{"_3dmet":{"prefix":"_3dmet","name":"3D Metabolites","description":"3DMET is a database collecting three-dimensional structures of natural metabolites.","pattern":"^B\\d{5}$","uri_format":"http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/3dmet:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.3dmet.dna.affrc.go.jp/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"01786mp71","wikidata":null,"gnd":null,"name":"National Institute of Agrobiological Sciences","partnered":false}],"example":"B00162","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"3DMET","edam.data":"2635","integbio":"nbdc00351","miriam":"3dmet","n2t":"3dmet","prefixcommons":"3dmet","wikidata.property":"P2796"},"synonyms":["3dmet"],"keywords":["3d structure","chemical","chemical compound","metabolite","structure"],"domain":null,"references":null,"publications":[{"pubmed":"29892514","doi":"10.2142/biophysico.15.0_87","pmc":"PMC5992871","arxiv":null,"title":"Chemical curation to improve data accuracy: recent development of the 3DMET database","year":2018},{"pubmed":"23293959","doi":"10.1021/ci300309k","pmc":null,"arxiv":null,"title":"Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures","year":2013}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":"Website has been down since 2023/2024","contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"_3dmet","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"aaindex":{"prefix":"aaindex","name":"AAindex","description":"Identifier of an entry from the AAindex database.","pattern":null,"uri_format":"http://www.genome.jp/dbget-bin/www_bget?aaindex:$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/aaindex:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.genome.ad.jp/aaindex/","repository":null,"contact":{"name":"Shuichi Kawashima","orcid":"0000-0001-7883-3756","email":"shuichi@hgc.jp","github":"skwsm","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"BUNA790102","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"1128","integbio":"nbdc00004","prefixcommons":"aaindex","wikidata.entity":"Q85738825"},"synonyms":[],"keywords":["protein","sequence"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/pull/1098"],"publications":[{"pubmed":"9847231","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"9053899","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"3244698","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17998252","doi":"10.1093/nar/gkm998","pmc":"PMC2238890","arxiv":null,"title":"AAindex: amino acid index database, progress report 2008","year":2007},{"pubmed":"10592278","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Sumir H. Pandit","orcid":"0000-0002-1216-4761","email":"sumirp77@gmail.com","github":"sumirp","wikidata":null}],"reviewer":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"aaindex","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"abs":{"prefix":"abs","name":"Annotated Regulatory Binding Sites","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.","pattern":"^A\\d+$","uri_format":"http://genome.crg.es/datasets/abs2005/entries/$1.html","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/abs:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://genome.crg.es/datasets/abs2005/","repository":null,"contact":{"name":"Enrique Blanco","orcid":"0000-0001-6261-7370","email":"enrique.blanco@crg.eu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"A0014","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"ABS","edam.data":"2741","fairsharing":"FAIRsharing.7mnebr","miriam":"abs","n2t":"abs","pathguide":"217","prefixcommons":"abs","wikidata.entity":"Q111134507"},"synonyms":[],"keywords":["binding site","biological regulation","biology","gene","interaction","molecular interaction","promoter","regulation","regulation of gene expression"],"domain":null,"references":null,"publications":[{"pubmed":"16381947","doi":"10.1093/nar/gkj116","pmc":"PMC1347478","arxiv":null,"title":"ABS: a database of Annotated regulatory Binding Sites from orthologous promoters","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"abs","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"arachnoserver":{"prefix":"arachnoserver","name":"ArachnoServer","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.","pattern":"^AS\\d{6}$","uri_format":"http://www.arachnoserver.org/toxincard.html?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/arachnoserver:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.arachnoserver.org/","repository":null,"contact":{"name":"Glenn King","orcid":"0000-0002-2308-2200","email":"glenn.king@imb.uq.edu.au","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"AS000060","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"ARACHNOSERVER","edam.data":"2578","fairsharing":"FAIRsharing.c54ywe","integbio":"nbdc01221","miriam":"arachnoserver","n2t":"arachnoserver","prefixcommons":"arachnoserver","re3data":"r3d100012902","uniprot.resource":"DB-0145","wikidata.entity":"Q4783563"},"synonyms":[],"keywords":["3d structure","drug","life science","organism-specific databases","peptide","protein","sequence","toxicity"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/pull/1141"],"publications":[{"pubmed":"29069336","doi":"10.1093/bioinformatics/btx661","pmc":null,"arxiv":null,"title":"ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins","year":2018},{"pubmed":"21036864","doi":"10.1093/nar/gkq1058","pmc":"PMC3013666","arxiv":null,"title":"ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures","year":2010},{"pubmed":"19674480","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Sumir H. Pandit","orcid":"0000-0002-1216-4761","email":"sumirp77@gmail.com","github":"sumirp","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"arachnoserver","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcE1HIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--2ce9f5f139fc6393edeb7f378166c9b5a7f868b9/Screenshot%20From%202025-06-04%2012-26-35.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"astd":{"prefix":"astd","name":"Alternative Splicing and Transcript Diversity database","description":"Identifier of an object from the ASTD database.","pattern":null,"uri_format":"http://www.ebi.ac.uk/astd/geneview.html?acc=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/astd:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.ebi.ac.uk/astd/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"ENSG00000136147","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":"ensembl","download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"edam.data":"2367","prefixcommons":"astd"},"synonyms":[],"keywords":["alternative splicing","gene","transcript"],"domain":null,"references":null,"publications":[{"pubmed":"19059335","doi":"10.1016/j.ygeno.2008.11.003","pmc":null,"arxiv":null,"title":"ASTD: The Alternative Splicing and Transcript Diversity database","year":2008}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":"This resource doesn't exist on the web anymore","contributor":null,"contributor_extras":null,"reviewer":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"astd","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"atc":{"prefix":"atc","name":"Anatomical Therapeutic Chemical Classification System","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.","pattern":"^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$","uri_format":"http://www.whocc.no/atc_ddd_index/?code=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/atc:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bioportal.purl","name":"BioPortal","description":"BioPortal assigned additional PURLs for ATC codes","homepage":"http://purl.bioontology.org/ontology/ATC","contact":null,"uri_format":"http://purl.bioontology.org/ontology/ATC/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.whocc.no/atc_ddd_index/","repository":null,"contact":{"name":"WHO Collaborating Centre for Drug Statistics Methodology","orcid":null,"email":"whocc@fhi.no","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"A10BA02","example_extras":[],"example_decoys":null,"license":null,"version":"2025_02_10","part_of":null,"part_of_database":null,"provides":null,"download_owl":"http://aber-owl.net/media/ontologies/ATC/1/atc.owl","download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"aberowl":"ATC","bartoc":"449","biocontext":"ATC","bioportal":"ATC","edam.data":"3103","fairsharing":"FAIRsharing.1a27h8","hl7":"6.73","miriam":"atc","n2t":"atc","prefixcommons":"atc","togoid":"Atc","wikidata.entity":"Q192093","wikidata.property":"P267"},"synonyms":["ATC_code","ATTC"],"keywords":["approved drug","atc code","biomedical science","chemical","chemical biology","drug","ontology","pharmacological family classification","pharmacology"],"domain":null,"references":null,"publications":[{"pubmed":"7368387","doi":null,"pmc":null,"arxiv":null,"title":"[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981]","year":1980},{"pubmed":"11214783","doi":"10.1007/s002280000200","pmc":null,"arxiv":null,"title":"Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable?","year":2000}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"atc","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"bind":{"prefix":"bind","name":"BIND accession number","description":"Accession number of an entry from the BIND database.","pattern":null,"uri_format":"http://www.bind.ca/Action?identifier=bindid&idsearch=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/bind:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://bind.ca","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"98346","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"BIND","edam.data":"1129","pathguide":"1","prefixcommons":"bind"},"synonyms":[],"keywords":["interaction","pathway","psi-mi","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"12519993","doi":"10.1093/nar/gkg056","pmc":"PMC165503","arxiv":null,"title":"BIND: the Biomolecular Interaction Network Database","year":2003},{"pubmed":"10871269","doi":"10.1093/bioinformatics/16.5.465","pmc":null,"arxiv":null,"title":"BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways","year":2000}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"bind","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"biocyc":{"prefix":"biocyc","name":"BioCyc","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.","pattern":"^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$","uri_format":"http://biocyc.org/getid?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/biocyc:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://biocyc.org","repository":null,"contact":{"name":"Peter D. Karp","orcid":"0000-0002-5876-6418","email":"pkarp@ai.sri.com","github":"pkarp111","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"05s570m15","wikidata":null,"gnd":null,"name":"SRI International","partnered":false}],"example":"ECOLI:CYT-D-UBIOX-CPLX","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"BIOCYC","edam.data":"2104","go.resource":"BioCyc","integbio":"nbdc00252","miriam":"biocyc","n2t":"biocyc","pathguide":"8","prefixcommons":"biocyc","uniprot.resource":"DB-0005"},"synonyms":[],"keywords":["bibliography/documents","biopax","dna","enzyme and pathway databases","genome","genome/gene","interaction/pathway","pathway","protein","rna","sbml","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"29447345","doi":"10.1093/bib/bbx085","pmc":"PMC6781571","arxiv":null,"title":"The BioCyc collection of microbial genomes and metabolic pathways","year":2019},{"pubmed":"26527732","doi":"10.1093/nar/gkv1164","pmc":"PMC4702838","arxiv":null,"title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases","year":2015},{"pubmed":"22102576","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16246909","doi":"10.1093/nar/gki892","pmc":"PMC1266070","arxiv":null,"title":"Expansion of the BioCyc collection of pathway/genome databases to 160 genomes","year":2005}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"biocyc","mastodon":null,"github_request_issue":null,"logo":"https://biocyc.org/graphics2021/BioCyc-logo-color-genome.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"biogrid.interaction":{"prefix":"biogrid.interaction","name":"BioGRID Interactions","description":"BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe.","pattern":"^\\d+$","uri_format":"https://thebiogrid.org/interaction/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://thebiogrid.org","repository":null,"contact":{"name":"Mike Tyers","orcid":"0000-0002-9713-9994","email":"md.tyers@umontreal.ca","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"2649230","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"2628"},"synonyms":[],"keywords":["biogrid"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"biogrid.interaction","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"bionumbers":{"prefix":"bionumbers","name":"BioNumbers","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.","pattern":"^\\d+$","uri_format":"https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/bionumbers:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://bionumbers.hms.harvard.edu","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0316ej306","wikidata":null,"gnd":null,"name":"Weizmann Institute","partnered":false}],"example":"104674","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"BIONUMBERS","edam.data":"2660","miriam":"bionumbers","n2t":"bionumbers","prefixcommons":"bionumbers"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"bionumbers","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"cabri":{"prefix":"cabri","name":"Common Access to Biological Resources and Information Project","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.","pattern":"^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$","uri_format":"http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"CABRI Cell Lines catalogue in Brussels (SRS)","description":"CABRI Cell Lines catalogue in Brussels (SRS)","homepage":"http://www.be.cabri.org/","contact":null,"uri_format":"http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.cabri.org/","repository":null,"contact":{"name":"Paolo Romano","orcid":"0000-0003-4694-3883","email":"paolo.romano@hsanmartino.it","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"dsmz_mutz-id:ACC 291","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"CABRI","edam.data":"2380","fairsharing":"FAIRsharing.qx2rvz","miriam":"cabri","n2t":"cabri","ncbi.resource":"CABRI"},"synonyms":[],"keywords":["applied microbiology","cell line","medical microbiology","microbiology","molecular biology","molecular microbiology","plasmid","virology"],"domain":null,"references":null,"publications":[{"pubmed":"18629057","doi":"10.1002/cfg.376","pmc":"PMC2447341","arxiv":null,"title":"Interoperability of CABRI Services and Biochemical Pathways Databases","year":2004},{"pubmed":"16231959","doi":"10.2165/00822942-200594030-00002","pmc":null,"arxiv":null,"title":"The role of informatics in the coordinated management of biological resources collections","year":2005}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"cabri","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"cas":{"prefix":"cas","name":"Chemical Abstracts Service Registry Number","description":"CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.","pattern":"^\\d{1,7}\\-\\d{2}\\-\\d$","uri_format":"https://commonchemistry.cas.org/detail?cas_rn=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/cas:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"hoelzel","name":"Hölzel Diagnostika","description":"Vendor page","homepage":"https://www.hoelzel-biotech.com","contact":null,"uri_format":"https://www.hoelzel-biotech.com/de/casinfo/cas/index/number/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"scholia","name":"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/","contact":null,"uri_format":"https://scholia.toolforge.org/cas/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://commonchemistry.cas.org/","repository":null,"contact":{"name":"Andrea Jacobs","orcid":"0000-0001-9316-9400","email":"ajacobs@cas.org","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"50-00-0","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"CAS","cheminf":"000446","edam.data":"1002","fairsharing":"FAIRsharing.r7Kwy7","go.resource":"CAS","hl7":"6.61","miriam":"cas","n2t":"cas","prefixcommons":"cas","wikidata.property":"P231"},"synonyms":["CASID","CAS_RN","SECONDARY_CAS_RN","cas_id"],"keywords":["chemical","chemical entity","physical chemistry","structure"],"domain":null,"references":null,"publications":[{"pubmed":"35559614","doi":"10.1021/acs.jcim.2c00268","pmc":"PMC9199008","arxiv":null,"title":"CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community","year":2022}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"cas","mastodon":null,"github_request_issue":null,"logo":"https://upload.wikimedia.org/wikipedia/en/2/2a/Chemical_Abstracts_Service_logo.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"cath":{"prefix":"cath","name":"CATH Protein Structural Domain Superfamily","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.","pattern":"^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$","uri_format":"http://www.cathdb.info/cathnode/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/cath:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.cathdb.info","repository":null,"contact":{"name":"Christine Orengo","orcid":"0000-0002-7141-8936","email":"c.orengo@ucl.ac.uk","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02jx3x895","wikidata":null,"gnd":null,"name":"University College London","partnered":false}],"example":"1.10.8.10","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"CATH","edam.data":"2700","fairsharing":"FAIRsharing.xgcyyn","integbio":"nbdc01888","miriam":"cath","n2t":"cath","prefixcommons":"cath","re3data":"r3d100012629"},"synonyms":[],"keywords":["3d structure","annotation","biology","classification","curated information","evolution","evolutionary biology","protein","sequence","structure"],"domain":null,"references":null,"publications":[{"pubmed":"9309224","doi":"10.1016/s0969-2126(97)00260-8","pmc":null,"arxiv":null,"title":"CATH--a hierarchic classification of protein domain structures","year":1997},{"pubmed":"39565206","doi":"10.1093/nar/gkae1087","pmc":null,"arxiv":null,"title":"CATH v4.4: major expansion of CATH by experimental and predicted structural data","year":2024},{"pubmed":"33237325","doi":"10.1093/nar/gkaa1079","pmc":"PMC7778904","arxiv":null,"title":"CATH: increased structural coverage of functional space","year":2021},{"pubmed":"30398663","doi":"10.1093/nar/gky1097","pmc":"PMC6323983","arxiv":null,"title":"CATH: expanding the horizons of structure-based functional annotations for genome sequences","year":2019},{"pubmed":"29112716","doi":"10.1093/nar/gkx1069","pmc":"PMC5753370","arxiv":null,"title":"Gene3D: Extensive prediction of globular domains in proteins","year":2018},{"pubmed":"27899584","doi":"10.1093/nar/gkw1098","pmc":"PMC5210570","arxiv":null,"title":"CATH: an expanded resource to predict protein function through structure and sequence","year":2016},{"pubmed":"27477482","doi":"10.1093/bioinformatics/btw473","pmc":"PMC5018379","arxiv":null,"title":"Functional classification of CATH superfamilies: a domain-based approach for protein function annotation","year":2016},{"pubmed":"26253692","doi":"10.1016/j.biochi.2015.08.004","pmc":"PMC4678953","arxiv":null,"title":"The history of the CATH structural classification of protein domains","year":2015},{"pubmed":"26139634","doi":"10.1093/bioinformatics/btv398","pmc":null,"arxiv":null,"title":"Functional classification of CATH superfamilies: a domain-based approach for protein function annotation","year":2015},{"pubmed":"25348408","doi":"10.1093/nar/gku947","pmc":"PMC4384018","arxiv":null,"title":"CATH: comprehensive structural and functional annotations for genome sequences","year":2014},{"pubmed":"11788987","doi":null,"pmc":null,"arxiv":null,"title":"The CATH protein family database: a resource for structural and functional annotation of genomes","year":2002},{"pubmed":null,"doi":"10.1016/j.jmb.2024.168551","pmc":null,"arxiv":null,"title":"CATH 2024: CATH-AlphaFlow Doubles the Number of Structures in CATH and Reveals Nearly 200 New Folds","year":2024}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"cath","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBcTBHIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--eebf623b75482e2f85ea3530dca48f801fca2ed1/Screenshot%20From%202025-06-24%2013-14-31.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"cath.domain":{"prefix":"cath.domain","name":"CATH domain","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.","pattern":"^\\w+$","uri_format":"http://www.cathdb.info/domain/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.cathdb.info/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"05wsetc54","wikidata":null,"gnd":null,"name":"Institute of Structural and Molecular Biology, University College London","partnered":false}],"example":"1cukA01","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"CATH.DOMAIN","edam.data":"1040","miriam":"cath.domain","n2t":"cath.domain"},"synonyms":[],"keywords":["cath"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"cath.domain","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"cdd":{"prefix":"cdd","name":"Conserved Domain Database","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.","pattern":"^(cd)?\\d{5}$","uri_format":"https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/cdd:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd","repository":null,"contact":{"name":"Aron Marchler-Bauer","orcid":"0000-0003-1516-0712","email":"bauer@ncbi.nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0060t0j89","wikidata":null,"gnd":null,"name":"National Library of Medicine, Maryland","partnered":false}],"example":"cd00400","example_extras":[],"example_decoys":null,"license":"http://www.nlm.nih.gov/copyright.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"CDD","edam.data":"2666","fairsharing":"FAIRsharing.b9st5p","go.resource":"CDD","integbio":"nbdc00401","miriam":"cdd","n2t":"cdd","ncbi.resource":"CDD","prefixcommons":"cdd","uniprot.resource":"DB-0214"},"synonyms":[],"keywords":["annotation","classification","family and domain databases","functional domain","image/movie","life science","literature curation","multiple sequence alignment","protein","protein domain","protein structure","sequence","sequence alignment","sequence feature","structure"],"domain":null,"references":null,"publications":[{"pubmed":"36477806","doi":"10.1093/nar/gkac1096","pmc":null,"arxiv":null,"title":"The conserved domain database in 2023","year":2022},{"pubmed":"27899674","doi":"10.1093/nar/gkw1129","pmc":null,"arxiv":null,"title":"CDD/SPARCLE: functional classification of proteins via subfamily domain architectures","year":2016},{"pubmed":"25414356","doi":"10.1093/nar/gku1221","pmc":"PMC4383992","arxiv":null,"title":"CDD: NCBI's conserved domain database","year":2014},{"pubmed":"23197659","doi":"10.1093/nar/gks1243","pmc":null,"arxiv":null,"title":"CDD: conserved domains and protein three-dimensional structure","year":2012},{"pubmed":"18984618","doi":"10.1093/nar/gkn845","pmc":"PMC2686570","arxiv":null,"title":"CDD: specific functional annotation with the Conserved Domain Database","year":2008},{"pubmed":"17135202","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15215404","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"12368255","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"cdd","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"chebi":{"prefix":"chebi","name":"Chemical Entities of Biological Interest","description":"Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.","pattern":"^\\d+$","uri_format":"http://purl.obolibrary.org/obo/CHEBI_$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.obolibrary.org/obo/CHEBI_$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/chebi:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"chebi-img","name":"ChEBI","description":"Image server from chebi","homepage":"https://www.ebi.ac.uk/chebi/","contact":null,"uri_format":"https://www.ebi.ac.uk/chebi/backend/api/public/compound/$1/structure/?width=300&height=300","first_party":true,"publications":null,"example":null,"status":null,"organization":null},{"code":"iedb.antigen","name":"Immune Epitope Database","description":"A comprehensive collection of data on immune epitopes, covering experimental data and resources, including antigens","homepage":"https://www.iedb.org","contact":null,"uri_format":"https://www.iedb.org/antigen/ChEBI:$1","first_party":null,"publications":null,"example":"60327","status":null,"organization":null}],"homepage":"http://www.ebi.ac.uk/chebi","repository":"https://github.com/ebi-chebi/ChEBI","contact":{"name":"Adnan Malik","orcid":"0000-0001-8123-5351","email":"amalik@ebi.ac.uk","github":"amalik01","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"138488","example_extras":["60327"],"example_decoys":null,"license":"CC-BY-4.0","version":"255","part_of":null,"part_of_database":null,"provides":null,"download_owl":"http://purl.obolibrary.org/obo/chebi.owl","download_obo":"http://purl.obolibrary.org/obo/chebi.obo","download_json":"http://purl.obolibrary.org/obo/chebi.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"CHEBI","banana_peel":null,"deprecated":false,"mappings":{"aberowl":"CHEBI","bartoc":"558","biocontext":"CHEBI","biodivportal":"CHEBI","bioportal":"CHEBI","cellosaurus.resource":"ChEBI","cheminf":"000407","edam.data":"1174","fairsharing":"FAIRsharing.62qk8w","go.resource":"CHEBI","integbio":"nbdc00027","miriam":"chebi","n2t":"chebi","obofoundry":"chebi","ols":"chebi","ontobee":"CHEBI","prefixcommons":"chebi","re3data":"r3d100012626","tib.ts":"chebi","togoid":"Chebi","wikidata.entity":"Q902623","wikidata.property":"P683"},"synonyms":["CHEBI","CHEBIID","ChEBI"],"keywords":["biochemistry","carbohydrate","chemical","chemical biology","chemical compound","chemical entity","chemistry","compound","dataplant","earth sciences","ess","lipid","lipidomics","metabolite","metabolomics","molecular entity","natural product","nfdi-matwerk","nfdi4cat","nfdi4chem","obo","ontology","ontology/terminology/nomenclature","proteomics","small molecule","structure","taxonomic classification"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/issues/1760"],"publications":[{"pubmed":"26467479","doi":"10.1093/nar/gkv1031","pmc":"PMC4702775","arxiv":null,"title":"ChEBI in 2016: Improved services and an expanding collection of metabolites","year":2015},{"pubmed":"23180789","doi":"10.1093/nar/gks1146","pmc":"PMC3531142","arxiv":null,"title":"The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013","year":2012},{"pubmed":"19854951","doi":"10.1093/nar/gkp886","pmc":"PMC2808869","arxiv":null,"title":"Chemical Entities of Biological Interest: an update","year":2009},{"pubmed":"19496059","doi":"10.1002/0471250953.bi1409s26","pmc":null,"arxiv":null,"title":"ChEBI: an open bioinformatics and cheminformatics resource","year":2009},{"pubmed":"17932057","doi":"10.1093/nar/gkm791","pmc":"PMC2238832","arxiv":null,"title":"ChEBI: a database and ontology for chemical entities of biological interest","year":2007},{"pubmed":null,"doi":"10.1093/nar/gkaf1271","pmc":null,"arxiv":null,"title":"ChEBI: re-engineered for a sustainable future","year":null}],"appears_in":["cdno","chiro","ecocore","ecto","envo","fobi","foodon","genepio","maxo","mco","ons","pcl","proco","scdo","uberon","xpo"],"depends_on":["bfo","ro"],"namespace_in_lui":true,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Muhammad Arsalan","orcid":"0009-0005-4625-8212","email":"muhammad@ebi.ac.uk","github":"theArsalanM","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"CHEBI","mastodon":null,"github_request_issue":null,"logo":"https://www.ebi.ac.uk/chebi/chebi_logo.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"chembl.compound":{"prefix":"chembl.compound","name":"ChEMBL Compound","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.","pattern":"^CHEMBL\\d+$","uri_format":"https://www.ebi.ac.uk/chembl/compound/inspect/$1","uri_format_resolvable":null,"rdf_uri_format":"http://rdf.ebi.ac.uk/resource/chembl/molecule/$1","providers":[],"homepage":"https://www.ebi.ac.uk/chembldb/","repository":null,"contact":{"name":"David Mendez Lopez","orcid":"0000-0002-0294-5484","email":"dmendez@ebi.ac.uk","github":"nclopezo","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"CHEMBL465070","example_extras":[],"example_decoys":null,"license":"CC-BY-SA-3.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.owl","download_obo":"https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.obo","download_json":"https://w3id.org/biopragmatics/resources/chembl.compound/chembl.compound.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"CHEMBL.COMPOUND","edam.data":"2646","miriam":"chembl.compound","n2t":"chembl.compound","togoid":"ChemblCompound","wikidata.property":"P592"},"synonyms":[],"keywords":["chemical","compound","ontology","small molecule"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"chembl.compound","mastodon":null,"github_request_issue":null,"logo":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg5LCdi4mEW56jpmM0YDjEwLtGUUy2F9I7m02I9hygI0OPugnZKlTrAgfBtug5yJS5RbpCXifID0pzA5Wxdc6un1UjCCtOJcvlkeoAFgzQspvplZcstYNwx8lBtvlYY8WJ-kLj-I891VIAO/s1600/Screenshot+2018-12-20+at+10.30.09.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"chemidplus":{"prefix":"chemidplus","name":"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.","pattern":"^\\d+\\-\\d+\\-\\d+$","uri_format":"https://chem.nlm.nih.gov/chemidplus/rn/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/chemidplus:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0060t0j89","wikidata":null,"gnd":null,"name":"National Library of Medicine, Maryland","partnered":false}],"example":"57-27-2","example_extras":[],"example_decoys":null,"license":"http://www.nlm.nih.gov/copyright.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"CHEMIDPLUS","edam.data":"2658","fairsharing":"FAIRsharing.5949vn","integbio":"nbdc01837","miriam":"chemidplus","n2t":"chemidplus","prefixcommons":"chemidplus"},"synonyms":["ChemIDplus"],"keywords":["3d structure","biomedical science","chemical compound","chemical structure","chemical structure image","chemistry","image/movie","molecular entity","molecules","structure"],"domain":null,"references":null,"publications":[{"pubmed":"11989279","doi":"10.1300/j115v21n01_04","pmc":null,"arxiv":null,"title":"ChemIDplus-super source for chemical and drug information","year":2002}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"chemidplus","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"chemspider":{"prefix":"chemspider","name":"ChemSpider","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.","pattern":"^\\d+$","uri_format":"http://www.chemspider.com/Chemical-Structure.$1.html","uri_format_resolvable":null,"rdf_uri_format":"http://rdf.chemspider.com/$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/chemspider:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.chemspider.com/","repository":null,"contact":{"name":"Harry E. Pence","orcid":"0000-0002-0412-9018","email":"pencehe@oneonta.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"025sbr097","wikidata":null,"gnd":null,"name":"Royal Society of Chemistry, Cambridge","partnered":false}],"example":"56586","example_extras":[],"example_decoys":null,"license":"http://www.rsc.org/Help/termsconditions.asp","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"CHEMSPIDER","cheminf":"000405","edam.data":"1173","fairsharing":"FAIRsharing.96f3gm","integbio":"nbdc01863","miriam":"chemspider","n2t":"chemspider","prefixcommons":"chemspider","re3data":"r3d100010205","wikidata.property":"P661"},"synonyms":["ChemSpiderID","Chemspider"],"keywords":["3d structure","chemical compound","chemical structure image","chemistry","image/movie","life science","molecular entity","molecules","structure"],"domain":null,"references":null,"publications":[{"pubmed":null,"doi":"10.1021/ed100697w","pmc":null,"arxiv":null,"title":"ChemSpider: An Online Chemical Information Resource","year":2010}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"chemspider","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"cosmic.gene":{"prefix":"cosmic.gene","name":"COSMIC Gene","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.","pattern":"^[A-Z0-9][A-Z0-9-]*$","uri_format":"http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/cosmic:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://cancer.sanger.ac.uk/cosmic/","repository":null,"contact":{"name":"John G Tate","orcid":"0000-0002-8315-6574","email":"jt6@sanger.ac.uk","github":"jgtate","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"05cy4wa09","wikidata":null,"gnd":null,"name":"Wellcome Trust Sanger Institute","partnered":false}],"example":"BRAF","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":"hgnc.symbol","download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"COSMIC","edam.data":"3264","fairsharing":"FAIRsharing.s5zmbp","miriam":"cosmic","n2t":"cosmic","prefixcommons":"cosmic"},"synonyms":["cosmic"],"keywords":["biomedical science","cancer","cosmic","dna","genetics","genome annotation","neoplasm","obsolete somatic mutation"],"domain":null,"references":null,"publications":[{"pubmed":"30371878","doi":"10.1093/nar/gky1015","pmc":"PMC6323903","arxiv":null,"title":"COSMIC: the Catalogue Of Somatic Mutations In Cancer","year":2019},{"pubmed":"25355519","doi":"10.1093/nar/gku1075","pmc":"PMC4383913","arxiv":null,"title":"COSMIC: exploring the world's knowledge of somatic mutations in human cancer","year":2014},{"pubmed":"20952405","doi":"10.1093/nar/gkq929","pmc":"PMC3013785","arxiv":null,"title":"COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer","year":2010},{"pubmed":"15188009","doi":"10.1038/sj.bjc.6601894","pmc":"PMC2409828","arxiv":null,"title":"The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"cosmic.gene","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"dbd":{"prefix":"dbd","name":"Transcription Factor Database","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.","pattern":"^\\d+$","uri_format":"http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/dbd:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.transcriptionfactor.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00tw3jy02","wikidata":null,"gnd":null,"name":"MRC Laboratory of Molecular Biology, Cambridge","partnered":false}],"example":"0045310","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"DBD","edam.data":"2716","miriam":"dbd","n2t":"dbd","pathguide":"496","prefixcommons":"dbd"},"synonyms":[],"keywords":["genome","regulation"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"dbd","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"dbest":{"prefix":"dbest","name":"dbEST","description":"The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.","pattern":"^([A-Z]+)?\\d+(\\.\\d+)?$","uri_format":"https://www.ncbi.nlm.nih.gov/nucest/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"dbEST through DNA Data Bank of Japan (DDBJ)","description":"dbEST through DNA Data Bank of Japan (DDBJ)","homepage":"http://www.ddbj.nig.ac.jp/","contact":null,"uri_format":"https://getentry.ddbj.nig.ac.jp/getentry/na/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/dbest:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"ebi","name":"dbEST through European Nucleotide Archive (ENA)","description":"dbEST through European Nucleotide Archive (ENA)","homepage":"https://www.ebi.ac.uk/ena","contact":null,"uri_format":"https://www.ebi.ac.uk/ena/data/view/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/nucest","repository":null,"contact":{"name":"Todd M Lowe","orcid":"0000-0003-3253-6021","email":"tmjlowe@ucsc.