diff --git a/docs/_data/bioregistry.yml b/docs/_data/bioregistry.yml index 548356dd0..f18f0e4c5 100644 --- a/docs/_data/bioregistry.yml +++ b/docs/_data/bioregistry.yml @@ -13,12 +13,6 @@ wikidata: database: Q23948774 property: P2796 -- deprecated: true - homepage: https://pictar.mdc-berlin.de/ - name: PicTar - prefix: pictar - synonyms: - - pictar-vert - miriam: deprecated: false description: The database of Annotated regulatory Binding Sites (from orthologous @@ -562,6 +556,9 @@ n2t: prefix: aspgd.protein prefix: aspgd.protein +- homepage: https://asrp.danforthcenter.org/ + name: Arabidopsis Small RNA Project + prefix: asrp - miriam: deprecated: false description: The Anatomical Therapeutic Chemical (ATC) classification system, @@ -1541,9 +1538,6 @@ version: 24-05-2019 version.iri: http://purl.obolibrary.org/obo/caro/2.0/beta/caro.owl prefix: caro -- homepage: https://asrp.danforthcenter.org/ - name: Arabidopsis Small RNA Project - prefix: asrp - miriam: deprecated: false description: CAS (Chemical Abstracts Service) is a division of the American Chemical @@ -4277,7 +4271,8 @@ version: '2020-06-10' version.iri: http://purl.obolibrary.org/obo/envo/releases/2020-06-10/envo.owl prefix: envo -- miriam: +- download: https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo + 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 @@ -4297,11 +4292,22 @@ obofoundry: contact: jaiswalp@science.oregonstate.edu contact.label: Pankaj Jaiswal - deprecated: true + deprecated: false license: CC-BY 4.0 - name: Plant Environment Ontology - prefix: eo - prefix: eo + name: Plant Experimental Conditions Ontology + prefix: peco + 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 + 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 + pattern: ^\d{7}$ + prefix: peco + synonyms: + - eo - ols: description: "L'ontologie EOL d\xE9crit les conditions d'environnement des \xE9\ levages d'animaux domestiques. Elle d\xE9crit plus particuli\xE8rement les modalit\xE9\ @@ -9648,7 +9654,8 @@ synonyms: - NIST Chemistry WebBook - NIST -- miriam: +- download: https://nmrml.org/cv/stable/nmrCV.owl + 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 @@ -9666,8 +9673,7 @@ deprecated: true name: NMR-instrument specific component of metabolomics investigations prefix: nmr - prefix: nmr -- ols: + 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 @@ -9694,7 +9700,9 @@ name: nuclear magnetic resonance CV prefix: nmrcv version: 1.1.0 - prefix: nmrcv + prefix: nmr + synonyms: + - nmrcv - miriam: deprecated: false description: NMR database for organic structures and their nuclear magnetic resonance @@ -9875,7 +9883,8 @@ version: '101' version.iri: http://purl.obolibrary.org/obo/obcs/2018-02-22/obcs.owl prefix: obcs -- miriam: +- download: https://github.com/obi-ontology/obi/raw/master/views/obi.obo + miriam: deprecated: false description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. @@ -10535,7 +10544,7 @@ - ORCID wikidata: database: Q51044 - database.label: ORCID iD + database.label: ORCID ID format: https://orcid.org/$1 pattern: 0000-000(1-[5-9]|2-[0-9]|3-[0-4])\d{3}-\d{3}[\dX] property: P496 @@ -11104,10 +11113,6 @@ version: '2019-09-19' version.iri: http://purl.obolibrary.org/obo/pdro/2019-09-19/pdro.owl prefix: pdro -- comment: All of these are typedefs in uberon now - deprecated: true - name: Uberon Property - prefix: ubprop - obofoundry: contact: bgee@sib.swiss contact.label: bgee @@ -11127,24 +11132,6 @@ prefix: pdumdv synonyms: - PdumDv -- download: https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo - obofoundry: - contact: jaiswalp@science.oregonstate.edu - contact.label: Pankaj Jaiswal - deprecated: false - license: CC-BY 4.0 - name: Plant Experimental Conditions Ontology - prefix: peco - ols: - description: A structured, controlled vocabulary which describes the treatments, - growing conditions, and/or study types used in plant biology experiments. - download: http://purl.obolibrary.org/obo/peco.owl - name: Plant Experimental