| Website | Homepage | Notes |
|---|---|---|
| ExplorEnz | https://www.enzyme-database.org | This is the resource officially recommended by IUBMB |
| IUBMB (via by Queen Mary) | https://iubmb.qmul.ac.uk/enzyme | This is a web-based version of the 1992 publication. |
| IntEnz | https://www.ebi.ac.uk/intenz | Shutdown in 2024 |
| ExPaSy | https://enzyme.expasy.org | |
| EnzymePortal | https://www.ebi.ac.uk/enzymeportal |
2.3.-.-) and without dashes (e.g., 2.3). 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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"echobase":{"prefix":"echobase","name":"EchoBASE","description":"EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.","pattern":"^EB\\d+$","uri_format":"http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$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/echobase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.york.ac.uk/","repository":null,"contact":{"name":"Gavin H. Thomas","orcid":"0000-0002-9763-1313","email":"gavin.thomas@york.ac.uk","github":"ghthomas","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"04m01e293","wikidata":null,"gnd":null,"name":"University of York","partnered":false}],"example":"EB0170","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":"ECHOBASE","go":"EchoBASE","miriam":"echobase","n2t":"echobase","prefixcommons":"echobase","re3data":"r3d100011646","uniprot":"DB-0020"},"synonyms":[],"keywords":["gene","gene expression","organism-specific databases"],"domain":null,"references":null,"publications":[{"pubmed":"15608209","doi":"10.1093/nar/gki028","pmc":"PMC539982","arxiv":null,"title":"EchoBASE: an integrated post-genomic database for Escherichia coli","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":"echobase","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ecocyc":{"prefix":"ecocyc","name":"EcoCyc","description":"EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.","pattern":null,"uri_format":"https://ecocyc.org/gene?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://ecocyc.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":null,"example":"AICARTRANSIMPCYCLO-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":{"go":"EcoCyc","integbio":"nbdc00262","ncbi":"ECOCYC","pathguide":"9","re3data":"r3d100011277"},"synonyms":[],"keywords":["biopax","genome/gene","interaction/pathway","metabolite","protein","rna","sbml","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"40304522","doi":"10.1128/ecosalplus.esp-0019-2024","pmc":null,"arxiv":null,"title":"The EcoCyc database (2025)","year":2025},{"pubmed":"34394059","doi":"10.3389/fmicb.2021.711077","pmc":"PMC8357350","arxiv":null,"title":"The EcoCyc Database in 2021","year":2021},{"pubmed":"27899573","doi":"10.1093/nar/gkw1003","pmc":"PMC5210515","arxiv":null,"title":"The EcoCyc database: reflecting new knowledge about Escherichia coli K-12","year":2016},{"pubmed":"26442933","doi":"10.1128/ecosalplus.esp-0009-2013","pmc":"PMC4243172","arxiv":null,"title":"The EcoCyc Database","year":2014},{"pubmed":"23143106","doi":"10.1093/nar/gks1027","pmc":"PMC3531154","arxiv":null,"title":"EcoCyc: fusing model organism databases with systems biology","year":2012},{"pubmed":"21097882","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":"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":"ecocyc","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ecogene":{"prefix":"ecogene","name":"EcoGene","description":"The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.","pattern":"^EG\\d+$","uri_format":"http://www.ecogene.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/ecogene:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://ecogene.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"EG10173","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":"EcoGene","miriam":"ecogene","n2t":"ecogene","ncbi":"EcoGene","prefixcommons":"ecogene","re3data":"r3d100010546"},"synonyms":[],"keywords":["genome","protein"],"domain":null,"references":null,"publications":[{"pubmed":"10592181","doi":"10.1093/nar/28.1.60","pmc":"PMC102481","arxiv":null,"title":"EcoGene: a genome sequence database for Escherichia coli K-12","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":"ecogene","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ega.dataset":{"prefix":"ega.dataset","name":"European Genome-phenome Archive Dataset","description":"The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.","pattern":"^EGAD\\d{11}$","uri_format":"https://www.ebi.ac.uk/ega/datasets/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"omicsdi","name":"EGA Dataset through OmicsDI","description":"EGA Dataset through OmicsDI","homepage":"https://www.omicsdi.org/","contact":null,"uri_format":"https://www.omicsdi.org/dataset/ega/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://ega-archive.org/","repository":null,"contact":{"name":"Thomas Keane","orcid":"0000-0001-7532-6898","email":"tk2@ebi.ac.uk","github":"tk2","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":"EGAD00000000001","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":"EGA.DATASET","miriam":"ega.dataset","n2t":"ega.dataset","re3data":"r3d100011242"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"34791407","doi":"10.1093/nar/gkab1059","pmc":"PMC8728218","arxiv":null,"title":"The European Genome-phenome Archive in 2021","year":2022},{"pubmed":"26111507","doi":"10.1038/ng.3312","pmc":"PMC5426533","arxiv":null,"title":"The European Genome-phenome Archive of human data consented for biomedical research","year":2015}],"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.dataset","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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":"1146","miriam":"emdb","n2t":"emdb","prefixcommons":"emdb","re3data":"r3d100010562","uniprot":"DB-0272"},"synonyms":[],"keywords":["3d structure databases","electron microscopy","protein"],"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":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ena.embl":{"prefix":"ena.embl","name":"European Nucleotide Archive","description":"The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers.","pattern":"^[A-Z]+[0-9]+(\\.\\d+)?$","uri_format":"https://www.ebi.ac.uk/ena/browser/view/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"","name":"ENA through GenBank","description":"ENA through GenBank","homepage":"https://www.ncbi.nlm.nih.gov/Genbank/","contact":null,"uri_format":"https://www.ncbi.nlm.nih.gov/nuccore/$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/ena:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/ena/","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":"BN000065","example_extras":[],"example_decoys":null,"license":"Apache-2.0","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":"ENA.EMBL","go":"ENA","integbio":"nbdc00432","miriam":"ena.embl","n2t":"ena.embl","prefixcommons":"ena","re3data":"r3d100010527","uniprot":"DB-0022"},"synonyms":["ena"],"keywords":["cdna/est","dna","genetic variation","genome/gene","method","repository","sequence","sequence databases"],"domain":null,"references":null,"publications":[{"pubmed":"33175160","doi":"10.1093/nar/gkaa1028","pmc":"PMC7778925","arxiv":null,"title":"The European Nucleotide Archive in 2020","year":2021},{"pubmed":"27899630","doi":"10.1093/nar/gkw1106","pmc":"PMC5210577","arxiv":null,"title":"European Nucleotide Archive in 2016","year":2016},{"pubmed":"26657633","doi":"10.1093/nar/gkv1323","pmc":"PMC4702924","arxiv":null,"title":"The International Nucleotide Sequence Database Collaboration","year":2015},{"pubmed":"26615190","doi":"10.1093/nar/gkv1311","pmc":"PMC4702917","arxiv":null,"title":"Biocuration of functional annotation at the European nucleotide archive","year":2015},{"pubmed":"25404130","doi":"10.1093/nar/gku1129","pmc":"PMC4383942","arxiv":null,"title":"Content discovery and retrieval services at the European Nucleotide Archive","year":2014},{"pubmed":"23203883","doi":"10.1093/nar/gks1175","pmc":"PMC3531187","arxiv":null,"title":"Facing growth in the European Nucleotide Archive","year":2012},{"pubmed":"20972220","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14681351","doi":"10.1093/nar/gkh120","pmc":"PMC308854","arxiv":null,"title":"The EMBL Nucleotide Sequence Database","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":"insdc.run","preferred_prefix":"ena.embl","mastodon":null,"github_request_issue":null,"logo":"https://www.ebi.ac.uk/ena/browser/assets/ENA_Logo_tagline.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"encode":{"prefix":"encode","name":"Encyclopedia of DNA Elements","description":"The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.","pattern":"^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$","uri_format":"https://www.encodeproject.org/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.encodeproject.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"ENCSR163RYW","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":"ENCODE","cellosaurus":"ENCODE","miriam":"encode","n2t":"encode","re3data":"r3d100013051"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"32728249","doi":"10.1038/s41586-020-2493-4","pmc":"PMC7410828","arxiv":null,"title":"Expanded encyclopaedias of DNA elements in the human and mouse genomes","year":2020},{"pubmed":"32728248","doi":"10.1038/s41586-020-2449-8","pmc":"PMC7410827","arxiv":null,"title":"Perspectives on ENCODE","year":2020},{"pubmed":"31751002","doi":"10.1002/cpbi.89","pmc":"PMC7307447","arxiv":null,"title":"The ENCODE Portal as an Epigenomics Resource","year":2019},{"pubmed":"31713622","doi":"10.1093/nar/gkz1062","pmc":"PMC7061942","arxiv":null,"title":"New developments on the Encyclopedia of DNA Elements (ENCODE) data portal","year":2020},{"pubmed":"29126249","doi":"10.1093/nar/gkx1081","pmc":"PMC5753278","arxiv":null,"title":"The Encyclopedia of DNA elements (ENCODE): data portal update","year":2018},{"pubmed":"28403240","doi":"10.1371/journal.pone.0175310","pmc":"PMC5389787","arxiv":null,"title":"SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata","year":2017},{"pubmed":"26980513","doi":"10.1093/database/baw001","pmc":"PMC4792520","arxiv":null,"title":"Principles of metadata organization at the ENCODE data coordination center","year":2016},{"pubmed":"26527727","doi":"10.1093/nar/gkv1160","pmc":"PMC4702836","arxiv":null,"title":"ENCODE data at the ENCODE portal","year":2015},{"pubmed":"25776021","doi":"10.1093/database/bav010","pmc":"PMC4360730","arxiv":null,"title":"Ontology application and use at the ENCODE DCC","year":2015},{"pubmed":"23193274","doi":"10.1093/nar/gks1172","pmc":"PMC3531152","arxiv":null,"title":"ENCODE data in the UCSC Genome Browser: year 5 update","year":2012},{"pubmed":"22075998","doi":"10.1093/nar/gkr1012","pmc":"PMC3245183","arxiv":null,"title":"ENCODE whole-genome data in the UCSC Genome Browser: update 2012","year":2011},{"pubmed":"21037257","doi":"10.1093/nar/gkq1017","pmc":"PMC3013645","arxiv":null,"title":"ENCODE whole-genome data in the UCSC genome browser (2011 update)","year":2010},{"pubmed":"19920125","doi":"10.1093/nar/gkp961","pmc":"PMC2808953","arxiv":null,"title":"ENCODE whole-genome data in the UCSC Genome Browser","year":2009},{"pubmed":"17166863","doi":"10.1093/nar/gkl1017","pmc":"PMC1781110","arxiv":null,"title":"The ENCODE Project at UC Santa Cruz","year":2006},{"pubmed":"15499007","doi":"10.1126/science.1105136","pmc":null,"arxiv":null,"title":"The ENCODE (ENCyclopedia Of DNA Elements) Project","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":"encode","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2610","go":"ENSEMBL","integbio":"nbdc00054","miriam":"ensembl","n2t":"ensembl","ncbi":"ENSEMBL","prefixcommons":"ensembl","re3data":"r3d100010228","uniprot":"DB-0023","wikidata":"P594","wikidata.entity":"Q7187"},"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":"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ensembl.bacteria":{"prefix":"ensembl.bacteria","name":"Ensembl Bacteria","description":"Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes.","pattern":"^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$","uri_format":"https://bacteria.ensembl.org/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/ensembl.bacteria:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://bacteria.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":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"MU9_3181","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":"ENSEMBL.BACTERIA","integbio":"nbdc00433","miriam":"ensembl.bacteria","n2t":"ensembl.bacteria","prefixcommons":"ensembl.bacteria","re3data":"r3d100011195","uniprot":"DB-0147"},"synonyms":[],"keywords":["genome","genome annotation databases","genome/gene","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"31598706","doi":"10.1093/nar/gkz890","pmc":"PMC6943047","arxiv":null,"title":"Ensembl Genomes 2020-enabling non-vertebrate genomic research","year":2020},{"pubmed":"26578574","doi":"10.1093/nar/gkv1209","pmc":"PMC4702859","arxiv":null,"title":"Ensembl Genomes 2016: more genomes, more complexity","year":2015},{"pubmed":"19884133","doi":"10.1093/nar/gkp871","pmc":"PMC2808935","arxiv":null,"title":"Ensembl Genomes: extending Ensembl across the taxonomic space","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":"ensembl.bacteria","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ensembl.fungi":{"prefix":"ensembl.fungi","name":"Ensembl Fungi","description":"Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.","pattern":"^[A-Z-a-z0-9]+$","uri_format":"https://fungi.ensembl.org/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/ensembl.fungi:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://fungi.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":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"CADAFLAT00006211","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":"ENSEMBL.FUNGI","go":"EnsemblFungi","integbio":"nbdc00434","miriam":"ensembl.fungi","n2t":"ensembl.fungi","prefixcommons":"ensembl.fungi","re3data":"r3d100011196","uniprot":"DB-0148"},"synonyms":[],"keywords":["genome","genome annotation databases","genome/gene","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"31598706","doi":"10.1093/nar/gkz890","pmc":"PMC6943047","arxiv":null,"title":"Ensembl Genomes 2020-enabling non-vertebrate genomic research","year":2020},{"pubmed":"26578574","doi":"10.1093/nar/gkv1209","pmc":"PMC4702859","arxiv":null,"title":"Ensembl Genomes 2016: more genomes, more complexity","year":2015},{"pubmed":"19884133","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":"ensembl.fungi","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ensembl.metazoa":{"prefix":"ensembl.metazoa","name":"Ensembl Metazoa","description":"Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes.","pattern":"^\\w+(\\.)