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"BP100000","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"DBEST","edam.data":"1105","fairsharing":"FAIRsharing.v9fya8","integbio":"nbdc00413","miriam":"dbest","n2t":"dbest","ncbi.resource":"dbEST","prefixcommons":"dbest","re3data":"r3d100010648"},"synonyms":[],"keywords":["bioinformatics","cdna","cdna/est","deoxyribonucleic acid","dna","dna sequencing assay","expression data","life science","repository","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"8401577","doi":"10.1038/ng0893-332","pmc":null,"arxiv":null,"title":"dbEST--database for \"expressed sequence tags\"","year":1993}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"dbest","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"dbprobe":{"prefix":"dbprobe","name":"dbProbe","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.","pattern":"^\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/probe/?term=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/dbprobe:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"1000000","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"DBPROBE","edam.data":"2719","miriam":"dbprobe","n2t":"dbprobe","ncbi.resource":"dbProbe","prefixcommons":"dbprobe"},"synonyms":[],"keywords":["nucleotide"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"dbprobe","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"dbsnp":{"prefix":"dbsnp","name":"dbSNP","description":"The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.","pattern":"^rs\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/snp/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/dbsnp:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"sib","name":"SNP2TFBS","description":"SNP2TFBS","homepage":"https://epd.expasy.org/","contact":null,"uri_format":"https://epd.expasy.org/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/snp/","repository":null,"contact":{"name":"Kim Dixon Pruitt","orcid":"0000-0001-7950-1374","email":"pruitt@ncbi.nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"rs121909098","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"dbSNP","cellosaurus.resource":"dbSNP","edam.data":"1106","fairsharing":"FAIRsharing.edxb58","go.resource":"dbSNP","hl7":"6.284","integbio":"nbdc00206","miriam":"dbsnp","n2t":"dbsnp","ncbi.resource":"dbSNP","prefixcommons":"dbsnp","re3data":"r3d100010652","togoid":"Dbsnp","uniprot.resource":"DB-0013","wikidata.property":"P6861"},"synonyms":[],"keywords":["genetic polymorphism","genetic variation","genetic variation databases","genome","life science","repository","sequence","snp","variant"],"domain":null,"references":null,"publications":[{"pubmed":"33095870","doi":"10.1093/nar/gkaa892","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17170002","doi":"10.1093/nar/gkl1031","pmc":"PMC1781113","arxiv":null,"title":"Database resources of the National Center for Biotechnology Information","year":2006},{"pubmed":"11125122","doi":"10.1093/nar/29.1.308","pmc":"PMC29783","arxiv":null,"title":"dbSNP: the NCBI database of genetic variation","year":2001},{"pubmed":"10592272","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"dbsnp","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"dip":{"prefix":"dip","name":"Database of Interacting Proteins","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","pattern":"^DIP(\\:)?\\-\\d{1,}[ENXS]$","uri_format":"https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/dip:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://dip.doe-mbi.ucla.edu/","repository":null,"contact":{"name":"David Eisenberg","orcid":"0000-0003-2432-5419","email":"david@mbi.ucla.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"046rm7j60","wikidata":null,"gnd":null,"name":"UCLA","partnered":false}],"example":"DIP-743N","example_extras":[],"example_decoys":null,"license":"http://dip.doe-mbi.ucla.edu/dip/termsofuse.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"DIP","edam.data":"2616","fairsharing":"FAIRsharing.qje0v8","integbio":"nbdc00049","miriam":"dip","n2t":"dip","pathguide":"3","prefixcommons":"dip","re3data":"r3d100010670","uniprot.resource":"DB-0016"},"synonyms":[],"keywords":["biology","interaction","interaction/pathway","protein","protein interactions","protein-protein interaction","protein-protein interaction databases","psi-mi","repository","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"14681454","doi":"10.1093/nar/gkh086","pmc":"PMC308820","arxiv":null,"title":"The Database of Interacting Proteins: 2004 update","year":2004},{"pubmed":"11752321","doi":"10.1093/nar/30.1.303","pmc":"PMC99070","arxiv":null,"title":"DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions","year":2002},{"pubmed":"1175232","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"11125102","doi":"10.1093/nar/29.1.239","pmc":"PMC29798","arxiv":null,"title":"DIP: The Database of Interacting Proteins: 2001 update","year":2001},{"pubmed":"10592249","doi":"10.1093/nar/28.1.289","pmc":"PMC102387","arxiv":null,"title":"DIP: the database of interacting proteins","year":2000}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"dip","mastodon":null,"github_request_issue":null,"logo":"https://dip.doe-mbi.ucla.edu/dip/img/dip_logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"disprot":{"prefix":"disprot","name":"DisProt","description":"DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature.","pattern":"^DP\\d{5}$","uri_format":"https://disprot.org/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/disprot:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://disprot.org/","repository":null,"contact":{"name":"Silvio C.E. Tosatto","orcid":"0000-0003-4525-7793","email":"silvio.tosatto@unipd.it","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00240q980","wikidata":null,"gnd":null,"name":"University of Padua","partnered":false}],"example":"DP00003","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"DISPROT","edam.data":"2723","fairsharing":"FAIRsharing.dt9z89","go.resource":"DisProt","integbio":"nbdc01798","miriam":"disprot","n2t":"disprot","prefixcommons":"disprot","re3data":"r3d100010561","uniprot.resource":"DB-0017"},"synonyms":[],"keywords":["3d structure","biocuration","biology","biomedical science","chemical structure","disease","family and domain databases","health/disease","interaction/pathway","intrinsically disordered proteins","protein","protein structure","sequence","structural biology","structure"],"domain":null,"references":null,"publications":[{"pubmed":"37904585","doi":"10.1093/nar/gkad928","pmc":null,"arxiv":null,"title":"DisProt in 2024: improving function annotation of intrinsically disordered proteins","year":2024},{"pubmed":"34850135","doi":"10.1093/nar/gkab1082","pmc":"PMC8728214","arxiv":null,"title":"DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation","year":2022},{"pubmed":"31713636","doi":"10.1093/nar/gkz975","pmc":"PMC7145575","arxiv":null,"title":"DisProt: intrinsic protein disorder annotation in 2020","year":2020},{"pubmed":"27899601","doi":"10.1093/nar/gkw1056","pmc":"PMC5210544","arxiv":null,"title":"DisProt 7.0: a major update of the database of disordered proteins","year":2016},{"pubmed":"17145717","doi":"10.1093/nar/gkl893","pmc":"PMC1751543","arxiv":null,"title":"DisProt: the Database of Disordered Proteins","year":2006},{"pubmed":"15310560","doi":"10.1093/bioinformatics/bth476","pmc":null,"arxiv":null,"title":"DisProt: a database of protein disorder","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"disprot","mastodon":null,"github_request_issue":null,"logo":"https://disprot.org/assets/DisProt_prot_vect_brownonly.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"doi":{"prefix":"doi","name":"Digital Object Identifier","description":"The Digital Object Identifier System is for identifying content objects in the digital environment.","pattern":"^10.\\d{2,9}/.*$","uri_format":"https://doi.org/$1","uri_format_resolvable":null,"rdf_uri_format":"http://dx.doi.org/$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/doi:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"doi_http","name":"Digital Object Identifier","description":"An alternate provider from the DOI website using HTTP","homepage":"https://www.doi.org","contact":null,"uri_format":"http://doi.org/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"dx_doi_http","name":"Digital Object Identifier","description":"An alternate provider from the DOI website using HTTP","homepage":"https://www.doi.org","contact":null,"uri_format":"http://dx.doi.org/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"dx_doi_https","name":"Digital Object Identifier","description":"An alternate provider from the DOI website using HTTPS","homepage":"https://www.doi.org","contact":null,"uri_format":"https://dx.doi.org/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"miriam_legacy","name":"Legacy MIRIAM URI","description":"A legacy MIRIAM URI that does not follow the standard pattern","homepage":"https://identifiers.org","contact":null,"uri_format":"http://identifiers.org/DOI/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"scholia","name":"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/","contact":null,"uri_format":"https://scholia.toolforge.org/doi/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.doi.org/","repository":null,"contact":{"name":"Jonathan Clark","orcid":"0000-0001-9551-9662","email":"jonathanmtclark@gmail.com","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"01fyxcz70","wikidata":null,"gnd":null,"name":"DOI Foundation","partnered":false}],"example":"10.1038/s41597-022-01807-3","example_extras":["10.1016/j.foodchem.2008.11.065","10.1093/acprof:oso/9780195159561.001.1","10.1139/z02-135","10.1333/s00897980202a","10.21/FQSQT4T3"],"example_decoys":null,"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"doi","banana_peel":null,"deprecated":false,"mappings":{"bartoc":"20716","biocontext":"DOI","biolink.resource":"doi","cellosaurus.resource":"DOI","edam.data":"1188","fairsharing":"FAIRsharing.hFLKCn","go.resource":"DOI","miriam":"doi","n2t":"doi","prefixcommons":"doi","wikidata.entity":"Q25670","wikidata.property":"P356"},"synonyms":[],"keywords":["bibliography","centrally registered identifier","subject agnostic"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/issues/287","https://github.com/biopragmatics/bioregistry/pull/316"],"publications":[{"pubmed":null,"doi":"10.1000/292","pmc":null,"arxiv":null,"title":"DOI URI Scheme","year":2024}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":"The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html) specifies that `https://doi.org/DOI` is the preferred format:\n\n> 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":null,"contributor_extras":[{"name":"Chris Mungall","orcid":"0000-0002-6601-2165","email":"cjmungall@lbl.gov","github":"cmungall","wikidata":null},{"name":"Daniel Himmelstein","orcid":"0000-0002-3012-7446","email":null,"github":"dhimmel","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"doi","mastodon":null,"github_request_issue":null,"logo":"https://upload.wikimedia.org/wikipedia/commons/1/11/DOI_logo.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"drugbank":{"prefix":"drugbank","name":"DrugBank","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.","pattern":"^DB\\d{5}$","uri_format":"https://go.drugbank.com/drugs/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/drugbank:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.drugbank.ca","repository":null,"contact":{"name":"David S. Wishart","orcid":"0000-0002-3207-2434","email":"david.wishart@ualberta.ca","github":"DavidWishartLab","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"DB14938","example_extras":[],"example_decoys":null,"license":"http://www.drugbank.ca/about","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"bartoc":"18377","biocontext":"DrugBank","cellosaurus.resource":"DrugBank","cheminf":"000406","edam.data":"2326","integbio":"nbdc01071","miriam":"drugbank","n2t":"drugbank","pathguide":"221","prefixcommons":"drugbank","re3data":"r3d100010544","togoid":"Drugbank","uniprot.resource":"DB-0019","wikidata.entity":"Q1122544","wikidata.property":"P715"},"synonyms":["DRUGBANK_ID","DrugBank"],"keywords":["chemical structure","chemistry databases","drug","interaction/pathway","protein","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"37953279","doi":"10.1093/nar/gkad976","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"24203711","doi":"10.1093/nar/gkt1068","pmc":"PMC3965102","arxiv":null,"title":"DrugBank 4.0: shedding new light on drug metabolism","year":2013},{"pubmed":"21059682","doi":"10.1093/nar/gkq1126","pmc":"PMC3013709","arxiv":null,"title":"DrugBank 3.0: a comprehensive resource for 'omics' research on drugs","year":2010},{"pubmed":"18048412","doi":"10.1093/nar/gkm958","pmc":"PMC2238889","arxiv":null,"title":"DrugBank: a knowledgebase for drugs, drug actions and drug targets","year":2007},{"pubmed":"16381955","doi":"10.1093/nar/gkj067","pmc":"PMC1347430","arxiv":null,"title":"DrugBank: a comprehensive resource for in silico drug discovery and exploration","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"drugbank","mastodon":null,"github_request_issue":null,"logo":"https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Drugbank_logo.svg/1280px-Drugbank_logo.svg.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ec":{"prefix":"ec","name":"Enzyme Nomenclature","description":"The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories.\n\nThe Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).\n\nThere are few notable resources providing access to the Enzyme Nomenclature:\n\n<table class=\"table table-striped\"><thead><tr><th>Website</th><th>Homepage</td><th>Notes</td></tr></thead><tbody><tr><td>ExplorEnz</td><td><a href=\"https://www.enzyme-database.org\">https://www.enzyme-database.org</a></td><td>This is the resource officially recommended by IUBMB</td></tr><tr><td>IUBMB (via by Queen Mary)</td><td><a href=\"https://iubmb.qmul.ac.uk/enzyme\">https://iubmb.qmul.ac.uk/enzyme</a></td><td>This is a web-based version of the <a href=\"https://archive.org/details/enzymenomenclatu0000inte_d6c2\">1992 publication</a>.</td></tr><tr><td>IntEnz</td><td><a href=\"https://www.ebi.ac.uk/intenz\">https://www.ebi.ac.uk/intenz</a></td><td>Shutdown in 2024</td></tr><tr><td>ExPaSy</td><td><a href=\"https://enzyme.expasy.org\">https://enzyme.expasy.org</a></td></tr><tr><td>EnzymePortal</td><td><a href=\"https://www.ebi.ac.uk/enzymeportal\">https://www.ebi.ac.uk/enzymeportal</a></td><td></td></tr></tbody></table>","pattern":"^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.[nB]\\d{1,3}|\\.-\\.-\\.-|\\.\\d{1,3}\\.-\\.-|\\.\\d{1,3}\\.\\d{1,3}\\.-)?$","uri_format":"https://www.enzyme-database.org/query.php?ec=$1","uri_format_resolvable":null,"rdf_uri_format":"https://purl.expasy.org/enzyme/EC/$1","providers":[{"code":"","name":"KEGG Ligand Database for Enzyme Nomenclature","description":"KEGG Ligand Database for Enzyme Nomenclature","homepage":"https://www.genome.jp/dbget-bin/www_bfind?enzyme","contact":null,"uri_format":"https://www.genome.jp/dbget-bin/www_bget?ec:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/intenz:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"enzymeportal","name":"EnzymePortal","description":" Enzyme Portal integrates publicly available information about enzymes, such as reaction mechanism, small-molecule chemistry, biochemical pathways and drug compounds.","homepage":"https://www.ebi.ac.uk/enzymeportal","contact":null,"uri_format":"https://www.ebi.ac.uk/enzymeportal/ec/$1","first_party":null,"publications":[{"pubmed":"28158609","doi":"10.1093/protein/gzx008","pmc":"PMC5421622","arxiv":null,"title":"An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge","year":2017}],"example":null,"status":null,"organization":null},{"code":"expasy","name":"Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)","description":"Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)","homepage":"https://enzyme.expasy.org/","contact":null,"uri_format":"https://enzyme.expasy.org/EC/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.enzyme-database.org","repository":null,"contact":{"name":"Kristian Axelsen","orcid":"0000-0003-3889-2879","email":"kristian.axelsen@sib.swiss","github":"kaxelsen","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00910ay07","wikidata":null,"gnd":null,"name":"International Union of Biochemistry and Molecular Biology","partnered":false}],"example":"1.1.1.1","example_extras":["2","2.-.-.-","2.3","2.3.-.-","2.3.1","2.3.1.-","2.3.1.n12","3.1.26.n2","3.4.24.B15"],"example_decoys":["100","2.","2.n1","2.3.","2.3.n1","2.3.1.","2.3.1.n","2.3.4.1.","2.-.-","2.-","2.3.4.1.-"],"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/ec/ec.owl","download_obo":"https://w3id.org/biopragmatics/resources/ec/ec.obo","download_json":"https://w3id.org/biopragmatics/resources/ec/ec.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"bartoc":"671","biocontext":"EC-CODE","edam.data":"1011","fairsharing":"FAIRsharing.rfLD2u","go.resource":"EC","integbio":"nbdc00508","miriam":"ec-code","n2t":"ec-code","ols":"ec","pathguide":"106","prefixcommons":"intenz","re3data":"r3d100010803","togoid":"Ec","uniprot.resource":"DB-0024","wikidata.entity":"Q741108","wikidata.property":"P591"},"synonyms":["EC","EC number","EC-CODE","ECCODE","EC_CODE","ec-code","eccode","intenz"],"keywords":["biochemistry","biopax","centrally registered identifier","classification","enzyme","enzyme and pathway databases","enzyme commission number","enzymology","function","ontology","ontology/terminology/nomenclature","protein","repository","rna"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/issues/681","https://github.com/biopragmatics/bioregistry/pull/1611"],"publications":[{"pubmed":"28158609","doi":"10.1093/protein/gzx008","pmc":"PMC5421622","arxiv":null,"title":"An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge","year":2017},{"pubmed":"14681451","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"10592255","doi":"10.1093/nar/28.1.304","pmc":"PMC102465","arxiv":null,"title":"The ENZYME database in 2000","year":2000}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":"The Nomenclature Committee website does not yet contain an official policy regarding the use of dashes in the hierarchical categorization of enzymes, so the Bioregistry's regular expression is permissive and accepts both EC identifiers with dashes (e.g. <code>2.3.-.-</code>) and without dashes (e.g., <code>2.3</code>). This means you may have to do post-processing of EC identifiers in data integration scenarios.","contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"EC","mastodon":null,"github_request_issue":null,"logo":"https://www.enzyme-database.org/images/banner_5.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ega":{"prefix":"ega","name":"European Genome-phenome Archive","description":"The European Genome-phenome Archive (EGA) is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. Jointly managed by the European Bioinformatics Institute (EMBL-EBI) in Cambridge (UK) and the Centre for Genomic Regulation (CRG) in Barcelona.","pattern":"^EGA[SCPNRXZDBF][0-9]{11}$","uri_format":"https://ega-archive.org/identifiers/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://ega-archive.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"EGAD00001008392","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"cellosaurus.resource":"EGA","edam.data":"2383","fairsharing":"FAIRsharing.mya1ff","miriam":"ega"},"synonyms":[],"keywords":["biology","biomedical science","biospecimen","cancer","clinical studies","covid-19","disease phenotype","dna sequence","genetic polymorphism","genome","genomics","genotype","microarray assay","phenomics","phenotype","rare disorder","rna-seq assay","single cell gene expression","whole genome sequencing assay"],"domain":null,"references":null,"publications":[{"pubmed":"26111507","doi":"10.1038/ng.3312","pmc":null,"arxiv":null,"title":"The European Genome-phenome Archive of human data consented for biomedical research","year":2015},{"pubmed":null,"doi":"10.1093/nar/gkab1059","pmc":null,"arxiv":null,"title":"The European Genome-phenome Archive in 2021","year":2021}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"ega","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZDg9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--e00754101f557d66dde0a63d5347b36a704a76d8/ega-logo.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"emdb":{"prefix":"emdb","name":"Electron Microscopy Data Bank","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.","pattern":"^EMD-\\d{4,5}$","uri_format":"https://www.ebi.ac.uk/pdbe/entry/emdb/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/emdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/pdbe/emdb/","repository":null,"contact":{"name":"Ardan Patwardhan","orcid":"0000-0001-7663-9028","email":"ardan@ebi.ac.uk","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"EMD-1001","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"EMDB","edam.data":"1146","fairsharing":"FAIRsharing.651n9j","miriam":"emdb","n2t":"emdb","prefixcommons":"emdb","re3data":"r3d100010562","uniprot.resource":"DB-0272"},"synonyms":[],"keywords":["3d structure databases","bioimaging","digital image processing","electron microscopy","epidemiology","microscopy","protein","structural biology","structure","virology","x-ray crystallography 3d molecular structure determination assay","x-ray diffraction"],"domain":null,"references":null,"publications":[{"pubmed":"26578576","doi":"10.1093/nar/gkv1126","pmc":"PMC4702818","arxiv":null,"title":"EMDataBank unified data resource for 3DEM","year":2015},{"pubmed":"20935055","doi":"10.1093/nar/gkq880","pmc":"PMC3013769","arxiv":null,"title":"EMDataBank.org: unified data resource for CryoEM","year":2010},{"pubmed":"12417136","doi":"10.1016/s0968-0004(02)02176-x","pmc":null,"arxiv":null,"title":"New electron microscopy database and deposition system","year":2002}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"emdb","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbllCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--18021442ee90695572715042ff5364d65b2a27a0/EMBD_logo_2017_light_background.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ensembl":{"prefix":"ensembl","name":"Ensembl Gene","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.","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])?))$","uri_format":"https://www.ensembl.org/id/$1","uri_format_resolvable":null,"rdf_uri_format":"http://rdf.ebi.ac.uk/resource/ensembl/$1","providers":[{"code":"","name":"Ensembl US East mirror","description":"Ensembl US East mirror","homepage":"http://useast.ensembl.org/","contact":null,"uri_format":"http://useast.ensembl.org/id/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"","name":"Ensembl Asia mirror","description":"Ensembl Asia mirror","homepage":"http://asia.ensembl.org/","contact":null,"uri_format":"http://asia.ensembl.org/id/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bgee","name":"Bgee","description":"Gene expression in various tissues","homepage":"https://bgee.org","contact":null,"uri_format":"https://bgee.org/?page=gene&gene_id=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/ensembl:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"ciliogenics","name":"CilioGenics","description":"CilioGenics is an integrated and open source, community friendly database for ciliary genes.","homepage":"https://ciliogenics.com","contact":null,"uri_format":"https://ciliogenics.com/?page=General%20info&query=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"digger","name":"Domain Interaction Graph Guided Explorer","description":"Digger integrates protein-protein interactions and domain-domain interactions into a joint graph and maps interacting residues to exons.","homepage":"https://exbio.wzw.tum.de/digger/","contact":null,"uri_format":"https://exbio.wzw.tum.de/digger/ID/gene/human/$1","first_party":null,"publications":[{"pubmed":"40337913","doi":"10.1093/nar/gkaf384","pmc":"PMC12230681","arxiv":null,"title":"DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders","year":2025}],"example":null,"status":null,"organization":null},{"code":"gnomad","name":"Genome Aggregation database","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","contact":null,"uri_format":"https://gnomad.broadinstitute.org/gene/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"opentargets.genetics","name":"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","contact":null,"uri_format":"https://genetics.opentargets.org/gene/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ensembl.org/","repository":null,"contact":{"name":"Paul Flicek","orcid":"0000-0002-3897-7955","email":"flicek@ebi.ac.uk","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"ENSG00000139618","example_extras":["ENSG00000049246.14","ENSG00000109819.9","ENSG00000132326.12","ENSG00000179094.16","ENST00000264867.7"],"example_decoys":null,"license":"http://www.ebi.ac.uk/Information/termsofuse.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"ENSEMBL","edam.data":"2610","go.resource":"ENSEMBL","integbio":"nbdc00054","miriam":"ensembl","n2t":"ensembl","ncbi.resource":"ENSEMBL","prefixcommons":"ensembl","re3data":"r3d100010228","uniprot.resource":"DB-0023","wikidata.entity":"Q7187","wikidata.property":"P594"},"synonyms":["Ensembl"],"keywords":["genome","genome annotation databases","genome/gene","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"40337913","doi":"10.1093/nar/gkaf384","pmc":"PMC12230681","arxiv":null,"title":"DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders","year":2025},{"pubmed":"39656687","doi":"10.1093/nar/gkae1071","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"34791404","doi":"10.1093/nar/gkab1049","pmc":"PMC8728283","arxiv":null,"title":"Ensembl 2022","year":2022},{"pubmed":"31691826","doi":"10.1093/nar/gkz966","pmc":"PMC7145704","arxiv":null,"title":"Ensembl 2020","year":2020},{"pubmed":"30407521","doi":"10.1093/nar/gky1113","pmc":"PMC6323964","arxiv":null,"title":"Ensembl 2019","year":2019},{"pubmed":"28365736","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"27899575","doi":"10.1093/nar/gkw1104","pmc":"PMC5210575","arxiv":null,"title":"Ensembl 2017","year":2016},{"pubmed":"27337980","doi":"10.1093/database/baw093","pmc":"PMC4919035","arxiv":null,"title":"The Ensembl gene annotation system","year":2016},{"pubmed":"27268795","doi":"10.1186/s13059-016-0974-4","pmc":"PMC4893825","arxiv":null,"title":"The Ensembl Variant Effect Predictor","year":2016},{"pubmed":"27141089","doi":"10.1093/database/baw053","pmc":"PMC4852398","arxiv":null,"title":"Ensembl comparative genomics resources","year":2016},{"pubmed":"26980512","doi":"10.1093/database/bav127","pmc":"PMC4792531","arxiv":null,"title":"ncRNA orthologies in the vertebrate lineage","year":2016},{"pubmed":"26896847","doi":"10.1093/database/bav096","pmc":"PMC4761110","arxiv":null,"title":"Ensembl comparative genomics resources","year":2016},{"pubmed":"26888907","doi":"10.1093/database/bav119","pmc":"PMC4756621","arxiv":null,"title":"Ensembl regulation resources","year":2016},{"pubmed":"26687719","doi":"10.1093/nar/gkv1157","pmc":"PMC4702834","arxiv":null,"title":"Ensembl 2016","year":2015},{"pubmed":"25887522","doi":"10.1186/s13059-015-0621-5","pmc":"PMC4407537","arxiv":null,"title":"The ensembl regulatory build","year":2015},{"pubmed":"25352552","doi":"10.1093/nar/gku1010","pmc":"PMC4383879","arxiv":null,"title":"Ensembl 2015","year":2014},{"pubmed":"25236461","doi":"10.1093/bioinformatics/btu613","pmc":"PMC4271150","arxiv":null,"title":"The Ensembl REST API: Ensembl Data for Any Language","year":2014},{"pubmed":"24363377","doi":"10.1093/bioinformatics/btt737","pmc":"PMC3967112","arxiv":null,"title":"WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis","year":2013},{"pubmed":"24316576","doi":"10.1093/nar/gkt1196","pmc":"PMC3964975","arxiv":null,"title":"Ensembl 2014","year":2013},{"pubmed":"23203987","doi":"10.1093/nar/gks1236","pmc":"PMC3531136","arxiv":null,"title":"Ensembl 2013","year":2012},{"pubmed":"22955987","doi":"10.1101/gr.135350.111","pmc":"PMC3431492","arxiv":null,"title":"GENCODE: the reference human genome annotation for The ENCODE Project","year":2012},{"pubmed":"22798491","doi":"10.1101/gr.137901.112","pmc":"PMC3460200","arxiv":null,"title":"Incorporating RNA-seq data into the zebrafish Ensembl genebuild","year":2012},{"pubmed":"22086963","doi":"10.1093/nar/gkr991","pmc":"PMC3245178","arxiv":null,"title":"Ensembl 2012","year":2011},{"pubmed":"21785142","doi":"10.1093/database/bar030","pmc":"PMC3170168","arxiv":null,"title":"Ensembl BioMarts: a hub for data retrieval across taxonomic space","year":2011},{"pubmed":"21400687","doi":"10.1002/0471142905.hg0611s69","pmc":"PMC3099348","arxiv":null,"title":"Disease and phenotype data at Ensembl","year":2011},{"pubmed":"21045057","doi":"10.1093/nar/gkq1064","pmc":"PMC3013672","arxiv":null,"title":"Ensembl 2011","year":2010},{"pubmed":"20562413","doi":"10.1093/bioinformatics/btq330","pmc":"PMC2916720","arxiv":null,"title":"Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor","year":2010},{"pubmed":"20459813","doi":"10.1186/1471-2105-11-240","pmc":"PMC2885371","arxiv":null,"title":"eHive: an artificial intelligence workflow system for genomic analysis","year":2010},{"pubmed":"20459810","doi":"10.1186/1471-2105-11-238","pmc":"PMC2882931","arxiv":null,"title":"A database and API for variation, dense genotyping and resequencing data","year":2010},{"pubmed":"20459808","doi":"10.1186/1471-2164-11-295","pmc":"PMC2894802","arxiv":null,"title":"Touring Ensembl: a practical guide to genome browsing","year":2010},{"pubmed":"20459805","doi":"10.1186/1471-2164-11-293","pmc":"PMC2894800","arxiv":null,"title":"Ensembl variation resources","year":2010},{"pubmed":"19906699","doi":"10.1093/nar/gkp972","pmc":"PMC2808936","arxiv":null,"title":"Ensembl's 10th year","year":2009},{"pubmed":"19033362","doi":"10.1093/nar/gkn828","pmc":"PMC2686571","arxiv":null,"title":"Ensembl 2009","year":2008},{"pubmed":"19029536","doi":"10.1101/gr.073585.107","pmc":"PMC2652215","arxiv":null,"title":"EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates","year":2008},{"pubmed":"18849525","doi":"10.1101/gr.076521.108","pmc":"PMC2577868","arxiv":null,"title":"Genome-wide nucleotide-level mammalian ancestor reconstruction","year":2008},{"pubmed":"18000006","doi":"10.1093/nar/gkm988","pmc":"PMC2238821","arxiv":null,"title":"Ensembl 2008","year":2007},{"pubmed":"17967807","doi":"10.1093/bfgp/elm025","pmc":null,"arxiv":null,"title":"Genome browsing with Ensembl: a practical overview","year":2007},{"pubmed":"17148474","doi":"10.1093/nar/gkl996","pmc":"PMC1761443","arxiv":null,"title":"Ensembl 2007","year":2006},{"pubmed":"16874317","doi":"10.1038/ng0806-853a","pmc":"PMC2610433","arxiv":null,"title":"TranscriptSNPView: a genome-wide catalog of mouse coding variation","year":2006},{"pubmed":"16381931","doi":"10.1093/nar/gkj133","pmc":"PMC1347495","arxiv":null,"title":"Ensembl 2006","year":2006},{"pubmed":"15608235","doi":"10.1093/nar/gki138","pmc":"PMC540092","arxiv":null,"title":"Ensembl 2005","year":2005},{"pubmed":"15145580","doi":"10.1016/j.tig.2004.04.002","pmc":null,"arxiv":null,"title":"Genome information resources - developments at Ensembl","year":2004},{"pubmed":"15123595","doi":"10.1101/gr.1862204","pmc":"PMC479129","arxiv":null,"title":"ESTGenes: alternative splicing from ESTs in Ensembl","year":2004},{"pubmed":"15123594","doi":"10.1101/gr.1866304","pmc":"PMC479128","arxiv":null,"title":"The Ensembl computing architecture","year":2004},{"pubmed":"15123591","doi":"10.1101/gr.1863004","pmc":"PMC479125","arxiv":null,"title":"The Ensembl Web site: mechanics of a genome browser","year":2004},{"pubmed":"15123590","doi":"10.1101/gr.1858004","pmc":"PMC479124","arxiv":null,"title":"The Ensembl automatic gene annotation system","year":2004},{"pubmed":"15123589","doi":"10.1101/gr.1859804","pmc":"PMC479123","arxiv":null,"title":"The Ensembl analysis pipeline","year":2004},{"pubmed":"15123588","doi":"10.1101/gr.1857204","pmc":"PMC479122","arxiv":null,"title":"The Ensembl core software libraries","year":2004},{"pubmed":"12519943","doi":"10.1093/nar/gkg083","pmc":"PMC165530","arxiv":null,"title":"Ensembl 2002: accommodating comparative genomics","year":2003},{"pubmed":"11752248","doi":"10.1093/nar/30.1.38","pmc":"PMC99161","arxiv":null,"title":"The Ensembl genome database project","year":2002}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"ensembl","mastodon":"ensembl@genomic.social","github_request_issue":null,"logo":"https://useast.ensembl.org/img/ebang-400dpi.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"epd":{"prefix":"epd","name":"Eukaryotic Promoter Database","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.","pattern":"^[A-Z-_0-9]+$","uri_format":"https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://epd.expasy.org/epd","repository":null,"contact":{"name":"Philipp Bucher","orcid":"0000-0002-0816-7775","email":"Philipp.Bucher@sib.swiss","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"002n09z45","wikidata":null,"gnd":null,"name":"SIB Swiss Institute of Bioinformatics","partnered":false}],"example":"TA_H3","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"EPD","edam.data":"2386","fairsharing":"FAIRsharing.yk1krv","integbio":"nbdc00438","miriam":"epd","n2t":"epd","ncbi.resource":"EPD"},"synonyms":[],"keywords":["bioinformatics","biology","dna sequence","genome/gene","promoter","sequence","transcription factor"],"domain":null,"references":null,"publications":[{"pubmed":"9847211","doi":"10.1093/nar/27.1.307","pmc":"PMC148166","arxiv":null,"title":"The Eukaryotic Promoter Database (EPD): recent developments","year":1999},{"pubmed":"9399872","doi":"10.1093/nar/26.1.353","pmc":"PMC147208","arxiv":null,"title":"The Eukaryotic Promoter Database EPD","year":1998},{"pubmed":"3808945","doi":"10.1093/nar/14.24.10009","pmc":"PMC341352","arxiv":null,"title":"Compilation and analysis of eukaryotic POL II promoter sequences","year":1986},{"pubmed":"28981707","doi":"10.1093/nar/gkx807","pmc":"PMC5753345","arxiv":null,"title":"The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics","year":2018},{"pubmed":"27899657","doi":"10.1093/nar/gkw1069","pmc":"PMC5210552","arxiv":null,"title":"The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms","year":2016},{"pubmed":"25378343","doi":"10.1093/nar/gku1111","pmc":"PMC4383928","arxiv":null,"title":"The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools","year":2014},{"pubmed":"23193273","doi":"10.1093/nar/gks1233","pmc":"PMC3531148","arxiv":null,"title":"EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era","year":2012},{"pubmed":"16381980","doi":"10.1093/nar/gkj146","pmc":"PMC1347508","arxiv":null,"title":"EPD in its twentieth year: towards complete promoter coverage of selected model organisms","year":2006},{"pubmed":"14681364","doi":"10.1093/nar/gkh122","pmc":"PMC308856","arxiv":null,"title":"The Eukaryotic Promoter Database EPD: the impact of in silico primer extension","year":2004},{"pubmed":"11752326","doi":"10.1093/nar/30.1.322","pmc":"PMC99099","arxiv":null,"title":"The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data","year":2002},{"pubmed":"10592254","doi":"10.1093/nar/28.1.302","pmc":"PMC102462","arxiv":null,"title":"The eukaryotic promoter database (EPD)","year":2000}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Sébastien Moretti","orcid":"0000-0003-3947-488X","email":"sebastien.moretti@sib.swiss","github":"smoretti","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"epd","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbTRCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--2bb2563b5fffe908d33560e31bf9e6885ac40441/Screenshot%20from%202022-08-02%2008-47-48.