Conditions Ontology - prefix: peco - version: '2020-08-21' - version.iri: http://purl.obolibrary.org/obo/peco/releases/2020-08-21/peco.owl - pattern: ^\d{7}$ - prefix: peco - deprecated: true download: https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo homepage: https://www.psidev.info/peff @@ -11445,6 +11432,12 @@ n2t: prefix: phytozome.locus prefix: phytozome.locus +- deprecated: true + homepage: https://pictar.mdc-berlin.de/ + name: PicTar + prefix: pictar + synonyms: + - pictar-vert - miriam: deprecated: false description: The Pathway Interaction Database is a highly-structured, curated @@ -12378,7 +12371,8 @@ prefix: reto version: 17-09-2019 prefix: reto -- obofoundry: +- download: http://purl.obolibrary.org/obo/rex.owl + obofoundry: deprecated: false download.obo: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo name: Physico-chemical process @@ -12702,6 +12696,21 @@ version.iri: http://purl.obolibrary.org/obo/rs/6.106/rs.owl pattern: ^\d{7}$ prefix: rs +- homepage: http://rna.rega.kuleuven.be/rnamods/ + name: The RNA Modification Database + prefix: rnamod + url: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1 +- comment: part of Sequence Ontology (SO). See https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/Ontology_Files/subsets/biosapiens.obo + name: Biosapiens + prefix: bs +- example: LL379-9 + homepage: https://loinc.org/ + name: Logical Observation Identifiers Names and Codes + prefix: loinc + url: https://loinc.org/$1/ +- homepage: https://www.wikidata.org + name: Wikipedia + prefix: wikipedia - download: https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo obofoundry: contact: batchelorc@rsc.org @@ -13245,7 +13254,8 @@ pattern: ^rs[0-9]+$ prefix: snp2tfbs prefix: snp2tfbs -- miriam: +- download: https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo + 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 @@ -13562,7 +13572,8 @@ n2t: prefix: swissregulon prefix: swissregulon -- obofoundry: +- download: https://github.com/allysonlister/swo/raw/master/release/swo.owl + obofoundry: contact: allyson.lister@oerc.ox.ac.uk contact.label: Allyson Lister deprecated: false @@ -14098,6 +14109,10 @@ n2t: prefix: ubio.namebank prefix: ubio.namebank +- comment: All of these are typedefs in uberon now + deprecated: true + name: Uberon Property + prefix: ubprop - homepage: https://genome.ucsc.edu/ name: UCSC Genome Browser prefix: ucsc @@ -14475,7 +14490,8 @@ - unipathway wikidata: database: Q85719315 -- obofoundry: +- download: https://github.com/obophenotype/upheno/blob/master/upheno.owl + obofoundry: contact: vasilevs@ohsu.edu contact.label: Nicole Vasilevsky deprecated: false diff --git a/docs/img/bioregistry_coverage.png b/docs/img/bioregistry_coverage.png index 2c081eb2b..486fee1ac 100644 Binary files a/docs/img/bioregistry_coverage.png and b/docs/img/bioregistry_coverage.png differ diff --git a/docs/img/external_overlap.png b/docs/img/external_overlap.png index b72a3ebbf..01c97ccdc 100644 Binary files a/docs/img/external_overlap.png and b/docs/img/external_overlap.png differ diff --git a/docs/img/has_attribute.png b/docs/img/has_attribute.png index 19839f6bd..961e19ed5 100644 Binary files a/docs/img/has_attribute.png and b/docs/img/has_attribute.png differ diff --git a/docs/img/license_coverage.png b/docs/img/license_coverage.png index f81a8f8a7..2c9d9d078 100644 Binary files a/docs/img/license_coverage.png and b/docs/img/license_coverage.png differ diff --git a/docs/img/licenses.png b/docs/img/licenses.png index cb592d5a7..0ac9a1a60 100644 Binary files a/docs/img/licenses.png and b/docs/img/licenses.png differ diff --git a/docs/img/xrefs.png b/docs/img/xrefs.png index 07cccbb46..9322b255b 100644 Binary files a/docs/img/xrefs.png and b/docs/img/xrefs.png differ diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 4289fa646..4912df367 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -1340,6 +1340,10 @@ "prefix": "broad" } }, + "bs": { + "comment": "part of Sequence Ontology (SO). See https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/Ontology_Files/subsets/biosapiens.obo", + "name": "Biosapiens" + }, "bspo": { "download": "https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo", "obofoundry": { @@ -4286,41 +4290,6 @@ "version.iri": "http://purl.obolibrary.org/obo/envo/releases/2020-06-10/envo.owl" } }, - "peco": { - "download": "https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo", - "obofoundry": { - "contact": "jaiswalp@science.oregonstate.edu", - "contact.label": "Pankaj Jaiswal", - "deprecated": false, - "license": "CC-BY 4.0", - "name": "Plant Experimental Conditions Ontology", - "prefix": "peco" - }, - "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", - "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" - }, - "pattern": "^\\d{7}$", - "miriam": { - "deprecated": false, - "description": "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.", - "id": "00000518", - "name": "Plant Environment Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^(P)?EO\\:\\d{7}$", - "prefix": "eo" - }, - "n2t": { - "prefix": "eo" - }, - "synonyms": [ - "eo" - ] - }, "eol": { "ols": { "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", @@ -7651,6 +7620,12 @@ "description": "A comprehensive compendium of human long non-coding RNAs", "name": "LNCipedia" }, + "loinc": { + "example": "LL379-9", + "homepage": "https://loinc.org/", + "name": "Logical Observation Identifiers Names and Codes", + "url": "https://loinc.org/$1/" + }, "lrg": { "miriam": { "deprecated": false, @@ -10527,7 +10502,7 @@ ], "wikidata": { "database": "Q51044", - "database.label": "ORCID iD", + "database.label": "ORCID ID", "format": "https://orcid.org/$1", "pattern": "0000-000(1-[5-9]|2-[0-9]|3-[0-4])\\d{3}-\\d{3}[\\dX]", "property": "P496", @@ -11096,6 +11071,41 @@ "PdumDv" ] }, + "peco": { + "download": "https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo", + "miriam": { + "deprecated": false, + "description": "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.", + "id": "00000518", + "name": "Plant Environment Ontology", + "namespaceEmbeddedInLui": true, + "pattern": "^(P)?EO\\:\\d{7}$", + "prefix": "eo" + }, + "n2t": { + "prefix": "eo" + }, + "obofoundry": { + "contact": "jaiswalp@science.oregonstate.edu", + "contact.label": "Pankaj Jaiswal", + "deprecated": false, + "license": "CC-BY 4.0", + "name": "Plant Experimental Conditions Ontology", + "prefix": "peco" + }, + "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", + "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" + }, + "pattern": "^\\d{7}$", + "synonyms": [ + "eo" + ] + }, "peff": { "deprecated": true, "download": "https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo", @@ -12553,6 +12563,11 @@ "prefix": "rnacentral" } }, + "rnamod": { + "homepage": "http://rna.rega.kuleuven.be/rnamods/", + "name": "The RNA Modification Database", + "url": "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1" + }, "rnamods": { "miriam": { "deprecated": false, @@ -12675,25 +12690,6 @@ }, "pattern": "^\\d{7}$" }, - "rnamod": { - "name": "The RNA Modification Database", - "homepage": "http://rna.rega.kuleuven.be/rnamods/", - "url": "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1" - }, - "bs": { - "name": "Biosapiens", - "comment": "part of Sequence Ontology (SO). See https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/Ontology_Files/subsets/biosapiens.obo" - }, - "loinc": { - "homepage": "https://loinc.org/", - "name": "Logical Observation Identifiers Names and Codes", - "url": "https://loinc.org/$1/", - "example": "LL379-9" - }, - "wikipedia": { - "homepage": "https://www.wikidata.org", - "name": "Wikipedia" - }, "rxno": { "download": "https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo", "obofoundry": { @@ -14970,6 +14966,10 @@ "webpage": "http://www.wikipathways.org" } }, + "wikipedia": { + "homepage": "https://www.wikidata.org", + "name": "Wikipedia" + }, "wikipedia.en": { "miriam": { "deprecated": false,