?\\d+$","uri_format":"https://metazoa.ensembl.org/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/ensembl.metazoa:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://metazoa.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":[{"ror":"02catss52","wikidata":null,"gnd":null,"name":"European Bioinformatics Institute","partnered":false}],"example":"FBtr0084214","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":"ENSEMBL.METAZOA","go":"EnsemblMetazoa","integbio":"nbdc00435","miriam":"ensembl.metazoa","n2t":"ensembl.metazoa","prefixcommons":"ensembl.metazoa","re3data":"r3d100011198","uniprot":"DB-0149"},"synonyms":[],"keywords":["genome","genome annotation databases","genome/gene","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"31598706","doi":"10.1093/nar/gkz890","pmc":"PMC6943047","arxiv":null,"title":"Ensembl Genomes 2020-enabling non-vertebrate genomic research","year":2020},{"pubmed":"26578574","doi":"10.1093/nar/gkv1209","pmc":"PMC4702859","arxiv":null,"title":"Ensembl Genomes 2016: more genomes, more complexity","year":2015},{"pubmed":"19884133","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":"ensembl.metazoa","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"envipath":{"prefix":"envipath","name":"enviPath","description":"enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.","pattern":"^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$","uri_format":"https://envipath.org/package/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://envipath.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea","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":{"integbio":"nbdc02011","miriam":"envipath","re3data":"r3d100012715"},"synonyms":[],"keywords":["bibliography/documents","chemical compound","environment","interaction/pathway","method"],"domain":null,"references":null,"publications":[{"pubmed":"34479624","doi":"10.1186/s13321-021-00543-x","pmc":"PMC8414759","arxiv":null,"title":"Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products","year":2021},{"pubmed":"28229138","doi":"10.1039/c6em00697c","pmc":null,"arxiv":null,"title":"Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data","year":2017},{"pubmed":"26582924","doi":"10.1093/nar/gkv1229","pmc":"PMC4702869","arxiv":null,"title":"enviPath--The environmental contaminant biotransformation pathway resource","year":2015}],"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":"envipath","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"eolife":{"prefix":"eolife","name":"Encyclopedia of Life","description":"A collaborative project intended to create an encyclopedia documenting all living species known to science","pattern":"^\\d+$","uri_format":"https://eol.org/pages/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://eol.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"1044544","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":{"re3data":"r3d100010229","wikidata":"P830"},"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":"eolife","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"facebase":{"prefix":"facebase","name":"FaceBase Data Repository","description":"FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.","pattern":"^FB\\d{8}$","uri_format":"https://www.facebase.org/data/record/#1/isa:dataset/accession=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.facebase.org","repository":null,"contact":{"name":"Yang Chai","orcid":"0000-0003-2477-7247","email":"ychai@usc.edu","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"03taz7m60","wikidata":null,"gnd":null,"name":"University of Southern California","partnered":false}],"example":"FB00000917","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":"FACEBASE","integbio":"nbdc02022","miriam":"facebase","n2t":"facebase","re3data":"r3d100013263"},"synonyms":[],"keywords":["bibliography/documents","expression","genome/gene","health/disease","image/movie","interaction/pathway","method","phenotype","protein","rna"],"domain":null,"references":null,"publications":[{"pubmed":"32958507","doi":"10.1242/dev.191213","pmc":"PMC7522026","arxiv":null,"title":"FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research","year":2020}],"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":"facebase","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"factgrid":{"prefix":"factgrid","name":"FactGrid","description":"A wikibase for linguistic knowledge","pattern":"^Q\\d+$","uri_format":"https://database.factgrid.de/viewer/item/$1","uri_format_resolvable":null,"rdf_uri_format":"https://database.factgrid.de/wiki/Item:Q24708","providers":[],"homepage":"https://database.factgrid.de","repository":null,"contact":{"name":"Olaf Simons","orcid":"0000-0001-9230-4666","email":"olaf.simons@pierre-marteau.com","github":"OlafSimons","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"Q24708","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":{"re3data":"r3d100013283"},"synonyms":[],"keywords":[],"domain":null,"references":["https://github.com/FactGrid"],"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":"factgrid","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"fairsharing":{"prefix":"fairsharing","name":"FAIRsharing","description":"The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.","pattern":"^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$","uri_format":"https://fairsharing.org/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://fairsharing.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"bsg-000052","example_extras":["FAIRsharing.CugtbQ"],"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":"FAIRSHARING","miriam":"fairsharing","n2t":"fairsharing","re3data":"r3d100010142"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"30940948","doi":"10.1038/s41587-019-0080-8","pmc":"PMC6785156","arxiv":null,"title":"FAIRsharing as a community approach to standards, repositories and policies","year":2019},{"pubmed":"27189610","doi":"10.1093/database/baw075","pmc":"PMC4869797","arxiv":null,"title":"BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences","year":2016},{"pubmed":null,"doi":"10.5281/zenodo.5106255","pmc":null,"arxiv":null,"title":"FAIRsharing, a FAIR-enabling service for repositories, standards and policies","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":"fairsharing","mastodon":"fairsharing@fediscience.org","github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"fishbase.species":{"prefix":"fishbase.species","name":"FishBase","description":"Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.","pattern":"^\\d+$","uri_format":"https://www.fishbase.ca/summary/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://fishbase.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"6472","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":{"integbio":"nbdc00270","re3data":"r3d100010912","wikidata":"P938"},"synonyms":["fishbase"],"keywords":["image/movie","ontology/terminology/nomenclature","organism"],"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":"fishbase.species","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"flowrepository":{"prefix":"flowrepository","name":"FlowRepository","description":"FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field.","pattern":"^FR\\-FCM\\-\\w{4}$","uri_format":"http://flowrepository.org/id/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://flowrepository.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"FR-FCM-ZYGW","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":{"integbio":"nbdc01698","miriam":"flowrepository","n2t":"flowrepository","re3data":"r3d100011280"},"synonyms":[],"keywords":["bibliography/documents","method"],"domain":null,"references":null,"publications":[{"pubmed":"22887982","doi":"10.1002/cyto.a.22106","pmc":null,"arxiv":null,"title":"FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications","year":2012},{"pubmed":"22752950","doi":"10.1002/0471142956.cy1018s61","pmc":null,"arxiv":null,"title":"Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org)","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":"flowrepository","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"1089","go":"FB","integbio":"nbdc00064","miriam":"fb","n2t":"fb","ncbi":"FLYBASE","pathguide":"460","prefixcommons":"flybase","re3data":"r3d100010591","rrid":"FlyBase","uniprot":"DB-0026","wikidata":"P3852"},"synonyms":["FB","FlyBase"],"keywords":["allele","anatomy","bibliography/documents","bio.tools","bioresource","blast","cdna/est","controlled term","dna","drosophilidae","expression","faseb list","gene","genetic variation","genetics","genome","genome/gene","genotype","health/disease","image","image collection","image/movie","interaction","interaction/pathway","life-cycle","movie","mutant","ontology","ontology/terminology/nomenclature","organism","organism-specific databases","phenotype","protein","repository","rna","rna-seq","sequence","stock","taxonomy","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":"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"foodb.compound":{"prefix":"foodb.compound","name":"FooDB compound","description":"FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.","pattern":"^FDB\\d+$","uri_format":"http://foodb.ca/compounds/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://foodb.ca/","repository":null,"contact":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":"FDB002100","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":"FOODB.COMPOUND","biolink":"foodb.compound","miriam":"foodb.compound","n2t":"foodb.compound","re3data":"r3d100012152","wikidata":"P8117"},"synonyms":["foodb"],"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":"foodb.compound","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"fungidb":{"prefix":"fungidb","name":"FungiDB","description":"FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.","pattern":"^[A-Za-z_0-9]+$","uri_format":"https://fungidb.org/fungidb/app/record/gene/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://fungidb.org/fungidb","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"CNBG_0001","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":"FUNGIDB","miriam":"fungidb","n2t":"fungidb","re3data":"r3d100011906"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"27259951","doi":"10.1016/j.fgb.2016.04.002","pmc":null,"arxiv":null,"title":"Database whiplash, crowdsourcing, and FungiDB","year":2016},{"pubmed":"24813190","doi":"10.1128/ec.00083-14","pmc":"PMC4135733","arxiv":null,"title":"Literature-based gene curation and proposed genetic nomenclature for cryptococcus","year":2014},{"pubmed":"22064857","doi":"10.1093/nar/gkr918","pmc":"PMC3245123","arxiv":null,"title":"FungiDB: an integrated functional genomics database for fungi","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":"fungidb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"gbif":{"prefix":"gbif","name":"Global Biodiversity Information Facility","description":"Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.","pattern":"^\\d+$","uri_format":"https://www.gbif.org/species/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.gbif.org/species","repository":null,"contact":{"name":"Tim Robertson","orcid":"0000-0001-6215-3617","email":"timrobertson100@gmail.com","github":"timrobertson100","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"4238","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":{"integbio":"nbdc00069","re3data":"r3d100000039","wikidata":"P846"},"synonyms":[],"keywords":["ontology/terminology/nomenclature","organism","repository"],"domain":null,"references":null,"publications":[{"pubmed":"25099149","doi":"10.1371/journal.pone.0102623","pmc":"PMC4123864","arxiv":null,"title":"The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet","year":2014}],"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":"gbif","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2292","go":"GenBank","integbio":"nbdc00276","prefixcommons":"genbank","re3data":"r3d100010528","uniprot":"DB-0028"},"synonyms":[],"keywords":["cdna/est","dna","genetic variation","genome/gene","repository","rna","sequence","sequence databases"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"genbase":{"prefix":"genbase","name":"GenBase","description":"GenBase is a genetic sequence database that accepts user submissions (mRNA, genomic DNAs, ncRNA, or small genomes such as organelles, viruses, plasmids, phages from any organism) and integrates data from INSDC.","pattern":null,"uri_format":"https://ngdc.cncb.ac.cn/genbase/search/gb/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://ngdc.cncb.ac.cn/genbase/?lang=en","repository":null,"contact":{"name":"Xuetong Zhao","orcid":"0000-0002-3019-8615","email":"zhaoxuetong@big.ac.cn","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"C_AA001108.1","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":{"re3data":"r3d100014353"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":"CTH: this is a provider of the INSDC resources, not a new prefix.","contributor":{"name":"Tanay Shah","orcid":"0009-0001-1912-5132","email":"shah.tanay2@northeastern.edu","github":"tanayshah2","wikidata":null},"contributor_extras":null,"reviewer":{"name":"Benjamin M. Gyori","orcid":"0000-0001-9439-5346","email":"b.gyori@northeastern.edu","github":"bgyori","wikidata":null},"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"genbase","mastodon":null,"github_request_issue":1140,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"genecards.gene":{"prefix":"genecards.gene","name":"GeneCards Gene","description":"The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.","pattern":"^[A-Za-z-0-9_]+(\\@)?$","uri_format":"https://www.genecards.org/cgi-bin/carddisp.pl?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/genecards:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.genecards.