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xlink:href="#DejaVuSans-38" x="63.623047"/> </g> </g> - <g id="text_233"> + <g id="text_243"> <!-- MIRIAM --> - <g style="fill: #262626" transform="translate(488.114715 2120.359706)scale(0.12 -0.12)"> + <g style="fill: #262626" transform="translate(73.418506 2301.999351)scale(0.12 -0.12)"> <use xlink:href="#DejaVuSans-4d"/> <use xlink:href="#DejaVuSans-49" x="86.279297"/> <use xlink:href="#DejaVuSans-52" x="115.771484"/> @@ -5564,9 +5758,9 @@ C 560.547651 2083.085828 564.186708 2084.818417 568.068788 2085.086206 <use xlink:href="#DejaVuSans-4d" x="283.154297"/> </g> </g> - <g id="text_234"> + <g id="text_244"> <!-- NCBI --> - <g style="fill: #262626" transform="translate(569.126315 2096.948057)scale(0.12 -0.12)"> + <g style="fill: #262626" transform="translate(156.555365 2277.231116)scale(0.12 -0.12)"> <use xlink:href="#DejaVuSans-4e"/> <use xlink:href="#DejaVuSans-43" x="74.804688"/> <use xlink:href="#DejaVuSans-42" x="144.628906"/> @@ -5574,80 +5768,80 @@ C 560.547651 2083.085828 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224.638438)scale(0.1 -0.1)"> <use xlink:href="#DejaVuSans-31"/> <use xlink:href="#DejaVuSans-36" x="63.623047"/> </g> @@ -448,7 +448,7 @@ z <g id="xtick_18"> <g id="text_18"> <!-- 17 --> - <g style="fill: #262626" transform="translate(455.816037 224.638438)scale(0.1 -0.1)"> + <g style="fill: #262626" transform="translate(437.899261 224.638438)scale(0.1 -0.1)"> <use xlink:href="#DejaVuSans-31"/> <use xlink:href="#DejaVuSans-37" x="63.623047"/> </g> @@ -457,7 +457,7 @@ z <g id="xtick_19"> <g id="text_19"> <!-- 18 --> - <g style="fill: #262626" transform="translate(479.230006 224.638438)scale(0.1 -0.1)"> + <g style="fill: #262626" transform="translate(460.295231 224.638438)scale(0.1 -0.1)"> <use xlink:href="#DejaVuSans-31"/> <use xlink:href="#DejaVuSans-38" x="63.623047"/> </g> @@ -466,7 +466,7 @@ z <g id="xtick_20"> <g id="text_20"> <!-- 19 --> - <g style="fill: #262626" transform="translate(502.643975 224.638438)scale(0.1 -0.1)"> + <g style="fill: #262626" 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transform="translate(367.85681 90.634579)scale(0.12 -0.12)"> <defs> <path id="DejaVuSans-68" d="M 3513 2113 L 3513 0 @@ -1584,7 +1601,7 @@ z <use xlink:href="#DejaVuSans-6e" x="1060.738281"/> </g> <!-- 16 external registries --> - <g style="fill: #262626" transform="translate(388.746074 103.632446)scale(0.12 -0.12)"> + <g style="fill: #262626" transform="translate(371.236498 104.071954)scale(0.12 -0.12)"> <use xlink:href="#DejaVuSans-31"/> <use xlink:href="#DejaVuSans-36" x="63.623047"/> <use xlink:href="#DejaVuSans-20" x="127.246094"/> @@ -1610,7 +1627,7 @@ z </g> </g> </g> - <g id="text_46"> + <g id="text_47"> <!-- https://github.com/biopragmatics/bioregistry (2022-07-30) --> <g style="fill: #808080; opacity: 0.5" transform="translate(574.33625 243.32375)rotate(-90)scale(0.08 -0.08)"> <defs> @@ -1753,7 +1770,7 @@ z </g> </g> <defs> - <clipPath id="pa9aa46526c"> + <clipPath id="p7da7db864a"> <rect x="50.092685" y="12.06" width="515.107315" height="197.98"/> </clipPath> </defs> diff --git a/exports/contexts/obo_synonyms.context.jsonld b/exports/contexts/obo_synonyms.context.jsonld index 3db929dae..4c3d45bfe 100644 --- a/exports/contexts/obo_synonyms.context.jsonld +++ b/exports/contexts/obo_synonyms.context.jsonld @@ -286,6 +286,7 @@ "MetaCyc": "https://metacyc.org/compound?orgid=META&id=", "MmusDv": "http://purl.obolibrary.org/obo/MmusDv_", "NBO": "http://purl.obolibrary.org/obo/NBO_", + "NCBI Taxonomy": "http://purl.obolibrary.org/obo/NCBITaxon_", "NCBIGene": "https://www.ncbi.nlm.nih.gov/gene/", "NCBIProtein": "https://www.ncbi.nlm.nih.gov/protein/", "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", diff --git a/exports/contexts/obo_synonyms.context.ttl b/exports/contexts/obo_synonyms.context.ttl index 017f118a9..fc77ba9de 100644 --- a/exports/contexts/obo_synonyms.context.ttl +++ b/exports/contexts/obo_synonyms.context.ttl @@ -288,6 +288,7 @@ [ sh:prefix "MetaCyc" ; sh:namespace "https://metacyc.org/compound?orgid=META&id=" ; sh:pattern "^[A-Za-z0-9+_.