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"flybase":{"prefix":"flybase","name":"FlyBase Gene","description":"FlyBase is the database of the Drosophila Genome Projects and of associated literature.","pattern":"^FB\\w{2}\\d{7}$","uri_format":"https://flybase.org/reports/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"The FlyBase Database","description":"The FlyBase Database","homepage":"http://flybase.org/","contact":null,"uri_format":"http://flybase.org/reports/$1.html","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"agr","name":"FlyBase through the Alliance of Genome Resources","description":"FlyBase through the Alliance of Genome Resources","homepage":"https://www.alliancegenome.org","contact":null,"uri_format":"https://www.alliancegenome.org/gene/FB:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/flybase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://bioentity.link/","repository":null,"contact":{"name":"Victoria K. Jenkins","orcid":"0000-0002-1567-7626","email":"vjenkins@morgan.harvard.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"FBgn0011293","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/flybase/flybase.owl","download_obo":"https://w3id.org/biopragmatics/resources/flybase/flybase.obo","download_json":"https://w3id.org/biopragmatics/resources/flybase/flybase.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"FlyBase","edam.data":"1089","fairsharing":"FAIRsharing.wrvze3","go.resource":"FB","integbio":"nbdc00064","miriam":"fb","n2t":"fb","ncbi.resource":"FLYBASE","pathguide":"460","prefixcommons":"flybase","re3data":"r3d100010591","rrid.resource":"FlyBase","uniprot.resource":"DB-0026","wikidata.property":"P3852"},"synonyms":["FB","FlyBase"],"keywords":["allele","anatomy","bibliography/documents","bio.tools","biocuration","bioinformatics","bioresource","blast","cdna","cdna/est","cell line","chromosomal aberration","clone library","comparative genomics","controlled term","crispr","digital curation","dna","drosophilidae","expression","expression data","faseb list","functional genomics","gene","gene model annotation","gene name","genetic variation","genetics","genome","genome/gene","genomics","genotype","go-term enrichment data","health/disease","image","image collection","image/movie","insertion sequence","interaction","interaction/pathway","life science","life-cycle","literature curation","molecular biology","molecular genetics","molecular interaction","molecular_function","movie","mutant","ontology","ontology/terminology/nomenclature","organism","organism-specific databases","orthologous","phenotype","prediction and recognition","protein","protein interactions","recombinant dna","regulatory ncrna-mediated post-transcriptional gene silencing","regulatory region","repository","rna","rna-seq","sequence","sequence feature","single balancer","stock","taxonomy","transposable element","video resource"],"domain":null,"references":null,"publications":[{"pubmed":"9847148","doi":"10.1093/nar/27.1.85","pmc":"PMC148103","arxiv":null,"title":"The FlyBase database of the Drosophila Genome Projects and community literature","year":1999},{"pubmed":"9399806","doi":"10.1093/nar/26.1.85","pmc":"PMC147222","arxiv":null,"title":"FlyBase: a Drosophila database","year":1998},{"pubmed":"9045212","doi":"10.1093/nar/25.1.63","pmc":"PMC146418","arxiv":null,"title":"FlyBase: a Drosophila database. The FlyBase consortium","year":1997},{"pubmed":"8594600","doi":"10.1093/nar/24.1.53","pmc":"PMC145580","arxiv":null,"title":"FlyBase: the Drosophila database","year":1996},{"pubmed":"8578603","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"7937045","doi":"10.1093/nar/22.17.3456","pmc":"PMC308301","arxiv":null,"title":"FlyBase--the Drosophila database. The FlyBase Consortium","year":1994},{"pubmed":"7925011","doi":"10.1242/dev.120.7.2077","pmc":null,"arxiv":null,"title":"FlyBase--the Drosophila genetic database","year":1994},{"pubmed":"38301657","doi":"10.1093/genetics/iyad211","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"33219682","doi":"10.1093/nar/gkaa1026","pmc":"PMC7779046","arxiv":null,"title":"FlyBase: updates to the Drosophila melanogaster knowledge base","year":2021},{"pubmed":"30364959","doi":"10.1093/nar/gky1003","pmc":"PMC6323960","arxiv":null,"title":"FlyBase 2.0: the next generation","year":2019},{"pubmed":"29761468","doi":"10.1007/978-1-4939-7737-6_16","pmc":"PMC5996772","arxiv":null,"title":"Using FlyBase to Find Functionally Related Drosophila Genes","year":2018},{"pubmed":"27930807","doi":"10.1002/cpbi.19","pmc":"PMC5152691","arxiv":null,"title":"Exploring FlyBase Data Using QuickSearch","year":2016},{"pubmed":"27799470","doi":"10.1093/nar/gkw1016","pmc":"PMC5210523","arxiv":null,"title":"FlyBase at 25: looking to the future","year":2016},{"pubmed":"26935103","doi":"10.1242/dmm.023317","pmc":"PMC4826978","arxiv":null,"title":"FlyBase portals to human disease research using Drosophila models","year":2016},{"pubmed":"26467478","doi":"10.1093/nar/gkv1046","pmc":"PMC4702782","arxiv":null,"title":"FlyBase: establishing a Gene Group resource for Drosophila melanogaster","year":2015},{"pubmed":"26109357","doi":"10.1534/g3.115.018929","pmc":"PMC4528329","arxiv":null,"title":"Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data","year":2015},{"pubmed":"26109356","doi":"10.1534/g3.115.018937","pmc":"PMC4528330","arxiv":null,"title":"Gene Model Annotations for Drosophila melanogaster: The Rule-Benders","year":2015},{"pubmed":"25398896","doi":"10.1093/nar/gku1099","pmc":"PMC4383921","arxiv":null,"title":"FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations","year":2014},{"pubmed":"24234449","doi":"10.1093/nar/gkt1092","pmc":"PMC3964969","arxiv":null,"title":"FlyBase 102--advanced approaches to interrogating FlyBase","year":2013},{"pubmed":"22554788","doi":"10.1093/database/bas024","pmc":"PMC3342516","arxiv":null,"title":"Directly e-mailing authors of newly published papers encourages community curation","year":2012},{"pubmed":"22127867","doi":"10.1093/nar/gkr1030","pmc":"PMC3245098","arxiv":null,"title":"FlyBase 101--the basics of navigating FlyBase","year":2011},{"pubmed":"18948289","doi":"10.1093/nar/gkn788","pmc":"PMC2686450","arxiv":null,"title":"FlyBase: enhancing Drosophila Gene Ontology annotations","year":2008},{"pubmed":"18641940","doi":"10.1007/978-1-59745-583-1_3","pmc":null,"arxiv":null,"title":"FlyBase : a database for the Drosophila research community","year":2008},{"pubmed":"18160408","doi":"10.1093/nar/gkm930","pmc":"PMC2238994","arxiv":null,"title":"FlyBase: integration and improvements to query tools","year":2007},{"pubmed":"17099233","doi":"10.1093/nar/gkl827","pmc":"PMC1669768","arxiv":null,"title":"FlyBase: genomes by the dozen","year":2006},{"pubmed":"16381917","doi":"10.1093/nar/gkj068","pmc":"PMC1347431","arxiv":null,"title":"FlyBase: anatomical data, images and queries","year":2006},{"pubmed":"15608223","doi":"10.1093/nar/gki046","pmc":"PMC540000","arxiv":null,"title":"FlyBase: genes and gene models","year":2005},{"pubmed":"12519974","doi":"10.1093/nar/gkg094","pmc":"PMC165541","arxiv":null,"title":"The FlyBase database of the Drosophila genome projects and community literature","year":2003},{"pubmed":"11752267","doi":"10.1093/nar/30.1.106","pmc":"PMC99082","arxiv":null,"title":"The FlyBase database of the Drosophila genome projects and community literature","year":2002},{"pubmed":"11465064","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"FlyBase","mastodon":null,"github_request_issue":null,"logo":"http://flybase.org/images/fly_logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"fma":{"prefix":"fma","name":"Foundational Model of Anatomy","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.","pattern":"^\\d+$","uri_format":"http://purl.org/sig/ont/fma/$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.org/sig/ont/fma/$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/fma:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://si.washington.edu/projects/fma","repository":"https://github.com/uw-sig/FMA","contact":{"name":"Jose Leonardo (Onard) Mejino","orcid":"0000-0003-2105-2283","email":"mejino@uw.edu","github":"Onard","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"63189","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":"5.1.0","part_of":null,"part_of_database":null,"provides":null,"download_owl":"http://purl.org/sig/ont/fma.owl","download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"FMA","banana_peel":null,"deprecated":true,"mappings":{"aberowl":"FMA","bartoc":"571","biocontext":"FMA","biolink.resource":"FMA","bioportal":"FMA","edam.data":"1182","fairsharing":"FAIRsharing.x56jsy","go.resource":"FMA","hl7":"6.119","integbio":"nbdc00273","miriam":"fma","n2t":"fma","obofoundry":"fma","ols":"fma","ontobee":"FMA","prefixcommons":"fma","wikidata.entity":"Q1406710","wikidata.property":"P1402"},"synonyms":["FMAID","FMA_RETIRED"],"keywords":["anatomy","biomedical science","human","neuroimaging measurement","obo","ontology","ontology/terminology/nomenclature","organism","owl","phenotype","radiology"],"domain":null,"references":null,"publications":[{"pubmed":"27235801","doi":"10.1016/j.artmed.2016.04.003","pmc":"PMC4915823","arxiv":null,"title":"From frames to OWL2: Converting the Foundational Model of Anatomy","year":2016},{"pubmed":"18688289","doi":"10.1016/j.websem.2007.12.001","pmc":"PMC2500209","arxiv":null,"title":"Translating the Foundational Model of Anatomy into OWL","year":2008},{"pubmed":"18360535","doi":"10.1016/j.websem.2006.05.007","pmc":"PMC2270940","arxiv":null,"title":"The foundational model of anatomy in OWL: Experience and perspectives","year":2006},{"pubmed":"17271570","doi":"10.1109/iembs.2004.1404513","pmc":null,"arxiv":null,"title":"The foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions","year":2004},{"pubmed":"16779026","doi":null,"pmc":"PMC1560487","arxiv":null,"title":"Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study","year":2005},{"pubmed":"14759821","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14759820","doi":"10.1016/j.jbi.2003.11.007","pmc":null,"arxiv":null,"title":"A reference ontology for biomedical informatics: the Foundational Model of Anatomy","year":2003}],"appears_in":[],"depends_on":[],"namespace_in_lui":true,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"FMA","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBYTg9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--16f323877b0cea5b9b3df9ea964ed441ad10cff1/fma.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"genbank":{"prefix":"genbank","name":"GenBank","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).","pattern":null,"uri_format":"https://www.ncbi.nlm.nih.gov/nucleotide/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/genbank:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/genbank","repository":null,"contact":{"name":"Eric P. Nawrocki","orcid":"0000-0002-2497-3427","email":"nawrocke@ncbi.nlm.nih.gov","github":"nawrockie","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"U49845","example_extras":[],"example_decoys":null,"license":"http://www.nlm.nih.gov/copyright.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"GenBank","cheminf":"000304","edam.data":"2292","fairsharing":"FAIRsharing.9kahy4","go.resource":"GenBank","integbio":"nbdc00276","prefixcommons":"genbank","re3data":"r3d100010528","uniprot.resource":"DB-0028"},"synonyms":[],"keywords":["bioinformatics","cdna/est","comparative genomics","covid-19","dna","dna sequencing assay","epigenomics","functional genomics","genetic variation","genome alignment","genome assembly","genome/gene","genomics","metagenomics","metaproteomics","microbiology","next generation sequencing","reference genome","repository","rna","rna-seq assay","sequence","sequence annotation","sequence databases","sequence variant","sequencing assay","transcriptomics","virology"],"domain":null,"references":null,"publications":[{"pubmed":"39558184","doi":"10.1093/nar/gkae1114","pmc":null,"arxiv":null,"title":"GenBank 2025 update","year":2024},{"pubmed":"32448124","doi":"10.1186/s12859-020-3537-3","pmc":"PMC7245624","arxiv":null,"title":"VADR: validation and annotation of virus sequence submissions to GenBank","year":2020},{"pubmed":"31665464","doi":"10.1093/nar/gkz956","pmc":"PMC7145611","arxiv":null,"title":"GenBank","year":2020},{"pubmed":"30365038","doi":"10.1093/nar/gky989","pmc":"PMC6323954","arxiv":null,"title":"GenBank","year":2019},{"pubmed":"29140468","doi":"10.1093/nar/gkx1094","pmc":"PMC5753231","arxiv":null,"title":"GenBank","year":2018},{"pubmed":"27899564","doi":"10.1093/nar/gkw1070","pmc":"PMC5210553","arxiv":null,"title":"GenBank","year":2016},{"pubmed":"26590407","doi":"10.1093/nar/gkv1276","pmc":"PMC4702903","arxiv":null,"title":"GenBank","year":2015},{"pubmed":"25414350","doi":"10.1093/nar/gku1216","pmc":"PMC4383990","arxiv":null,"title":"GenBank","year":2014},{"pubmed":"24217914","doi":"10.1093/nar/gkt1030","pmc":"PMC3965104","arxiv":null,"title":"GenBank","year":2013},{"pubmed":"23193287","doi":"10.1093/nar/gks1195","pmc":"PMC3531190","arxiv":null,"title":"GenBank","year":2012},{"pubmed":"22144687","doi":"10.1093/nar/gkr1202","pmc":"PMC3245039","arxiv":null,"title":"GenBank","year":2011},{"pubmed":"21071399","doi":"10.1093/nar/gkq1079","pmc":"PMC3013681","arxiv":null,"title":"GenBank","year":2010},{"pubmed":"18940867","doi":"10.1093/nar/gkn723","pmc":"PMC2686462","arxiv":null,"title":"GenBank","year":2008},{"pubmed":"18073190","doi":"10.1093/nar/gkm929","pmc":"PMC2238942","arxiv":null,"title":"GenBank","year":2007},{"pubmed":"17170002","doi":"10.1093/nar/gkl1031","pmc":"PMC1781113","arxiv":null,"title":"Database resources of the National Center for Biotechnology Information","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"genbank","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"genedb":{"prefix":"genedb","name":"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.","pattern":"^[\\w\\d\\.-]*$","uri_format":"https://www.genedb.org/gene/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/genedb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.genedb.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"LinJ.20.0070","example_extras":[],"example_decoys":null,"license":"http://www.sanger.ac.uk/legal","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"GENEDB","edam.data":"1035","go.resource":"GeneDB","integbio":"nbdc00469","miriam":"genedb","n2t":"genedb","ncbi.resource":"GeneDB","prefixcommons":"genedb","re3data":"r3d100010626","wikidata.property":"P3382"},"synonyms":[],"keywords":["genome","genome/gene","protein","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"22116062","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14681429","doi":"10.1093/nar/gkh007","pmc":"PMC308742","arxiv":null,"title":"GeneDB: a resource for prokaryotic and eukaryotic organisms","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"genedb","mastodon":null,"github_request_issue":null,"logo":"https://www.genedb.org/errors/genedb_logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"geo":{"prefix":"geo","name":"Gene Expression Omnibus","description":"The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.","pattern":"^G(PL|SM|SE|DS)\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/geo:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/geo/","repository":null,"contact":{"name":"Tanya Barrett","orcid":"0000-0002-9448-8064","email":"barrett@ncbi.nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"GDS1234","example_extras":[],"example_decoys":null,"license":"http://www.nlm.nih.gov/copyright.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":"_","deprecated":false,"mappings":{"cellosaurus.resource":"GEO","edam.data":"1147","fairsharing":"FAIRsharing.5hc8vt","go.resource":"GEO","integbio":"nbdc00080","miriam":"geo","n2t":"geo","prefixcommons":"geo","re3data":"r3d100010283"},"synonyms":[],"keywords":["array design","cdna/est","clone library","comparative genomics","differential gene expression profiling","epigenomics","expression","expression data","gene array","gene expression","genome","genomics","image/movie","life science","microarray assay","mirna","mirna-mediated post-transcriptional gene silencing","mrna","next generation sequencing","omics","phenomics","raw microarray data","repository","sequence","sequencing assay","transcriptomics"],"domain":null,"references":null,"publications":[{"pubmed":"37933855","doi":"10.1093/nar/gkad965","pmc":null,"arxiv":null,"title":"NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update","year":2024},{"pubmed":"23193258","doi":"10.1093/nar/gks1193","pmc":"PMC3531084","arxiv":null,"title":"NCBI GEO: archive for functional genomics data sets--update","year":2012},{"pubmed":"21097893","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18940857","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17160034","doi":"10.1038/nbt1206-1471","pmc":"PMC2270403","arxiv":null,"title":"NCBI GEO standards and services for microarray data","year":2006},{"pubmed":"17099226","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16939800","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16888359","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15608262","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"11752295","doi":"10.1093/nar/30.1.207","pmc":"PMC99122","arxiv":null,"title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","year":2002},{"pubmed":"10693778","doi":"10.1038/35001676","pmc":null,"arxiv":null,"title":"One-stop shop for microarray data","year":2000},{"pubmed":null,"doi":"10.5281/zenodo.5706412","pmc":null,"arxiv":null,"title":"MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing Experiment - a proposal for standards in functional genomic data reporting","year":2012}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"geo","mastodon":null,"github_request_issue":null,"logo":"https://www.ncbi.nlm.nih.gov/geo/img/geo_main.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"glycomedb":{"prefix":"glycomedb","name":"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.","pattern":"^\\w+$","uri_format":"https://glytoucan.org/Structures/Glycans/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/glycomedb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://glytoucan.org/","repository":null,"contact":{"name":"René Ranzinger","orcid":"0000-0003-3147-448X","email":"rr@uga.edu","github":"ReneRanzinger","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"04cdgtt98","wikidata":null,"gnd":null,"name":"DKFZ TP3, Heidelberg","partnered":false}],"example":"G77500AY","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"GLYCOMEDB","edam.data":"2664","fairsharing":"FAIRsharing.k5k0yh","integbio":"nbdc00899","miriam":"glycomedb","n2t":"glycomedb","prefixcommons":"glycomedb","re3data":"r3d100011527"},"synonyms":[],"keywords":["carbohydrate","chemical structure","life science","molecular entity","molecules","sequence","small molecule","small molecules","structure"],"domain":null,"references":null,"publications":[{"pubmed":"25753706","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21045056","doi":"10.1093/nar/gkq1014","pmc":"PMC3013643","arxiv":null,"title":"GlycomeDB--a unified database for carbohydrate structures","year":2010},{"pubmed":"19759275","doi":"10.1093/glycob/cwp137","pmc":null,"arxiv":null,"title":"Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences","year":2009},{"pubmed":"18803830","doi":"10.1186/1471-2105-9-384","pmc":"PMC2567997","arxiv":null,"title":"GlycomeDB - integration of open-access carbohydrate structure databases","year":2008}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":"glytoucan","preferred_prefix":"glycomedb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"gmelin":{"prefix":"gmelin","name":"Gmelin's Handbook of Inorganic Chemistry","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.","pattern":"^[1-9][0-9]{1,6}$","uri_format":null,"uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://link.springer.com/bookseries/562","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"1466","example_extras":["606","80"],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"1004","wikidata.property":"P1578"},"synonyms":[],"keywords":[],"domain":null,"references":["https://en.wikipedia.org/wiki/Gmelin_database"],"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":true,"has_canonical":null,"preferred_prefix":"gmelin","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"go":{"prefix":"go","name":"Gene Ontology","description":"The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.","pattern":"^\\d{7}$","uri_format":"http://purl.obolibrary.org/obo/GO_$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.obolibrary.org/obo/GO_$1","providers":[{"code":"","name":"GO Browser","description":"GO Browser","homepage":"http://www.informatics.jax.org/searches/GO_form.shtml","contact":null,"uri_format":"http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/go:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"go_site","name":"GO Site Link","description":"A non-PURL link through the GO site","homepage":"http://www.geneontology.org","contact":null,"uri_format":"http://www.geneontology.org/GO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"jax","name":"Jackson Laboratories","description":"The JAX endpoint for exploring GO","homepage":"http://www.informatics.jax.org","contact":null,"uri_format":"http://www.informatics.jax.org/vocab/gene_ontology/GO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"miriam_obo_legacy","name":"MIRIAM OBO Legacy","description":"An old URI style for MIRIAM + GO","homepage":"https://identifiers.org/","contact":null,"uri_format":"http://identifiers.org/obo.go/GO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"nextprot","name":"neXtProt GO Browser","description":"The neXtProt endpoint for exploring GO","homepage":"https://www.nextprot.org/","contact":null,"uri_format":"https://www.nextprot.org/term/GO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"pantherdb","name":"PatherDB","description":"GO Browser in PantherDB","homepage":"http://www.pantherdb.org/panther","contact":null,"uri_format":"http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"purlorg","name":"PURL.org Legacy","description":null,"homepage":null,"contact":null,"uri_format":"http://purl.org/obo/owl/GO#GO_$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"quickgo","name":"QuickGO","description":"Gene Ontology browser from the EBI","homepage":"https://www.ebi.ac.uk/QuickGO/","contact":null,"uri_format":"https://www.ebi.ac.uk/QuickGO/term/GO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"quickgo.legacy","name":"QuickGO (Legacy URL)","description":"QuickGO (Gene Ontology browser)","homepage":"https://www.ebi.ac.uk/QuickGO/","contact":null,"uri_format":"https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://geneontology.org/","repository":"https://github.com/geneontology/go-ontology","contact":{"name":"Suzi Aleksander","orcid":"0000-0001-6787-2901","email":"suzia@stanford.edu","github":"suzialeksander","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"0032571","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":"2026-07-26","part_of":null,"part_of_database":null,"provides":null,"download_owl":"http://purl.obolibrary.org/obo/go.owl","download_obo":"http://purl.obolibrary.org/obo/go.obo","download_json":"http://purl.obolibrary.org/obo/go.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"GO","banana_peel":null,"deprecated":false,"mappings":{"aberowl":"GO","agroportal":"GO","bartoc":"572","biocontext":"GO","bioportal":"GO","edam.data":"1176","fairsharing":"FAIRsharing.6xq0ee","go.resource":"GO","hl7":"6.128","integbio":"nbdc00074","miriam":"go","n2t":"go","ncbi.resource":"GO","obofoundry":"go","ols":"go","ontobee":"GO","pathguide":"272","prefixcommons":"go","re3data":"r3d100014165","tib.ts":"go","togoid":"Go","uniprot.resource":"DB-0037","wikidata.entity":"Q135085","wikidata.property":"P686"},"synonyms":["gobp","gobpid","gocc","goccid","gomf","gomfid"],"keywords":["annotation","biocuration","biological_process","cellular_component","dataplant","expression data","function","gene","gene functional annotation","genome/gene","go-term enrichment data","knowledge representation","life science","life sciences, biology","medicine","molecular_function","obo","omics","ontologies","ontology","ontology/terminology/nomenclature","protein","rna","sequence annotation","transcript"],"domain":null,"references":null,"publications":[{"pubmed":"41413728","doi":"10.1093/nar/gkaf1292","pmc":null,"arxiv":null,"title":"The Gene Ontology knowledgebase in 2026","year":2026},{"pubmed":"36866529","doi":"10.1093/genetics/iyad031","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"33290552","doi":"10.1093/nar/gkaa1113","pmc":"PMC7779012","arxiv":null,"title":"The Gene Ontology resource: enriching a GOld mine","year":2021},{"pubmed":"30395331","doi":"10.1093/nar/gky1055","pmc":"PMC6323945","arxiv":null,"title":"The Gene Ontology Resource: 20 years and still GOing strong","year":2019},{"pubmed":"25428369","doi":"10.1093/nar/gku1179","pmc":"PMC4383973","arxiv":null,"title":"Gene Ontology Consortium: going forward","year":2014},{"pubmed":"23895341","doi":"10.1186/1471-2164-14-513","pmc":"PMC3733925","arxiv":null,"title":"Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology","year":2013},{"pubmed":"23161678","doi":"10.1093/nar/gks1050","pmc":"PMC3531070","arxiv":null,"title":"Gene Ontology annotations and resources","year":2012},{"pubmed":"22102568","doi":"10.1093/nar/gkr1028","pmc":"PMC3245151","arxiv":null,"title":"The Gene Ontology: enhancements for 2011","year":2011},{"pubmed":"19920128","doi":"10.1093/nar/gkp1018","pmc":"PMC2808930","arxiv":null,"title":"The Gene Ontology in 2010: extensions and refinements","year":2009},{"pubmed":"19578431","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14681407","doi":"10.1093/nar/gkh036","pmc":"PMC308770","arxiv":null,"title":"The Gene Ontology (GO) database and informatics resource","year":2004},{"pubmed":"10802651","doi":"10.1038/75556","pmc":"PMC3037419","arxiv":null,"title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","year":2000}],"appears_in":["agro","chiro","cl","ecocore","ecto","envo","maxo","pcl","pco","planp","uberon","xpo","zp"],"depends_on":["cl","ncbitaxon","ro","uberon"],"namespace_in_lui":true,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"James Alastair McLaughlin","orcid":"0000-0002-8361-2795","email":"jmcl@ebi.ac.uk","github":"jamesamcl","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"GO","mastodon":"go@genomic.social","github_request_issue":null,"logo":"https://obofoundry.org/images/go_logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"hamap":{"prefix":"hamap","name":"High-quality Automated and Manual Annotation of microbial Proteomes","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.","pattern":"^MF_\\d+$","uri_format":"https://hamap.expasy.org/unirule/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/hamap:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://hamap.expasy.org/","repository":null,"contact":{"name":"Alan Bridge","orcid":"0000-0003-2148-9135","email":"alan.bridge@isb-sib.ch","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"002n09z45","wikidata":null,"gnd":null,"name":"SIB Swiss Institute of Bioinformatics","partnered":false}],"example":"MF_01400","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"HAMAP","edam.data":"2766","fairsharing":"FAIRsharing.63m4ss","go.resource":"HAMAP","miriam":"hamap","n2t":"hamap","prefixcommons":"hamap","uniprot.resource":"DB-0041"},"synonyms":[],"keywords":["family and domain databases","life science","polypeptide region","protein","sequence annotation"],"domain":null,"references":null,"publications":[{"pubmed":"25348399","doi":"10.1093/nar/gku1002","pmc":"PMC4383873","arxiv":null,"title":"HAMAP in 2015: updates to the protein family classification and annotation system","year":2014},{"pubmed":"23193261","doi":"10.1093/nar/gks1157","pmc":"PMC3531088","arxiv":null,"title":"HAMAP in 2013, new developments in the protein family classification and annotation system","year":2012}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"hamap","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--ca50c6050260c6ee4769280a49fff47fa8daa924/HAMAP_Red_Logo_trans.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"hgmd":{"prefix":"hgmd","name":"Human Gene Mutation Database","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.","pattern":"^[A-Z_0-9]+$","uri_format":"http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.hgmd.cf.ac.uk/ac/index.php","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"03kk7td41","wikidata":null,"gnd":null,"name":"Cardiff University, Cardiff","partnered":false}],"example":"CALM1","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"HGMD","edam.data":"3265","integbio":"nbdc00097","miriam":"hgmd","n2t":"hgmd"},"synonyms":[],"keywords":["cdna/est","genome/gene","health/disease","sequence"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"hgmd","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"hgnc":{"prefix":"hgnc","name":"HUGO Gene Nomenclature Committee","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.","pattern":"^\\d{1,5}$","uri_format":"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/hgnc:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"gencc","name":"The Gene Curation Coalition","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","contact":null,"uri_format":"https://search.thegencc.org/genes/HGNC:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"indra","name":"INDRA Database","description":"A large scale database of biomedical statements.","homepage":"https://db.indra.bio","contact":null,"uri_format":"https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC","first_party":null,"publications":[{"pubmed":"36938926","doi":"10.15252/msb.202211325","pmc":"PMC10167483","arxiv":null,"title":"Automated assembly of molecular mechanisms at scale from text mining and curated databases","year":2023},{"pubmed":"29175850","doi":"10.15252/msb.20177651","pmc":"PMC5731347","arxiv":null,"title":"From word models to executable models of signaling networks using automated assembly","year":2017}],"example":null,"status":null,"organization":null}],"homepage":"http://www.genenames.org","repository":null,"contact":{"name":"Elspeth Bruford","orcid":"0000-0002-8380-5247","email":"elspeth@genenames.org","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"16793","example_extras":[],"example_decoys":null,"license":"CC0-1.0","version":"dev","part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/hgnc/hgnc.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/hgnc/hgnc.obo","download_json":"https://w3id.org/biopragmatics/resources/hgnc/hgnc.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"aberowl":"HGNC","bartoc":"20688","biocontext":"HGNC","bioportal":"HGNC","cellosaurus.resource":"HGNC","edam.data":"2298","fairsharing":"FAIRsharing.amcv1e","go.resource":"HGNC","hl7":"6.281","miriam":"hgnc","n2t":"hgnc","ncbi.resource":"HGNC","ols":"hgnc","prefixcommons":"hgnc","togoid":"Hgnc","uniprot.resource":"DB-0042","wikidata.property":"P354"},"synonyms":[],"keywords":["classification","gene","gene name","life science","ncrna","ontology","organism-specific databases","protein","pseudogene"],"domain":null,"references":null,"publications":[{"pubmed":"41287213","doi":"10.1093/nar/gkaf1329","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"36938926","doi":"10.15252/msb.202211325","pmc":"PMC10167483","arxiv":null,"title":"Automated assembly of molecular mechanisms at scale from text mining and curated databases","year":2023},{"pubmed":"33152070","doi":"10.1093/nar/gkaa980","pmc":"PMC7779007","arxiv":null,"title":"Genenames.org: the HGNC and VGNC resources in 2021","year":2021},{"pubmed":"30304474","doi":"10.1093/nar/gky930","pmc":"PMC6324057","arxiv":null,"title":"Genenames.org: the HGNC and VGNC resources in 2019","year":2019},{"pubmed":"295268","doi":"10.1159/000131404","pmc":null,"arxiv":null,"title":"International system for human gene nomenclature (1979) ISGN (1979)","year":1979},{"pubmed":"29175850","doi":"10.15252/msb.20177651","pmc":"PMC5731347","arxiv":null,"title":"From word models to executable models of signaling networks using automated assembly","year":2017}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"hgnc","mastodon":null,"github_request_issue":null,"logo":"https://www.genenames.org/img/hgnc/logo/hgnc-logo-dark-bckgrnd-large.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"hmdb":{"prefix":"hmdb","name":"Human Metabolome Database","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.","pattern":"^HMDB\\d+$","uri_format":"http://www.hmdb.ca/metabolites/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/hmdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.hmdb.ca/","repository":null,"contact":{"name":"David S. Wishart","orcid":"0000-0002-3207-2434","email":"david.wishart@ualberta.ca","github":"DavidWishartLab","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0160cpw27","wikidata":null,"gnd":null,"name":"University of Alberta","partnered":false}],"example":"HMDB00001","example_extras":[],"example_decoys":null,"license":"http://www.hmdb.ca/about#cite","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"HMDB","cheminf":"000408","edam.data":"2622","fairsharing":"FAIRsharing.sye5js","integbio":"nbdc00909","miriam":"hmdb","n2t":"hmdb","pathguide":"244","prefixcommons":"hmdb","re3data":"r3d100011285","togoid":"Hmdb","wikidata.property":"P2057"},"synonyms":["HMDB"],"keywords":["biochemistry","bioinformatics","chemical","chemical entity","classification","compound","health/disease","human","interaction/pathway","life science","lipid","metabolite","metabolomics","molecular biology","molecular entity","omics","phenomics","protein","proteomics","rna","sequence","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"34986597","doi":"10.1093/nar/gkab1062","pmc":"PMC8728138","arxiv":null,"title":"HMDB 5.0: the Human Metabolome Database for 2022","year":2022},{"pubmed":"29140435","doi":"10.1093/nar/gkx1089","pmc":"PMC5753273","arxiv":null,"title":"HMDB 4.0: the human metabolome database for 2018","year":2018},{"pubmed":"23161693","doi":"10.1093/nar/gks1065","pmc":"PMC3531200","arxiv":null,"title":"HMDB 3.0--The Human Metabolome Database in 2013","year":2012},{"pubmed":"18953024","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17202168","doi":"10.1093/nar/gkl923","pmc":"PMC1899095","arxiv":null,"title":"HMDB: the Human Metabolome Database","year":2007}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"hmdb","mastodon":null,"github_request_issue":null,"logo":"https://www.hmdb.ca/assets/hmdb_logo-f7bd764aa882bbbb2cfb8930f5f784e60576755c3de62a23a6d99c845cbff7e3.