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"ABL1","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":"GENECARDS","integbio":"nbdc00242","miriam":"genecards","n2t":"genecards","prefixcommons":"genecards","re3data":"r3d100012015","uniprot":"DB-0030"},"synonyms":["genecards"],"keywords":["cdna/est","expression","genetic variation","genome","genome/gene","health/disease","organism-specific databases","protein","rna"],"domain":null,"references":null,"publications":[{"pubmed":"9789091","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"9097728","doi":"10.1016/s0168-9525(97)01103-7","pmc":null,"arxiv":null,"title":"GeneCards: integrating information about genes, proteins and diseases","year":1997},{"pubmed":"27357693","doi":"10.1186/s12864-016-2722-2","pmc":"PMC4928145","arxiv":null,"title":"VarElect: the phenotype-based variation prioritizer of the GeneCards Suite","year":2016},{"pubmed":"27322403","doi":"10.1002/cpbi.5","pmc":null,"arxiv":null,"title":"The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses","year":2016},{"pubmed":"27048349","doi":"10.1093/database/baw030","pmc":"PMC4820835","arxiv":null,"title":"Genic insights from integrated human proteomics in GeneCards","year":2016},{"pubmed":"26983021","doi":"10.1089/omi.2015.0168","pmc":"PMC4799705","arxiv":null,"title":"GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data","year":2016},{"pubmed":"25725062","doi":"10.1093/database/bav006","pmc":"PMC4343183","arxiv":null,"title":"PathCards: multi-source consolidation of human biological pathways","year":2015},{"pubmed":"20689021","doi":"10.1093/database/baq020","pmc":"PMC2938269","arxiv":null,"title":"GeneCards Version 3: the human gene integrator","year":2010},{"pubmed":"12424129","doi":"10.1093/bioinformatics/18.11.1542","pmc":null,"arxiv":null,"title":"GeneCards 2002: towards a complete, object-oriented, human gene compendium","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":"genecards.gene","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"1035","go":"GeneDB","integbio":"nbdc00469","miriam":"genedb","n2t":"genedb","ncbi":"GeneDB","prefixcommons":"genedb","re3data":"r3d100010626","wikidata":"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"GEO","edam":"1147","go":"GEO","integbio":"nbdc00080","miriam":"geo","n2t":"geo","prefixcommons":"geo","re3data":"r3d100010283"},"synonyms":[],"keywords":["cdna/est","expression","gene expression","genome","image/movie","repository","sequence"],"domain":null,"references":null,"publications":[{"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"geonames":{"prefix":"geonames","name":"GeoNames","description":"The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.","pattern":"^\\d+$","uri_format":"https://www.geonames.org/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.geonames.org","repository":null,"contact":{"name":"Marc Wick","orcid":null,"email":"marc@geonames.org","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"3532759","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/geonames/geonames.owl","download_obo":"https://w3id.org/biopragmatics/resources/geonames/geonames.obo","download_json":"https://w3id.org/biopragmatics/resources/geonames/geonames.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"bartoc":"1674","biodivportal":"GEONAMES","fairsharing":"FAIRsharing.6dba71","re3data":"r3d100010245"},"synonyms":["Geomames","Geonamaes"],"keywords":["geographic location","geography","geoinformatics","ontology"],"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":"geonames","mastodon":null,"github_request_issue":null,"logo":"https://www.geonames.org/img/globe.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"giardiadb":{"prefix":"giardiadb","name":"GiardiaDB","description":"GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","pattern":"^\\w+$","uri_format":"https://giardiadb.org/giardiadb/app/record/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/giardiadb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://giardiadb.org/giardiadb/","repository":null,"contact":{"name":"Omar S. Harb","orcid":"0000-0003-4446-6200","email":"oharb@upenn.edu","github":"ramobrah","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"GL50803_102438","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":"GIARDIADB","integbio":"nbdc01782","miriam":"giardiadb","n2t":"giardiadb","prefixcommons":"giardiadb","re3data":"r3d100012458"},"synonyms":[],"keywords":["cdna/est","cell/organelle","eukaryotic","expression","genome","genome/gene","ontology/terminology/nomenclature","organism","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"18824479","doi":"10.1093/nar/gkn631","pmc":"PMC2686445","arxiv":null,"title":"GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis","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":"giardiadb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"github":{"prefix":"github","name":"github","description":"GitHub is an online host of Git source code repositories.","pattern":"^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$","uri_format":"https://github.com/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://github.com/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"biopragmatics/bioregistry","example_extras":["biopragmatics","cthoyt"],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"miriam":"github","re3data":"r3d100010375","wikidata":"P2037"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"github","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"glycomedb":{"prefix":"glycomedb","name":"GlycomeDB","description":"GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.","pattern":"^\\w+$","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":"2664","integbio":"nbdc00899","miriam":"glycomedb","n2t":"glycomedb","prefixcommons":"glycomedb","re3data":"r3d100011527"},"synonyms":[],"keywords":["carbohydrate","chemical structure","molecules","sequence","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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"glytoucan":{"prefix":"glytoucan","name":"GlyTouCan","description":"GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.","pattern":"^G[0-9]{5}[A-Z]{2}$","uri_format":"https://glytoucan.org/Structures/Glycans/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"glygen","name":"GlyGen","description":"GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. ","homepage":"https://www.glygen.org/","contact":null,"uri_format":"https://glygen.org/glycan/$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":"003qdfg20","wikidata":null,"gnd":null,"name":"Soka University, Hachioji, Tokyo","partnered":false}],"example":"G00054MO","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":"GLYTOUCAN","integbio":"nbdc02434","miriam":"glytoucan","n2t":"glytoucan","re3data":"r3d100012388","togoid":"Glytoucan"},"synonyms":["glygen"],"keywords":["carbohydrate","chemical structure","expression","glycan","health/disease","interaction/pathway","portal","protein","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"28922742","doi":"10.1093/glycob/cwx066","pmc":"PMC5881658","arxiv":null,"title":"GlyTouCan: an accessible glycan structure repository","year":2017},{"pubmed":"26476458","doi":"10.1093/nar/gkv1041","pmc":"PMC4702779","arxiv":null,"title":"GlyTouCan 1.0--The international glycan structure repository","year":2015}],"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":"glytoucan","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"gmd":{"prefix":"gmd","name":"Golm Metabolome Database","description":"Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.","pattern":"^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$","uri_format":"http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://gmd.mpimp-golm.mpg.de/","repository":null,"contact":{"name":"Joachim Kopka","orcid":"0000-0001-9675-4883","email":"kopka@mpimp-golm.mpg.de","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"01fbde567","wikidata":null,"gnd":null,"name":"Max Planck Institute of Molecular Plant Physiology, Potsdam","partnered":false}],"example":"68513255-fc44-4041-bc4b-4fd2fae7541d","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":"GMD","miriam":"gmd","n2t":"gmd","re3data":"r3d100011046"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"20526350","doi":"10.1007/s11306-010-0198-7","pmc":"PMC2874469","arxiv":null,"title":"Decision tree supported substructure prediction of metabolites from GC-MS profiles","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":"gmd","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"gnpis":{"prefix":"gnpis","name":"GnpIS","description":"GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.","pattern":"^[A-Za-z0-9]+$","uri_format":"https://urgi.versailles.inra.fr/gnpis/#result/term=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://urgi.versailles.inra.fr/gnpis/","repository":null,"contact":{"name":"Hadi Quesneville","orcid":"0000-0003-3001-4908","email":"hadi.quesneville@versailles.inra.fr","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"AY109603","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":"GNPIS","miriam":"gnpis","n2t":"gnpis","re3data":"r3d100012647"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"23959375","doi":"10.1093/database/bat058","pmc":"PMC3746681","arxiv":null,"title":"GnpIS: an information system to integrate genetic and genomic data from plants and fungi","year":2013}],"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":"gnpis","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2026-06-15","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":"1176","fairsharing":"FAIRsharing.6xq0ee","go":"GO","hl7":"2.16.840.1.113883.6.128","integbio":"nbdc00074","miriam":"go","n2t":"go","ncbi":"GO","obofoundry":"go","ols":"go","ontobee":"GO","pathguide":"272","prefixcommons":"go","re3data":"r3d100014165","tib":"go","togoid":"Go","uniprot":"DB-0037","wikidata":"P686","wikidata.entity":"Q135085"},"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"gold":{"prefix":"gold","name":"Genomes Online Database","description":"The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.","pattern":"^[A-Z][a-z][0-9]+$","uri_format":"https://gold.jgi.doe.gov/resolver?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/gold:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://gold.jgi.doe.gov/","repository":null,"contact":{"name":"TBK Reddy","orcid":"0000-0002-0871-5567","email":"tbreddy@lbl.gov","github":"TBKReddy","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"Gs0000008","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://raw.githubusercontent.com/cmungall/gold-ontology/refs/heads/main/gold.owl","download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"fairsharing":"FAIRsharing.4c40ed","integbio":"nbdc00483","miriam":"gold","ols":"gold","prefixcommons":"gold","re3data":"r3d100010808"},"synonyms":[],"keywords":["bibliography/documents","classification","computer science","genome","genome/gene","linguistics","natural language processing","ontology","portal","repository"],"domain":null,"references":null,"publications":[{"pubmed":"39498478","doi":"10.1093/nar/gkae1000","pmc":null,"arxiv":null,"title":"Genomes OnLine Database (GOLD) v.10: new features and updates","year":2024},{"pubmed":"33152092","doi":"10.1093/nar/gkaa983","pmc":"PMC7778979","arxiv":null,"title":"Genomes OnLine Database (GOLD) v.8: overview and updates","year":2021},{"pubmed":"30357420","doi":"10.1093/nar/gky977","pmc":"PMC6323969","arxiv":null,"title":"Genomes OnLine database (GOLD) v.7: updates and new features","year":2019},{"pubmed":"27794040","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"19914934","doi":"10.1093/nar/gkp848","pmc":"PMC2808860","arxiv":null,"title":"The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata","year":2009},{"pubmed":"17981842","doi":"10.1093/nar/gkm884","pmc":"PMC2238992","arxiv":null,"title":"The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata","year":2007},{"pubmed":"11125068","doi":"10.1093/nar/29.1.126","pmc":"PMC29859","arxiv":null,"title":"Genomes OnLine Database (GOLD): a monitor of genome projects world-wide","year":2001},{"pubmed":"10498782","doi":"10.1093/bioinformatics/15.9.773","pmc":null,"arxiv":null,"title":"Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide","year":1999}],"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":"gold","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"greengenes":{"prefix":"greengenes","name":"GreenGenes","description":"A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.","pattern":"^\\d+$","uri_format":"http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_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/greengenes:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://greengenes.lbl.gov/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"100000","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":true,"mappings":{"biocontext":"GREENGENES","integbio":"nbdc01824","miriam":"greengenes","n2t":"greengenes","ncbi":"Greengenes","prefixcommons":"greengenes","re3data":"r3d100010549"},"synonyms":[],"keywords":["genome/gene","rna","sequence","taxonomy"],"domain":null,"references":null,"publications":[{"pubmed":"16820507","doi":"10.1128/aem.03006-05","pmc":"PMC1489311","arxiv":null,"title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","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":"greengenes","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"gudmap":{"prefix":"gudmap","name":"Genitourinary Development Molecular Anatomy Project","description":"The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.","pattern":"^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$","uri_format":"https://gudmap.org/id/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.gudmap.org/","repository":null,"contact":{"name":"Simon Douglas Harding","orcid":"0000-0002-9262-8318","email":"simon.harding@ed.ac.uk","github":"simondharding","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"Q-2958","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":"GUDMAP","miriam":"gudmap","n2t":"gudmap","re3data":"r3d100012193"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"21652655","doi":"10.1242/dev.063594","pmc":"PMC3188593","arxiv":null,"title":"The GUDMAP database--an online resource for genitourinary research","year":2011},{"pubmed":"18287559","doi":"10.1681/asn.2007101078","pmc":null,"arxiv":null,"title":"GUDMAP: the genitourinary developmental molecular anatomy project","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":"gudmap","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2622","integbio":"nbdc00909","miriam":"hmdb","n2t":"hmdb","pathguide":"244","prefixcommons":"hmdb","re3data":"r3d100011285","togoid":"Hmdb","wikidata":"P2057"},"synonyms":["HMDB"],"keywords":["chemical","classification","compound","health/disease","human","interaction/pathway","metabolite","protein","rna","sequence"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"hpa":{"prefix":"hpa","name":"Human Protein Atlas","description":"The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.","pattern":"^ENSG\\d{11}$","uri_format":"http://www.proteinatlas.