%-:]+$" ], [ sh:prefix "MmusDv" ; sh:namespace "http://purl.obolibrary.org/obo/MmusDv_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "NBO" ; sh:namespace "http://purl.obolibrary.org/obo/NBO_" ; sh:pattern "^\d{7}$" ], + [ sh:prefix "NCBI Taxonomy" ; sh:namespace "http://purl.obolibrary.org/obo/NCBITaxon_" ; sh:pattern "^\d+$" ], [ sh:prefix "NCBIGene" ; sh:namespace "https://www.ncbi.nlm.nih.gov/gene/" ; sh:pattern "^\d+$" ], [ sh:prefix "NCBIProtein" ; sh:namespace "https://www.ncbi.nlm.nih.gov/protein/" ; sh:pattern "^(\w+\d+(\.\d+)?)|(NP_\d+)$" ], [ sh:prefix "NCBITaxon" ; sh:namespace "http://purl.obolibrary.org/obo/NCBITaxon_" ; sh:pattern "^\d+$" ], diff --git a/exports/metaregistry/metaregistry.tsv b/exports/metaregistry/metaregistry.tsv index 61822ea8a..37e3e8b99 100644 --- a/exports/metaregistry/metaregistry.tsv +++ b/exports/metaregistry/metaregistry.tsv @@ -20,5 +20,6 @@ ols Ontology Lookup Service https://www.ebi.ac.uk/ols The Ontology Lookup Servic ontobee OntoBee http://www.ontobee.org/ Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. AGRO Yongqun Oliver He yongqunh@med.umich.edu yongqunh http://www.ontobee.org/ontology/$1 http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2 lookup prefixcc Prefix.cc https://prefix.cc/ A web-developer centric archive of prefixes and URI prefixes https://prefix.cc/context.jsonld foaf Richard Cyganiak richard@cyganiak.de cygri https://prefix.cc/$1 prefixcommons Prefix Commons https://prefixcommons.org A registry of commonly used prefixes in the life sciences and linked data https://raw.githubusercontent.com/prefixcommons/data-ingest/master/yml/lsregistry.yml CHEBI Michel Dumontier michel.dumontier@gmail.com micheldumontier https://prefixcommons.org/?q=$1 +re3data Registry of Research Data Repositories https://www.re3data.org Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines. r3d100010772 Michael Witt mwitt@purdue.edu mwittin https://www.re3data.org/repository/$1 uniprot UniProt Cross-ref database https://www.uniprot.org/database/ 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. https://www.uniprot.org/database/?format=rdf 0174 Alex Bateman agb@ebi.ac.uk bateman-research https://www.uniprot.org/database/DB-$1 wikidata Wikidata Property https://www.wikidata.org An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries. P683 WikiData Support info@wikidata.org https://www.wikidata.org/wiki/Property:$1 diff --git a/exports/metaregistry/metaregistry.yml b/exports/metaregistry/metaregistry.yml index 1b90d84db..3a6b118ec 100644 --- a/exports/metaregistry/metaregistry.yml +++ b/exports/metaregistry/metaregistry.yml @@ -867,6 +867,47 @@ prefixcommons: name: Prefix Commons prefix: prefixcommons provider_uri_format: https://prefixcommons.org/?q=$1 +re3data: + availability: + alternate_providers: missing + contact: present + description: required + example: missing + fair: false + fair_note: The API for Re3data does not provide a bulk download + homepage: required + license: present + name: required + pattern: missing + provider: missing + search: true + synonyms: missing + version: missing + bioregistry_prefix: re3data + contact: + email: mwitt@purdue.edu + github: mwittin + name: Michael Witt + orcid: 0000-0003-4221-7956 + description: Re3data is a global registry of research data repositories that covers + research data repositories from different academic disciplines. + example: r3d100010772 + governance: + accepts_external_contributions: true + comments: null + curates: true + curation: opaque-review + imports: false + public_version_control: false + review_team: private + scope: general + status: active + homepage: https://www.re3data.org + license: CC 0 + name: Registry of Research Data Repositories + prefix: re3data + provider_uri_format: https://www.re3data.org/repository/$1 + short_name: re3data uniprot: availability: alternate_providers: missing diff --git a/exports/rdf/bioregistry.jsonld b/exports/rdf/bioregistry.jsonld index 3b91cf122..b7c36b335 100644 --- a/exports/rdf/bioregistry.jsonld +++ b/exports/rdf/bioregistry.jsonld @@ -34,6 +34,7 @@ "prefixcommons": "https://prefixcommons.org/?q=", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "re3data": "https://www.re3data.org/repository/", "uniprot.resource": "https://www.uniprot.org/database/DB-", "wikidata": "https://www.wikidata.org/wiki/Property:", "xml": "http://www.w3.org/XML/1998/namespace", @@ -41,1890 +42,1893 @@ }, "@graph": [ { - "@id": "https://bioregistry.io/metaregistry/cellosaurus/NHCDR", + "@id": "https://bioregistry.io/registry/opmi", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/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.", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/cellosaurus" + "@id": "https://bioregistry.io/metaregistry/bioregistry" + }, + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "Ontology of Precision Medicine and Investigation" + }, + "http://www.w3.org/2004/02/skos/core#exactMatch": [ + { + "@id": "https://bioportal.bioontology.org/ontologies/OPMI" + }, + { + "@id": "http://www.obofoundry.org/ontology/opmi" + }, + { + "@id": "http://www.ontobee.org/ontology/OPMI" + }, + { + "@id": "https://www.ebi.ac.uk/ols/ontologies/opmi" + }, + { + "@id": "http://aber-owl.net/ontology/OPMI" + } + ], + "http://xmlns.com/foaf/0.1/homepage": "https://github.com/OPMI/opmi", + "https://bioregistry.io/schema/#0000005": "0000101", + "https://bioregistry.io/schema/#0000006": "http://purl.obolibrary.org/obo/OPMI_$1", + "https://bioregistry.io/schema/#0000008": "^\\d{7}$", + "https://bioregistry.io/schema/#0000012": false, + "https://bioregistry.io/schema/#0000018": [ + { + "@id": "https://bioregistry.io/registry/labo" + }, + { + "@id": "https://bioregistry.io/registry/scdo" + } + ], + "https://bioregistry.io/schema/#0000019": { + "@id": "https://orcid.org/0000-0001-9189-9661" } }, { - "@id": "https://registry.identifiers.org/registry/pride.project", + "@id": "http://www.ontobee.org/ontology/HSAPDV", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" + "@id": "https://bioregistry.io/metaregistry/ontobee" } }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/GMD.REF", + "@id": "http://www.ontobee.org/ontology/HSO", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biocontext" + "@id": "https://bioregistry.io/metaregistry/ontobee" } }, { - "@id": "http://www.obofoundry.org/ontology/sbo", + "@id": "https://registry.identifiers.org/registry/aop.relationships", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/obofoundry" + "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://www.ebi.ac.uk/ols/ontologies/mamo", + "@id": "https://bioregistry.io/registry/xml", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/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. 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