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"icd10":{"prefix":"icd10","name":"International Classification of Diseases, 10th Revision","description":"The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.","pattern":"^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$","uri_format":"https://icd.who.int/browse10/2019/en#/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/icd:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"icd10_2008","name":"ICD-10 Version 2008","description":"The 2008 revision of ICD-10","homepage":"https://icd.who.int/browse10/2008/en#","contact":null,"uri_format":"https://icd.who.int/browse10/2008/en#/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"icd10_2010","name":"ICD-10 Version 2010","description":"The 2010 revision of ICD-10","homepage":"https://icd.who.int/browse10/2010/en#","contact":null,"uri_format":"https://icd.who.int/browse10/2010/en#/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"icd10_2014","name":"ICD-10 Version 2014","description":"The 2014 revision of ICD-10","homepage":"https://icd.who.int/browse10/2014/en#","contact":null,"uri_format":"https://icd.who.int/browse10/2014/en#/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"icd10_2015","name":"ICD-10 Version 2015","description":"The 2015 revision of ICD-10","homepage":"https://icd.who.int/browse10/2015/en#","contact":null,"uri_format":"https://icd.who.int/browse10/2015/en#/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"icd10_2016","name":"ICD-10 Version 2016","description":"The 2016 revision of ICD-10","homepage":"https://icd.who.int/browse10/2016/en#","contact":null,"uri_format":"https://icd.who.int/browse10/2016/en#/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"icdcodelookup","name":"ICD Code Lookup","description":"This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general.","homepage":"https://icdcodelookup.com/icd-10/codes","contact":null,"uri_format":"https://icdcodelookup.com/icd-10/codes/$1","first_party":null,"publications":null,"example":null,"status":{"value":"hijacked","date":"2025-10-25","contributor":"0000-0003-4423-4370","notes":null},"organization":null}],"homepage":"https://icd.who.int/browse10","repository":null,"contact":{"name":"Robert Jakob","orcid":"0000-0001-6542-7548","email":"jakobr@who.int","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"C34","example_extras":["A01.1","G00","R25","R25-R29","R25.3","V20","XVIII"],"example_decoys":["G00X","C34.90","C4A.8","C91.Z","C91.Z0"],"license":"https://cdn.who.int/media/docs/default-source/publishing-policies/copyright/who-faq-licensing-icd-10.pdf","version":"ICD10_1998","part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/icd10/icd10.owl","download_obo":"https://w3id.org/biopragmatics/resources/icd10/icd10.obo","download_json":"https://w3id.org/biopragmatics/resources/icd10/icd10.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"bartoc":"447","biocontext":"ICD","biolink.resource":"ICD10","bioportal":"ICD10","edam.data":"2611","fairsharing":"FAIRsharing.nj16g","hl7":"6.3","miriam":"icd","n2t":"icd","prefixcommons":"icd","wikidata.entity":"Q50018","wikidata.property":"P494"},"synonyms":["ICD","ICD-10","ICD10","ICD10WHO"],"keywords":["biomedical science","classification","diagnosis","disease","epidemiology","global health","health science","icd","ontology","taxonomy"],"domain":null,"references":["https://www.who.int/about/policies/publishing/copyright"],"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Joe Flack","orcid":"0000-0002-2906-7319","email":null,"github":"joeflack4","wikidata":null},{"name":"Nicolas Matentzoglu","orcid":"0000-0002-7356-1779","email":"nicolas.matentzoglu@gmail.com","github":"matentzn","wikidata":null},{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"icd10","mastodon":null,"github_request_issue":null,"logo":"https://upload.wikimedia.org/wikipedia/commons/a/a4/Icd10codeslogo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"imgt.hla":{"prefix":"imgt.hla","name":"IMGT HLA","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.","pattern":"^[A-Z0-9*:]+$","uri_format":"https://www.ebi.ac.uk/ipd/imgt/hla/alleles/?query=eq(name,%22$1%22)","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/imgthla:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/imgt/hla/allele.html","repository":null,"contact":{"name":"Steven G. E. Marsh","orcid":"0000-0003-2855-4120","email":"steven.marsh@ucl.ac.uk","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"A*01:01:01:01","example_extras":[],"example_decoys":null,"license":"CC","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"IMGT.HLA","cellosaurus.resource":"IPD-IMGT/HLA","edam.data":"2773","fairsharing":"FAIRsharing.e28v7g","go.resource":"IMGT_HLA","integbio":"nbdc00106","miriam":"imgt.hla","n2t":"imgt.hla","ncbi.resource":"IMGT/HLA","prefixcommons":"imgthla","re3data":"r3d100010804"},"synonyms":["IPD-IMGT/HLA"],"keywords":["allele","biomedical science","cell/organelle","dna","dna sequence","genetic polymorphism","genome/gene","human leukocyte antigen complex","immunogenetics","immunology","major histocompatibility complex","multiple sequence alignment","nucleic acid sequence","nucleic acid sequence alignment","ontology/terminology/nomenclature","protein","rna","sequence","sequence alignment","sequence annotation","sequence variant"],"domain":null,"references":null,"publications":[{"pubmed":"31667505","doi":"10.1093/nar/gkz950","pmc":"PMC7145640","arxiv":null,"title":"IPD-IMGT/HLA Database","year":2020},{"pubmed":"26826444","doi":"10.1016/j.humimm.2016.01.020","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"25414341","doi":"10.1093/nar/gku1161","pmc":"PMC4383959","arxiv":null,"title":"The IPD and IMGT/HLA database: allele variant databases","year":2014},{"pubmed":"25048120","doi":"10.1007/978-1-4939-1115-8_5","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18838392","doi":"10.1093/nar/gkn662","pmc":"PMC2686596","arxiv":null,"title":"The IMGT/HLA database","year":2008},{"pubmed":"18449991","doi":"10.1007/978-1-60327-118-9_3","pmc":null,"arxiv":null,"title":"The IMGT/HLA database","year":2007},{"pubmed":"16944494","doi":"10.1002/humu.20406","pmc":null,"arxiv":null,"title":"The IMGT/HLA and IPD databases","year":2006},{"pubmed":"16381979","doi":"10.1093/nar/gkj088","pmc":"PMC1347451","arxiv":null,"title":"IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences","year":2006},{"pubmed":"12520010","doi":"10.1093/nar/gkg070","pmc":"PMC165517","arxiv":null,"title":"IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex","year":2003},{"pubmed":"11125094","doi":"10.1093/nar/29.1.210","pmc":"PMC29780","arxiv":null,"title":"IMGT/HLA Database--a sequence database for the human major histocompatibility complex","year":2001},{"pubmed":"10777106","doi":"10.1034/j.1399-0039.2000.550314.x","pmc":null,"arxiv":null,"title":"IMGT/HLA database--a sequence database for the human major histocompatibility complex","year":2000}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"imgt.hla","mastodon":null,"github_request_issue":null,"logo":"https://www.ebi.ac.uk/ipd/imgt/hla/assets/images/hla_logo_2014-e4fa904dc2.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"interpro":{"prefix":"interpro","name":"InterPro","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.","pattern":"^IPR\\d{6}$","uri_format":"https://www.ebi.ac.uk/interpro/entry/InterPro/$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.obolibrary.org/obo/IPR_$1","providers":[{"code":"","name":"Bio2RDF","description":"Bio2RDF","homepage":"http://bio2rdf.org/","contact":null,"uri_format":"http://bio2rdf.org/interpro:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/interpro:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.ebi.ac.uk/interpro/index.html","repository":null,"contact":{"name":"Alex Bateman","orcid":"0000-0002-6982-4660","email":"agb@ebi.ac.uk","github":"bateman-research","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"IPR016380","example_extras":[],"example_decoys":null,"license":"CC0-1.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/interpro/interpro.owl","download_obo":"https://w3id.org/biopragmatics/resources/interpro/interpro.obo","download_json":"https://w3id.org/biopragmatics/resources/interpro/interpro.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"IPR","biolink.resource":"interpro","edam.data":"1133","fairsharing":"FAIRsharing.pda11d","go.resource":"InterPro","integbio":"nbdc00108","miriam":"interpro","n2t":"interpro","ncbi.resource":"InterPro","obofoundry":"ipr","prefixcommons":"interpro","re3data":"r3d100010798","togoid":"Interpro","uniprot.resource":"DB-0052","wikidata.entity":"Q114677890","wikidata.property":"P2926"},"synonyms":["IP","IPR","InterPro"],"keywords":["bioinformatics","biology","classification","conserved region","domain","family and domain databases","function analysis","functional domain","genome","molecular_function","ontology","polypeptide region","prediction and recognition","protein","protein binding domain","protein domain","sequence","sequencing assay"],"domain":null,"references":null,"publications":[{"pubmed":"39565202","doi":"10.1093/nar/gkae1082","pmc":null,"arxiv":null,"title":"InterPro: the protein sequence classification resource in 2025","year":2024},{"pubmed":"36350672","doi":"10.1093/nar/gkac993","pmc":"PMC9825450","arxiv":null,"title":"InterPro in 2022","year":2023},{"pubmed":"33156333","doi":"10.1093/nar/gkaa977","pmc":"PMC7778928","arxiv":null,"title":"The InterPro protein families and domains database: 20 years on","year":2021},{"pubmed":"30398656","doi":"10.1093/nar/gky1100","pmc":"PMC6323941","arxiv":null,"title":"InterPro in 2019: improving coverage, classification and access to protein sequence annotations","year":2019},{"pubmed":"22301074","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"22096229","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21785143","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18836194","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15980438","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15608177","doi":"10.1093/nar/gki106","pmc":"PMC540060","arxiv":null,"title":"InterPro, progress and status in 2005","year":2005}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"interpro","mastodon":null,"github_request_issue":null,"logo":"https://content.embl.org/sites/default/files/03-2025/interpro_newlogo-2-scaled-1.jpg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"isbn":{"prefix":"isbn","name":"International Standard Book Number","description":"The International Standard Book Number (ISBN) is for identifying printed books.","pattern":"^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$","uri_format":"https://www.worldcat.org/isbn/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"ISBNDB - ISBN Database","description":"ISBNDB - ISBN Database","homepage":"http://isbndb.com/","contact":null,"uri_format":"http://isbndb.com/search-all.html?kw=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/isbn:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"google.isbn","name":"Google Books","description":"Google Books provider for ISBN numbers","homepage":"https://books.google.com","contact":null,"uri_format":"https://books.google.com/books?isbn=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"isbnsearch","name":"ISBN Search","description":"ISBN Search is an unofficial search engine for ISBNs.","homepage":"https://isbnsearch.org","contact":null,"uri_format":"https://isbnsearch.org/isbn/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.worldcat.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02nv42w72","wikidata":null,"gnd":null,"name":"OCLC Online Computer Library Center, Inc. Ohio","partnered":false}],"example":"9789211613865","example_extras":["978-92-1-161386-5"],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"ISBN-13","biolink.resource":"isbn","edam.data":"2634","go.resource":"ISBN","miriam":"isbn","n2t":"isbn","prefixcommons":"isbn"},"synonyms":["ISBN-10","ISBN-13"],"keywords":["bibliography"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"isbn","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"kegg.compound":{"prefix":"kegg.compound","name":"KEGG Compound","description":"KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.","pattern":"^C\\d+$","uri_format":"https://www.kegg.jp/entry/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/kegg.compound:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.genome.jp/kegg/ligand.html","repository":null,"contact":{"name":"Minoru Kanehisa","orcid":"0000-0001-6123-540X","email":"kanehisa@kuicr.kyoto-u.ac.jp","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"C12345","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":"kegg","part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"KEGG.COMPOUND","edam.data":"2605","integbio":"nbdc00814","miriam":"kegg.compound","n2t":"kegg.compound","prefixcommons":"kegg.compound"},"synonyms":["KEGG COMPOUND","KEGG.COMPOUND"],"keywords":["chemical compound","chemical structure","dna","interaction/pathway","protein","rna","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"22700311","doi":"10.1002/0471250953.bi0112s38","pmc":null,"arxiv":null,"title":"Using the KEGG database resource","year":2012},{"pubmed":"20460463","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"19327755","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17921532","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17400247","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14505407","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"kegg.compound","mastodon":null,"github_request_issue":null,"logo":"https://www.genome.jp/Fig/kegg128.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"kegg.drug":{"prefix":"kegg.drug","name":"KEGG Drug","description":"KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.","pattern":"^D\\d+$","uri_format":"https://www.kegg.jp/entry/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/kegg.drug:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.genome.jp/kegg/drug/","repository":null,"contact":{"name":"Minoru Kanehisa","orcid":"0000-0001-6123-540X","email":"kanehisa@kuicr.kyoto-u.ac.jp","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"D00123","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":"kegg","part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"KEGG.DRUG","edam.data":"2609","integbio":"nbdc00812","miriam":"kegg.drug","n2t":"kegg.drug","prefixcommons":"kegg.drug"},"synonyms":["KEGG DRUG","KEGG.DRUG"],"keywords":["chemical structure","drug","interaction/pathway","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"16381885","doi":"10.1093/nar/gkj102","pmc":"PMC1347464","arxiv":null,"title":"From genomics to chemical genomics: new developments in KEGG","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"kegg.drug","mastodon":null,"github_request_issue":null,"logo":"https://www.genome.jp/Fig/kegg128.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"kegg.glycan":{"prefix":"kegg.glycan","name":"KEGG Glycan","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.","pattern":"^G\\d+$","uri_format":"https://www.kegg.jp/entry/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/kegg.glycan:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.genome.jp/kegg/glycan/","repository":null,"contact":{"name":"Minoru Kanehisa","orcid":"0000-0001-6123-540X","email":"kanehisa@kuicr.kyoto-u.ac.jp","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"G00123","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":"kegg","part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"KEGG.GLYCAN","edam.data":"2613","integbio":"nbdc00533","miriam":"kegg.glycan","n2t":"kegg.glycan","prefixcommons":"kegg.glycan"},"synonyms":[],"keywords":["carbohydrate","chemical structure","interaction/pathway","protein","rna","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"19327755","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18546491","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16362924","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16159923","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16014746","doi":"10.1093/glycob/cwj010","pmc":null,"arxiv":null,"title":"KEGG as a glycome informatics resource","year":2005},{"pubmed":"15215393","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"kegg.glycan","mastodon":null,"github_request_issue":null,"logo":"https://www.genome.jp/Fig/kegg128.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"kegg.pathway":{"prefix":"kegg.pathway","name":"KEGG pathway","description":"KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.","pattern":"^\\w{2,4}\\d{5}$","uri_format":"https://www.kegg.jp/pathway/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/kegg.pathway:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.genome.jp/kegg/pathway.html","repository":null,"contact":{"name":"Minoru Kanehisa","orcid":"0000-0001-6123-540X","email":"kanehisa@kuicr.kyoto-u.ac.jp","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"rsk00410","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"KEGG.PATHWAY","biolink.resource":"KEGG.PATHWAY","edam.data":"2343","go.resource":"KEGG_PATHWAY","miriam":"kegg.pathway","n2t":"kegg.pathway","prefixcommons":"kegg.pathway"},"synonyms":["KEGG-path","KEGG_PATHWAY"],"keywords":["kegg","pathway"],"domain":null,"references":null,"publications":[{"pubmed":"22700311","doi":"10.1002/0471250953.bi0112s38","pmc":null,"arxiv":null,"title":"Using the KEGG database resource","year":2012}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"kegg.pathway","mastodon":null,"github_request_issue":null,"logo":"https://www.genome.jp/Fig/kegg128.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"kegg.reaction":{"prefix":"kegg.reaction","name":"KEGG Reaction","description":"KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.","pattern":"^R\\d+$","uri_format":"https://www.kegg.jp/entry/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/kegg.reaction:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"gotenzymes","name":null,"description":"Contains identifiers for enzyme reactions from GotEnzymes, an interactive database of enzyme parameter predictions. Enzyme parameters are essential for quantitatively understanding, modelling, and engineering cells. Each identifier represents a singular reaction, but the database allows browsing using reactions, genes, compounds, organisms, EC codes, and domains.","homepage":"https://metabolicatlas.org/gotenzymes","contact":{"name":"Jens Nielsen","orcid":"0000-0002-9955-6003","email":"nielsenj@chalmers.se","github":null,"wikidata":null},"uri_format":"https://metabolicatlas.org/gotenzymes/$1","first_party":null,"publications":[{"pubmed":"36169223","doi":"10.1093/nar/gkac831","pmc":"PMC9825421","arxiv":null,"title":"GotEnzymes: an extensive database of enzyme parameter predictions","year":2023}],"example":null,"status":null,"organization":null}],"homepage":"https://www.genome.jp/kegg/reaction/","repository":null,"contact":{"name":"Minoru Kanehisa","orcid":"0000-0001-6123-540X","email":"kanehisa@kuicr.kyoto-u.ac.jp","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"R00100","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":"kegg","part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"KEGG.REACTION","edam.data":"2608","go.resource":"KEGG_REACTION","integbio":"nbdc00818","miriam":"kegg.reaction","n2t":"kegg.reaction","prefixcommons":"kegg.reaction"},"synonyms":["KEGG_REACTION"],"keywords":["chemical structure","classification","enzyme","interaction/pathway","pathway","protein","rna"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/pull/1656"],"publications":[{"pubmed":"36169223","doi":"10.1093/nar/gkac831","pmc":"PMC9825421","arxiv":null,"title":"GotEnzymes: an extensive database of enzyme parameter predictions","year":2023},{"pubmed":"22700311","doi":"10.1002/0471250953.bi0112s38","pmc":null,"arxiv":null,"title":"Using the KEGG database resource","year":2012},{"pubmed":"20435670","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"19477985","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17516640","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15600352","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14505407","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"kegg.reaction","mastodon":null,"github_request_issue":null,"logo":"https://www.genome.jp/Fig/kegg128.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"lipidbank":{"prefix":"lipidbank","name":"LipidBank","description":"LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.","pattern":"^\\w+\\d+$","uri_format":"https://lipidbank.jp/data/$1.cdx","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/lipidbank:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://lipidbank.jp/index.html","repository":null,"contact":{"name":"Etsuko Yasugi","orcid":"0000-0003-1898-4426","email":"e-yasugi@umin.ac.jp","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"BBA0001","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"LIPIDBANK","edam.data":"2665","integbio":"nbdc00126","miriam":"lipidbank","n2t":"lipidbank","prefixcommons":"lipidbank"},"synonyms":[],"keywords":["chemical structure","image/movie","lipid","molecule","structure"],"domain":null,"references":null,"publications":[{"pubmed":"12058481","doi":null,"pmc":null,"arxiv":null,"title":"[LIPIDBANK for Web, the newly developed lipid database]","year":2002}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"lipidbank","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"lipidmaps":{"prefix":"lipidmaps","name":"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.","pattern":"^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$","uri_format":"http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/lipidmaps:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"scholia","name":"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/","contact":null,"uri_format":"https://scholia.toolforge.org/lipidmaps/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://lipidmaps.org","repository":null,"contact":{"name":"Edward A Dennis","orcid":"0000-0003-3738-3140","email":"edennis@ucsd.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"LMPR0102010012","example_extras":[],"example_decoys":null,"license":"http://www.lipidmaps.org/about/terms_of_use.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"LIPIDMAPS","cheminf":"000564","edam.data":"2625","fairsharing":"FAIRsharing.cpneh8","integbio":"nbdc02669","miriam":"lipidmaps","n2t":"lipidmaps","ols":"lipidmaps","pathguide":"503","prefixcommons":"lipidmaps","re3data":"r3d100012315","togoid":"Lipidmaps","wikidata.property":"P2063"},"synonyms":["LIPID MAPS","LIPID_MAPS_class","LIPID_MAPS_instance"],"keywords":["biomedical science","chemical structure","classification","data analysis","endocrinology","interaction/pathway","life science","lipid","mass spectrum","metabolomics","omics","ontology/terminology/nomenclature","small molecule","structure","systems biology","taxonomic classification","taxonomy"],"domain":null,"references":null,"publications":[{"pubmed":"37855672","doi":"10.1093/nar/gkad896","pmc":null,"arxiv":null,"title":"LIPID MAPS: update to databases and tools for the lipidomics community","year":2023},{"pubmed":"33564392","doi":"10.12688/f1000research.28022.2","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"33037133","doi":"10.1194/jlr.s120001025","pmc":null,"arxiv":null,"title":"Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures","year":2020},{"pubmed":"23549332","doi":"10.1194/jlr.m033506","pmc":null,"arxiv":null,"title":"Shorthand notation for lipid structures derived from mass spectrometry","year":2013},{"pubmed":"19098281","doi":"10.1194/jlr.r800095-jlr200","pmc":"PMC2674711","arxiv":null,"title":"Update of the LIPID MAPS comprehensive classification system for lipids","year":2008},{"pubmed":"17584797","doi":"10.1093/nar/gkm324","pmc":"PMC1933166","arxiv":null,"title":"LIPID MAPS online tools for lipid research","year":2007},{"pubmed":"17098933","doi":"10.1093/nar/gkl838","pmc":"PMC1669719","arxiv":null,"title":"LMSD: LIPID MAPS structure database","year":2006},{"pubmed":"16381922","doi":"10.1093/nar/gkj122","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15722563","doi":"10.1194/jlr.e400004-jlr200","pmc":null,"arxiv":null,"title":"A comprehensive classification system for lipids","year":2005},{"pubmed":"","doi":" 10.1101/2020.04.09.033894","pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"lipidmaps","mastodon":null,"github_request_issue":null,"logo":"https://www.lipidmaps.org/assets/images/logos/lipid_maps_transparent_sm.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"macie":{"prefix":"macie","name":"Mechanism, Annotation and Classification in Enzymes","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.","pattern":"^M\\d{4}$","uri_format":"https://www.ebi.ac.uk/thornton-srv/m-csa/search/?s=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/macie:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/thornton-srv/m-csa/about/","repository":null,"contact":{"name":"Gemma L. Holliday","orcid":"0000-0002-6731-6398","email":"gemma.l.holliday@gmail.com","github":"GLHolliday79","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"M0001","example_extras":[],"example_decoys":null,"license":"http://www.ebi.ac.uk/Information/termsofuse.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"MACIE","edam.data":"2641","fairsharing":"FAIRsharing.7xkx69","miriam":"macie","n2t":"macie","prefixcommons":"macie"},"synonyms":[],"keywords":["chemical bond modification","enzymatic reaction","enzyme","enzyme commission number","life science","molecular interaction","pathway","reaction data"],"domain":null,"references":null,"publications":[{"pubmed":"17082206","doi":"10.1093/nar/gkl774","pmc":"PMC1634735","arxiv":null,"title":"MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms","year":2006},{"pubmed":"16188925","doi":"10.1093/bioinformatics/bti693","pmc":"PMC2748267","arxiv":null,"title":"MACiE: a database of enzyme reaction mechanisms","year":2005}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"macie","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"merops.entry":{"prefix":"merops.entry","name":"MEROPS Entry","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.","pattern":"^[SCTAGMNUIXCP]{1,2}\\d{2,3}\\.(([ABP]\\d{2})|\\d{3})$","uri_format":"https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/merops:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/merops","repository":null,"contact":{"name":"Neil D Rawlings","orcid":"0000-0001-5557-7665","email":"ndr@ebi.ac.uk","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"05cy4wa09","wikidata":null,"gnd":null,"name":"Wellcome Trust Sanger Institute","partnered":false}],"example":"I31.952","example_extras":["A01.P01","C101.001","C13.P01","M12.P03","P02.027","S01.001","S01.P08","T01.P02","XM02.001"],"example_decoys":null,"license":"http://merops.sanger.ac.uk/about/availability.shtml","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"MEROPS.INHIBITOR","edam.data":"2629","go.resource":"MEROPS","miriam":"merops.inhibitor","n2t":"merops.inhibitor","prefixcommons":"merops","uniprot.resource":"DB-0059"},"synonyms":["merops.inhibitor"],"keywords":["enzyme","protein","protein family/group databases","structure"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/issues/439"],"publications":[{"pubmed":"9847218","doi":"10.1093/nar/27.1.325","pmc":"PMC148173","arxiv":null,"title":"MEROPS: the peptidase database","year":1999},{"pubmed":"8439290","doi":"10.1042/bj2900205","pmc":"PMC1132403","arxiv":null,"title":"Evolutionary families of peptidases","year":1993},{"pubmed":"29145643","doi":"10.1093/nar/gkx1134","pmc":"PMC5753285","arxiv":null,"title":"The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database","year":2018},{"pubmed":"26527717","doi":"10.1093/nar/gkv1118","pmc":"PMC4702814","arxiv":null,"title":"Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors","year":2015},{"pubmed":"26455268","doi":"10.1016/j.biochi.2015.10.003","pmc":"PMC4756867","arxiv":null,"title":"Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation","year":2015},{"pubmed":"22086950","doi":"10.1093/nar/gkr987","pmc":"PMC3245014","arxiv":null,"title":"MEROPS: the database of proteolytic enzymes, their substrates and inhibitors","year":2011},{"pubmed":"17991683","doi":"10.1093/nar/gkm954","pmc":"PMC2238837","arxiv":null,"title":"MEROPS: the peptidase database","year":2007}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"merops.entry","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"mesh":{"prefix":"mesh","name":"Medical Subject Headings","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.","pattern":"^(C|D|Q)\\d+$","uri_format":"https://meshb.nlm.nih.gov/record/ui?ui=$1","uri_format_resolvable":null,"rdf_uri_format":"http://id.nlm.nih.gov/mesh/$1","providers":[{"code":"","name":"MeSH Linked Data at National Library of Medicine","description":"MeSH Linked Data at National Library of Medicine","homepage":"http://id.nlm.nih.gov/mesh/","contact":null,"uri_format":"http://id.nlm.nih.gov/mesh/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/mesh:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bioportal.purl","name":"BioPortal","description":"The BioPortal version of MeSH. Should be re-coded to `bioportal`, see https://github.com/biopragmatics/bioregistry/pull/1066.","homepage":"https://bioportal.bioontology.org/ontologies/MESH","contact":null,"uri_format":"http://purl.bioontology.org/ontology/MESH/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"mesh.2008","name":"Legacy 2008 MeSH URL","description":"Appears in birnlex","homepage":"http://id.nlm.nih.gov/mesh/","contact":null,"uri_format":"http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi?field=uid&term=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"mesh.json-ld","name":"Medical Subject Headings (JSON-LD)","description":"The MeSH version in JSON-LD.","homepage":"http://id.nlm.nih.gov/mesh/","contact":null,"uri_format":"https://id.nlm.nih.gov/mesh/$1.json-ld","first_party":true,"publications":null,"example":null,"status":null,"organization":null},{"code":"mesh.n3","name":"Medical Subject Headings (N3)","description":"The MeSH version in N3.","homepage":"http://id.nlm.nih.gov/mesh/","contact":null,"uri_format":"https://id.nlm.nih.gov/mesh/$1.n3","first_party":true,"publications":null,"example":null,"status":null,"organization":null},{"code":"mesh.ttl","name":"Medical Subject Headings (TTL)","description":"The MeSH version in TTL.","homepage":"http://id.nlm.nih.gov/mesh/","contact":null,"uri_format":"https://id.nlm.nih.gov/mesh/$1.ttl","first_party":true,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.nlm.nih.gov/","repository":null,"contact":{"name":"NLM Customer Service","orcid":null,"email":"custserv@nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0060t0j89","wikidata":null,"gnd":null,"name":"National Library of Medicine, Maryland","partnered":false}],"example":"C063233","example_extras":["D000001","Q000473"],"example_decoys":null,"license":"CC0-1.0","version":"2026_2025_08_15","part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/mesh/mesh.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/mesh/mesh.obo","download_json":"https://w3id.org/biopragmatics/resources/mesh/mesh.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"aberowl":"MESH","bartoc":"391","biocontext":"MESH","biolink.resource":"MESH","bioportal":"MESH","cellosaurus.resource":"MeSH","edam.data":"1177","fairsharing":"FAIRsharing.qnkw45","go.resource":"MeSH","hl7":"6.177","integbio":"nbdc00132","miriam":"mesh","n2t":"mesh","ols":"mesh","prefixcommons":"mesh","togoid":"Mesh","wikidata.entity":"Q199897","wikidata.property":"P486"},"synonyms":["MESH","MESHA","MESHC","MESHCS","MESHD","MESHPP","MESH_DESCRIPTOR_UI","MESH_SUPPLEMENTAL_RECORD_UI","MSH","MSH2010_2010_02_22","MeSH","meshUID"],"keywords":["bioinformatics","biomedical science","classification","data retrieval","life science","literature curation","metascience","ontology","ontology/terminology/nomenclature","phenotype","topics"],"domain":null,"references":null,"publications":[{"pubmed":"20623263","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15360776","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"13982385","doi":null,"pmc":"PMC197951","arxiv":null,"title":"Medical subject headings","year":1963}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Roman Baum","orcid":"0000-0001-5246-9351","email":"baum@zbmed.de","github":"rombaum","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"mesh","mastodon":null,"github_request_issue":null,"logo":"https://meshb.nlm.nih.gov/public/img/meshLogo.jpg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"mge":{"prefix":"mge","name":"Aclame","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.","pattern":"^\\d+$","uri_format":"http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/aclame:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://aclame.ulb.ac.be/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"2","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"mge","banana_peel":null,"deprecated":true,"mappings":{"biocontext":"ACLAME","edam.data":"2631","integbio":"nbdc00355","miriam":"mge","n2t":"mge","prefixcommons":"aclame"},"synonyms":["aclame"],"keywords":["dna","gene","genome","genome/gene","ontology/terminology/nomenclature","protein"],"domain":null,"references":null,"publications":[{"pubmed":"19933762","doi":"10.1093/nar/gkp938","pmc":"PMC2808911","arxiv":null,"title":"ACLAME: a CLAssification of Mobile genetic Elements, update 2010","year":2009},{"pubmed":"18238785","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18234706","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17614261","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17482656","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17064288","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14681355","doi":"10.1093/nar/gkh084","pmc":"PMC308818","arxiv":null,"title":"ACLAME: a CLAssification of Mobile genetic Elements","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":true,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"mge","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"mgi":{"prefix":"mgi","name":"Mouse Genome Informatics","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.","pattern":"^\\d+$","uri_format":"http://www.informatics.jax.org/accession/MGI:$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"agr","name":"MGI through the Alliance of Genome Resources","description":"MGI through the Alliance of Genome Resources","homepage":"https://www.alliancegenome.org","contact":null,"uri_format":"https://www.alliancegenome.org/gene/MGI:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/mgi:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"mgi.marker","name":"MGI Marker","description":"MGI Marker","homepage":"http://www.informatics.jax.org/marker","contact":null,"uri_format":"http://www.informatics.jax.org/marker/MGI:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.informatics.jax.org/","repository":null,"contact":{"name":"Joel Richardson","orcid":"0000-0003-3342-5753","email":"joel.richardson@jax.org","github":"JoelRichardson","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"021sy4w91","wikidata":null,"gnd":null,"name":"The Jackson Laboratory","partnered":false}],"example":"6017782","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/mgi/mgi.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/mgi/mgi.obo.gz","download_json":"https://w3id.org/biopragmatics/resources/mgi/mgi.