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/hpa:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.proteinatlas.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"ENSG00000026508","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":"HPA","go":"HPA","miriam":"hpa","n2t":"hpa","prefixcommons":"hpa","re3data":"r3d100010931","uniprot":"DB-0046"},"synonyms":[],"keywords":["organism-specific databases","protein","structure"],"domain":null,"references":null,"publications":[{"pubmed":"28818916","doi":"10.1126/science.aan2507","pmc":null,"arxiv":null,"title":"A pathology atlas of the human cancer transcriptome","year":2017},{"pubmed":"28495876","doi":"10.1126/science.aal3321","pmc":null,"arxiv":null,"title":"A subcellular map of the human proteome","year":2017},{"pubmed":"27044256","doi":"10.15252/msb.20155865","pmc":"PMC4848759","arxiv":null,"title":"Transcriptomics resources of human tissues and organs","year":2016},{"pubmed":"25613900","doi":"10.1126/science.1260419","pmc":null,"arxiv":null,"title":"Proteomics. Tissue-based map of the human proteome","year":2015},{"pubmed":"21139605","doi":"10.1038/nbt1210-1248","pmc":null,"arxiv":null,"title":"Towards a knowledge-based Human Protein Atlas","year":2010},{"pubmed":"18853439","doi":"10.1002/path.2440","pmc":null,"arxiv":null,"title":"The Human Protein Atlas--a tool for pathology","year":2008},{"pubmed":"18669619","doi":"10.1074/mcp.r800013-mcp200","pmc":null,"arxiv":null,"title":"A genecentric Human Protein Atlas for expression profiles based on antibodies","year":2008},{"pubmed":"16127175","doi":"10.1074/mcp.m500279-mcp200","pmc":null,"arxiv":null,"title":"A human protein atlas for normal and cancer tissues based on antibody proteomics","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":"hpa","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"hprd":{"prefix":"hprd","name":"Human Protein Reference Database","description":"The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.","pattern":"^\\d+$","uri_format":"http://www.hprd.org/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/hprd:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.hprd.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"04hqfvm50","wikidata":null,"gnd":null,"name":"Institute of Bioinformatics, International Tech Park, Bangalore","partnered":false}],"example":"00001","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":"HPRD","integbio":"nbdc00103","miriam":"hprd","n2t":"hprd","pathguide":"14","prefixcommons":"hprd","re3data":"r3d100010978"},"synonyms":[],"keywords":["cdna/est","health/disease","protein","psi-mi","sequence","structure"],"domain":null,"references":null,"publications":[{"pubmed":"18988627","doi":"10.1093/nar/gkn892","pmc":"PMC2686490","arxiv":null,"title":"Human Protein Reference Database--2009 update","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":"hprd","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"hpscreg":{"prefix":"hpscreg","name":"Human Pluripotent Stem Cell Registry","description":"hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines).","pattern":"^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$","uri_format":"https://hpscreg.eu/cell-line/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://hpscreg.eu/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"05tpsgh61","wikidata":null,"gnd":null,"name":"Fraunhofer Institute for Biomedical Engineering","partnered":false}],"example":"BCRTi001-A","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":"hPSCreg","miriam":"hpscreg","n2t":"hpscreg","re3data":"r3d100012863"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"32707486","doi":"10.1016/j.scr.2020.101887","pmc":null,"arxiv":null,"title":"Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)","year":2020},{"pubmed":"32679065","doi":"10.1016/j.stemcr.2020.06.014","pmc":"PMC7419703","arxiv":null,"title":"A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells","year":2020},{"pubmed":"31450190","doi":"10.1016/j.scr.2019.101539","pmc":null,"arxiv":null,"title":"A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC","year":2019},{"pubmed":"29320760","doi":"10.1016/j.stemcr.2017.12.002","pmc":"PMC5768986","arxiv":null,"title":"A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells","year":2018},{"pubmed":"26400179","doi":"10.1093/nar/gkv963","pmc":"PMC4702942","arxiv":null,"title":"hPSCreg--the human pluripotent stem cell registry","year":2015}],"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":"hpscreg","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"hydra":{"prefix":"hydra","name":"The Hydra Core Vocabulary","description":"A lightweight vocabulary for hypermedia-driven Web APIs","pattern":null,"uri_format":null,"uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.w3.org/ns/hydra/spec/latest/core/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"TemplatedLink","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":{"lov":"hydra","re3data":"r3d100011525","zazuko":"hydra"},"synonyms":[],"keywords":["rdf"],"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":"hydra","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"idog":{"prefix":"idog","name":"Integrated Resource for Domestic Dog","description":"Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses.","pattern":"^\\d+$","uri_format":"https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://ngdc.cncb.ac.cn/idog/","repository":null,"contact":{"name":"Yiming Bao","orcid":"0000-0002-9922-9723","email":"baoym@big.ac.cn","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"4","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":{"integbio":"nbdc02480","re3data":"r3d100012176"},"synonyms":[],"keywords":["bibliography/documents","expression","genetic variation","genome/gene","health/disease","interaction/pathway","organism","phenotype","sequence"],"domain":null,"references":["https://github.com/biopragmatics/bioregistry/pull/725"],"publications":[{"pubmed":"30371881","doi":"10.1093/nar/gky1041","pmc":"PMC6323916","arxiv":null,"title":"iDog: an integrated resource for domestic dogs and wild canids","year":2019}],"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":"idog","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"idr":{"prefix":"idr","name":"Image Data Resource","description":"Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.","pattern":"^[0-9]{4}$","uri_format":"https://idr.openmicroscopy.org/search/?query=Name:idr$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://idr.openmicroscopy.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"03h2bxq36","wikidata":null,"gnd":null,"name":"University of Dundee","partnered":false}],"example":"0001","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"miriam":"idr","re3data":"r3d100012435"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"28775673","doi":"10.1038/nmeth.4326","pmc":"PMC5536224","arxiv":null,"title":"The Image Data Resource: A Bioimage Data Integration and Publication Platform","year":2017}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"idr","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"iedb.assay":{"prefix":"iedb.assay","name":"Immune Epitope Database Assays","description":"Identifiers for specific experimental assays that serve as evidence for immune-related studies.","pattern":"^\\d+$","uri_format":"https://www.iedb.org/assay/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"cedar","name":"Cancer Epitope Database and Analysis Resource","description":"Cancer Epitope Database and Analysis Resource (CEDAR) is a specialized interface providing cancer-focused access to IEDB data with domain-specific analysis tools and workflows.","homepage":"https://cedar.iedb.org/","contact":null,"uri_format":"https://cedar.iedb.org/assay/$1","first_party":null,"publications":[{"pubmed":"40779104","doi":"10.1007/978-1-0716-4566-6_3","pmc":null,"arxiv":null,"title":"Using the Cancer Epitope Database and Analysis Resource (CEDAR)","year":2025}],"example":null,"status":null,"organization":null}],"homepage":"https://www.iedb.org/","repository":null,"contact":{"name":"Randi Vita","orcid":"0000-0001-8957-7612","email":"rvita@liai.org","github":"rvita","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"1691753","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":{"integbio":"nbdc00924","re3data":"r3d100012702"},"synonyms":[],"keywords":["bibliography/documents","health/disease","immunology","protein","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"40779104","doi":"10.1007/978-1-0716-4566-6_3","pmc":null,"arxiv":null,"title":"Using the Cancer Epitope Database and Analysis Resource (CEDAR)","year":2025},{"pubmed":"25300482","doi":"10.1093/nar/gku938","pmc":"PMC4384014","arxiv":null,"title":"The immune epitope database (IEDB) 3.0","year":2014},{"pubmed":"22681406","doi":"10.1111/j.1365-2567.2012.03611.x","pmc":"PMC3461392","arxiv":null,"title":"The immune epitope database: a historical retrospective of the first decade","year":2012},{"pubmed":"19906713","doi":"10.1093/nar/gkp1004","pmc":"PMC2808938","arxiv":null,"title":"The immune epitope database 2.0","year":2009},{"pubmed":"16312048","doi":null,"pmc":null,"arxiv":null,"title":"The immune epitope database and analysis resource: from vision to blueprint","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Mufaddal Naguthanawala","orcid":"0009-0009-5240-7463","email":"m.naguthana@hotmail.com","github":"nagutm","wikidata":null},"contributor_extras":null,"reviewer":{"name":"Benjamin M. Gyori","orcid":"0000-0001-9439-5346","email":"b.gyori@northeastern.edu","github":"bgyori","wikidata":null},"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"iedb.assay","mastodon":null,"github_request_issue":1204,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"igsr":{"prefix":"igsr","name":"International Genome Sample Resource","description":"The 1000 Genomes Project is an international collaboration to produce an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts. This resource will support genome-wide association studies and other medical research studies.\nThe genomes of about 2500 unidentified people from about 25 populations around the world will be sequenced using next-generation sequencing technologies. The results of the study will be freely and publicly accessible to researchers worldwide.\nThe International Genome Sample Resource (IGSR) has been established at EMBL-EBI to continue supporting data generated by the 1000 Genomes Project, supplemented with new data and new analysis.","pattern":null,"uri_format":"https://www.internationalgenome.org/data-portal/sample/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.internationalgenome.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":"NA06985","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":"IGSR","re3data":"r3d100010180"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"31584097","doi":"10.1093/nar/gkz836","pmc":"PMC6943028","arxiv":null,"title":"The International Genome Sample Resource (IGSR) collection of open human genomic variation resources","year":2020},{"pubmed":"26432245","doi":"10.1038/nature15393","pmc":"PMC4750478","arxiv":null,"title":"A global reference for human genetic variation","year":2015}],"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":"igsr","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"imex":{"prefix":"imex","name":"International Molecular Exchange","description":"The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.","pattern":"^\\d+(-\\d+)?$","uri_format":"https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$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/imex:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"ebi","name":"IMEx Consortium running at EBI","description":"IMEx Consortium running at EBI","homepage":"https://www.imexconsortium.org/","contact":null,"uri_format":"https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"intact.search","name":"IntAct Search","description":"Search page on IntAct","homepage":"https://www.ebi.ac.uk/intact","contact":null,"uri_format":"https://www.ebi.ac.uk/intact/search?query=IM-$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/intact/","repository":null,"contact":{"name":"Sandra Orchard","orcid":"0000-0002-8878-3972","email":"orchard@ebi.ac.uk","github":"sandraorchard","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":"19210-3","example_extras":["19210"],"example_decoys":null,"license":"http://disber.net/imexdrupal/node/5","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":"IM","banana_peel":"-","deprecated":false,"mappings":{"biocontext":"IMEX","miriam":"imex","n2t":"imex","pathguide":"422","prefixcommons":"imex","re3data":"r3d100010669"},"synonyms":[],"keywords":["interaction","molecule","psi-mi"],"domain":null,"references":null,"publications":[{"pubmed":"17893861","doi":"10.1002/pmic.200700286","pmc":null,"arxiv":null,"title":"Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition","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":"imex","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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":"IPD-IMGT/HLA","edam":"2773","go":"IMGT_HLA","integbio":"nbdc00106","miriam":"imgt.hla","n2t":"imgt.hla","ncbi":"IMGT/HLA","prefixcommons":"imgthla","re3data":"r3d100010804"},"synonyms":["IPD-IMGT/HLA"],"keywords":["cell/organelle","dna","genome/gene","ontology/terminology/nomenclature","protein","rna","sequence"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"imgt.primerdb":{"prefix":"imgt.primerdb","name":"IMGT/PRIMER-DB","description":"The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).","pattern":null,"uri_format":"http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList","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/imgt.primerdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://imgt.org/IMGTPrimerDB/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"IPP900099","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":{"prefixcommons":"imgt.primerdb","re3data":"r3d100012535"},"synonyms":[],"keywords":["dna"],"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":"imgt.primerdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"innatedb":{"prefix":"innatedb","name":"A Knowledge Resource for Innate Immunity Interactions and Pathways","description":"InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection. The database covers the innate immunity interactome by integrating known interactions and pathways from major public databases.","pattern":null,"uri_format":"http://www.innatedb.ca/getGeneCard.do?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/innatedb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.innatedb.ca/","repository":null,"contact":{"name":"David Lynn","orcid":"0000-0003-4664-1404","email":"david.lynn@flinders.edu.au","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"20021","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":{"integbio":"nbdc01870","pathguide":"264","prefixcommons":"innatedb","re3data":"r3d100010676"},"synonyms":[],"keywords":["gene","genome/gene","health/disease","immunology","interaction","interaction/pathway","organism","pathway","protein","psi-mi"],"domain":null,"references":null,"publications":[{"pubmed":"23180781","doi":"10.1093/nar/gks1147","pmc":"PMC3531080","arxiv":null,"title":"InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation","year":2012}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"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":"innatedb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"insdc.sra":{"prefix":"insdc.sra","name":"Sequence Read Archive","description":"The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.","pattern":"^[SED]R[APRSXZ]\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/sra/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"ddbj","name":"DDBJ Sequence Read Archive (DRA)","description":"DDBJ Sequence Read Archive (DRA)","homepage":"https://www.ddbj.nig.ac.jp/dra/index-e.html","contact":null,"uri_format":"https://ddbj.nig.ac.jp/resource/sra-experiment/$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/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/sra","repository":null,"contact":{"name":"Hugh P Shanahan","orcid":"0000-0003-1374-6015","email":"Hugh.Shanahan@rhul.ac.uk","github":"hughshanahan","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":"SRX000007","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":"INSDC.SRA","miriam":"insdc.sra","n2t":"insdc.sra","re3data":"r3d100010775"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"25960871","doi":"10.1186/s13742-015-0064-7","pmc":"PMC4425880","arxiv":null,"title":"Investigation into the annotation of protocol sequencing steps in the sequence read archive","year":2015},{"pubmed":"22009675","doi":"10.1093/nar/gkr854","pmc":"PMC3245110","arxiv":null,"title":"The Sequence Read Archive: explosive growth of sequencing data","year":2011},{"pubmed":"18045790","doi":"10.1093/nar/gkm1000","pmc":"PMC2238880","arxiv":null,"title":"Database resources of the National Center for Biotechnology Information","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":"insdc.sra","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"intact":{"prefix":"intact","name":"IntAct protein interaction","description":"IntAct provides a freely available, open source database system and analysis tools for protein interaction data.","pattern":"^EBI\\-[0-9]+$","uri_format":"https://www.ebi.ac.uk/intact/interaction/$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/intact:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/intact/","repository":null,"contact":{"name":"Kalpana Panneerselvam","orcid":"0000-0003-2534-198X","email":"kalpanap@ebi.ac.uk","github":"Kalpanapanneerselvam","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":"EBI-2307691","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":{"biocontext":"INTACT","go":"IntAct","integbio":"nbdc00507","miriam":"intact","n2t":"intact","pathguide":"111","prefixcommons":"intact","re3data":"r3d100010671","togoid":"Intact","uniprot":"DB-0051"},"synonyms":[],"keywords":["interaction","interaction/pathway","metabolite","protein","protein-protein interaction databases","psi-mi","repository"],"domain":null,"references":null,"publications":[{"pubmed":"39401100","doi":"10.1002/cpz1.70018","pmc":null,"arxiv":null,"title":"IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions","year":2024},{"pubmed":"24234451","doi":"10.1093/nar/gkt1115","pmc":"PMC3965093","arxiv":null,"title":"The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases","year":2013},{"pubmed":"22121220","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21716279","doi":"10.1038/nmeth.1637","pmc":"PMC3246345","arxiv":null,"title":"PSICQUIC and PSISCORE: accessing and scoring molecular interactions","year":2011},{"pubmed":"19850723","doi":"10.1093/nar/gkp878","pmc":"PMC2808934","arxiv":null,"title":"The IntAct molecular interaction database in 2010","year":2009},{"pubmed":"17925023","doi":"10.1186/1741-7007-5-44","pmc":"PMC2189715","arxiv":null,"title":"Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions","year":2007},{"pubmed":"14681455","doi":"10.1093/nar/gkh052","pmc":"PMC308786","arxiv":null,"title":"IntAct: an open source molecular interaction database","year":2004}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Sucharitha Balu","orcid":"0000-0001-7456-0594","email":"sbalu@ebi.ac.uk","github":"CP-SB","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"intact","mastodon":null,"github_request_issue":null,"logo":"https://raw.githubusercontent.com/intact-portal/intact-portal-documentation/master/assets/logo_gradient_250x82_transparentbg_300dpi.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"interpro","edam":"1133","go":"InterPro","integbio":"nbdc00108","miriam":"interpro","n2t":"interpro","ncbi":"InterPro","obofoundry":"ipr","prefixcommons":"interpro","re3data":"r3d100010798","togoid":"Interpro","uniprot":"DB-0052","wikidata":"P2926","wikidata.entity":"Q114677890"},"synonyms":["IP","IPR","InterPro"],"keywords":["classification","domain","family and domain databases","ontology","protein","sequence"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"irefweb":{"prefix":"irefweb","name":"iRefWeb","description":"iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.","pattern":"^\\d+$","uri_format":"http://wodaklab.org/iRefWeb/interaction/show/$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/irefweb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://wodaklab.org/iRefWeb/","repository":null,"contact":{"name":"Shoshana J. Wodak","orcid":"0000-0002-0701-6545","email":"shoshana@sickkids.ca","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"617102","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":"IREFWEB","miriam":"irefweb","n2t":"irefweb","pathguide":"300","prefixcommons":"irefweb","re3data":"r3d100012725"},"synonyms":[],"keywords":["interaction","protein","psi-mi"],"domain":null,"references":null,"publications":[{"pubmed":"20940177","doi":"10.1093/database/baq023","pmc":"PMC2963317","arxiv":null,"title":"iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence","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":"irefweb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"itis":{"prefix":"itis","name":"Integrated Taxonomic Information System","description":"Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world.","pattern":"^\\d+$","uri_format":"https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.itis.gov/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"589462","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/itis/itis.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/itis/itis.obo","download_json":"https://w3id.org/biopragmatics/resources/itis/itis.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"bartoc":"17791","integbio":"nbdc00916","re3data":"r3d100011213","wikidata":"P815","wikidata.entity":"Q82575"},"synonyms":[],"keywords":["bibliography/documents","ontology","ontology/terminology/nomenclature","organism","repository","taxonomy"],"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":"itis","mastodon":null,"github_request_issue":null,"logo":"https://www.itis.gov/Static/images/ITIS-Logo.jpg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"kaggle":{"prefix":"kaggle","name":"Kaggle","description":"Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.","pattern":"^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$","uri_format":"https://www.kaggle.com/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://kaggle.com","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"024bc3e07","wikidata":null,"gnd":null,"name":"Google Incorporated","partnered":false}],"example":"nasa/kepler-exoplanet-search-results","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":{"miriam":"kaggle","n2t":"kaggle","re3data":"r3d100012705"},"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":"kaggle","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"licebase":{"prefix":"licebase","name":"LiceBase","description":"Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.","pattern":"^[A-Za-z0-9\\-\\/]+$","uri_format":"https://licebase.org/?q=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://licebase.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"EMLSAT00000003403","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":"LICEBASE","integbio":"nbdc02217","miriam":"licebase","n2t":"licebase","re3data":"r3d100013547"},"synonyms":[],"keywords":["genome/gene","image/movie","organism","rna","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":"licebase","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2625","integbio":"nbdc02669","miriam":"lipidmaps","n2t":"lipidmaps","ols":"lipidmaps","pathguide":"503","prefixcommons":"lipidmaps","re3data":"r3d100012315","togoid":"Lipidmaps","wikidata":"P2063"},"synonyms":["LIPID MAPS","LIPID_MAPS_class","LIPID_MAPS_instance"],"keywords":["chemical structure","classification","interaction/pathway","lipid","ontology/terminology/nomenclature","structure","taxonomy"],"domain":null,"references":null,"publications":[{"pubmed":"37855672","doi":"10.1093/nar/gkad896","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"33564392","doi":"10.12688/f1000research.28022.2","pmc":null,"arxiv":null,"title":null,"year":null},{"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"maizegdb.locus":{"prefix":"maizegdb.locus","name":"MaizeGDB Locus","description":"MaizeGDB is the maize research community's central repository for genetics and genomics information.","pattern":"^\\d+$","uri_format":"http://www.maizegdb.org/cgi-bin/displaylocusrecord.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/maizegdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.maizegdb.org/","repository":null,"contact":{"name":"Margaret R. Woodhouse","orcid":"0000-0003-2164-8300","email":"margaret.woodhouse@usda.gov","github":"margaretwoodhouse","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"25011","example_extras":[],"example_decoys":null,"license":"public-domain","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":"MAIZEGDB.LOCUS","go":"MaizeGDB_Locus","integbio":"nbdc00129","miriam":"maizegdb.locus","n2t":"maizegdb.locus","ncbi":"MaizeGDB","prefixcommons":"maizegdb","re3data":"r3d100010795","uniprot":"DB-0058"},"synonyms":["MaizeGDB"],"keywords":["bioresource","cdna/est","dna","expression","genetic variation","genome","genome/gene","image/movie","interaction/pathway","organism","organism-specific databases","portal","protein","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"34416864","doi":"10.1186/s12870-021-03173-5","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"31555312","doi":"10.3389/fpls.2019.01050","pmc":"PMC6724615","arxiv":null,"title":"MaizeDIG: Maize Database of Images and Genomes","year":2019},{"pubmed":"30407532","doi":"10.1093/nar/gky1046","pmc":"PMC6323944","arxiv":null,"title":"MaizeGDB 2018: the maize multi-genome genetics and genomics database","year":2019},{"pubmed":"26519406","doi":"10.1007/978-1-4939-3167-5_9","pmc":null,"arxiv":null,"title":"MaizeGDB: The Maize Genetics and Genomics Database","year":2016},{"pubmed":"26432828","doi":"10.1093/nar/gkv1007","pmc":"PMC4702771","arxiv":null,"title":"MaizeGDB update: new tools, data and interface for the maize model organism database","year":2015},{"pubmed":"21565781","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18769488","doi":"10.1155/2008/496957","pmc":"PMC2518694","arxiv":null,"title":"MaizeGDB: The maize model organism database for basic, translational, and applied research","year":2008},{"pubmed":"17202174","doi":"10.1093/nar/gkl1048","pmc":"PMC1899092","arxiv":null,"title":"MaizeGDB's new data types, resources and activities","year":2007},{"pubmed":"14681441","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":"maizegdb.locus","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"matrixdb":{"prefix":"matrixdb","name":"MatrixDB","description":"MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides","pattern":null,"uri_format":"http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$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/matrixdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://matrixdb.univ-lyon1.fr/","repository":null,"contact":{"name":"Sylvie Ricard-Blum","orcid":"0000-0001-9263-1851","email":"sylvie.ricard-blum@univ-lyon1.fr","github":"ricardblum","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"MULT_4_VAR1_bovine","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":{"integbio":"nbdc01222","pathguide":"298","prefixcommons":"matrixdb","re3data":"r3d100010672"},"synonyms":[],"keywords":["carbohydrate","interaction","interaction/pathway","metabolite","protein","psi-mi","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"30371822","doi":"10.1093/nar/gky1035","pmc":"PMC6324007","arxiv":null,"title":"MatrixDB: integration of new data with a focus on glycosaminoglycan interactions","year":2019},{"pubmed":"25378329","doi":"10.1093/nar/gku1091","pmc":"PMC4383919","arxiv":null,"title":"MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities","year":2014},{"pubmed":"20852260","doi":"10.1093/nar/gkq830","pmc":"PMC3013758","arxiv":null,"title":"MatrixDB, the extracellular matrix interaction database","year":2010},{"pubmed":"20213321","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"19147664","doi":"10.1093/bioinformatics/btp025","pmc":"PMC2647840","arxiv":null,"title":"MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions","year":2009}],"appears_in":["complexportal"],"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":[{"name":"Sucharitha Balu","orcid":"0000-0001-7456-0594","email":"sbalu@ebi.ac.uk","github":"CP-SB","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"matrixdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"mdm":{"prefix":"mdm","name":"Medical Data Models","description":"The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.","pattern":"^\\d+$","uri_format":"https://medical-data-models.org/forms/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://medical-data-models.org/","repository":null,"contact":{"name":"Bernd