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"MGI","banana_peel":null,"deprecated":false,"mappings":{"biocontext":"MGI","cellosaurus.resource":"MGI","edam.data":"3274","fairsharing":"FAIRsharing.fcwyhz","go.resource":"MGI","integbio":"nbdc00568","miriam":"mgi","n2t":"mgi","ncbi.resource":"MGI","prefixcommons":"mgi","re3data":"r3d100010266","rrid.resource":"MGI","uniprot.resource":"DB-0060","wikidata.property":"P671"},"synonyms":["MGD","MGI"],"keywords":["allele","animal genetics","animal model","biology","blast","chromosomal element nomenclature","covid-19","cytogenetic map","data analysis service","disease","disease course","expression","expression data","function","gene","gene expression","gene name","genetic polymorphism","genetics","genome","genome map","genome/gene","genomics","genotype","go-term enrichment data","gold standard","homologous","human disease","human health","image","model","molecular neuroanatomy resource","mutation","ontology","organism-specific databases","orthology","pathology","pathway","phenotype","qtl","recombinase","region","sequence","single nucleotide polymorphism","snp","strain","tumor"],"domain":null,"references":null,"publications":[{"pubmed":"8091224","doi":"10.1126/science.8091224","pmc":null,"arxiv":null,"title":"A database for mouse development","year":1994},{"pubmed":"38531069","doi":"10.1093/genetics/iyae031","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"30407599","doi":"10.1093/nar/gky1056","pmc":"PMC6323923","arxiv":null,"title":"Mouse Genome Database (MGD) 2019","year":2019},{"pubmed":"30335138","doi":"10.1093/nar/gky922","pmc":"PMC6324054","arxiv":null,"title":"The mouse Gene Expression Database (GXD): 2019 update","year":2019},{"pubmed":"28838066","doi":"10.1093/ilar/ilx013","pmc":"PMC5886341","arxiv":null,"title":"Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse","year":2017},{"pubmed":"27933520","doi":"10.1007/978-1-4939-6427-7_3","pmc":null,"arxiv":null,"title":"Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research","year":2017},{"pubmed":"27899570","doi":"10.1093/nar/gkw1040","pmc":"PMC5210536","arxiv":null,"title":"Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse","year":2016},{"pubmed":"24285300","doi":"10.1093/nar/gkt1225","pmc":"PMC3964950","arxiv":null,"title":"The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse","year":2013},{"pubmed":"23175610","doi":"10.1093/nar/gks1115","pmc":"PMC3531104","arxiv":null,"title":"The mouse genome database: genotypes, phenotypes, and models of human disease","year":2012},{"pubmed":"22075990","doi":"10.1093/nar/gkr974","pmc":"PMC3245042","arxiv":null,"title":"The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse","year":2011},{"pubmed":"19274630","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18428715","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15608240","doi":"10.1093/nar/gki113","pmc":"PMC540067","arxiv":null,"title":"The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology","year":2005},{"pubmed":"15602912","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":true,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"MGI","mastodon":null,"github_request_issue":null,"logo":"https://www.informatics.jax.org/webshare/images/mgi_logo.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"mint":{"prefix":"mint","name":"Molecular Interaction Database","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.","pattern":"^\\d{1,7}$","uri_format":"https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"The Molecular INTeraction database (MINT)","description":"The Molecular INTeraction database (MINT)","homepage":"http://mint.bio.uniroma2.it/mint/","contact":null,"uri_format":"https://mint.bio.uniroma2.it/index.php/results-interactions/?id=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/mint:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://mint.bio.uniroma2.it","repository":null,"contact":{"name":"Luana Licata","orcid":"0000-0001-5084-9000","email":"luana.licata@gmail.com","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"6978836","example_extras":[],"example_decoys":null,"license":"http://dip.doe-mbi.ucla.edu/dip/termsofuse.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"MINT","banana_peel":"-","deprecated":false,"mappings":{"biocontext":"MINT","edam.data":"2615","fairsharing":"FAIRsharing.2bdvmk","miriam":"mint","n2t":"mint","pathguide":"17","prefixcommons":"mint","re3data":"r3d100010414","uniprot.resource":"DB-0158"},"synonyms":[],"keywords":["interaction","life science","molecular interaction","protein","protein interactions","protein-protein interaction databases","proteomics","psi-mi"],"domain":null,"references":null,"publications":[{"pubmed":"22096227","doi":"10.1093/nar/gkr930","pmc":"PMC3244991","arxiv":null,"title":"MINT, the molecular interaction database: 2012 update","year":2011},{"pubmed":"19897547","doi":"10.1093/nar/gkp983","pmc":"PMC2808973","arxiv":null,"title":"MINT, the molecular interaction database: 2009 update","year":2009},{"pubmed":"17135203","doi":"10.1093/nar/gkl950","pmc":"PMC1751541","arxiv":null,"title":"MINT: the Molecular INTeraction database","year":2006},{"pubmed":"11911893","doi":"10.1016/s0014-5793(01)03293-8","pmc":null,"arxiv":null,"title":"MINT: a Molecular INTeraction database","year":2002}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"mint","mastodon":null,"github_request_issue":null,"logo":"https://mint.bio.uniroma2.it/wp-content/uploads/2017/11/cropped-mint-1-e1509905882312.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"mirbase":{"prefix":"mirbase","name":"miRBase pre-miRNA","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).","pattern":"^MI\\d{7}$","uri_format":"http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/mirbase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.mirbase.org","repository":null,"contact":{"name":"Sam Griffiths-Jones","orcid":"0000-0001-6043-807X","email":"sam.griffiths-jones@manchester.ac.uk","github":"samgriffithsjones","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"MI0026471","example_extras":[],"example_decoys":null,"license":"public-domain","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/mirbase/mirbase.owl","download_obo":"https://w3id.org/biopragmatics/resources/mirbase/mirbase.obo","download_json":"https://w3id.org/biopragmatics/resources/mirbase/mirbase.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"MIRBASE","biolink.resource":"mirbase","edam.data":"2642","fairsharing":"FAIRsharing.hmgte8","integbio":"nbdc00136","miriam":"mirbase","n2t":"mirbase","ncbi.resource":"miRBase","pathguide":"210","prefixcommons":"mirbase","re3data":"r3d100010566","togoid":"Mirbase","wikidata.property":"P2870"},"synonyms":[],"keywords":["biology","crowdsourcing","gene","mirbase","mirna","ontology","ribonucleic acid","rna","rna sequence","sequence","transcript"],"domain":null,"references":null,"publications":[{"pubmed":"30423142","doi":"10.1093/nar/gky1141","pmc":"PMC6323917","arxiv":null,"title":"miRBase: from microRNA sequences to function","year":2019},{"pubmed":"24275495","doi":"10.1093/nar/gkt1181","pmc":"PMC3965103","arxiv":null,"title":"miRBase: annotating high confidence microRNAs using deep sequencing data","year":2013},{"pubmed":"21037258","doi":"10.1093/nar/gkq1027","pmc":"PMC3013655","arxiv":null,"title":"miRBase: integrating microRNA annotation and deep-sequencing data","year":2010},{"pubmed":"17991681","doi":"10.1093/nar/gkm952","pmc":"PMC2238936","arxiv":null,"title":"miRBase: tools for microRNA genomics","year":2007},{"pubmed":"16381832","doi":"10.1093/nar/gkj112","pmc":"PMC1347474","arxiv":null,"title":"miRBase: microRNA sequences, targets and gene nomenclature","year":2006},{"pubmed":"14681370","doi":"10.1093/nar/gkh023","pmc":"PMC308757","arxiv":null,"title":"The microRNA Registry","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"mirbase","mastodon":null,"github_request_issue":null,"logo":"https://www.mirbase.org/static/images/mirbase-logo_new.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"miriam":{"prefix":"miriam","name":"Identifiers.org namespace","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.","pattern":"^[0-9a-z_:\\.-]+$","uri_format":"https://registry.identifiers.org/registry/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://identifiers.org","repository":"https://github.com/identifiers-org/registry-data","contact":{"name":"Henning Hermjakob","orcid":"0000-0001-8479-0262","email":"hhe@ebi.ac.uk","github":"hHermjakob","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"pubmed","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"1162","miriam":"identifiers.namespace"},"synonyms":["identifiers.namespace"],"keywords":["miriam","registry"],"domain":null,"references":null,"publications":[{"pubmed":"22140103","doi":"10.1093/nar/gkr1097","pmc":"PMC3245029","arxiv":null,"title":"Identifiers.org and MIRIAM Registry: community resources to provide persistent identification","year":2011},{"pubmed":"18078503","doi":"10.1186/1752-0509-1-58","pmc":"PMC2259379","arxiv":null,"title":"MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology","year":2007},{"pubmed":"16333295","doi":"10.1038/nbt1156","pmc":null,"arxiv":null,"title":"Minimum information requested in the annotation of biochemical models (MIRIAM)","year":2005}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"miriam","mastodon":null,"github_request_issue":null,"logo":"https://identifiers.org/identifiers_logo.9d30579d.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"mmdb":{"prefix":"mmdb","name":"Molecular Modeling Database","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.","pattern":"^\\d{1,5}$","uri_format":"http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/mmdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure","repository":null,"contact":{"name":"Siqian He","orcid":"0000-0002-1707-4167","email":"siqian.he@nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0060t0j89","wikidata":null,"gnd":null,"name":"National Library of Medicine, Maryland","partnered":false}],"example":"50885","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"MMDB","edam.data":"2667","miriam":"mmdb","n2t":"mmdb","pathguide":"508","prefixcommons":"mmdb"},"synonyms":[],"keywords":["dna","interaction","protein","small molecule","structure"],"domain":null,"references":null,"publications":[{"pubmed":"17135201","doi":"10.1093/nar/gkl952","pmc":"PMC1751549","arxiv":null,"title":"MMDB: annotating protein sequences with Entrez's 3D-structure database","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"mmdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"modeldb":{"prefix":"modeldb","name":"ModelDB","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.","pattern":"^\\d+$","uri_format":"https://modeldb.science/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/modeldb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://modeldb.science","repository":null,"contact":{"name":"Perry Miller","orcid":"0000-0002-5176-943X","email":"perry.miller@yale.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"45539","example_extras":[],"example_decoys":null,"license":"http://senselab.med.yale.edu/ModelDB/HowToCite.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"MODELDB","edam.data":"2669","fairsharing":"FAIRsharing.5rb3fk","integbio":"nbdc02085","miriam":"modeldb","n2t":"modeldb","prefixcommons":"modeldb","re3data":"r3d100011330"},"synonyms":[],"keywords":["behavior","bibliography/documents","cell/organelle","computational biology","life science","method","modeldb","monoatomic ion channel activity","neurobiology","neuron"],"domain":null,"references":null,"publications":[{"pubmed":"8930855","doi":"10.1136/jamia.1996.97084512","pmc":"PMC116323","arxiv":null,"title":"ModelDB: an environment for running and storing computational models and their results applied to neuroscience","year":1996},{"pubmed":"27629590","doi":"10.1007/s10827-016-0623-7","pmc":"PMC5279891","arxiv":null,"title":"Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience","year":2016},{"pubmed":"15218350","doi":"10.1023/b:jcns.0000023869.22017.2e","pmc":"PMC3732827","arxiv":null,"title":"ModelDB: A Database to Support Computational Neuroscience","year":2004},{"pubmed":"15055399","doi":"10.1385/ni:1:1:135","pmc":"PMC3728921","arxiv":null,"title":"ModelDB: making models publicly accessible to support computational neuroscience","year":2003}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"modeldb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ncbi.genome":{"prefix":"ncbi.genome","name":"NCBI Genome","description":"This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.","pattern":"^\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/genome/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.ncbi.nlm.nih.gov/genome","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"51","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"NCBIGenome","edam.data":"2787","re3data":"r3d100010785"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"ncbi.genome","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ncbigene":{"prefix":"ncbigene","name":"NCBI Gene","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.","pattern":"^\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/gene/$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.uniprot.org/geneid/$1","providers":[{"code":"","name":"Bio2RDF","description":"Bio2RDF","homepage":"http://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/ncbigene:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/ncbigene:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"marrvel","name":"Model organism Aggregated Resources for Rare Variant ExpLoration","description":"Helps browse potential orthologs in model organisms for a given gene","homepage":"http://marrvel.org","contact":null,"uri_format":"http://marrvel.org/model/gene/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"scholia","name":"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/","contact":null,"uri_format":"https://scholia.toolforge.org/ncbi-gene/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/gene","repository":null,"contact":{"name":"Terence D. Murphy","orcid":"0000-0001-9311-9745","email":"murphyte@ncbi.nlm.nih.gov","github":"murphyte","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"100010","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"NCBIGene","biolink.resource":"NCBIGene","edam.data":"1027","fairsharing":"FAIRsharing.5h3maw","go.resource":"NCBIGene","hl7":"6.340","integbio":"nbdc00073","miriam":"ncbigene","n2t":"ncbigene","ncbi.resource":"GeneID","prefixcommons":"ncbigene","re3data":"r3d100010650","togoid":"Ncbigene","uniprot.resource":"DB-0118","wikidata.property":"P351"},"synonyms":["EGID","EntrezGene","GeneID","NCBIGene","NCBI_GeneID","entrez","entrez gene/locuslink","nihgeneid"],"keywords":["chromosome","deoxyribonucleic acid","dna","dna sequence","expression data","gene","gene expression","genetics","genome","genome annotation databases","genome/gene","genomics","homologous","organelle","phenotype","plasmid","protein","repository","sequence","structure","transcript"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/issues/983"],"publications":[{"pubmed":"25355515","doi":"10.1093/nar/gku1055","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21115458","doi":"10.1093/nar/gkq1237","pmc":"PMC3013746","arxiv":null,"title":"Entrez Gene: gene-centered information at NCBI","year":2010},{"pubmed":"15608257","doi":"10.1093/nar/gki031","pmc":"PMC539985","arxiv":null,"title":"Entrez Gene: gene-centered information at NCBI","year":2005}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Rhiannon Cameron","orcid":"0000-0002-9578-0788","email":"rcameron@sfu.com","github":"cmrn-rhi","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"NCBIGene","mastodon":null,"github_request_issue":null,"logo":"https://www.ncbi.nlm.nih.gov/corehtml/logo256.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ncbigi":{"prefix":"ncbigi","name":"GenInfo Identifier","description":"A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number.","pattern":"^\\d+$","uri_format":"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.ncbi.nlm.nih.gov/genbank/sequenceids","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"568815597","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"NCBIGI","edam.data":"2314","go.resource":"NCBI_gi","ncbi.resource":"GI"},"synonyms":["NCBI_gi","ncbi.gi"],"keywords":[],"domain":null,"references":["https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html","https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Format/exercises/qa_accession_vs_gi.html"],"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":"genbank","preferred_prefix":"ncbigi","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ncbitaxon":{"prefix":"ncbitaxon","name":"NCBI Taxonomy","description":"The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.","pattern":"^(\\d+)|([a-zA-Z_]+)$","uri_format":"http://purl.obolibrary.org/obo/NCBITaxon_$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.obolibrary.org/obo/NCBITaxon_$1","providers":[{"code":"","name":"Bio2RDF","description":"Bio2RDF","homepage":"https://bio2rdf.org/","contact":null,"uri_format":"https://bio2rdf.org/taxonomy:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"","name":"Taxonomy through UniProt PURL","description":"Taxonomy through UniProt PURL","homepage":"https://www.uniprot.org/taxonomy/","contact":null,"uri_format":"https://purl.uniprot.org/taxonomy/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/taxonomy:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bioportal.purl","name":"BioPortal","description":"BioPortal assigns their own PURLs to entities in NCBI taxonomy database.","homepage":"https://purl.bioontology.org/ontology/NCBITAXON","contact":null,"uri_format":"http://purl.bioontology.org/ontology/NCBITAXON/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"ebi","name":"European Nucleotide Archive (ENA)","description":"European Nucleotide Archive (ENA)","homepage":"https://www.ebi.ac.uk/ena/","contact":null,"uri_format":"https://www.ebi.ac.uk/ena/data/view/Taxon:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"ena","name":"ENA Taxon Browser","description":null,"homepage":"https://www.ebi.ac.uk/ena","contact":null,"uri_format":"https://www.ebi.ac.uk/ena/browser/view/Taxon:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"ena.xml","name":"ENA Taxon XML","description":null,"homepage":"https://www.ebi.ac.uk/ena","contact":null,"uri_format":"https://www.ebi.ac.uk/ena/browser/api/xml/Taxon:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"scholia","name":"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/","contact":null,"uri_format":"https://scholia.toolforge.org/ncbi-taxon/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://github.com/obophenotype/ncbitaxon","repository":"https://github.com/obophenotype/ncbitaxon","contact":{"name":"Conrad L Schoch","orcid":"0000-0003-1839-5322","email":"schoch2@ncbi.nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"2170610","example_extras":["subclass"],"example_decoys":null,"license":"CC0-1.0","version":"2026-07-12","part_of":null,"part_of_database":null,"provides":null,"download_owl":"http://purl.obolibrary.org/obo/ncbitaxon.owl","download_obo":"http://purl.obolibrary.org/obo/ncbitaxon.obo.gz","download_json":"http://purl.obolibrary.org/obo/ncbitaxon.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"aberowl":"NCBITAXON","bartoc":"509","biocontext":"TAXONOMY","biodivportal":"NCBITAXON","bioportal":"NCBITAXON","cellosaurus.resource":"NCBI_TaxID","edam.data":"1179","fairsharing":"FAIRsharing.fj07xj","go.resource":"NCBITaxon","hl7":"6.205","miriam":"taxonomy","n2t":"taxonomy","ncbi.resource":"taxon","obofoundry":"ncbitaxon","ols":"ncbitaxon","ontobee":"NCBITaxon","prefixcommons":"taxonomy","re3data":"r3d100010415","togoid":"Taxonomy","wikidata.entity":"Q81661717","wikidata.property":"P685"},"synonyms":["NCBI Taxonomy","NCBITaxon","NCBITaxonomyID","NCBI_Taxon_ID","NCBI_taxid","TAX","TaxonomyID","ncbiTaxUID","taxid","taxon","taxonomy","uniprot.taxonomy"],"keywords":["classification","dna","evolutionary biology","genomics","knowledge and information systems","life science","obo","omics","ontology","organism","phylogenetics","protein","proteomics","structure","taxonomic classification","taxonomy"],"domain":null,"references":null,"publications":[{"pubmed":"32761142","doi":"10.1093/database/baaa062","pmc":"PMC7408187","arxiv":null,"title":"NCBI Taxonomy: a comprehensive update on curation, resources and tools","year":2020},{"pubmed":"29140468","doi":"10.1093/nar/gkx1094","pmc":"PMC5753231","arxiv":null,"title":"GenBank","year":2018},{"pubmed":"22139910","doi":"10.1093/nar/gkr1178","pmc":"PMC3245000","arxiv":null,"title":"The NCBI Taxonomy database","year":2011},{"pubmed":null,"doi":"10.5281/zenodo.8065005","pmc":null,"arxiv":null,"title":"obophenotype/ncbitaxon: 2023-06-20 Release (v2023-06-20)","year":2023}],"appears_in":["agro","chiro","cl","clo","ecto","envo","foodon","gallont","genepio","go","hso","mco","ons","pcl","pco","uberon","vbo"],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"NCBITaxon","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"neuromorpho":{"prefix":"neuromorpho","name":"NeuroMorpho","description":"NeuroMorpho.Org is a centrally curated inventory of  digitally reconstructed neurons.","pattern":"^\\w+$","uri_format":"http://neuromorpho.org/neuron_info.jsp?neuron_name=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/neuromorpho:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://neuromorpho.org/index.jsp","repository":null,"contact":{"name":"Giorgio Ascoli","orcid":"0000-0002-0964-676X","email":"Ascoli@gmu.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"Rosa2","example_extras":[],"example_decoys":null,"license":"CC-BY-3.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"NEUROMORPHO","edam.data":"2657","miriam":"neuromorpho","n2t":"neuromorpho","prefixcommons":"neuromorpho"},"synonyms":[],"keywords":["anatomy","structure"],"domain":null,"references":null,"publications":[{"pubmed":"16552417","doi":"10.1038/nrn1885","pmc":null,"arxiv":null,"title":"Mobilizing the base of neuroscience data: the case of neuronal morphologies","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"neuromorpho","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"neurondb":{"prefix":"neurondb","name":"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.","pattern":"^\\d+$","uri_format":"http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/neurondb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://senselab.med.yale.edu/NeuronDB/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"265","example_extras":[],"example_decoys":null,"license":"CC-BY-3.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"NEURONDB","edam.data":"2656","miriam":"neurondb","n2t":"neurondb","prefixcommons":"neurondb"},"synonyms":[],"keywords":["anatomy","structure"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"neurondb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"omim":{"prefix":"omim","name":"Online Mendelian Inheritance in Man","description":"Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.","pattern":"^\\d+$","uri_format":"https://omim.org/MIM:$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"OMIM mirror at John Hopkins","description":"OMIM mirror at John Hopkins","homepage":"http://mirror.omim.org/","contact":null,"uri_format":"http://mirror.omim.org/entry/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/omim:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"legacy","name":"OMIM","description":"This is the actual endpoint for OMIM entries","homepage":"https://www.omim.org","contact":null,"uri_format":"https://www.omim.org/entry/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"miriam_legacy","name":"MIRIAM Legacy","description":"Legacy URLs for identifiers.org","homepage":"http://identifiers.org","contact":null,"uri_format":"http://identifiers.org/omim/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"ncbi.omim","name":"NCBI","description":"An NCBI endpoint for OMIM entries","homepage":"http://www.ncbi.nlm.nih.gov/omim","contact":null,"uri_format":"http://www.ncbi.nlm.nih.gov/omim/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"purl","name":"OMIM PURL (not in use)","description":"An extra purl that was registred, but probably won't be used.","homepage":"https://www.omim.org","contact":null,"uri_format":"https://purl.org/mim/MIM:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"purl2","name":"OMIM PURL (not in use)","description":"An extra purl that was registred, but probably won't be used.","homepage":"https://www.omim.org","contact":null,"uri_format":"https://omim.org/OMIM:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://omim.org/","repository":null,"contact":{"name":"Ada Hamosh","orcid":"0000-0002-1780-5230","email":"ahamosh@jhmi.edu","github":"ahamosh","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00za53h95","wikidata":null,"gnd":null,"name":"Johns Hopkins University, Baltimore, Maryland","partnered":false}],"example":"603903","example_extras":[],"example_decoys":null,"license":"https://www.omim.org/help/agreement","version":"2025_08_04","part_of":null,"part_of_database":null,"provides":null,"download_owl":"http://aber-owl.net/media/ontologies/OMIM/1/omim.owl","download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"aberowl":"OMIM","biocontext":"OMIM","bioportal":"OMIM","edam.data":"1153","fairsharing":"FAIRsharing.b084yh","go.resource":"OMIM","hl7":"6.174","integbio":"nbdc00154","miriam":"mim","n2t":"mim","ncbi.resource":"MIM","prefixcommons":"omim","uniprot.resource":"DB-0062","wikidata.entity":"Q7187","wikidata.property":"P492"},"synonyms":["OMIM","mim"],"keywords":["bibliography/documents","biomedical science","disease","disease course","gene","gene expression","genetic disorder","genetic variation","genome/gene","genotype","health/disease","omim","ontology","organism-specific databases","phenotype"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/issues/497"],"publications":[{"pubmed":"30445645","doi":"10.1093/nar/gky1151","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"25428349","doi":"10.1093/nar/gku1205","pmc":"PMC4383985","arxiv":null,"title":"OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders","year":2014},{"pubmed":"18842627","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15608251","doi":"10.1093/nar/gki033","pmc":"PMC539987","arxiv":null,"title":"Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders","year":2005}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"omim","mastodon":null,"github_request_issue":null,"logo":"https://omim.org/static/omim/icons/OMIM_davinciman.001.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"panther.pathway":{"prefix":"panther.pathway","name":"PANTHER Pathway","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.","pattern":"^P\\d{5}$","uri_format":"http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.pantherdb.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"01rq8ck58","wikidata":null,"gnd":null,"name":"Keck School of Medicine, University of Southern California","partnered":false}],"example":"P00024","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PANTHER.PATHWAY","edam.data":"1161","miriam":"panther.pathway","n2t":"panther.pathway"},"synonyms":[],"keywords":["panther"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"panther.pathway","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pdb":{"prefix":"pdb","name":"PDB Structure","description":"The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.","pattern":"^[0-9][A-Za-z0-9]{3}$","uri_format":"https://www.wwpdb.org/pdb?id=pdb_0000$1","uri_format_resolvable":null,"rdf_uri_format":"https://rdf.wwpdb.org/pdb/$1","providers":[{"code":"","name":"Proteopedia","description":"Proteopedia","homepage":"http://www.proteopedia.org/","contact":null,"uri_format":"http://proteopedia.org/wiki/index.php/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pdbj:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"dionysus","name":"DIONYSUS","description":"DIONYSUS is a database of protein-carbohydrate interfaces, offering annotated data and tools for exploring interaction patterns and annotating proteins.","homepage":"www.dsimb.inserm.fr/DIONYSUS","contact":null,"uri_format":"https://www.dsimb.inserm.fr/DIONYSUS/structure/$1","first_party":null,"publications":[{"pubmed":"39436020","doi":"10.1093/nar/gkae890","pmc":null,"arxiv":null,"title":"DIONYSUS: a database of protein-carbohydrate interfaces","year":2024}],"example":null,"status":null,"organization":null},{"code":"ebi","name":"Protein Databank through PDBsum","description":"Protein Databank through PDBsum","homepage":"https://www.ebi.ac.uk/pdbsum/","contact":null,"uri_format":"https://www.ebi.ac.uk/pdbsum/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"furna","name":"furna","description":"FURNA (Functions of RNAs) is a database of ligand-RNA interactions and Gene Ontology annotations for RNAs in the Protein Data Bank (PDB).","homepage":"https://seq2fun.dcmb.med.umich.edu/furna/","contact":null,"uri_format":"https://seq2fun.dcmb.med.umich.edu/furna/pdb.cgi?pdbid=$1","first_party":null,"publications":[{"pubmed":"39074139","doi":"10.1371/journal.pbio.3002476","pmc":"PMC11309384","arxiv":null,"title":"FURNA: A database for functional annotations of RNA structures","year":2024}],"example":"157d","status":null,"organization":null},{"code":"pdbe","name":"Protein Databank in Europe (PDBe)","description":"Protein Databank in Europe (PDBe)","homepage":"http://www.pdbe.org/","contact":null,"uri_format":"https://www.ebi.ac.uk/pdbe/entry/pdb/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"pdbj","name":"Protein Data Bank Japan (PDBj)","description":"Protein Data Bank Japan (PDBj)","homepage":"http://www.pdbj.org/","contact":null,"uri_format":"https://pdbj.org/mine/summary/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"proteinsplus","name":"ProteinsPlus","description":"Database of protein-ligand interactions.","homepage":"https://proteins.plus/","contact":null,"uri_format":"https://proteins.plus/$1","first_party":null,"publications":[{"pubmed":"40326518","doi":"10.1093/nar/gkaf377","pmc":null,"arxiv":null,"title":"ProteinsPlus: a publicly available resource for protein structure mining","year":2025}],"example":null,"status":null,"organization":null},{"code":"rcsb","name":"RCSB PDB","description":"RCSB PDB","homepage":"https://www.rcsb.org/","contact":null,"uri_format":"https://www.rcsb.org/structure/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"rnaprodb","name":"RNA Protein Database","description":"RNAproDB assists research in structural analysis of RNA-protein complexes by providing information about the nucleic acid structure as well as interacting proteins.","homepage":"https://rnaprodb.usc.edu","contact":null,"uri_format":"https://rnaprodb.usc.edu/$1","first_party":null,"publications":[{"pubmed":"40126909","doi":"10.1016/j.jmb.2025.169012","pmc":null,"arxiv":null,"title":"RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions","year":2025}],"example":null,"status":null,"organization":null},{"code":"sabdab","name":"The Structural Antibody Database","description":"SAbDab is a database containing all the antibody structures available in the PDB. Each structure is annotated with a number of properties including experimental details, antibody nomenclature (e.g. heavy-light pairings), curated affinity data and sequence annotations.","homepage":"https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab","contact":null,"uri_format":"https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/structureviewer/?pdb=$1","first_party":null,"publications":[{"pubmed":"24214988","doi":"10.1093/nar/gkt1043","pmc":"PMC3965125","arxiv":null,"title":"SAbDab: the structural antibody database","year":2013}],"example":"9ii2","status":null,"organization":null}],"homepage":"https://www.wwpdb.org/","repository":null,"contact":{"name":"Haruki Nakamura","orcid":"0000-0001-6690-5863","email":"harukin@protein.osaka-u.ac.jp","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"2gc4","example_extras":["157d","9ii2"],"example_decoys":null,"license":"CC0-1.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PDB","edam.data":"1127","fairsharing":"FAIRsharing.rs2815","integbio":"nbdc00613","miriam":"pdb","n2t":"pdb","ncbi.resource":"PDB","pathguide":"398","prefixcommons":"pdbj","re3data":"r3d100010910","togoid":"Pdb","uniprot.resource":"DB-0172","wikidata.property":"P638"},"synonyms":["RCSB_PDB","pdbe","pdbj","wwpdb"],"keywords":["3d structure","3d structure databases","bioinformatics","covid-19","dna","epidemiology","function analysis","image/movie","protein","proteomics","repository","rna","structural biology","structure","virology"],"domain":null,"references":null,"publications":[{"pubmed":"40326518","doi":"10.1093/nar/gkaf377","pmc":null,"arxiv":null,"title":"ProteinsPlus: a publicly available resource for protein structure mining","year":2025},{"pubmed":"40126909","doi":"10.1016/j.jmb.2025.169012","pmc":null,"arxiv":null,"title":"RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions","year":2025},{"pubmed":"39436020","doi":"10.1093/nar/gkae890","pmc":null,"arxiv":null,"title":"DIONYSUS: a database of protein-carbohydrate interfaces","year":2024},{"pubmed":"39074139","doi":"10.1371/journal.pbio.3002476","pmc":"PMC11309384","arxiv":null,"title":"FURNA: A database for functional annotations of RNA structures","year":2024},{"pubmed":"34664328","doi":"10.1002/pro.4211","pmc":"PMC8740847","arxiv":null,"title":"Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data","year":2021},{"pubmed":"28815765","doi":"10.1002/pro.3273","pmc":"PMC5734392","arxiv":null,"title":"New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)","year":2017},{"pubmed":"27789697","doi":"10.1093/nar/gkw962","pmc":"PMC5210648","arxiv":null,"title":"Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures","year":2016},{"pubmed":"24214988","doi":"10.1093/nar/gkt1043","pmc":"PMC3965125","arxiv":null,"title":"SAbDab: the structural antibody database","year":2013},{"pubmed":"22110033","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21976737","doi":"10.1093/nar/gkr811","pmc":"PMC3245181","arxiv":null,"title":"Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format","year":2011},{"pubmed":"21796434","doi":"10.1007/s10822-011-9460-y","pmc":null,"arxiv":null,"title":"Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr","year":2011},{"pubmed":"20798081","doi":"10.1093/database/baq021","pmc":"PMC2997606","arxiv":null,"title":"PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan","year":2010},{"pubmed":"12099029","doi":null,"pmc":null,"arxiv":null,"title":"[Development of PDBj: Advanced database for protein structures]","year":2002}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pdb","mastodon":null,"github_request_issue":null,"logo":"https://cdn.rcsb.org/wwpdb/img/core/wwpdb-logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"peptideatlas.peptide":{"prefix":"peptideatlas.peptide","name":"PeptideAtlas Peptide","description":"The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools.","pattern":"^PAp[0-9]{8}$","uri_format":"https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/peptideatlas:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.peptideatlas.org/","repository":null,"contact":{"name":"Eric W. Deutsch","orcid":"0000-0001-8732-0928","email":"edeutsch@systemsbiology.org","github":"edeutsch","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02tpgw303","wikidata":null,"gnd":null,"name":"Institute for Systems Biology","partnered":false}],"example":"PAp00000009","example_extras":[],"example_decoys":null,"license":"http://www.peptideatlas.org/publications.php","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PEPTIDEATLAS","edam.data":"2626","fairsharing":"FAIRsharing.dvyrsz","integbio":"nbdc01812","miriam":"peptideatlas","n2t":"peptideatlas","prefixcommons":"peptideatlas","re3data":"r3d100010889","uniprot.resource":"DB-0071"},"synonyms":["peptideatlas"],"keywords":["annotation","mass spectrometry","mass spectrum","protein","proteomic databases","proteomics","sequence","structure"],"domain":null,"references":null,"publications":[{"pubmed":"18451766","doi":"10.1038/embor.2008.56","pmc":"PMC2373374","arxiv":null,"title":"PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows","year":2008},{"pubmed":"16381952","doi":"10.1093/nar/gkj040","pmc":"PMC1347403","arxiv":null,"title":"The PeptideAtlas project","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"peptideatlas.peptide","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pfam":{"prefix":"pfam","name":"Pfam protein family","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.","pattern":"^PF\\d{5}$","uri_format":"https://www.ebi.ac.uk/interpro/entry/pfam/$1","uri_format_resolvable":null,"rdf_uri_format":"http://pfam.janelia.org/family/#$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pfam:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"sanger","name":"Sanger Pfam Mirror","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":"http://pfam.sanger.ac.uk/","contact":null,"uri_format":"http://pfam.sanger.ac.uk/family?entry=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"xfam","name":"Xfam","description":"Pfam's familes in their old home in the xfam.org","homepage":"https://pfam.xfam.org","contact":null,"uri_format":"https://pfam.xfam.org/family?acc=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/interpro/","repository":null,"contact":{"name":"Alex Bateman","orcid":"0000-0002-6982-4660","email":"agb@ebi.ac.uk","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"PF11779","example_extras":[],"example_decoys":null,"license":"CC0-1.