Müller","orcid":"0000-0003-3062-8192","email":"bernd.mueller@zbmed.de","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"4776","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":"MDM","miriam":"mdm","n2t":"mdm","re3data":"r3d100013816"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"26868052","doi":"10.1093/database/bav121","pmc":"PMC4750548","arxiv":null,"title":"Portal of medical data models: information infrastructure for medical research and healthcare","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":"mdm","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"metabolights":{"prefix":"metabolights","name":"MetaboLights Compound","description":"MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.","pattern":"^MTBL[CS]\\d+$","uri_format":"https://www.ebi.ac.uk/metabolights/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"omicsdi","name":"MataboLights through OmicsDI","description":"MataboLights through OmicsDI","homepage":"https://www.omicsdi.org/","contact":null,"uri_format":"https://www.omicsdi.org/dataset/metabolights_dataset/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ebi.ac.uk/metabolights/","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":"MTBLS1","example_extras":[],"example_decoys":null,"license":"Apache-2.0","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":"METABOLIGHTS","cellosaurus":"MetaboLights","integbio":"nbdc02124","miriam":"metabolights","n2t":"metabolights","re3data":"r3d100011556","wikidata":"P3890"},"synonyms":[],"keywords":["bibliography/documents","chemical structure","metabolite","method"],"domain":null,"references":null,"publications":[{"pubmed":"28830114","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"27010336","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"23683662","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"23630246","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"23109552","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"23060735","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":"metabolights","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"metacyc.compound":{"prefix":"metacyc.compound","name":"MetaCyc Compound","description":"MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.","pattern":"^[A-Za-z0-9+_.%-:]+$","uri_format":"https://metacyc.org/compound?orgid=META&id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://metacyc.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":"CPD-10330","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":"METACYC.COMPOUND","go":"MetaCyc","integbio":"nbdc00907","miriam":"metacyc.compound","n2t":"metacyc.compound","pathguide":"10","re3data":"r3d100011294"},"synonyms":["MetaCyc"],"keywords":["biopax","genome/gene","image/movie","interaction/pathway","metabolite","protein","rna","sbml"],"domain":null,"references":null,"publications":[{"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":"24225315","doi":"10.1093/nar/gkt1103","pmc":"PMC3964957","arxiv":null,"title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases","year":2013},{"pubmed":"22102576","doi":"10.1093/nar/gkr1014","pmc":"PMC3245006","arxiv":null,"title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases","year":2011},{"pubmed":"17965431","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"16381923","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"14681452","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"11752254","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"10592180","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":"metacyc.compound","mastodon":null,"github_request_issue":null,"logo":"https://metacyc.org/graphics2021/MetaCyc-logo-color.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"metlin":{"prefix":"metlin","name":"Metabolite and Tandem Mass Spectrometry Database","description":"The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.","pattern":"^\\d{4}$","uri_format":"http://metlin.scripps.edu/metabo_info.php?molid=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://masspec.scripps.edu/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02dxx6824","wikidata":null,"gnd":null,"name":"Scripps Research Institute, San Diego","partnered":false}],"example":"1455","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"biocontext":"METLIN","miriam":"metlin","n2t":"metlin","re3data":"r3d100012311"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"metlin","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"mgi":{"prefix":"mgi","name":"Mouse Genome Informatics","description":"The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.","pattern":"^\\d+$","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":"MGI","edam":"3274","go":"MGI","integbio":"nbdc00568","miriam":"mgi","n2t":"mgi","ncbi":"MGI","prefixcommons":"mgi","re3data":"r3d100010266","rrid":"MGI","uniprot":"DB-0060","wikidata":"P671"},"synonyms":["MGD","MGI"],"keywords":["animal model","blast","data analysis service","expression","function","gene","gene expression","genetics","genome","genome/gene","genotype","gold standard","human disease","human health","image","model","molecular neuroanatomy resource","ontology","organism-specific databases","orthology","pathology","pathway","phenotype","recombinase","sequence","single nucleotide polymorphism","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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"microscope":{"prefix":"microscope","name":"MicroScope","description":"MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.","pattern":"^\\d+$","uri_format":"http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.genoscope.cns.fr/agc/microscope","repository":null,"contact":{"name":"MEDIGUE Claudine","orcid":"0000-0002-3905-1054","email":"cmedigue@genoscope.cns.fr","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"5601141","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":"MICROSCOPE","miriam":"microscope","n2t":"microscope","re3data":"r3d100012928"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"23193269","doi":"10.1093/nar/gks1194","pmc":"PMC3531135","arxiv":null,"title":"MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data","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":"microscope","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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":"2615","miriam":"mint","n2t":"mint","pathguide":"17","prefixcommons":"mint","re3data":"r3d100010414","uniprot":"DB-0158"},"synonyms":[],"keywords":["interaction","protein","protein-protein interaction databases","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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"mirbase","edam":"2642","integbio":"nbdc00136","miriam":"mirbase","n2t":"mirbase","ncbi":"miRBase","pathguide":"210","prefixcommons":"mirbase","re3data":"r3d100010566","togoid":"Mirbase","wikidata":"P2870"},"synonyms":[],"keywords":["gene","ontology","rna","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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"mmrrc":{"prefix":"mmrrc","name":"Mutant Mouse Resource and Research Centers","description":"The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.","pattern":"^\\d+$","uri_format":"http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.mmrrc.org","repository":null,"contact":{"name":"Franziska B. Grieder","orcid":"0000-0002-3070-8224","email":"f.grieder@nih.gov","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02t0qr014","wikidata":null,"gnd":null,"name":"University of North Carolina","partnered":false}],"example":"70","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":"MMRRC","cellosaurus":"MMRRC","miriam":"mmrrc","n2t":"mmrrc","re3data":"r3d100013715","rrid":"MMRRC"},"synonyms":[],"keywords":["cryopreserved","database","embryonic stem cell","embryonic stem cell line","faseb list","mouse strain","mutant","mutant mouse strain","stem cell","transgenic"],"domain":null,"references":null,"publications":[{"pubmed":"12102564","doi":null,"pmc":null,"arxiv":null,"title":"Mutant Mouse Regional Resource Center Program: a resource for distribution of mouse models for biomedical research","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":"mmrrc","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2669","integbio":"nbdc02085","miriam":"modeldb","n2t":"modeldb","prefixcommons":"modeldb","re3data":"r3d100011330"},"synonyms":[],"keywords":["bibliography/documents","cell/organelle","method"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"mona":{"prefix":"mona","name":"MoNA spectrum ID","description":"identifier for spectra in the MassBank of North America database","pattern":null,"uri_format":"https://massbank.us/spectra/display/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://massbank.us","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"FiehnLib001006","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"re3data":"r3d100012318","wikidata":"P13537"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"mona","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"mycobank":{"prefix":"mycobank","name":"MycoBank","description":"MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.","pattern":"^\\d+$","uri_format":"https://www.mycobank.org/page/Name%20details%20page/$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/mycobank:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.mycobank.org/","repository":null,"contact":{"name":"Vincent Robert","orcid":"0000-0002-9370-4677","email":"vrobert@unistra.fr","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"030a5r161","wikidata":null,"gnd":null,"name":"CBS-KNAW Fungal Biodiversity Centre, Utrecht","partnered":false}],"example":"349124","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":"MYCOBANK","integbio":"nbdc01815","miriam":"mycobank","n2t":"mycobank","ncbi":"MycoBank","prefixcommons":"mycobank","re3data":"r3d100011222"},"synonyms":[],"keywords":["classification","ontology/terminology/nomenclature","organism","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"24563843","doi":"10.5598/imafungus.2013.04.02.16","pmc":"PMC3905949","arxiv":null,"title":"MycoBank gearing up for new horizons","year":2013}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Carlos Moreno","orcid":"0000-0003-0066-1717","email":"carlosm@ebi.ac.uk","github":"CarMoreno","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"mycobank","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"nasc":{"prefix":"nasc","name":"NASC code","description":"The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.","pattern":"^(\\w+)?\\d+$","uri_format":"http://arabidopsis.info/StockInfo?NASC_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/nasc:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://arabidopsis.info/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"N1899","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":"NASC","miriam":"nasc","n2t":"nasc","prefixcommons":"nasc","re3data":"r3d100010906"},"synonyms":[],"keywords":["genome"],"domain":null,"references":null,"publications":[{"pubmed":"14681484","doi":"10.1093/nar/gkh133","pmc":"PMC308867","arxiv":null,"title":"NASCArrays: a repository for microarray data generated by NASC's transcriptomics service","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":"nasc","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ncbi.assembly":{"prefix":"ncbi.assembly","name":"Assembly","description":"A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.","pattern":"^[a-zA-Z0-9_\\.]+$","uri_format":"https://www.ncbi.nlm.nih.gov/datasets/genome/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.ncbi.nlm.nih.gov/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02meqm098","wikidata":null,"gnd":null,"name":"National Center for Biotechnology Information","partnered":false}],"example":"GCF_000005845.2","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"NCBIAssembly","miriam":"assembly","re3data":"r3d100012688"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"ncbi.assembly","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ncbi.genome":{"prefix":"ncbi.genome","name":"NCBI Genome","description":"This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.","pattern":"^\\d+$","uri_format":"https://www.ncbi.nlm.nih.gov/genome/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.ncbi.nlm.nih.gov/genome","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"51","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"NCBIGenome","edam":"2787","re3data":"r3d100010785"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null},"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"ncbi.genome","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ncbigene":{"prefix":"ncbigene","name":"NCBI Gene","description":"Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.","pattern":"^\\d+$","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":"NCBIGene","edam":"1027","go":"NCBIGene","hl7":"2.16.840.1.113883.6.340","integbio":"nbdc00073","miriam":"ncbigene","n2t":"ncbigene","ncbi":"GeneID","prefixcommons":"ncbigene","re3data":"r3d100010650","togoid":"Ncbigene","uniprot":"DB-0118","wikidata":"P351"},"synonyms":["EGID","EntrezGene","GeneID","NCBIGene","NCBI_GeneID","entrez","entrez gene/locuslink","nihgeneid"],"keywords":["dna","gene","genome","genome annotation databases","genome/gene","repository","sequence"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ncbiprotein":{"prefix":"ncbiprotein","name":"NCBI Protein","description":"The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.","pattern":"^\\w+_?\\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/ncbi.protein:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.ncbi.nlm.nih.gov/protein","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":"CAA71118.1","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":"NCBIProtein","go":"NCBI_NP","integbio":"nbdc00636","miriam":"ncbiprotein","n2t":"ncbiprotein","prefixcommons":"ncbi.protein","re3data":"r3d100010776"},"synonyms":[],"keywords":["protein","repository","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":"NCBIProtein","mastodon":null,"github_request_issue":null,"logo":"https://www.ncbi.nlm.nih.gov/corehtml/logo256.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"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":"2026-05-13","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","agroportal":"TAX","bartoc":"509","biocontext":"TAXONOMY","biodivportal":"TAXON","bioportal":"NCBITAXON","cellosaurus":"NCBI_TaxID","edam":"1179","fairsharing":"FAIRsharing.fj07xj","go":"NCBITaxon","hl7":"2.16.840.1.113883.6.205","lov":"tax","miriam":"taxonomy","n2t":"taxonomy","ncbi":"taxon","obofoundry":"ncbitaxon","ols":"ncbitaxon","ontobee":"NCBITaxon","prefixcommons":"taxonomy","re3data":"r3d100010415","togoid":"Taxonomy","wikidata":"P685","wikidata.entity":"Q81661717"},"synonyms":["NCBI Taxonomy","NCBITaxon","NCBITaxonomyID","NCBI_Taxon_ID","NCBI_taxid","TAX","TaxonomyID","ncbiTaxUID","taxid","taxon","taxonomy","uniprot.taxonomy"],"keywords":["biology","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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ndex":{"prefix":"ndex","name":"Network Data Exchange","description":"The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.","pattern":null,"uri_format":"https://www.ndexbio.org/viewer/networks/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.ndexbio.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"aa78a43f-9c4d-11eb-9e72-0ac135e8bacf","example_extras":[],"example_decoys":null,"license":"BSD","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":{"re3data":"r3d100012690"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"34570431","doi":"10.1002/cpz1.258","pmc":"PMC8544027","arxiv":null,"title":"NDEx: Accessing Network Models and Streamlining Network Biology Workflows","year":2021},{"pubmed":"29092941","doi":"10.1158/0008-5472.can-17-0606","pmc":"PMC5679399","arxiv":null,"title":"NDEx 2.0: A Clearinghouse for Research on Cancer Pathways","year":2017},{"pubmed":"28150243","doi":"10.1007/978-1-4939-6783-4_13","pmc":null,"arxiv":null,"title":"NDEx: A Community Resource for Sharing and Publishing of Biological Networks","year":2017},{"pubmed":"26594663","doi":"10.1016/j.cels.2015.10.001","pmc":"PMC4649937","arxiv":null,"title":"NDEx, the Network Data Exchange","year":2015}],"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":"ndex","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"nmrshiftdb2":{"prefix":"nmrshiftdb2","name":"NMRShiftDB structure","description":"NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties.","pattern":"^[0-9]+$","uri_format":"https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://nmrshiftdb.nmr.uni-koeln.de","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"00rcxh774","wikidata":null,"gnd":null,"name":"University of Cologne","partnered":false}],"example":"234","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":{"miriam":"nmrshiftdb2","re3data":"r3d100010316","wikidata":"P9405"},"synonyms":["NMRShiftDB"],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"25998807","doi":"10.1002/mrc.4263","pmc":null,"arxiv":null,"title":"Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories","year":2015},{"pubmed":"15464159","doi":"10.1016/j.phytochem.2004.08.027","pmc":null,"arxiv":null,"title":"NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database","year":2004},{"pubmed":"14632418","doi":"10.1021/ci0341363","pmc":null,"arxiv":null,"title":"NMRShiftDB-constructing a free chemical information system with open-source components","year":2003}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":[{"name":"Benjamin M. Gyori","orcid":"0000-0001-9439-5346","email":"b.gyori@northeastern.edu","github":"bgyori","wikidata":null}],"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"nmrshiftdb2","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"odc.sci":{"prefix":"odc.sci","name":"Open Data Commons for Spinal Cord Injury","description":"The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.","pattern":"^[0-9]*$","uri_format":"https://odc-sci.org/data/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://odc-sci.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0168r3w48","wikidata":null,"gnd":null,"name":"University of California, San Diego","partnered":false}],"example":"602","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":{"miriam":"odc.sci","re3data":"r3d100014071"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"31608767","doi":"10.1089/neu.2019.6674","pmc":"PMC7071068","arxiv":null,"title":"FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research","year":2019},{"pubmed":"28576567","doi":"10.1016/j.expneurol.2017.05.012","pmc":"PMC6448396","arxiv":null,"title":"Developing a data sharing community for spinal cord injury research","year":2017},{"pubmed":"26466022","doi":"10.1038/ncomms9581","pmc":"PMC4634208","arxiv":null,"title":"Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury","year":2015},{"pubmed":"25349910","doi":"10.1038/nn.3838","pmc":"PMC4728080","arxiv":null,"title":"Big data from small data: data-sharing in the 'long tail' of neuroscience","year":2014},{"pubmed":"25077610","doi":"10.1089/neu.2014.3399","pmc":"PMC4186058","arxiv":null,"title":"Development of a database for translational spinal cord injury research","year":2014},{"pubmed":"23544088","doi":"10.1371/journal.pone.0059712","pmc":"PMC3609747","arxiv":null,"title":"Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats","year":2013},{"pubmed":"22207883","doi":"10.1007/s12975-011-0121-1","pmc":"PMC3236294","arxiv":null,"title":"Syndromics: a bioinformatics approach for neurotrauma research","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":"odc.sci","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"pandit":{"prefix":"pandit","name":"Protein and Associated NucleotideDomains with Inferred Trees","description":"PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.","pattern":null,"uri_format":"http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$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/pandit:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.ebi.ac.uk/goldman-srv/pandit","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":"PF00004","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":"pfam","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":{"integbio":"nbdc00607","prefixcommons":"pandit","re3data":"r3d100011232"},"synonyms":[],"keywords":["classification","dna","protein","sequence","structure"],"domain":null,"references":null,"publications":[{"pubmed":"16381879","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":{"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":"pandit","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"pathwaycommons":{"prefix":"pathwaycommons","name":"Pathway Commons","description":"Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.","pattern":"^\\d+$","uri_format":"http://www.pathwaycommons.org/pc/record2.do?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/pathwaycommons:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.pathwaycommons.org/pc/","repository":null,"contact":{"name":"Chris Sander","orcid":"0000-0001-6059-6270","email":"chris@sanderlab.org","github":"sanderlab","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02yrq0923","wikidata":null,"gnd":null,"name":"Memorial Sloan Kettering Cancer Center","partnered":false}],"example":"485991","example_extras":[],"example_decoys":null,"license":"http://www.pathwaycommons.org/pc/about.do","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":"PATHWAYCOMMONS","miriam":"pathwaycommons","n2t":"pathwaycommons","prefixcommons":"pathwaycommons","re3data":"r3d100012731","uniprot":"DB-0253"},"synonyms":[],"keywords":["enzyme and pathway databases","pathway"],"domain":null,"references":null,"publications":[{"pubmed":"31647099","doi":"10.1093/nar/gkz946/5606621","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"21071392","doi":"10.1093/nar/gkq1039","pmc":"PMC3013659","arxiv":null,"title":"Pathway Commons, a web resource for biological pathway data","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":"pathwaycommons","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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":"1127","go":"PDB","integbio":"nbdc00613","miriam":"pdb","n2t":"pdb","ncbi":"PDB","pathguide":"398","prefixcommons":"pdbj","re3data":"r3d100010910","togoid":"Pdb","uniprot":"DB-0172","wikidata":"P638"},"synonyms":["RCSB_PDB","pdbe","pdbj","wwpdb"],"keywords":["3d structure","3d structure databases","dna","image/movie","protein","repository","rna","structure"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2626","integbio":"nbdc01812","miriam":"peptideatlas","n2t":"peptideatlas","prefixcommons":"peptideatlas","re3data":"r3d100010889","uniprot":"DB-0071"},"synonyms":["peptideatlas"],"keywords":["mass spectrometry","protein","proteomic databases","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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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":"1138","go":"Pfam","integbio":"nbdc00163","miriam":"pfam","n2t":"pfam","ncbi":"PFAM","prefixcommons":"pfam","re3data":"r3d100012850","togoid":"Pfam","uniprot":"DB-0073","wikidata":"P3519"},"synonyms":["PF"],"keywords":["classification","domain","family and domain databases","ontology","protein","sequence"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"pgx":{"prefix":"pgx","name":"Progenetix","description":"The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs.","pattern":"^\\w{3,15}[-_]\\w[\\w.-]{3,128}$","uri_format":"https://progenetix.org/services/ids/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://progenetix.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02crff812","wikidata":null,"gnd":null,"name":"University of Zurich","partnered":false}],"example":"pgxbs-kftva5zv","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":"PGX","cellosaurus":"Progenetix","miriam":"pgx","n2t":"pgx","re3data":"r3d100012820"},"synonyms":["Progenetix"],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"25428357","doi":"10.1093/nar/gku1123","pmc":"PMC4383937","arxiv":null,"title":"arrayMap 2014: an updated cancer genome resource","year":2014},{"pubmed":"24476156","doi":"10.1186/1471-2164-15-82","pmc":"PMC3909908","arxiv":null,"title":"Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens","year":2014},{"pubmed":"24225322","doi":"10.1093/nar/gkt1108","pmc":"PMC3965091","arxiv":null,"title":"Progenetix: 12 years of oncogenomic data curation","year":2013},{"pubmed":"22629346","doi":"10.1371/journal.pone.0036944","pmc":"PMC3356349","arxiv":null,"title":"arrayMap: a reference resource for genomic copy number imbalances in human malignancies","year":2012},{"pubmed":"18088415","doi":"10.1186/1471-2407-7-226","pmc":"PMC2225423","arxiv":null,"title":"Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data","year":2007},{"pubmed":"16568815","doi":"10.2144/000112102","pmc":null,"arxiv":null,"title":"Online database and bioinformatics toolbox to support data mining in cancer cytogenetics","year":2006},{"pubmed":"11751233","doi":"10.1093/bioinformatics/17.12.1228","pmc":null,"arxiv":null,"title":"Progenetix.net: an online repository for molecular cytogenetic aberration data","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":"pgx","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"phagedive":{"prefix":"phagedive","name":"PhageDive","description":"PhageDive is a database for bacteriophages and archaeal viruses. It provides information regarding taxonomy, host strain, phage morphology, life cycle, origin and genomic data.","pattern":"^\\d+$","uri_format":"https://phagedive.dsmz.de/strain/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://phagedive.dsmz.de","repository":null,"contact":{"name":"Johannes Wittmann","orcid":"0000-0002-7275-9927","email":"johannes.wittmann@dsmz.de","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"3","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":{"re3data":"r3d100014540"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"39373542","doi":"10.1093/nar/gkae878","pmc":"PMC11701545","arxiv":null,"title":"PhageDive: the comprehensive strain database of prokaryotic viral diversity","year":2025}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Mufaddal Naguthanawala","orcid":"0009-0009-5240-7463","email":"m.naguthana@hotmail.com","github":"nagutm","wikidata":null},"contributor_extras":null,"reviewer":{"name":"Benjamin M. Gyori","orcid":"0000-0001-9439-5346","email":"b.gyori@northeastern.edu","github":"bgyori","wikidata":null},"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"phagedive","mastodon":null,"github_request_issue":1454,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2649","pathguide":"117","prefixcommons":"pharmgkb","re3data":"r3d100012325","wikidata":"P7001"},"synonyms":[],"keywords":["biopax","classification","gene","gene expression","pathway"],"domain":null,"references":null,"publications":[{"pubmed":"22103613","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"11908751","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":"pharmgkb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"phenolexplorer":{"prefix":"phenolexplorer","name":"Phenol-Explorer","description":"Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.","pattern":"^\\d+$","uri_format":"http://phenol-explorer.eu/foods/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.phenol-explorer.eu/foods/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"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":"PHENOLEXPLORER","miriam":"phenolexplorer","n2t":"phenolexplorer","re3data":"r3d100012197"},"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":"phenolexplorer","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"planttfdb":{"prefix":"planttfdb","name":"Plant Transcription Factor Database","description":"The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.","pattern":"^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$","uri_format":"http://planttfdb.cbi.pku.edu.cn/tf.php?