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/pfam/pfam.owl","download_obo":"https://w3id.org/biopragmatics/resources/pfam/pfam.obo","download_json":"https://w3id.org/biopragmatics/resources/pfam/pfam.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PFAM","edam.data":"1138","fairsharing":"FAIRsharing.y3scf6","go.resource":"Pfam","integbio":"nbdc00163","miriam":"pfam","n2t":"pfam","ncbi.resource":"PFAM","prefixcommons":"pfam","re3data":"r3d100012850","togoid":"Pfam","uniprot.resource":"DB-0073","wikidata.property":"P3519"},"synonyms":["PF"],"keywords":["biocuration","biology","classification","domain","evolution","evolutionary relationship between proteins via sequence similarity","family and domain databases","function analysis","functional domain","multiple sequence alignment","ontology","pfam","polypeptide region","prediction and recognition","protein","protein binding domain","protein domain","proteome","sequence","sequence alignment","sequence motif","sequence similarity"],"domain":null,"references":["https://twitter.com/PfamDB/status/1555149527228813314"],"publications":[{"pubmed":"9847196","doi":"10.1093/nar/27.1.260","pmc":"PMC148151","arxiv":null,"title":"Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins","year":1999},{"pubmed":"9399864","doi":"10.1093/nar/26.1.320","pmc":"PMC147209","arxiv":null,"title":"Pfam: multiple sequence alignments and HMM-profiles of protein domains","year":1998},{"pubmed":"9223186","doi":"10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l","pmc":null,"arxiv":null,"title":"Pfam: a comprehensive database of protein domain families based on seed alignments","year":1997},{"pubmed":"39540428","doi":"10.1093/nar/gkae997","pmc":null,"arxiv":null,"title":"The Pfam protein families database: embracing AI/ML","year":2024},{"pubmed":"33125078","doi":"10.1093/nar/gkaa913","pmc":"PMC7779014","arxiv":null,"title":"Pfam: The protein families database in 2021","year":2021},{"pubmed":"30357350","doi":"10.1093/nar/gky995","pmc":"PMC6324024","arxiv":null,"title":"The Pfam protein families database in 2019","year":2019},{"pubmed":"26673716","doi":"10.1093/nar/gkv1344","pmc":"PMC4702930","arxiv":null,"title":"The Pfam protein families database: towards a more sustainable future","year":2015},{"pubmed":"24288371","doi":"10.1093/nar/gkt1223","pmc":"PMC3965110","arxiv":null,"title":"Pfam: the protein families database","year":2013},{"pubmed":"22127870","doi":"10.1093/nar/gkr1065","pmc":"PMC3245129","arxiv":null,"title":"The Pfam protein families database","year":2011},{"pubmed":"19920124","doi":"10.1093/nar/gkp985","pmc":"PMC2808889","arxiv":null,"title":"The Pfam protein families database","year":2009},{"pubmed":"18039703","doi":"10.1093/nar/gkm960","pmc":"PMC2238907","arxiv":null,"title":"The Pfam protein families database","year":2007},{"pubmed":"16381856","doi":"10.1093/nar/gkj149","pmc":"PMC1347511","arxiv":null,"title":"Pfam: clans, web tools and services","year":2006},{"pubmed":"14681378","doi":"10.1093/nar/gkh121","pmc":"PMC308855","arxiv":null,"title":"The Pfam protein families database","year":2004},{"pubmed":"11752314","doi":"10.1093/nar/30.1.276","pmc":"PMC99071","arxiv":null,"title":"The Pfam protein families database","year":2002},{"pubmed":"10592242","doi":"10.1093/nar/28.1.263","pmc":"PMC102420","arxiv":null,"title":"The Pfam protein families database","year":2000}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pfam","mastodon":null,"github_request_issue":null,"logo":"https://upload.wikimedia.org/wikipedia/commons/0/03/Pfam_logo.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pfam.clan":{"prefix":"pfam.clan","name":"Pfam protein clan","description":"Higher order grouping of Pfam families","pattern":"^CL\\d+$","uri_format":"https://www.ebi.ac.uk/interpro/set/pfam/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"xfam","name":"Xfam","description":"Pfam's clans in their old home in the xfam.org","homepage":"https://pfam.xfam.org","contact":null,"uri_format":"https://pfam.xfam.org/clan/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://pfam.xfam.org","repository":null,"contact":{"name":"Alex Bateman","orcid":"0000-0002-6982-4660","email":"agb@ebi.ac.uk","github":"bateman-research","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"CL0192","example_extras":[],"example_decoys":null,"license":"CC0-1.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/pfam.clan/pfam.clan.owl","download_obo":"https://w3id.org/biopragmatics/resources/pfam.clan/pfam.clan.obo","download_json":"https://w3id.org/biopragmatics/resources/pfam.clan/pfam.clan.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"2758"},"synonyms":[],"keywords":["ontology","pfam","protein family"],"domain":null,"references":["https://twitter.com/PfamDB/status/1555149527228813314"],"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pfam.clan","mastodon":null,"github_request_issue":null,"logo":"https://upload.wikimedia.org/wikipedia/commons/0/03/Pfam_logo.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pharmgkb":{"prefix":"pharmgkb","name":"PharmGKB","description":"unique identifier for an entity in the PharmGKB knowledgebase","pattern":"^PA[1-9]\\d*$","uri_format":"https://www.clinpgx.org/accession/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pharmgkb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.pharmgkb.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"PA134955224","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"2649","fairsharing":"FAIRsharing.t7yckc","pathguide":"117","prefixcommons":"pharmgkb","re3data":"r3d100012325","wikidata.property":"P7001"},"synonyms":[],"keywords":["approved drug","biomedical science","biopax","classification","drug","drug metabolism","expression data","gene","gene expression","gene-disease association","genetics","genotype","life science","pathway","pharmacogenomics","phenotype","sequence variant"],"domain":null,"references":null,"publications":[{"pubmed":"22103613","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"11908751","doi":"10.1038/sj.tpj.6500035","pmc":null,"arxiv":null,"title":"Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base","year":2002}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pharmgkb","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaFFCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--7b5a4cbda608fcf58b6992075869e40ea5f34044/wordmark.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pharmgkb.disease":{"prefix":"pharmgkb.disease","name":"PharmGKB Disease","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.","pattern":"^PA\\d+$","uri_format":"http://www.pharmgkb.org/disease/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pharmgkb.disease:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.pharmgkb.org/","repository":null,"contact":{"name":"Teri E Klein","orcid":"0000-0001-5527-6475","email":"teri.klein@stanford.edu","github":"TeriKlein","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"PA447218","example_extras":[],"example_decoys":null,"license":"CC-BY-SA-4.0","version":null,"part_of":"pharmgkb","part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.owl","download_obo":"https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.obo","download_json":"https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PHARMGKB.DISEASE","biolink.resource":"PHARMGKB.DISEASE","edam.data":"2651","miriam":"pharmgkb.disease","n2t":"pharmgkb.disease","prefixcommons":"pharmgkb.disease"},"synonyms":[],"keywords":["ontology","pharmacogenomics"],"domain":null,"references":null,"publications":[{"pubmed":"22103613","doi":"10.2217/bmm.11.94","pmc":"PMC3339046","arxiv":null,"title":"From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource","year":2011},{"pubmed":"11908751","doi":"10.1038/sj.tpj.6500035","pmc":null,"arxiv":null,"title":"Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base","year":2001}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pharmgkb.disease","mastodon":null,"github_request_issue":null,"logo":"https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pharmgkb.drug":{"prefix":"pharmgkb.drug","name":"PharmGKB Drug","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.","pattern":"^PA\\d+$","uri_format":"http://www.pharmgkb.org/drug/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pharmgkb.drug:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.pharmgkb.org/","repository":null,"contact":{"name":"Teri E Klein","orcid":"0000-0001-5527-6475","email":"teri.klein@stanford.edu","github":"TeriKlein","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"PA448710","example_extras":[],"example_decoys":null,"license":"CC-BY-SA-4.0","version":null,"part_of":"pharmgkb","part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.owl","download_obo":"https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.obo","download_json":"https://w3id.org/biopragmatics/resources/pharmgkb.drug/pharmgkb.drug.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PHARMGKB.DRUG","biolink.resource":"PHARMGKB.DRUG","edam.data":"2652","miriam":"pharmgkb.drug","n2t":"pharmgkb.drug","prefixcommons":"pharmgkb.drug"},"synonyms":[],"keywords":["drug","ontology","pharmacogenomics"],"domain":null,"references":null,"publications":[{"pubmed":"22103613","doi":"10.2217/bmm.11.94","pmc":"PMC3339046","arxiv":null,"title":"From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource","year":2011},{"pubmed":"11908751","doi":"10.1038/sj.tpj.6500035","pmc":null,"arxiv":null,"title":"Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base","year":2001}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pharmgkb.drug","mastodon":null,"github_request_issue":null,"logo":"https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pharmgkb.pathways":{"prefix":"pharmgkb.pathways","name":"PharmGKB pathway","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. \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.","pattern":"^PA\\d+$","uri_format":"http://www.pharmgkb.org/pathway/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pharmgkb.pathways:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.pharmgkb.org/","repository":null,"contact":{"name":"Teri E Klein","orcid":"0000-0001-5527-6475","email":"teri.klein@stanford.edu","github":"TeriKlein","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"PA146123006","example_extras":[],"example_decoys":null,"license":"CC-BY-SA-4.0","version":null,"part_of":"pharmgkb","part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.owl","download_obo":"https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.obo","download_json":"https://w3id.org/biopragmatics/resources/pharmgkb.pathways/pharmgkb.pathways.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PHARMGKB.PATHWAYS","biolink.resource":"PHARMGKB.PATHWAYS","edam.data":"2650","miriam":"pharmgkb.pathways","n2t":"pharmgkb.pathways","prefixcommons":"pharmgkb.pathways"},"synonyms":[],"keywords":["ontology","pathway","pharmacogenomics"],"domain":null,"references":null,"publications":[{"pubmed":"22103613","doi":"10.2217/bmm.11.94","pmc":"PMC3339046","arxiv":null,"title":"From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource","year":2011},{"pubmed":"11908751","doi":"10.1038/sj.tpj.6500035","pmc":null,"arxiv":null,"title":"Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base","year":2001}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pharmgkb.pathways","mastodon":null,"github_request_issue":null,"logo":"https://rxgenomix.com/wp-content/uploads/2019/10/pharmgKB.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pid.pathway":{"prefix":"pid.pathway","name":"NCI Pathway Interaction Database: Pathway","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.","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$","uri_format":"http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pid:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ndexbio.org/index.html#/networkset/8a2d7ee9-1513-11e9-bb6a-0ac135e8bacf","repository":null,"contact":{"name":"Carl F. Schaefer","orcid":"0000-0002-5941-3390","email":"schaefec@mail.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"eff796f3-6195-11e5-8ac5-06603eb7f303","example_extras":[],"example_decoys":null,"license":"http://www.cancer.gov/global/web/policies/allpages#5","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/pid.pathway/pid.pathway.owl","download_obo":"https://w3id.org/biopragmatics/resources/pid.pathway/pid.pathway.obo","download_json":"https://w3id.org/biopragmatics/resources/pid.pathway/pid.pathway.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"PID.PATHWAY","edam.data":"2344","miriam":"pid.pathway","n2t":"pid.pathway","pathguide":"119","prefixcommons":"pid"},"synonyms":["pid"],"keywords":["biopax","gene","ontology","pathway","protein","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"18832364","doi":"10.1093/nar/gkn653","pmc":"PMC2686461","arxiv":null,"title":"PID: the Pathway Interaction Database","year":2008}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pid.pathway","mastodon":null,"github_request_issue":null,"logo":"https://home.ndexbio.org/img/pid-logo-ndex.jpg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pir":{"prefix":"pir","name":"Protein Information Resource","description":"The Protein Information Resource (PIR) had its final release in 2004 and is now a part of UniProt","pattern":null,"uri_format":"https://proteininformationresource.org/cgi-bin/nbrfget?uid=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://proteininformationresource.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0425gsx30","wikidata":null,"gnd":null,"name":"Protein Information Resource","partnered":false}],"example":"B44282","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"edam.data":"1100","go.resource":"PIR","integbio":"nbdc00167","ncbi.resource":"PIR","uniprot.resource":"DB-0078"},"synonyms":[],"keywords":["protein","sequence","sequence databases"],"domain":null,"references":null,"publications":[{"pubmed":"17569631","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"12520019","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"11752247","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"11125041","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"10869023","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"10592177","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pir","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pirsf":{"prefix":"pirsf","name":"PIR Superfamily Classification System","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.","pattern":"^PIRSF\\d{6}$","uri_format":"https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pirsf:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://pir.georgetown.edu/","repository":null,"contact":{"name":"Cathy H. Wu","orcid":"0000-0001-6379-8601","email":"wuc@udel.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00hjz7x27","wikidata":null,"gnd":null,"name":"Georgetown University Medical Center","partnered":false}],"example":"PIRSF000100","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PIRSF","edam.data":"1136","fairsharing":"FAIRsharing.vssch2","go.resource":"PIRSF","miriam":"pirsf","n2t":"pirsf","prefixcommons":"pirsf","uniprot.resource":"DB-0079"},"synonyms":[],"keywords":["family and domain databases","life science","protein","proteomics","sequence cluster","structure"],"domain":null,"references":null,"publications":[{"pubmed":"14681371","doi":"10.1093/nar/gkh097","pmc":"PMC308831","arxiv":null,"title":"PIRSF: family classification system at the Protein Information Resource","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pirsf","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"po":{"prefix":"po","name":"Plant Ontology","description":"The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.","pattern":"^\\d+$","uri_format":"http://purl.obolibrary.org/obo/PO_$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.obolibrary.org/obo/PO_$1","providers":[{"code":"amigo","name":"Plant Ontology through Amigo","description":"Plant Ontology through Amigo","homepage":"http://www.plantontology.org/","contact":null,"uri_format":"https://browser.planteome.org/amigo/term/PO:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/po:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://browser.planteome.org/amigo","repository":"https://github.com/Planteome/plant-ontology","contact":{"name":"Pankaj Jaiswal","orcid":"0000-0002-1005-8383","email":"jaiswalp@science.oregonstate.edu","github":"jaiswalp","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"0009089","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":"2026-01-09","part_of":null,"part_of_database":null,"provides":null,"download_owl":"http://purl.obolibrary.org/obo/po.owl","download_obo":"http://purl.obolibrary.org/obo/po.obo","download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"PO","banana_peel":null,"deprecated":false,"mappings":{"aberowl":"PO","agroportal":"PO","biocontext":"PO","biodivportal":"PO","bioportal":"PO","cellosaurus.resource":"PO","edam.data":"1180","fairsharing":"FAIRsharing.3ngg40","go.resource":"PO","miriam":"po","n2t":"po","obofoundry":"po","ols":"po","ontobee":"PO","prefixcommons":"po","tib.ts":"po","wikidata.entity":"Q7201529"},"synonyms":[],"keywords":["botany","classification","dataplant","earth sciences","ess","expression data","genomics","life cycle","life science","obo","omics","ontology","plant anatomy","structure","whole plant development stage"],"domain":null,"references":null,"publications":[{"pubmed":"29186578","doi":"10.1093/nar/gkx1152","pmc":"PMC5753347","arxiv":null,"title":"The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics","year":2018},{"pubmed":"26519402","doi":"10.1007/978-1-4939-3167-5_5","pmc":null,"arxiv":null,"title":"The Plant Ontology: A Tool for Plant Genomics","year":2016},{"pubmed":"25562316","doi":"10.1371/journal.pbio.1002033","pmc":"PMC4285398","arxiv":null,"title":"Finding our way through phenotypes","year":2015},{"pubmed":"23220694","doi":"10.1093/pcp/pcs163","pmc":"PMC3583023","arxiv":null,"title":"The plant ontology as a tool for comparative plant anatomy and genomic analyses","year":2012},{"pubmed":"18629207","doi":"10.1002/cfg.496","pmc":"PMC2447502","arxiv":null,"title":"Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages","year":2005},{"pubmed":"18628842","doi":"10.1002/cfg.154","pmc":"PMC2447263","arxiv":null,"title":"The Plant Ontology Consortium and plant ontologies","year":2002},{"pubmed":"18194960","doi":"10.1093/nar/gkm908","pmc":"PMC2238838","arxiv":null,"title":"The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations","year":2008}],"appears_in":["agro","ecocore","envo","gallont","genepio"],"depends_on":[],"namespace_in_lui":true,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"PO","mastodon":null,"github_request_issue":null,"logo":"https://raw.githubusercontent.com/Planteome/plant-ontology/refs/heads/master/Planteome_profile.jpg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pubchem.bioassay":{"prefix":"pubchem.bioassay","name":"PubChem-bioassay","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.","pattern":"^\\d+$","uri_format":"https://pubchem.ncbi.nlm.nih.gov/bioassay/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pubchem.bioassay:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay","repository":null,"contact":{"name":"Kim Dixon Pruitt","orcid":"0000-0001-7950-1374","email":"pruitt@ncbi.nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"1018","example_extras":[],"example_decoys":null,"license":"http://www.nlm.nih.gov/copyright.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PUBCHEM.BIOASSAY","edam.data":"2638","go.resource":"PubChem_BioAssay","integbio":"nbdc00640","miriam":"pubchem.bioassay","n2t":"pubchem.bioassay","prefixcommons":"pubchem.bioassay"},"synonyms":["pubchem.aid","pubchem.assay"],"keywords":["bibliography/documents","chemical compound","image/movie","metabolite","method","pubchem","repository","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"22140110","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17170002","doi":"10.1093/nar/gkl1031","pmc":"PMC1781113","arxiv":null,"title":"Database resources of the National Center for Biotechnology Information","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pubchem.bioassay","mastodon":null,"github_request_issue":null,"logo":"https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pubchem.compound":{"prefix":"pubchem.compound","name":"PubChem compound","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.","pattern":"^\\d+$","uri_format":"https://pubchem.ncbi.nlm.nih.gov/compound/$1","uri_format_resolvable":null,"rdf_uri_format":"http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pubchem.compound:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"scholia","name":"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/","contact":null,"uri_format":"https://scholia.toolforge.org/pubchem/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://pubchem.ncbi.nlm.nih.gov/","repository":null,"contact":{"name":"Evan E Bolton","orcid":"0000-0002-5959-6190","email":"bolton@ncbi.nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"100101","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PUBCHEM.COMPOUND","biolink.resource":"CID","cellosaurus.resource":"PubChem","cheminf":"000140","edam.data":"2639","fairsharing":"FAIRsharing.qt3w7z","go.resource":"PubChem_Compound","integbio":"nbdc02626","miriam":"pubchem.compound","n2t":"pubchem.compound","prefixcommons":"pubchem.compound","re3data":"r3d100010129","togoid":"PubchemCompound","wikidata.property":"P662"},"synonyms":["CID","DSSTox_CID","PUBCHEM_CID","PubChem_Compound_CID","Pubchem","pubchem_id"],"keywords":["assay","bibliography/documents","chemical","chemical compound","chemical structure","chemistry","compound","epidemiology","metabolite","method","protein","pubchem","repository","small molecule","structure","virology"],"domain":null,"references":null,"publications":[{"pubmed":"33151290","doi":"10.1093/nar/gkaa971","pmc":"PMC7778930","arxiv":null,"title":"PubChem in 2021: new data content and improved web interfaces","year":2021},{"pubmed":"30371825","doi":"10.1093/nar/gky1033","pmc":"PMC6324075","arxiv":null,"title":"PubChem 2019 update: improved access to chemical data","year":2019},{"pubmed":"27899599","doi":"10.1093/nar/gkw1118","pmc":"PMC5210581","arxiv":null,"title":"PubChem BioAssay: 2017 update","year":2016},{"pubmed":"24198245","doi":"10.1093/nar/gkt978","pmc":"PMC3965008","arxiv":null,"title":"PubChem BioAssay: 2014 update","year":2013},{"pubmed":"22140110","doi":"10.1093/nar/gkr1132","pmc":"PMC3245056","arxiv":null,"title":"PubChem's BioAssay Database","year":2011},{"pubmed":"20970519","doi":"10.1016/j.drudis.2010.10.003","pmc":"PMC3010383","arxiv":null,"title":"PubChem as a public resource for drug discovery","year":2010},{"pubmed":"19498078","doi":"10.1093/nar/gkp456","pmc":"PMC2703903","arxiv":null,"title":"PubChem: a public information system for analyzing bioactivities of small molecules","year":2009},{"pubmed":"17170002","doi":"10.1093/nar/gkl1031","pmc":"PMC1781113","arxiv":null,"title":"Database resources of the National Center for Biotechnology Information","year":2006},{"pubmed":null,"doi":"10.1093/nar/gkac956","pmc":null,"arxiv":null,"title":"PubChem 2023 update","year":2022}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pubchem.compound","mastodon":null,"github_request_issue":null,"logo":"https://pubchem.ncbi.nlm.nih.gov/pcfe/logo/PubChem_logo_splash.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"pubmed":{"prefix":"pubmed","name":"PubMed","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.","pattern":"^\\d+$","uri_format":"https://pubmed.ncbi.nlm.nih.gov/$1/","uri_format_resolvable":null,"rdf_uri_format":"http://rdf.ncbi.nlm.nih.gov/pubchem/reference/$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/pubmed:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"epmc","name":"Europe PMC","description":"Europe PMC","homepage":"http://europepmc.org/","contact":null,"uri_format":"http://europepmc.org/abstract/MED/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"hubmed","name":"HubMed","description":"HubMed","homepage":"http://www.hubmed.org/","contact":null,"uri_format":"https://www.hubmed.org/?term=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"pubmed.new","name":"PubMed (new)","description":"New-style link for pubmed","homepage":"https://pubmed.ncbi.nlm.nih.gov","contact":null,"uri_format":"https://pubmed.ncbi.nlm.nih.gov/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"scholia","name":"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/","contact":null,"uri_format":"https://scholia.toolforge.org/pubmed/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"uniprot.citation","name":"UniProt","description":"UniProt mints PURLs for citations identifiers","homepage":"https://uniprot.org/","contact":null,"uri_format":"http://purl.uniprot.org/citations/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"uniprot.pubmed","name":"UniProt","description":"UniProt mints PURLs for PubMed identifiers","homepage":"https://uniprot.org/","contact":null,"uri_format":"http://purl.uniprot.org/pubmed/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/PubMed/","repository":null,"contact":{"name":"Jeff Beck","orcid":"0000-0002-1798-9797","email":"beck@ncbi.nlm.nih.gov","github":"jeffbeckncbi","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"16333295","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PUBMED","cellosaurus.resource":"PubMed","edam.data":"1187","fairsharing":"FAIRsharing.a5sv8m","go.resource":"PMID","integbio":"nbdc00179","miriam":"pubmed","n2t":"pubmed","prefixcommons":"pubmed","togoid":"Pubmed","wikidata.entity":"Q2082879","wikidata.property":"P698"},"synonyms":["MEDLINE","PMID","PubMed","PubMed ID","pmid"],"keywords":["bibliography","bibliography/documents","biomedical science","earth science","environmental science","life science","literature","traditional medicine"],"domain":null,"references":null,"publications":[{"pubmed":"16381840","doi":"10.1093/nar/gkj158","pmc":"PMC1347520","arxiv":null,"title":"Database resources of the National Center for Biotechnology Information","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"pubmed","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"reactome":{"prefix":"reactome","name":"Reactome","description":"The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.","pattern":"^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$","uri_format":"https://reactome.org/content/detail/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/reactome:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"browser","name":"Reactome Pathway Browser","description":"An interactive view over pathways.","homepage":"https://reactome.org/PathwayBrowser/","contact":null,"uri_format":"https://reactome.org/PathwayBrowser/#/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"pathwaycommons","name":"Pathway Commons","description":"Pathway diagram drawn with Cytoscape","homepage":"https://www.pathwaycommons.org","contact":null,"uri_format":"https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.reactome.org/","repository":null,"contact":{"name":"Peter D'Eustachio","orcid":"0000-0002-5494-626X","email":"deustp01@med.nyu.edu","github":"deustp01","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"R-BTA-418592","example_extras":[],"example_decoys":null,"license":"CC0-1.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/reactome/reactome.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/reactome/reactome.obo","download_json":"https://w3id.org/biopragmatics/resources/reactome/reactome.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"REACTOME","cheminf":"000411","edam.data":"1155","go.resource":"Reactome","integbio":"nbdc00185","miriam":"reactome","n2t":"reactome","pathguide":"103","prefixcommons":"reactome","re3data":"r3d100010861","togoid":"ReactomePathway","wikidata.property":"P3937"},"synonyms":["RE","REACT","Reactome","reactome.pathway"],"keywords":["biopax","expression","human","interaction/pathway","ontology","pathway","protein","psi-mi","reaction","sbml"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/pull/1086"],"publications":[{"pubmed":"29145629","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15608231","doi":"10.1093/nar/gki072","pmc":"PMC540026","arxiv":null,"title":"Reactome: a knowledgebase of biological pathways","year":2005}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Sierra Moxon","orcid":"0000-0002-8719-7760","email":"smoxon@lbl.gov","github":"sierra-moxon","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"reactome","mastodon":null,"github_request_issue":null,"logo":"https://reactome.org/templates/favourite/images/logo/logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"rebase":{"prefix":"rebase","name":"Restriction Enzyme Database","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.","pattern":"^\\d+$","uri_format":"http://rebase.neb.com/rebase/enz/$1.html","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/rebase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://rebase.neb.com/rebase/","repository":null,"contact":{"name":"Richard John Roberts","orcid":"0000-0002-4348-0169","email":"roberts@neb.com","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"04ywg3445","wikidata":null,"gnd":null,"name":"New England Biolabs, Ipswich, Massachusetts","partnered":false}],"example":"101","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"REBASE","edam.data":"2325","fairsharing":"FAIRsharing.9sb9qh","go.resource":"REBASE","integbio":"nbdc00648","miriam":"rebase","n2t":"rebase","pathguide":"72","prefixcommons":"rebase","re3data":"r3d100012171","uniprot.resource":"DB-0089","wikidata.property":"P4866"},"synonyms":[],"keywords":["bioresource","deoxyribonucleic acid","dna","enzyme","genome","life science","protein","protein family/group databases","repository","ribonucleic acid","rna","sequence","small molecule","structure"],"domain":null,"references":null,"publications":[{"pubmed":"36318248","doi":"10.1093/nar/gkac975","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"25378308","doi":"10.1093/nar/gku1046","pmc":"PMC4383893","arxiv":null,"title":"REBASE--a database for DNA restriction and modification: enzymes, genes and genomes","year":2014},{"pubmed":"19846593","doi":"10.1093/nar/gkp874","pmc":"PMC2808884","arxiv":null,"title":"REBASE--a database for DNA restriction and modification: enzymes, genes and genomes","year":2009}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"rebase","mastodon":null,"github_request_issue":null,"logo":"https://rebase.neb.com/rebase/rebase_header_crop3_gray_url_use.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"refseq":{"prefix":"refseq","name":"Reference Sequence Collection","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.","pattern":"^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$","uri_format":"https://www.ncbi.nlm.nih.gov/protein/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/refseq:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/projects/RefSeq/","repository":null,"contact":{"name":"Kim Dixon Pruitt","orcid":"0000-0001-7950-1374","email":"pruitt@ncbi.nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"NP_012345","example_extras":["WP_029104145.1"],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"RefSeq","edam.data":"1098","fairsharing":"FAIRsharing.4jg0qw","go.resource":"RefSeq","hl7":"6.280","integbio":"nbdc00187","miriam":"refseq","n2t":"refseq","prefixcommons":"refseq","re3data":"r3d100010285","uniprot.resource":"DB-0117"},"synonyms":["REFSEQ_PROT"],"keywords":["cdna/est","cell/organelle","computational biology","deoxyribonucleic acid","dna","genetics","genome","genome/gene","life science","protein","ribonucleic acid","rna","sequence","sequence databases","sequencing assay","transcript"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/issues/545"],"publications":[{"pubmed":"39526381","doi":"10.1093/nar/gkae1038","pmc":null,"arxiv":null,"title":"NCBI RefSeq: reference sequence standards through 25 years of curation and annotation","year":2024},{"pubmed":"26553804","doi":"10.1093/nar/gkv1189","pmc":"PMC4702849","arxiv":null,"title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","year":2015},{"pubmed":"22121212","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18927115","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17130148","doi":"10.1093/nar/gkl842","pmc":"PMC1716718","arxiv":null,"title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins","year":2006},{"pubmed":"10592200","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Sebastian Lobentanzer","orcid":"0000-0003-3399-6695","email":null,"github":"slobentanzer","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":"ncbiprotein","preferred_prefix":"refseq","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"resid":{"prefix":"resid","name":"Protein covalent bond","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.","pattern":"^AA\\d{4}$","uri_format":"https://proteininformationresource.org/cgi-bin/resid?id=$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.obolibrary.org/obo/RESID_$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/resid:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://proteininformationresource.org/resid","repository":null,"contact":{"name":"John Garavelli","orcid":"0000-0002-4131-735X","email":"john.garavelli@ebi.ac.uk","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00hjz7x27","wikidata":null,"gnd":null,"name":"Georgetown University Medical Center","partnered":false}],"example":"AA0001","example_extras":[],"example_decoys":null,"license":"http://www.ebi.ac.uk/Information/termsofuse.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"RESID","edam.data":"2619","go.resource":"RESID","miriam":"resid","n2t":"resid","obofoundry":"resid","prefixcommons":"resid","wikidata.entity":"Q114677910"},"synonyms":[],"keywords":["protein","small molecule","structure"],"domain":null,"references":null,"publications":[{"pubmed":"15174124","doi":"10.1002/pmic.200300764","pmc":null,"arxiv":null,"title":"Annotation of post-translational modifications in the Swiss-Prot knowledge base","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"RESID","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"rfam":{"prefix":"rfam","name":"RNA family database","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.","pattern":"^RF\\d{5}$","uri_format":"https://rfam.org/family/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://rfam.org/","repository":null,"contact":{"name":"Anton I Petrov","orcid":"0000-0001-7279-2682","email":"apetrov@ebi.ac.uk","github":"AntonPetrov","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"RF00230","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"RFAM","edam.data":"2356","fairsharing":"FAIRsharing.fex4c8","go.resource":"Rfam","integbio":"nbdc00654","miriam":"rfam","n2t":"rfam","ncbi.resource":"RFAM","togoid":"Rfam","wikidata.property":"P3523"},"synonyms":[],"keywords":["bibliography/documents","cis","cis-regulatory modules","classification","curated information","genetics","multiple sequence alignment","ncrna","regulatory region","ribonucleic acid","rna","rna splicing","sequence","transcript"],"domain":null,"references":null,"publications":[{"pubmed":"39526405","doi":"10.1093/nar/gkae1023","pmc":null,"arxiv":null,"title":"Rfam 15: RNA families database in 2025","year":2024},{"pubmed":"29112718","doi":"10.1093/nar/gkx1038","pmc":"PMC5753348","arxiv":null,"title":"Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families","year":2018},{"pubmed":"25392425","doi":"10.1093/nar/gku1063","pmc":"PMC4383904","arxiv":null,"title":"Rfam 12.0: updates to the RNA families database","year":2014},{"pubmed":"21062808","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18953034","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18945806","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15608160","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"12520045","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"rfam","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"rgd":{"prefix":"rgd","name":"Rat Genome Database","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.","pattern":"^\\d{4,}$","uri_format":"http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"agr","name":"RGD through the Alliance of Genome Resources","description":"RGD through the Alliance of Genome Resources","homepage":"https://www.alliancegenome.org","contact":null,"uri_format":"https://www.alliancegenome.org/gene/RGD:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/rgd:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://rgd.mcw.edu/","repository":null,"contact":{"name":"Jennifer R Smith","orcid":"0000-0002-6443-9376","email":"jrsmith@mcw.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00qqv6244","wikidata":null,"gnd":null,"name":"Medical College of Wisconsin","partnered":false}],"example":"7499841","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/rgd/rgd.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/rgd/rgd.obo","download_json":"https://w3id.org/biopragmatics/resources/rgd/rgd.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"RGD","cellosaurus.resource":"RGD","edam.data":"2620","fairsharing":"FAIRsharing.pfg82t","go.resource":"RGD","integbio":"nbdc00188","miriam":"rgd","n2t":"rgd","ncbi.resource":"RGD","pathguide":"267","prefixcommons":"rgd","re3data":"r3d100010417","rrid.resource":"RGD","togoid":"Rgd","uniprot.resource":"DB-0091","wikidata.property":"P3853"},"synonyms":["RGD"],"keywords":["behavior","biomedical science","bioresource","comparative genomics","congenic rat","data analysis service","deoxyribonucleic acid","disease","disease course","dna","est","faseb list","function","gene","gene functional annotation","genetic","genetic variation","genome","genome/gene","genomic","genomics","genotype","gold standard","health/disease","human","immunology","inbred rat strain","interaction/pathway","interactome","knockout","map","marker","model organism","molecular medicine","mouse","mutant","ontology","ontology/terminology/nomenclature","organism","organism supplier","organism-specific databases","pathway","phenomics","phenotype","physiology","proteomics","qtl","quantitative genetics","rat","recombinant inbred rat","repository","sequence","strain","translational medicine","variation","veterinary medicine","xenobiotic metabolic process"],"domain":null,"references":null,"publications":[{"pubmed":"39841812","doi":"10.1093/database/baae132","pmc":"PMC11753291","arxiv":null,"title":"Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database","year":null},{"pubmed":"35380657","doi":"10.1093/genetics/iyac005","pmc":"PMC8982048","arxiv":null,"title":"MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses","year":2022},{"pubmed":"34741192","doi":"10.1007/s00335-021-09932-x","pmc":"PMC8570235","arxiv":null,"title":"The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research","year":2021},{"pubmed":"31713623","doi":"10.1093/nar/gkz1041","pmc":"PMC7145519","arxiv":null,"title":"The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform","year":2020},{"pubmed":"31228152","doi":"10.1007/978-1-4939-9581-3_3","pmc":null,"arxiv":null,"title":"Rat Genome Databases, Repositories, and Tools","year":2019},{"pubmed":"31228151","doi":"10.1007/978-1-4939-9581-3_2","pmc":null,"arxiv":null,"title":"Rat Genome Assemblies, Annotation, and Variant Repository","year":2019},{"pubmed":"31228150","doi":"10.1007/978-1-4939-9581-3_1","pmc":null,"arxiv":null,"title":"The Rat: A Model Used in Biomedical Research","year":2019},{"pubmed":"30938777","doi":"10.1093/database/baz037","pmc":"PMC6444380","arxiv":null,"title":"Quantitative phenotype analysis to identify, validate and compare rat disease models","year":2019},{"pubmed":"30753478","doi":"10.1093/database/baz014","pmc":"PMC6369425","arxiv":null,"title":"Integrated curation and data mining for disease and phenotype models at the Rat Genome Database","year":2019},{"pubmed":"29761460","doi":"10.1007/978-1-4939-7737-6_8","pmc":"PMC6487669","arxiv":null,"title":"A Primer for the Rat Genome Database (RGD)","year":2018},{"pubmed":"28838068","doi":"10.1093/ilar/ilw041","pmc":"PMC6057551","arxiv":null,"title":"Rat Genome and Model Resources","year":2017},{"pubmed":"27736745","doi":"10.1242/dmm.026021","pmc":"PMC5087824","arxiv":null,"title":"Exploring human disease using the Rat Genome Database","year":2016},{"pubmed":"27602200","doi":"10.1016/j.csbj.2015.11.006","pmc":"PMC4700298","arxiv":null,"title":"Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass","year":2015},{"pubmed":"27287925","doi":"10.1152/physiolgenomics.00046.2016","pmc":"PMC5005459","arxiv":null,"title":"Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database","year":2016},{"pubmed":"27009807","doi":"10.1093/database/baw034","pmc":"PMC4805243","arxiv":null,"title":"The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database","year":2016},{"pubmed":"25355511","doi":"10.1093/nar/gku1026","pmc":"PMC4383884","arxiv":null,"title":"The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease","year":2014},{"pubmed":"25265995","doi":"10.1186/s40246-014-0017-8","pmc":"PMC4191248","arxiv":null,"title":"Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease","year":2014},{"pubmed":"23603846","doi":"10.1093/database/bat015","pmc":"PMC3630803","arxiv":null,"title":"PhenoMiner: quantitative phenotype curation at the rat genome database","year":2013},{"pubmed":"23434633","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21478484","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"19956751","doi":"10.1371/journal.pcbi.1000582","pmc":"PMC2775909","arxiv":null,"title":"The rat genome database curators: who, what, where, why","year":2009},{"pubmed":"18996890","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17151068","doi":"10.1093/nar/gkl988","pmc":"PMC1761441","arxiv":null,"title":"The Rat Genome Database, update 2007--easing the path from disease to data and back again","year":2006},{"pubmed":"10400928","doi":null,"pmc":null,"arxiv":null,"title":"A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat","year":1999},{"pubmed":null,"doi":"10.3390/genes13122304","pmc":null,"arxiv":null,"title":"Ontological Analysis of Coronavirus Associated Human Genes at the COVID-19 Disease Portal","year":2022},{"pubmed":null,"doi":"10.1093/genetics/iyad042","pmc":null,"arxiv":null,"title":"2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource","year":2023}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"rgd","mastodon":null,"github_request_issue":null,"logo":"https://rgd.mcw.edu/rgdweb//common/images/rgd_logo.jpg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"rhea":{"prefix":"rhea","name":"Rhea reaction","description":"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.\n\nRhea 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.","pattern":"^\\d{5}$","uri_format":"https://www.rhea-db.org/rhea/$1","uri_format_resolvable":null,"rdf_uri_format":"http://rdf.rhea-db.org/$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/rhea:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.rhea-db.org/","repository":null,"contact":{"name":"Anne Morgat","orcid":"0000-0002-1216-2969","email":"anne.morgat@sib.swiss","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"002n09z45","wikidata":null,"gnd":null,"name":"SIB Swiss Institute of Bioinformatics","partnered":false}],"example":"12345","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/rhea/rhea.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/rhea/rhea.obo","download_json":"https://w3id.org/biopragmatics/resources/rhea/rhea.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"RHEA","edam.data":"2644","fairsharing":"FAIRsharing.pn1sr5","go.resource":"RHEA","integbio":"nbdc02083","miriam":"rhea","n2t":"rhea","pathguide":"310","prefixcommons":"rhea","re3data":"r3d100010891","togoid":"Rhea","wikidata.entity":"Q24265951"},"synonyms":["RHEA"],"keywords":["annotation","biochemistry","biocuration","biopax","chemical entity","chemical formula","curated information","enzymatic reaction","interaction/pathway","life science","metabolite","ontology","protein","reaction","reaction data","small molecule","transport"],"domain":null,"references":null,"publications":[{"pubmed":"34755880","doi":"10.1093/nar/gkab1016","pmc":"PMC8728268","arxiv":null,"title":"Rhea, the reaction knowledgebase in 2022","year":2022},{"pubmed":"31688925","doi":"10.1093/bioinformatics/btz817","pmc":"PMC7162351","arxiv":null,"title":"Enzyme annotation in UniProtKB using Rhea","year":2020},{"pubmed":"30272209","doi":"10.1093/nar/gky876","pmc":"PMC6324061","arxiv":null,"title":"Updates in Rhea: SPARQLing biochemical reaction data","year":2019},{"pubmed":"27789701","doi":"10.1093/nar/gkw990","pmc":"PMC5210663","arxiv":null,"title":"Updates in Rhea - an expert curated resource of biochemical reactions","year":2016},{"pubmed":"25332395","doi":"10.1093/nar/gku961","pmc":"PMC4384025","arxiv":null,"title":"Updates in Rhea--a manually curated resource of biochemical reactions","year":2014},{"pubmed":"22135291","doi":"10.1093/nar/gkr1126","pmc":"PMC3245052","arxiv":null,"title":"Rhea--a manually curated resource of biochemical reactions","year":2011}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"rhea","mastodon":null,"github_request_issue":null,"logo":"https://www.rhea-db.org/style/images/rhea_logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"rnacentral":{"prefix":"rnacentral","name":"RNACentral","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.","pattern":"^URS[0-9A-F]{10}(\\_\\d+)?$","uri_format":"https://rnacentral.org/rna/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://rnacentral.org/","repository":null,"contact":{"name":"Blake A Sweeney","orcid":"0000-0002-6497-2883","email":"bsweeney@ebi.ac.uk","github":"blakesweeney","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"URS0000759CF4","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"RNACENTRAL","edam.data":"3856","fairsharing":"FAIRsharing.KcCjL7","go.resource":"RNAcentral","integbio":"nbdc02671","miriam":"rnacentral","n2t":"rnacentral","ncbi.resource":"RNAcentral","togoid":"Rnacentral","wikidata.property":"P8697"},"synonyms":["LNCRNADB"],"keywords":["bibliography/documents","bioinformatics","biology","expression","genome/gene","ncrna","nucleic acid sequence","organism","portal","rna","rna sequence","sequence","sequence annotation","transcript"],"domain":null,"references":null,"publications":[{"pubmed":"30395267","doi":"10.1093/nar/gky1034","pmc":"PMC6324050","arxiv":null,"title":"RNAcentral: a hub of information for non-coding RNA sequences","year":2019},{"pubmed":"27794554","doi":"10.1093/nar/gkw1008","pmc":"PMC5210518","arxiv":null,"title":"RNAcentral: a comprehensive database of non-coding RNA sequences","year":2016}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"rnacentral","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ2tHIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--d676fd0c08b74e109bad17a62cf6016687ec37d5/rnacentral-logo-128x128.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"sabiork.reaction":{"prefix":"sabiork.reaction","name":"SABIO-RK Reaction","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.","pattern":"^\\d+$","uri_format":"http://sabiork.h-its.org/reacdetails.jsp?reactid=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/sabiork.reaction:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://sabiork.h-its.org/","repository":null,"contact":{"name":"Ulrike Wittig","orcid":"0000-0002-9077-5664","email":"ulrike.wittig@h-its.org","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"01f7bcy98","wikidata":null,"gnd":null,"name":"Heidelberg Institute for Theoretical Studies  (HITS gGmbH)","partnered":false}],"example":"75","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"SABIORK.REACTION","edam.data":"2309","fairsharing":"FAIRsharing.cwx04e","miriam":"sabiork.reaction","n2t":"sabiork.reaction","pathguide":"226","prefixcommons":"sabiork.reaction","re3data":"r3d100011052","uniprot.resource":"DB-0177"},"synonyms":["SABIO-RK"],"keywords":["biochemistry","biopax","enzyme","enzyme and pathway databases","kinetics","life science","pathway","reaction","reaction data","sbml","systems biology"],"domain":null,"references":null,"publications":[{"pubmed":"37002681","doi":"10.1093/database/baad011","pmc":null,"arxiv":null,"title":"Improved insights into the SABIO-RK database via visualization","year":2023},{"pubmed":"29092055","doi":"10.1093/nar/gkx1065","pmc":null,"arxiv":null,"title":"SABIO-RK: an updated resource for manually curated biochemical reaction kinetics","year":2018},{"pubmed":"24165050","doi":"10.1111/febs.12562","pmc":null,"arxiv":null,"title":"Challenges for an enzymatic reaction kinetics database","year":2014},{"pubmed":"22102587","doi":"10.1093/nar/gkr1046","pmc":"PMC3245076","arxiv":null,"title":"SABIO-RK--database for biochemical reaction kinetics","year":2011}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"sabiork.reaction","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ3NHIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--02f2e1ce3178a109b41747cff268358715024698/logo_SABIO.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"scop":{"prefix":"scop","name":"Structural Classification of Proteins - Unique Identifier","description":"SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.).","pattern":"^\\d+$","uri_format":"http://scop.berkeley.edu/sunid=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/scop:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"gendis","name":"Genomic Distribution of structural Superfamilies","description":"GenDiS is a repository of SCOP-identified homologous sequences of structural superfamily members.","homepage":"https://caps.ncbs.res.in/gendis3/home","contact":null,"uri_format":"https://caps.ncbs.res.in/gendis3/superfamily_display/$1","first_party":null,"publications":[{"pubmed":"40343712","doi":"10.1093/database/baaf035","pmc":"PMC12063530","arxiv":null,"title":"GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database","year":2025}],"example":null,"status":null,"organization":null},{"code":"mrc","name":"SCOP at UK Medical Research council (MRC)","description":"SCOP at UK Medical Research council (MRC)","homepage":"https://scop.mrc-lmb.cam.ac.uk","contact":null,"uri_format":"https://scop.mrc-lmb.cam.ac.uk/term/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://scop.berkeley.edu","repository":null,"contact":{"name":"John-Marc Chandonia","orcid":"0000-0002-5153-9079","email":"JMChandonia@lbl.gov","github":"jmchandonia","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"01an7q238","wikidata":null,"gnd":null,"name":"University of California, Berkeley","partnered":false}],"example":"47419","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"SCOP","edam.data":"1042","fairsharing":"FAIRsharing.wjzty","miriam":"scop","n2t":"scop","prefixcommons":"scop"},"synonyms":["scop.sun","scop.sunid"],"keywords":["life science","polypeptide region","protein","structure"],"domain":null,"references":["https://scop.berkeley.edu/help/#stableidentifiers"],"publications":[{"pubmed":"9847194","doi":"10.1093/nar/27.1.254","pmc":"PMC148149","arxiv":null,"title":"SCOP: a Structural Classification of Proteins database","year":1999},{"pubmed":"9016544","doi":"10.1093/nar/25.1.236","pmc":"PMC146380","arxiv":null,"title":"SCOP: a structural classification of proteins database","year":1997},{"pubmed":"40343712","doi":"10.1093/database/baaf035","pmc":"PMC12063530","arxiv":null,"title":"GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database","year":2025},{"pubmed":"10592240","doi":"10.1093/nar/28.1.257","pmc":"PMC102479","arxiv":null,"title":"SCOP: a structural classification of proteins database","year":2000},{"pubmed":"10089491","doi":"10.1107/s0907444998009172","pmc":null,"arxiv":null,"title":"SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data","year":1998}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"scop","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbkFFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--a73ab0bd167ea1cddb9a506a0b8a3461acbaa4ac/scop_logo.358e74fa.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"scop.sccs":{"prefix":"scop.sccs","name":"SCOP(e) concise classification string","description":"This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family.","pattern":null,"uri_format":"http://scop.berkeley.edu/sccs=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://scop.berkeley.edu","repository":null,"contact":{"name":"John-Marc Chandonia","orcid":"0000-0002-5153-9079","email":"JMChandonia@lbl.gov","github":"jmchandonia","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"a.39.1.1","example_extras":["a","a.39","a.39.1"],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"1041"},"synonyms":[],"keywords":["scop"],"domain":null,"references":["https://scop.berkeley.edu/help/#stableidentifiers"],"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"scop.sccs","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"scop.sid":{"prefix":"scop.sid","name":"Structural Classification of Protein - Stable Domain Identifier","description":"A 7-character sid consists of \"d\" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1.","pattern":null,"uri_format":"http://scop.berkeley.edu/sid=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://scop.berkeley.edu","repository":null,"contact":{"name":"John-Marc Chandonia","orcid":"0000-0002-5153-9079","email":"JMChandonia@lbl.gov","github":"jmchandonia","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"d4akea1","example_extras":["d1cph.1","d9hvpa_"],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"1039"},"synonyms":[],"keywords":["scop"],"domain":null,"references":["https://scop.berkeley.edu/help/#stableidentifiers"],"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"scop.sid","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"sgd":{"prefix":"sgd","name":"Saccharomyces Genome Database","description":"The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.","pattern":"^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$","uri_format":"https://www.yeastgenome.org/locus/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"Bio2RDF","description":"Bio2RDF","homepage":"http://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/sgd:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"agr","name":"SGD through the Alliance of Genome Resources","description":"SGD through the Alliance of Genome Resources","homepage":"https://www.alliancegenome.org","contact":null,"uri_format":"https://www.alliancegenome.org/gene/SGD:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/sgd:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.yeastgenome.org/","repository":null,"contact":{"name":"J. Michael Cherry","orcid":"0000-0001-9163-5180","email":"cherry@genome.stanford.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00f54p054","wikidata":null,"gnd":null,"name":"Stanford University","partnered":false}],"example":"S000002493","example_extras":[],"example_decoys":null,"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/sgd/sgd.owl","download_obo":"https://w3id.org/biopragmatics/resources/sgd/sgd.obo","download_json":"https://w3id.org/biopragmatics/resources/sgd/sgd.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"SGD","edam.data":"2632","fairsharing":"FAIRsharing.pzvw40","go.resource":"SGD","integbio":"nbdc00202","miriam":"sgd","n2t":"sgd","ncbi.resource":"SGD","prefixcommons":"sgd","re3data":"r3d100010419","togoid":"Sgd","uniprot.resource":"DB-0095","wikidata.property":"P3406"},"synonyms":[],"keywords":["ars","bibliography/documents","bioresource","chromatin remodeling","chromosomal element nomenclature","chromosome, centromeric region","epigenetics","eukaryotic","expression","expression data","gene","gene array","gene model annotation","gene name","genome","genome/gene","go-term enrichment data","image/movie","interaction/pathway","life science","literature annotations defined by experimental results","molecular interaction","nucleotide","ontology","ontology/terminology/nomenclature","organism","organism-specific databases","orthologous","phenotype","plasmid","protein","protein domain","proteomics","pseudogene","reference genome","rna","sequence","sequence feature","sgd","strain","synthetic genetic array","transcriptomics","transposable element"],"domain":null,"references":null,"publications":[{"pubmed":"9885151","doi":"10.1002/(sici)1097-0061(199812)14:16<1453::aid-yea348>3.0.co;2-g","pmc":"PMC3037831","arxiv":null,"title":"Expanding yeast knowledge online","year":1998},{"pubmed":"9851918","doi":"10.1126/science.282.5396.2022","pmc":"PMC3057080","arxiv":null,"title":"Comparison of the complete protein sets of worm and yeast: orthology and divergence","year":1998},{"pubmed":"9847146","doi":"10.1093/nar/27.1.74","pmc":"PMC148101","arxiv":null,"title":"Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure","year":1999},{"pubmed":"9399804","doi":"10.1093/nar/26.1.73","pmc":"PMC147204","arxiv":null,"title":"SGD: Saccharomyces Genome Database","year":1998},{"pubmed":"9297238","doi":"10.1126/science.277.5330.1259","pmc":"PMC3039837","arxiv":null,"title":"Yeast as a model organism","year":1997},{"pubmed":"9169866","doi":null,"pmc":"PMC3057085","arxiv":null,"title":"Genetic and physical maps of Saccharomyces cerevisiae","year":1997},{"pubmed":"9159100","doi":"10.1073/pnas.94.11.5506","pmc":"PMC34160","arxiv":null,"title":"Molecular linguistics: extracting information from gene and protein sequences","year":1997},{"pubmed":"7660459","doi":null,"pmc":null,"arxiv":null,"title":"Genetic nomenclature guide. Saccharomyces cerevisiae","year":1995},{"pubmed":"39530598","doi":"10.1093/genetics/iyae185","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"39345624","doi":"10.1101/2024.09.16.613348","pmc":"PMC11430078","arxiv":null,"title":"Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements","year":2024},{"pubmed":"26989152","doi":"10.1093/database/baw020","pmc":"PMC4795930","arxiv":null,"title":"From one to many: expanding the Saccharomyces cerevisiae reference genome panel","year":2016},{"pubmed":"26631132","doi":"10.1101/pdb.top083840","pmc":"PMC5673599","arxiv":null,"title":"The Saccharomyces Genome Database: A Tool for Discovery","year":2015},{"pubmed":"26631126","doi":"10.1101/pdb.prot088922","pmc":"PMC5673602","arxiv":null,"title":"The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations","year":2015},{"pubmed":"26631125","doi":"10.1101/pdb.prot088914","pmc":"PMC5673600","arxiv":null,"title":"The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component","year":2015},{"pubmed":"26631124","doi":"10.1101/pdb.prot088906","pmc":"PMC5673598","arxiv":null,"title":"The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining","year":2015},{"pubmed":"26631123","doi":"10.1101/pdb.prot088898","pmc":"PMC5673601","arxiv":null,"title":"The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes","year":2015},{"pubmed":"26578556","doi":"10.1093/nar/gkv1250","pmc":"PMC4702884","arxiv":null,"title":"The Saccharomyces Genome Database Variant Viewer","year":2015},{"pubmed":"25997651","doi":"10.1002/dvg.22862","pmc":"PMC4545726","arxiv":null,"title":"Biocuration at the Saccharomyces genome database","year":2015},{"pubmed":"25781462","doi":"10.1371/journal.pone.0120671","pmc":"PMC4363492","arxiv":null,"title":"AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae","year":2015},{"pubmed":"25313161","doi":"10.1093/nar/gku975","pmc":"PMC4384031","arxiv":null,"title":"The complex portal--an encyclopaedia of macromolecular complexes","year":2014},{"pubmed":"25052702","doi":"10.1093/database/bau075","pmc":"PMC4105709","arxiv":null,"title":"Standardized description of scientific evidence using the Evidence Ontology (ECO)","year":2014},{"pubmed":"24374639","doi":"10.1534/g3.113.008995","pmc":"PMC3962479","arxiv":null,"title":"The reference genome sequence of Saccharomyces cerevisiae: then and now","year":2014},{"pubmed":"24265222","doi":"10.1093/nar/gkt1158","pmc":"PMC3965049","arxiv":null,"title":"Saccharomyces genome database provides new regulation data","year":2013},{"pubmed":"23842463","doi":"10.1093/database/bat054","pmc":"PMC3706743","arxiv":null,"title":"A guide to best practices for Gene Ontology (GO) manual annotation","year":2013},{"pubmed":"23487186","doi":"10.1093/database/bat012","pmc":"PMC3595989","arxiv":null,"title":"The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database","year":2013},{"pubmed":"23396302","doi":"10.1093/database/bat004","pmc":"PMC3567487","arxiv":null,"title":"The YeastGenome app: the Saccharomyces Genome Database at your fingertips","year":2013},{"pubmed":"22434836","doi":"10.1093/database/bas001","pmc":"PMC3308158","arxiv":null,"title":"CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations","year":2012},{"pubmed":"22434830","doi":"10.1093/database/bar062","pmc":"PMC3308152","arxiv":null,"title":"YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit","year":2012},{"pubmed":"22434826","doi":"10.1093/database/bar057","pmc":"PMC3308148","arxiv":null,"title":"Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report","year":2012},{"pubmed":"22110037","doi":"10.1093/nar/gkr1029","pmc":"PMC3245034","arxiv":null,"title":"Saccharomyces Genome Database: the genomics resource of budding yeast","year":2011},{"pubmed":"21411447","doi":"10.1093/database/bar004","pmc":"PMC3067894","arxiv":null,"title":"Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study","year":2011},{"pubmed":"20157474","doi":"10.1093/database/bap001","pmc":"PMC2790299","arxiv":null,"title":"New mutant phenotype data curation system in the Saccharomyces Genome Database","year":2009},{"pubmed":"19906697","doi":"10.1093/nar/gkp917","pmc":"PMC2808950","arxiv":null,"title":"Saccharomyces Genome Database provides mutant phenotype data","year":2009},{"pubmed":"19577472","doi":"10.1016/j.tim.2009.04.005","pmc":"PMC3057094","arxiv":null,"title":"Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns","year":2009},{"pubmed":"17982175","doi":"10.1093/nar/gkm909","pmc":"PMC2238894","arxiv":null,"title":"Gene Ontology annotations at SGD: new data sources and annotation methods","year":2007},{"pubmed":"17142221","doi":"10.1093/nar/gkl931","pmc":"PMC1669759","arxiv":null,"title":"Expanded protein information at SGD: new pages and proteome browser","year":2006},{"pubmed":"17001629","doi":"10.1002/yea.1400","pmc":"PMC3040122","arxiv":null,"title":"Saccharomyces cerevisiae S288C genome annotation: a working hypothesis","year":2006},{"pubmed":"16381907","doi":"10.1093/nar/gkj117","pmc":"PMC1347479","arxiv":null,"title":"Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome","year":2006},{"pubmed":"15608219","doi":"10.1093/nar/gki023","pmc":"PMC539977","arxiv":null,"title":"Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)","year":2005},{"pubmed":"15153302","doi":"10.1093/bib/5.1.9","pmc":"PMC3037832","arxiv":null,"title":"Saccharomyces genome database: underlying principles and organisation","year":2004},{"pubmed":"14681421","doi":"10.1093/nar/gkh033","pmc":"PMC308767","arxiv":null,"title":"Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms","year":2004},{"pubmed":"12519985","doi":"10.1093/nar/gkg054","pmc":"PMC165501","arxiv":null,"title":"Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins","year":2003},{"pubmed":"12073322","doi":"10.1016/s0076-6879(02)50972-1","pmc":null,"arxiv":null,"title":"Saccharomyces Genome Database","year":2002},{"pubmed":"11752257","doi":"10.1093/nar/30.1.69","pmc":"PMC99086","arxiv":null,"title":"Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)","year":2002},{"pubmed":"11125055","doi":"10.1093/nar/29.1.80","pmc":"PMC29796","arxiv":null,"title":"Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data","year":2001},{"pubmed":"10592186","doi":"10.1093/nar/28.1.77","pmc":"PMC102447","arxiv":null,"title":"Integrating functional genomic information into the Saccharomyces genome database","year":2000},{"pubmed":null,"doi":"10.1002/9780470089941.et1104s01","pmc":null,"arxiv":null,"title":"Using Model Organism Databases (MODs)","year":2009}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"sgd","mastodon":null,"github_request_issue":null,"logo":"https://cherrylab.stanford.edu/sites/g/files/sbiybj20496/files/styles/card_1900x950/public/media/image/sgd-banner-higher_res_0.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"smpdb":{"prefix":"smpdb","name":"Small Molecule Pathway Database","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.","pattern":"^SMP\\d+$","uri_format":"https://smpdb.ca/view/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/smpdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://smpdb.ca/","repository":null,"contact":{"name":"David S. Wishart","orcid":"0000-0002-3207-2434","email":"david.wishart@ualberta.ca","github":"DavidWishartLab","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0160cpw27","wikidata":null,"gnd":null,"name":"University of Alberta","partnered":false}],"example":"SMP0000219","example_extras":[],"example_decoys":null,"license":"http://www.smpdb.ca/about#cite","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"SMPDB","biolink.resource":"PathWhiz","edam.data":"2659","fairsharing":"FAIRsharing.y1zyaq","integbio":"nbdc00908","miriam":"smpdb","n2t":"smpdb","pathguide":"311","prefixcommons":"smpdb"},"synonyms":["SMP"],"keywords":["biopax","chemical","chemical entity","chemical structure image","human","image/movie","interaction/pathway","life science","metabolite","pathway","protein","protein structure","sbml","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"24203708","doi":"10.1093/nar/gkt1067","pmc":"PMC3965088","arxiv":null,"title":"SMPDB 2.0: big improvements to the Small Molecule Pathway Database","year":2013},{"pubmed":"19948758","doi":"10.1093/nar/gkp1002","pmc":"PMC2808928","arxiv":null,"title":"SMPDB: The Small Molecule Pathway Database","year":2009}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"smpdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"string":{"prefix":"string","name":"Search Tool for Retrieval of Interacting Genes/Proteins","description":"STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\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.","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})$","uri_format":"https://string-db.org/cgi/network?identifier=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"STRING at Heidelberg","description":"STRING at Heidelberg","homepage":"http://string.embl.de/","contact":null,"uri_format":"https://string.embl.de/cgi/network?identifier=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/string:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://string-db.org/","repository":null,"contact":{"name":"Peer Bork","orcid":"0000-0002-2627-833X","email":"bork@embl.de","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"03mstc592","wikidata":null,"gnd":null,"name":"EMBL, Heidelberg","partnered":false}],"example":"P53350","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":"uniprot","download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"STRING","edam.data":"2302","fairsharing":"FAIRsharing.9b7wvk","integbio":"nbdc00690","miriam":"string","n2t":"string","pathguide":"93","prefixcommons":"string","re3data":"r3d100010604","uniprot.resource":"DB-0141"},"synonyms":[],"keywords":["association","biology","classification","interaction","interaction/pathway","life science","prediction and recognition","protein","protein interactions","protein-protein interaction databases","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"39558183","doi":"10.1093/nar/gkae1113","pmc":null,"arxiv":null,"title":"The STRING database in 2025: protein networks with directionality of regulation","year":2024},{"pubmed":"36370105","doi":"10.1093/nar/gkac1000","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"30476243","doi":"10.1093/nar/gky1131","pmc":"PMC6323986","arxiv":null,"title":"STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","year":2019},{"pubmed":"27924014","doi":"10.1093/nar/gkw937","pmc":"PMC5210637","arxiv":null,"title":"The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible","year":2016},{"pubmed":"26614125","doi":"10.1093/bioinformatics/btv696","pmc":"PMC4896368","arxiv":null,"title":"SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles","year":2015},{"pubmed":"25352553","doi":"10.1093/nar/gku1003","pmc":"PMC4383874","arxiv":null,"title":"STRING v10: protein-protein interaction networks, integrated over the tree of life","year":2014},{"pubmed":"23203871","doi":"10.1093/nar/gks1094","pmc":"PMC3531103","arxiv":null,"title":"STRING v9.1: protein-protein interaction networks, with increased coverage and integration","year":2012},{"pubmed":"18940858","doi":"10.1093/nar/gkn760","pmc":"PMC2686466","arxiv":null,"title":"STRING 8--a global view on proteins and their functional interactions in 630 organisms","year":2008},{"pubmed":"17098935","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15608232","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"12519996","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"10982861","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"string","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"t3db":{"prefix":"t3db","name":"Toxin and Toxin Target Database","description":"Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.","pattern":"^T3D\\d+$","uri_format":"http://www.t3db.org/toxins/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/t3db:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.t3db.org/","repository":null,"contact":{"name":"David Wishart","orcid":"0000-0002-3207-2434","email":"david.wishart@ualberta.ca","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0160cpw27","wikidata":null,"gnd":null,"name":"University of Alberta","partnered":false}],"example":"T3D0001","example_extras":[],"example_decoys":null,"license":"http://www.t3db.org/about#cite","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"T3DB","edam.data":"2662","fairsharing":"FAIRsharing.psn0h2","miriam":"t3db","n2t":"t3db","pathguide":"326","prefixcommons":"t3db","re3data":"r3d100012189"},"synonyms":[],"keywords":["bioinformatics","biomedical science","chemistry","drug","drug metabolism","exposomics","mass spectrum","medical toxicology","molecular entity","molecule","nuclear magnetic resonance spectroscopy","pesticides","protein","toxicology","xenobiotic metabolic process"],"domain":null,"references":null,"publications":[{"pubmed":"25378312","doi":"10.1093/nar/gku1004","pmc":"PMC4383875","arxiv":null,"title":"T3DB: the toxic exposome database","year":2014},{"pubmed":"19897546","doi":"10.1093/nar/gkp934","pmc":"PMC2808899","arxiv":null,"title":"T3DB: a comprehensively annotated database of common toxins and their targets","year":2009}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"t3db","mastodon":null,"github_request_issue":null,"logo":"https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaGNFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--4767ec568a9519169473e68911fa244c9bbc23cb/Screenshot%20from%202024-03-26%2008-41-24.png?disposition=inline","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"tcdb":{"prefix":"tcdb","name":"Transporter Classification Database","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.","pattern":"^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$","uri_format":"http://www.tcdb.org/search/result.php?tc=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/tcdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.tcdb.org","repository":null,"contact":{"name":"Milton H. Saier, Jr.","orcid":"0000-0001-5530-0017","email":"msaier@ucsd.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"5.A.1.1.1","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"TCDB","edam.data":"2756","fairsharing":"FAIRsharing.p3bzqb","go.resource":"TCDB","miriam":"tcdb","n2t":"tcdb","pathguide":"104","prefixcommons":"tcdb","uniprot.resource":"DB-0135","wikidata.property":"P7260"},"synonyms":["TC"],"keywords":["annotation","cell biology","computational biology","disease","function analysis","knowledge and information systems","life science","molecular_function","phylogenetics","protein","protein family/group databases","structure","transport"],"domain":null,"references":null,"publications":[{"pubmed":"33170213","doi":"10.1093/nar/gkaa1004","pmc":"PMC7778945","arxiv":null,"title":"The Transporter Classification Database (TCDB): 2021 update","year":2021},{"pubmed":"26546518","doi":"10.1093/nar/gkv1103","pmc":"PMC4702804","arxiv":null,"title":"The Transporter Classification Database (TCDB): recent advances","year":2015},{"pubmed":"24225317","doi":"10.1093/nar/gkt1097","pmc":"PMC3964967","arxiv":null,"title":"The transporter classification database","year":2013},{"pubmed":"19022853","doi":"10.1093/nar/gkn862","pmc":"PMC2686586","arxiv":null,"title":"The Transporter Classification Database: recent advances","year":2008},{"pubmed":"16381841","doi":"10.1093/nar/gkj001","pmc":"PMC1334385","arxiv":null,"title":"TCDB: the Transporter Classification Database for membrane transport protein analyses and information","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"tcdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"tigrfam":{"prefix":"tigrfam","name":"TIGRFAMS","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.","pattern":"^TIGR\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/cdd?term=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/tigrfams:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"049r1ts75","wikidata":null,"gnd":null,"name":"J. Craig Venter Institute","partnered":false}],"example":"TIGR00010","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"TIGRFAM","edam.data":"1141","miriam":"tigrfam","n2t":"tigrfam","ncbi.resource":"TIGRFAM","prefixcommons":"tigrfams","uniprot.resource":"DB-0270"},"synonyms":[],"keywords":["family and domain databases","protein"],"domain":null,"references":["https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt","https://github.com/biopragmatics/bioregistry/issues/366"],"publications":[{"pubmed":"33270901","doi":"10.1093/nar/gkaa1105","pmc":null,"arxiv":null,"title":null,"year":null}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Chris Mungall","orcid":"0000-0002-6601-2165","email":"cjmungall@lbl.gov","github":"cmungall","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"tigrfam","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"topdb":{"prefix":"topdb","name":"Topology Data Bank of Transmembrane Proteins","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.","pattern":"^[A-Z0-9]+$","uri_format":"http://topdb.enzim.hu/?m=show&id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/topdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://topdb.enzim.hu/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"04t4pws42","wikidata":null,"gnd":null,"name":"Institute of Enzymology, Hungarian Academy of Sciences, Budapest","partnered":false}],"example":"AP00378","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"TOPDB","edam.data":"2789","miriam":"topdb","n2t":"topdb","prefixcommons":"topdb"},"synonyms":[],"keywords":["protein"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"topdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ttd.drug":{"prefix":"ttd.drug","name":"TTD Drug","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.","pattern":"^\\w+$","uri_format":"https://db.idrblab.net/ttd/data/drug/details/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://db.idrblab.net/ttd","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"D0N5OV","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"TTD.DRUG","edam.data":"2653","miriam":"ttd.drug","n2t":"ttd.drug"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"ttd.drug","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"ttd.target":{"prefix":"ttd.target","name":"TTD Target","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.","pattern":"^t\\d+$","uri_format":"https://db.idrblab.net/ttd/data/target/details/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://db.idrblab.net/ttd","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"t59328","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"TTD.TARGET","edam.data":"2654","miriam":"ttd.target","n2t":"ttd.target"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"ttd.target","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"umls":{"prefix":"umls","name":"Unified Medical Language System Concept Unique Identifier","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.","pattern":"^C\\d+$","uri_format":"https://uts.nlm.nih.gov/uts/umls/concept/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.nlm.nih.gov/research/umls","repository":null,"contact":{"name":"Olivier Bodenreider","orcid":"0000-0003-4769-4217","email":"olivier@nlm.nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"C2584994","example_extras":[],"example_decoys":null,"license":"https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"bartoc":"20052","biocontext":"UMLS","edam.data":"1181","hl7":"6.86","miriam":"umls","n2t":"umls","wikidata.entity":"Q455338","wikidata.property":"P2892"},"synonyms":["UMLS","UMLS CUI","UMLS_CUI","umls.cui"],"keywords":["biomedicine","umls"],"domain":null,"references":null,"publications":[{"pubmed":"14681409","doi":"10.1093/nar/gkh061","pmc":"PMC308795","arxiv":null,"title":"The Unified Medical Language System (UMLS): integrating biomedical terminology","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"umls","mastodon":null,"github_request_issue":null,"logo":"https://uts.nlm.nih.gov/uts/assets/images/umls_tree_sm.jpg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"unimod":{"prefix":"unimod","name":"Unimod protein modification database for mass spectrometry","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).","pattern":"^\\d+$","uri_format":"http://www.unimod.org/modifications_view.php?editid1=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.unimod.org/","repository":null,"contact":{"name":"John Cottrell","orcid":"0000-0003-3843-0818","email":"jcottrell@matrixscience.com","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"1200","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/unimod.owl","download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"UNIMOD","edam.data":"3757","fairsharing":"FAIRsharing.zZHCUQ","miriam":"unimod","n2t":"unimod","ols":"unimod"},"synonyms":[],"keywords":["bioinformatics","mass spectrometry assay","mass spectrum","ontology","protein","protein modification process"],"domain":null,"references":null,"publications":[{"pubmed":"15174123","doi":"10.1002/pmic.200300744","pmc":null,"arxiv":null,"title":"Unimod: Protein modifications for mass spectrometry","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"unimod","mastodon":null,"github_request_issue":null,"logo":"https://www.unimod.org/images/logo.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"uniparc":{"prefix":"uniparc","name":"UniParc","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.","pattern":"^UPI[A-F0-9]{10}$","uri_format":"https://www.uniprot.org/uniparc/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/uniparc:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.uniprot.org/uniparc/","repository":null,"contact":{"name":"Alex Bateman","orcid":"0000-0002-6982-4660","email":"agb@ebi.ac.uk","github":"bateman-research","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"017yq1n41","wikidata":null,"gnd":null,"name":"The Uniprot Consortium","partnered":false}],"example":"UPI000000000A","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"UNIPARC","edam.data":"2392","go.resource":"UniParc","miriam":"uniparc","n2t":"uniparc","prefixcommons":"uniparc","re3data":"r3d100011519","togoid":"Uniparc"},"synonyms":[],"keywords":["protein","structure"],"domain":null,"references":null,"publications":[{"pubmed":"14681372","doi":"10.1093/nar/gkh131","pmc":"PMC308865","arxiv":null,"title":"UniProt: the Universal Protein knowledgebase","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"uniparc","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"uniprot":{"prefix":"uniprot","name":"UniProt Protein","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.","pattern":"^([OPQ]\\d[A-Z0-9]{3}\\d|[A-NR-Z]\\d([A-Z][A-Z0-9]{2}\\d){1,2})$","uri_format":"http://purl.uniprot.org/uniprot/$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.uniprot.org/uniprot/$1","providers":[{"code":"aipd","name":"Autoinhibited Protein Database","description":"A curated database standardizing information on autoinhibited proteins.","homepage":"http://ssbio.cau.ac.kr/databases/AiPD/","contact":null,"uri_format":"http://165.194.60.211:9006/detail/$1","first_party":null,"publications":[{"pubmed":"39192607","doi":"10.1093/database/baae085","pmc":"PMC11349611","arxiv":null,"title":"Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms","year":2024}],"example":null,"status":null,"organization":null},{"code":"bfvd","name":"Big Fantastic Virus Database","description":"Predicted protein structures for viral sequences","homepage":"https://bfvd.foldseek.com","contact":null,"uri_format":"https://bfvd.foldseek.com/cluster/$1","first_party":null,"publications":[{"pubmed":"39574394","doi":"10.1093/nar/gkae1119","pmc":null,"arxiv":null,"title":"BFVD-a large repository of predicted viral protein structures","year":2024}],"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/uniprot:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"describeprot","name":"DescribePROT","description":"Structural and functional descriptors for proteins at the amino acid level","homepage":"http://biomine.cs.vcu.edu/servers/DESCRIBEPROT","contact":null,"uri_format":"http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/result_v2.php?uniprot=$1","first_party":null,"publications":[{"pubmed":"39576581","doi":"10.1007/978-1-0716-4196-5_10","pmc":null,"arxiv":null,"title":"DescribePROT Database of Residue-Level Protein Structure and Function Annotations","year":2024}],"example":null,"status":null,"organization":null},{"code":"drugbank","name":"DrugBank Polypeptide","description":"DrugBank PolyPeptide.","homepage":"https://go.drugbank.com","contact":null,"uri_format":"https://go.drugbank.com/polypeptides/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"iedb.antigen","name":"Immune Epitope Database","description":"A comprehensive collection of data on immune epitopes, covering experimental data and resources, including antigens","homepage":"https://www.iedb.org/","contact":null,"uri_format":"https://www.iedb.org/antigen/UNIPROT:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"indra","name":"INDRA Database","description":"A large scale database of biomedical statements.","homepage":"https://db.indra.bio","contact":null,"uri_format":"https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@UP","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"iptmnet","name":"iPTMnet","description":"Protein post translational modification information","homepage":"https://research.bioinformatics.udel.edu/iptmnet","contact":null,"uri_format":"https://research.bioinformatics.udel.edu/iptmnet/entry/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"ncbi","name":"UniProt through NCBI","description":"UniProt through NCBI","homepage":"https://www.ncbi.nlm.nih.gov/protein/","contact":null,"uri_format":"https://www.ncbi.nlm.nih.gov/protein/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"oglcnac","name":"The O-GlcNAc Database","description":"A comprehensive catalog of O-GlcNAcylated proteins","homepage":"https://www.oglcnac.mcw.edu","contact":null,"uri_format":"https://www.oglcnac.mcw.edu/search/?query_protein=$1","first_party":null,"publications":[{"pubmed":"39379619","doi":"10.1007/s00216-024-05571-8","pmc":null,"arxiv":null,"title":"The O-GlcNAc database: introducing new features and tools developed from community feedback","year":2024}],"example":null,"status":null,"organization":null},{"code":"oma","name":"Orthologous Matrix Browser","description":"The OMA project is a method and database for the inference of orthologs among complete genomes.","homepage":"https://omabrowser.org/oma/home/","contact":null,"uri_format":"http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p2=orthologs&p1=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"omnipath","name":"OmniPathDB","description":"Molecular interations endpoint from OmniPathDB","homepage":"https://omnipathdb.org/","contact":null,"uri_format":"https://omnipathdb.org/interactions/?fields=sources,references&partners=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"pharos","name":"Pharos","description":"Part of the Illuminating the Druggable Genome project","homepage":"https://pharos.nih.gov/idg","contact":null,"uri_format":"https://pharos.nih.gov/idg/targets/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"proteinsplus","name":"ProteinsPlus","description":"Database of protein-ligand interactions.","homepage":"https://proteins.plus/","contact":null,"uri_format":"https://proteins.plus/$1","first_party":null,"publications":[{"pubmed":"40326518","doi":"10.1093/nar/gkaf377","pmc":null,"arxiv":null,"title":"ProteinsPlus: a publicly available resource for protein structure mining","year":2025}],"example":null,"status":null,"organization":null},{"code":"scholia","name":"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/","contact":null,"uri_format":"https://scholia.toolforge.org/uniprot/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.uniprot.org","repository":null,"contact":{"name":"Alex Bateman","orcid":"0000-0002-6982-4660","email":"agb@ebi.ac.uk","github":"bateman-research","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"017yq1n41","wikidata":null,"gnd":null,"name":"The Uniprot Consortium","partnered":false}],"example":"P0DP23","example_extras":["A0A023GPI8","A2BC19","P12345","Q8WZ42"],"example_decoys":["Q5BJF6-3","Q5BJF6.1","P08069#PRO_0000016681"],"license":"CC-BY-4.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/uniprot/uniprot.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/uniprot/uniprot.obo.gz","download_json":"https://w3id.org/biopragmatics/resources/uniprot/uniprot.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"UniProtKB","biolink.resource":"UniProtKB","cellosaurus.resource":"UniProtKB","edam.data":"3021","fairsharing":"FAIRsharing.wf28wm","go.resource":"UniProtKB","integbio":"nbdc00221","miriam":"uniprot","n2t":"uniprot","ncbi.resource":"UniProt","prefixcommons":"uniprot","re3data":"r3d100011521","togoid":"Uniprot","wikidata.property":"P352"},"synonyms":["SwissProt","UP","UniProt","UniProtKB","Uniprot ID","uniprot/swiss-prot"],"keywords":["biology","ontology","protein","repository","sequence","taxonomic classification"],"domain":null,"references":["https://www.uniprot.org/help/accession_numbers"],"publications":[{"pubmed":"40326518","doi":"10.1093/nar/gkaf377","pmc":null,"arxiv":null,"title":"ProteinsPlus: a publicly available resource for protein structure mining","year":2025},{"pubmed":"39576581","doi":"10.1007/978-1-0716-4196-5_10","pmc":null,"arxiv":null,"title":"DescribePROT Database of Residue-Level Protein Structure and Function Annotations","year":2024},{"pubmed":"39574394","doi":"10.1093/nar/gkae1119","pmc":null,"arxiv":null,"title":"BFVD-a large repository of predicted viral protein structures","year":2024},{"pubmed":"39552041","doi":"10.1093/nar/gkae1010","pmc":null,"arxiv":null,"title":"UniProt: the Universal Protein Knowledgebase in 2025","year":2024},{"pubmed":"39379619","doi":"10.1007/s00216-024-05571-8","pmc":null,"arxiv":null,"title":"The O-GlcNAc database: introducing new features and tools developed from community feedback","year":2024},{"pubmed":"39192607","doi":"10.1093/database/baae085","pmc":"PMC11349611","arxiv":null,"title":"Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms","year":2024},{"pubmed":"16381842","doi":"10.1093/nar/gkj161","pmc":"PMC1347523","arxiv":null,"title":"The Universal Protein Resource (UniProt): an expanding universe of protein information","year":2006}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Mufaddal Naguthanawala","orcid":"0009-0009-5240-7463","email":"m.naguthana@hotmail.com","github":"nagutm","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"uniprot","mastodon":null,"github_request_issue":null,"logo":"https://www.uniprot.org/uniprot-logo.img.0df091.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"uniref":{"prefix":"uniref","name":"UniRef","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.","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})$","uri_format":"https://www.uniprot.org/uniref/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/uniref:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.uniprot.org/","repository":null,"contact":{"name":"Alex Bateman","orcid":"0000-0002-6982-4660","email":"agb@ebi.ac.uk","github":"bateman-research","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"017yq1n41","wikidata":null,"gnd":null,"name":"The Uniprot Consortium","partnered":false}],"example":"UniRef90_P00750","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"edam.data":"2346","miriam":"uniref","prefixcommons":"uniref","re3data":"r3d100011518"},"synonyms":[],"keywords":["gene","protein","uniprot"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"uniref","mastodon":null,"github_request_issue":null,"logo":"https://www.uniprot.org/uniprot-logo.img.0df091.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"unists":{"prefix":"unists","name":"UniSTS","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.","pattern":"^\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/unists:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"456789","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"UNISTS","edam.data":"2389","miriam":"unists","n2t":"unists","ncbi.resource":"UniSTS","prefixcommons":"unists"},"synonyms":[],"keywords":["gene","protein"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"unists","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"unite":{"prefix":"unite","name":"Unite","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.","pattern":"^UDB\\d{6}$","uri_format":"http://unite.ut.ee/bl_forw.php?nimi=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/unite:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://unite.ut.ee/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"UDB000691","example_extras":[],"example_decoys":null,"license":"CC","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"UNITE","edam.data":"2390","integbio":"nbdc01905","miriam":"unite","n2t":"unite","ncbi.resource":"UNITE","prefixcommons":"unite","re3data":"r3d100011316"},"synonyms":[],"keywords":["dna","genome/gene","organism","sequence","taxonomy"],"domain":null,"references":null,"publications":[{"pubmed":"30371820","doi":"10.1093/nar/gky1022","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"20409185","doi":"10.1111/j.1469-8137.2009.03160.x","pmc":null,"arxiv":null,"title":"The UNITE database for molecular identification of fungi--recent updates and future perspectives","year":2010}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"unite","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"upa":{"prefix":"upa","name":"Unipathway","description":"A manually curated resource for the representation and annotation of metabolic pathways","pattern":"^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$","uri_format":"http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1","uri_format_resolvable":null,"rdf_uri_format":"http://purl.obolibrary.org/obo/UPA_$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/unipathway:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://github.com/geneontology/unipathway","repository":"https://github.com/geneontology/unipathway","contact":{"name":"Anne Morgat","orcid":"0000-0002-1216-2969","email":"Anne.Morgat@sib.swiss","github":"amorgat","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"UCR00513","example_extras":[],"example_decoys":null,"license":"CC-BY-3.0","version":"2024-03-06","part_of":null,"part_of_database":null,"provides":null,"download_owl":"http://purl.obolibrary.org/obo/upa.owl","download_obo":"https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo","download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"UNIPATHWAY","bioportal":"UPA","edam.data":"2645","go.resource":"UniPathway","obofoundry":"upa","ols":"upa","ontobee":"UPA","pathguide":"414","prefixcommons":"unipathway","wikidata.entity":"Q85719315"},"synonyms":["UPa","unipathway","unipathway.pathway"],"keywords":["obo","ontology","pathway"],"domain":null,"references":null,"publications":[{"pubmed":"22102589","doi":"10.1093/nar/gkr1023","pmc":"PMC3245108","arxiv":null,"title":"UniPathway: a resource for the exploration and annotation of metabolic pathways","year":2011}],"appears_in":[],"depends_on":["ro"],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"UPA","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"wikipathways":{"prefix":"wikipathways","name":"WikiPathways","description":"WikiPathways is a database of biological pathways maintained by and for the scientific community.","pattern":"^WP\\d{1,5}(\\_r\\d+)?$","uri_format":"http://www.wikipathways.org/instance/$1","uri_format_resolvable":null,"rdf_uri_format":"http://identifiers.org/wikipathways/$1","providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/wikipathways:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"scholia","name":"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.\n","homepage":"https://scholia.toolforge.org/","contact":null,"uri_format":"https://scholia.toolforge.org/wikipathways/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.wikipathways.org/","repository":null,"contact":{"name":"Egon Willighagen","orcid":"0000-0001-7542-0286","email":"egon.willighagen@gmail.com","github":"egonw","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02jz4aj89","wikidata":null,"gnd":null,"name":"Maastricht University","partnered":false}],"example":"WP732","example_extras":[],"example_decoys":null,"license":"CC0-1.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.owl","download_obo":"https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.obo","download_json":"https://w3id.org/biopragmatics/resources/wikipathways/wikipathways.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"WIKIPATHWAYS","edam.data":"3952","fairsharing":"FAIRsharing.g7b4rj","integbio":"nbdc02116","miriam":"wikipathways","n2t":"wikipathways","ols":"wikipathways","pathguide":"237","prefixcommons":"wikipathways","re3data":"r3d100013316","togoid":"Wikipathways","wikidata.entity":"Q7999828","wikidata.property":"P2410"},"synonyms":[],"keywords":["biological regulation","biopax","drug interaction","epidemiology","genetic interaction (sensu unexpected)","image/movie","interaction/pathway","molecular interaction","ontology","pathway","protein","protein interactions","reaction data","signaling","virology","wikipathways"],"domain":null,"references":null,"publications":[{"pubmed":"37941138","doi":"10.1093/nar/gkad960","pmc":"PMC10767877","arxiv":null,"title":"WikiPathways 2024: next generation pathway database","year":2024},{"pubmed":"33211851","doi":"10.1093/nar/gkaa1024","pmc":"PMC7779061","arxiv":null,"title":"WikiPathways: connecting communities","year":2021},{"pubmed":"29136241","doi":"10.1093/nar/gkx1064","pmc":"PMC5753270","arxiv":null,"title":"WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research","year":2018},{"pubmed":"26481357","doi":"10.1093/nar/gkv1024","pmc":"PMC4702772","arxiv":null,"title":"WikiPathways: capturing the full diversity of pathway knowledge","year":2015},{"pubmed":"22096230","doi":"10.1093/nar/gkr1074","pmc":"PMC3245032","arxiv":null,"title":"WikiPathways: building research communities on biological pathways","year":2011},{"pubmed":"19649250","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18651794","doi":"10.1371/journal.pbio.0060184","pmc":"PMC2475545","arxiv":null,"title":"WikiPathways: pathway editing for the people","year":2008}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Egon Willighagen","orcid":"0000-0001-7542-0286","email":"egon.willighagen@gmail.com","github":"egonw","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"wikipathways","mastodon":"wikipathways@fosstodon.org","github_request_issue":null,"logo":"https://www.wikipathways.org/assets/img/wikipathways-logo-horizontal.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"wormbase":{"prefix":"wormbase","name":"WormBase","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.","pattern":"^(CE[0-9]{5}|WB[A-Z][a-z]+\\d+)$","uri_format":"https://www.wormbase.org/get?name=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"agr","name":"WormBase through the Alliance of Genome Resources","description":"WormBase through the Alliance of Genome Resources","homepage":"https://www.alliancegenome.org","contact":null,"uri_format":"https://www.alliancegenome.org/gene/WB:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/wormbase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"wormbase.c_elegans","name":"WormBase C. Elegans Gene Portal","description":"Pages describing C. Elegans genes.","homepage":"http://www.wormbase.org","contact":null,"uri_format":"http://www.wormbase.org/species/c_elegans/gene/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.wormbase.org/","repository":null,"contact":{"name":"Todd W Harris","orcid":"0000-0003-3406-163X","email":"todd@wormbase.org","github":"tharris","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"WBGene00000001","example_extras":[],"example_decoys":null,"license":"CC0-1.0","version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"WormBase","biolink.resource":"WBVocab","edam.data":"1805","fairsharing":"FAIRsharing.zx1td8","go.resource":"WB_REF","integbio":"nbdc00740","miriam":"wb","n2t":"wb","ncbi.resource":"WormBase","pathguide":"426","prefixcommons":"wormbase","re3data":"r3d100010424","rrid.resource":"WB-STRAIN:WBStrain","uniprot.resource":"DB-0110","wikidata.property":"P3860"},"synonyms":["WB","WB_REF","wb","wormbase"],"keywords":["anatomy","bibliography/documents","binding site","bioresource","blast","c elegans","catalog","cdna/est","clone library","cross linking","cytogenetic map","database","disease","expression","expression data","faseb list","gene","gene expression","gene function","gene mapping","gene name","gene prediction","geneotype","genetic interaction (sensu unexpected)","genetic polymorphism","genetic variation","genome","genome map","genome/gene","genomic sequence","genomics","go-term enrichment data","health/disease","image/movie","immunoglobulin complex, circulating","life cycle","life science","mass spectrum","model organisms","molecular interaction","ontology/terminology/nomenclature","organism","organism-specific databases","ortholog","orthologous","orthology assignment","phenotype","promoter","protein","protein domain","protein expression","protein interactions","pseudogene","reagent","regulation of gene expression","regulatory ncrna-mediated post-transcriptional gene silencing","repository","roundworm","sequence","sequence feature","small molecule","snp","strain","trans spliced","transposon family","utr","wormmart"],"domain":null,"references":null,"publications":[{"pubmed":"38573366","doi":"10.1093/genetics/iyae050","pmc":null,"arxiv":null,"title":"WormBase 2024: status and transitioning to Alliance infrastructure","year":2024},{"pubmed":"31642470","doi":"10.1093/nar/gkz920","pmc":"PMC7145598","arxiv":null,"title":"WormBase: a modern Model Organism Information Resource","year":2020},{"pubmed":"29069413","doi":"10.1093/nar/gkx998","pmc":"PMC5753391","arxiv":null,"title":"WormBase 2017: molting into a new stage","year":2018},{"pubmed":"27899279","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"26578572","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"24194605","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"24058818","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"23160413","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"22067452","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21595960","doi":"10.1186/1471-2105-12-175","pmc":"PMC3213741","arxiv":null,"title":"Toward an interactive article: integrating journals and biological databases","year":2011},{"pubmed":"21543339","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21071413","doi":"10.1093/nar/gkq1116","pmc":"PMC3013707","arxiv":null,"title":"The BioGRID Interaction Database: 2011 update","year":2010},{"pubmed":"21059240","doi":"10.1186/1471-2105-11-550","pmc":"PMC2992068","arxiv":null,"title":"Localizing triplet periodicity in DNA and cDNA sequences","year":2010},{"pubmed":"19921742","doi":"10.1002/mrd.21130","pmc":"PMC2830379","arxiv":null,"title":"Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology","year":2010},{"pubmed":"19920128","doi":"10.1093/nar/gkp1018","pmc":"PMC2808930","arxiv":null,"title":"The Gene Ontology in 2010: extensions and refinements","year":2009},{"pubmed":"19910365","doi":"10.1093/nar/gkp952","pmc":"PMC2808986","arxiv":null,"title":"WormBase: a comprehensive resource for nematode research","year":2009},{"pubmed":"19622167","doi":"10.1186/1471-2105-10-228","pmc":"PMC2719631","arxiv":null,"title":"Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation","year":2009},{"pubmed":"19578431","doi":"10.1371/journal.pcbi.1000431","pmc":"PMC2699109","arxiv":null,"title":"The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species","year":2009},{"pubmed":"19099578","doi":"10.1186/1471-2105-9-549","pmc":"PMC2651883","arxiv":null,"title":"nGASP--the nematode genome annotation assessment project","year":2008},{"pubmed":"17991679","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"17099234","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16988424","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16381915","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15608221","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"15489338","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14681445","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"12519966","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"11125056","doi":"10.1093/nar/29.1.82","pmc":"PMC29781","arxiv":null,"title":"WormBase: network access to the genome and biology of Caenorhabditis elegans","year":2001}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Chris Mungall","orcid":"0000-0002-6601-2165","email":"cjmungall@lbl.gov","github":"cmungall","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"WormBase","mastodon":null,"github_request_issue":null,"logo":"https://wormbase.org/img/logo/logo_wormbase_gradient.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null},"xenbase":{"prefix":"xenbase","name":"Xenbase","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.","pattern":"^XB\\-\\w+\\-\\d+$","uri_format":"https://www.xenbase.org/entry/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"bio2rdf","name":"Bio2RDF","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.","homepage":"https://bio2rdf.org","contact":null,"uri_format":"http://bio2rdf.org/xenbase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.xenbase.org/","repository":null,"contact":{"name":"Troy Pells","orcid":"0000-0002-2340-5356","email":"troy_pells@yahoo.ca","github":"pellst","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"03yjb2x39","wikidata":null,"gnd":null,"name":"University of Calgary","partnered":false}],"example":"XB-GENE-922462","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"Xenbase","biolink.resource":"Xenbase","edam.data":"2738","fairsharing":"FAIRsharing.jrv6wj","go.resource":"Xenbase","miriam":"xenbase","n2t":"xenbase","ncbi.resource":"Xenbase","prefixcommons":"xenbase","re3data":"r3d100011331","uniprot.resource":"DB-0129"},"synonyms":["Xenbase"],"keywords":["anatomy","cell biology","chip-seq assay","developmental biology","differential gene expression profiling","differential protein expression profiling","disease course","expression","expression data","functional genomics","gene expression","genetics","genome","genomics","go-term enrichment data","immunoglobulin complex, circulating","mirna","model organisms","next generation sequencing","organism-specific databases","phenotype","proteomics","reagent","rna-seq assay","strain"],"domain":null,"references":null,"publications":[{"pubmed":"36755307","doi":"10.1093/genetics/iyad018","pmc":null,"arxiv":null,"title":"Xenbase: Key Features and Resources of the Xenopus Model Organism Knowledgebase","year":2023},{"pubmed":"35833709","doi":"10.1242/dev.200356","pmc":null,"arxiv":null,"title":"Normal Table of Xenopus development: a new graphical resource","year":2022},{"pubmed":"35317743","doi":"10.1186/s12859-022-04636-8","pmc":"PMC8939077","arxiv":null,"title":"The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development","year":2022},{"pubmed":"31733057","doi":"10.1093/nar/gkz933","pmc":"PMC7145613","arxiv":null,"title":"Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database","year":2020},{"pubmed":"30863320","doi":"10.3389/fphys.2019.00154","pmc":"PMC6399412","arxiv":null,"title":"Xenbase: Facilitating the Use of","year":2019},{"pubmed":"29761462","doi":"10.1007/978-1-4939-7737-6_10","pmc":"PMC6853059","arxiv":null,"title":"Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database","year":2018},{"pubmed":"29059324","doi":"10.1093/nar/gkx936","pmc":"PMC5753396","arxiv":null,"title":"Xenbase: a genomic, epigenomic and transcriptomic model organism database","year":2018},{"pubmed":"27039265","doi":"10.1016/j.ydbio.2016.03.030","pmc":"PMC5045824","arxiv":null,"title":"Xenopus genomic data and browser resources","year":2016},{"pubmed":"25380782","doi":"10.1093/database/bau108","pmc":"PMC4224262","arxiv":null,"title":"The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud","year":2014},{"pubmed":"25313157","doi":"10.1093/nar/gku956","pmc":"PMC4384024","arxiv":null,"title":"Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes","year":2014},{"pubmed":"24139024","doi":"10.1186/2041-1480-4-31","pmc":"PMC3816597","arxiv":null,"title":"Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase","year":2013},{"pubmed":"19884130","doi":"10.1093/nar/gkp953","pmc":"PMC2808955","arxiv":null,"title":"Xenbase: gene expression and improved integration","year":2009}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"xenbase","mastodon":null,"github_request_issue":null,"logo":"https://www.xenbase.org/xenbase/img/Xenbase-Logo-Small.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata.property":null,"wikidata_entity":null,"go.resource":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi.resource":null,"uniprot.resource":null,"biolink.resource":null,"cellosaurus.resource":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam.data":null,"re3data":null,"hl7":null,"bartoc":null,"rrid.resource":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib.ts":null,"biodivportal":null}}