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/planttfdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://planttfdb.cbi.pku.edu.cn","repository":null,"contact":{"name":"Ge Gao","orcid":"0000-0001-6470-8815","email":"gaog@mail.cbi.pku.edu.cn","github":"gao-ge","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02v51f717","wikidata":null,"gnd":null,"name":"Peking University","partnered":false}],"example":"Ath_AT1G01030.1","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":"PLANTTFDB","miriam":"planttfdb","n2t":"planttfdb","pathguide":"497","prefixcommons":"planttfdb","re3data":"r3d100011301"},"synonyms":[],"keywords":["dna","gene","protein","regulation","rna","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"27924042","doi":"10.1093/nar/gkw982","pmc":"PMC5210657","arxiv":null,"title":"PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants","year":2016},{"pubmed":"25750178","doi":"10.1093/molbev/msv058","pmc":"PMC4476157","arxiv":null,"title":"An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors","year":2015},{"pubmed":"24174544","doi":"10.1093/nar/gkt1016","pmc":"PMC3965000","arxiv":null,"title":"PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors","year":2013}],"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":"planttfdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"plasmodb":{"prefix":"plasmodb","name":"PlasmoDB","description":"AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","pattern":"^\\w+$","uri_format":"http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_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/plasmodb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://plasmodb.org/plasmo/","repository":null,"contact":{"name":"Omar S. Harb","orcid":"0000-0003-4446-6200","email":"oharb@upenn.edu","github":"ramobrah","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"PF11_0344","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":"PLASMODB","go":"PlasmoDB","integbio":"nbdc01783","miriam":"plasmodb","n2t":"plasmodb","ncbi":"ApiDB_PlasmoDB","pathguide":"514","prefixcommons":"plasmodb","re3data":"r3d100011569"},"synonyms":["ApiDB_PlasmoDB"],"keywords":["cdna/est","expression","genome","genome/gene","health/disease","ontology/terminology/nomenclature","organism","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"18957442","doi":"10.1093/nar/gkn814","pmc":"PMC2686598","arxiv":null,"title":"PlasmoDB: a functional genomic database for malaria parasites","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":"plasmodb","mastodon":null,"github_request_issue":null,"logo":"https://sites.psu.edu/llinaslab/files/2020/05/plasmodb_logogif-e1590176740521.jpg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"pombase":{"prefix":"pombase","name":"PomBase","description":"PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets.","pattern":"^S\\w+(\\.)?\\w+(\\.)?$","uri_format":"https://www.pombase.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/pombase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.pombase.org/","repository":null,"contact":{"name":"Valerie Wood","orcid":"0000-0001-6330-7526","email":"vw253@cam.ac.uk","github":"ValWood","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"SPCC13B11.01","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/pombase/pombase.owl","download_obo":"https://w3id.org/biopragmatics/resources/pombase/pombase.obo","download_json":"https://w3id.org/biopragmatics/resources/pombase/pombase.json","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"PomBase","biolink":"PomBase","go":"PomBase","integbio":"nbdc00332","miriam":"pombase","n2t":"pombase","ncbi":"PomBase","prefixcommons":"pombase","re3data":"r3d100011478","uniprot":"DB-0031","wikidata":"P6245"},"synonyms":["PomBase"],"keywords":["genome/gene","ontology","organism-specific databases","repository","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"38376816","doi":"10.1093/genetics/iyae007","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"30321395","doi":"10.1093/nar/gky961","pmc":"PMC6324063","arxiv":null,"title":"PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information","year":2019},{"pubmed":"27334346","doi":"10.1186/s12915-016-0276-z","pmc":"PMC4918006","arxiv":null,"title":"Model organism databases: essential resources that need the support of both funders and users","year":2016},{"pubmed":"25361970","doi":"10.1093/nar/gku1040","pmc":"PMC4383888","arxiv":null,"title":"PomBase 2015: updates to the fission yeast database","year":2014},{"pubmed":"24885854","doi":"10.1186/1471-2105-15-155","pmc":"PMC4039540","arxiv":null,"title":"A method for increasing expressivity of Gene Ontology annotations using a compositional approach","year":2014},{"pubmed":"24574118","doi":"10.1093/bioinformatics/btu103","pmc":"PMC4058955","arxiv":null,"title":"Canto: an online tool for community literature curation","year":2014},{"pubmed":"23658422","doi":"10.1093/bioinformatics/btt266","pmc":"PMC3694669","arxiv":null,"title":"FYPO: the fission yeast phenotype 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":"22039153","doi":"10.1093/nar/gkr853","pmc":"PMC3245111","arxiv":null,"title":"PomBase: a comprehensive online resource for fission yeast","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":"pombase","mastodon":null,"github_request_issue":null,"logo":"https://www.pombase.org/assets/pombase-logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"pride":{"prefix":"pride","name":"Proteomics Identification Database Ontology","description":"The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays.","pattern":"^\\d{7}$","uri_format":"http://purl.obolibrary.org/obo/PRIDE_$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/pride:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://github.com/PRIDE-Utilities/pride-ontology","repository":"https://github.com/PRIDE-Utilities/pride-ontology","contact":{"name":"Yasset Perez-Riverol","orcid":"0000-0001-6579-6941","email":"yperez@ebi.ac.uk","github":"ypriverol","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":"0000006","example_extras":[],"example_decoys":null,"license":"http://www.ebi.ac.uk/Information/termsofuse.html","version":"2026-06-01","part_of":null,"part_of_database":null,"provides":null,"download_owl":"https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.owl","download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":true,"mappings":{"aberowl":"PRIDE","biocontext":"PRIDE","integbio":"nbdc00312","miriam":"pride","n2t":"pride","ols":"pride","prefixcommons":"pride","re3data":"r3d100010137","uniprot":"DB-0130"},"synonyms":[],"keywords":["ontology","protein","proteomic databases","repository"],"domain":null,"references":null,"publications":[{"pubmed":"39494541","doi":"10.1093/nar/gkae1011","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"34723319","doi":"10.1093/nar/gkab1038","pmc":"PMC8728295","arxiv":null,"title":"The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences","year":2022},{"pubmed":"30395289","doi":"10.1093/nar/gky1106","pmc":"PMC6323896","arxiv":null,"title":"The PRIDE database and related tools and resources in 2019: improving support for quantification data","year":2019},{"pubmed":"26527722","doi":"10.1093/nar/gkv1145","pmc":"PMC4702828","arxiv":null,"title":"2016 update of the PRIDE database and its related tools","year":2015},{"pubmed":"25047258","doi":"10.1002/pmic.201400120","pmc":null,"arxiv":null,"title":"How to submit MS proteomics data to ProteomeXchange via the PRIDE database","year":2014},{"pubmed":"24727771","doi":"10.1038/nbt.2839","pmc":"PMC3986813","arxiv":null,"title":"ProteomeXchange provides globally coordinated proteomics data submission and dissemination","year":2014},{"pubmed":"23203882","doi":"10.1093/nar/gks1262","pmc":"PMC3531176","arxiv":null,"title":"The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013","year":2012},{"pubmed":"19906717","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"18428683","doi":"10.1002/0471250953.bi1308s21","pmc":null,"arxiv":null,"title":"Using the Proteomics Identifications Database (PRIDE)","year":2008},{"pubmed":"18033805","doi":"10.1093/nar/gkm1021","pmc":"PMC2238846","arxiv":null,"title":"PRIDE: new developments and new datasets","year":2007},{"pubmed":"16381953","doi":"10.1093/nar/gkj138","pmc":"PMC1347500","arxiv":null,"title":"PRIDE: a public repository of protein and peptide identifications for the proteomics community","year":2006},{"pubmed":"16041671","doi":"10.1002/pmic.200401303","pmc":null,"arxiv":null,"title":"PRIDE: the proteomics identifications database","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":"pride","mastodon":null,"github_request_issue":null,"logo":"https://www.proteomexchange.org/pride_logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"CID","cellosaurus":"PubChem","cheminf":"000140","edam":"2639","go":"PubChem_Compound","integbio":"nbdc02626","miriam":"pubchem.compound","n2t":"pubchem.compound","prefixcommons":"pubchem.compound","re3data":"r3d100010129","togoid":"PubchemCompound","wikidata":"P662"},"synonyms":["CID","DSSTox_CID","PUBCHEM_CID","PubChem_Compound_CID","Pubchem","pubchem_id"],"keywords":["bibliography/documents","chemical","chemical compound","chemical structure","compound","metabolite","method","protein","repository","structure"],"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}],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"1155","go":"Reactome","integbio":"nbdc00185","miriam":"reactome","n2t":"reactome","pathguide":"103","prefixcommons":"reactome","re3data":"r3d100010861","togoid":"ReactomePathway","wikidata":"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2325","go":"REBASE","integbio":"nbdc00648","miriam":"rebase","n2t":"rebase","pathguide":"72","prefixcommons":"rebase","re3data":"r3d100012171","uniprot":"DB-0089","wikidata":"P4866"},"synonyms":[],"keywords":["bioresource","dna","enzyme","genome","protein","protein family/group databases","repository","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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"1098","go":"RefSeq","hl7":"2.16.840.1.113883.6.280","integbio":"nbdc00187","miriam":"refseq","n2t":"refseq","prefixcommons":"refseq","re3data":"r3d100010285","uniprot":"DB-0117"},"synonyms":["REFSEQ_PROT"],"keywords":["cdna/est","cell/organelle","dna","genome/gene","protein","rna","sequence","sequence databases"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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":"RGD","edam":"2620","go":"RGD","integbio":"nbdc00188","miriam":"rgd","n2t":"rgd","ncbi":"RGD","pathguide":"267","prefixcommons":"rgd","re3data":"r3d100010417","rrid":"RGD","togoid":"Rgd","uniprot":"DB-0091","wikidata":"P3853"},"synonyms":["RGD"],"keywords":["behavior","bioresource","comparative genomics","congenic rat","data analysis service","disease","dna","est","faseb list","function","gene","genetic","genetic variation","genome","genome/gene","genomic","genotype","gold standard","health/disease","human","immunology","inbred rat strain","interaction/pathway","knockout","map","marker","model organism","mouse","mutant","ontology","ontology/terminology/nomenclature","organism","organism supplier","organism-specific databases","pathway","phenotype","physiology","proteomics","qtl","rat","recombinant inbred rat","repository","sequence","strain","variation"],"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}],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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/rhea:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.rhea-db.org/","repository":null,"contact":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":"2644","go":"RHEA","integbio":"nbdc02083","miriam":"rhea","n2t":"rhea","pathguide":"310","prefixcommons":"rhea","re3data":"r3d100010891","togoid":"Rhea","wikidata.entity":"Q24265951"},"synonyms":["RHEA"],"keywords":["biopax","interaction/pathway","metabolite","ontology","protein","reaction","small molecule"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2309","miriam":"sabiork.reaction","n2t":"sabiork.reaction","pathguide":"226","prefixcommons":"sabiork.reaction","re3data":"r3d100011052","uniprot":"DB-0177"},"synonyms":["SABIO-RK"],"keywords":["biopax","enzyme and pathway databases","kinetics","pathway","reaction","sbml"],"domain":null,"references":null,"publications":[{"pubmed":"29092055","doi":"10.1093/nar/gkx1065","pmc":null,"arxiv":null,"title":null,"year":null},{"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":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"sasbdb":{"prefix":"sasbdb","name":"Small Angle Scattering Biological Data Bank","description":"Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.","pattern":"^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$","uri_format":"http://www.sasbdb.org/data/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.sasbdb.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"050589e39","wikidata":null,"gnd":null,"name":"European Molecular Biology Lab Hamburg Outstation","partnered":false}],"example":"SASDAX8","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":"SASBDB","miriam":"sasbdb","n2t":"sasbdb","re3data":"r3d100012273","uniprot":"DB-0258"},"synonyms":[],"keywords":["3d structure databases"],"domain":null,"references":null,"publications":[{"pubmed":"31576635","doi":"10.1002/pro.3731","pmc":"PMC6933840","arxiv":null,"title":"SASBDB: Towards an automatically curated and validated repository for biological scattering data","year":2019},{"pubmed":"25352555","doi":"10.1093/nar/gku1047","pmc":"PMC4383894","arxiv":null,"title":"SASBDB, a repository for biological small-angle scattering data","year":2014}],"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":"sasbdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"sciflection":{"prefix":"sciflection","name":"Sciflection","description":"Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions","pattern":"^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$","uri_format":"https://sciflection.com/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://sciformation.com/sciflection.html","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"5ede4273-b26c-4ea4-adb7-3ce294ab3397","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"miriam":"sciflection","re3data":"r3d100013413"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"sciflection","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"sgd":{"prefix":"sgd","name":"Saccharomyces Genome Database","description":"The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.","pattern":"^((S\\d+$)|(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":"2632","go":"SGD","integbio":"nbdc00202","miriam":"sgd","n2t":"sgd","ncbi":"SGD","prefixcommons":"sgd","re3data":"r3d100010419","togoid":"Sgd","uniprot":"DB-0095","wikidata":"P3406"},"synonyms":[],"keywords":["bibliography/documents","bioresource","eukaryotic","expression","gene","genome","genome/gene","image/movie","interaction/pathway","nucleotide","ontology","ontology/terminology/nomenclature","organism","organism-specific databases","protein","rna","sequence"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"sgn":{"prefix":"sgn","name":"Sol Genomics Network","description":"The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.","pattern":"^\\d+$","uri_format":"http://solgenomics.net/phenome/locus_display.pl?locus_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/sgn:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://solgenomics.net/","repository":null,"contact":{"name":"Lukas A. Mueller","orcid":"0000-0001-8640-1750","email":"lam87@cornell.edu","github":"lukasmueller","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"0001","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":"SGN","go":"SGN","integbio":"nbdc02414","miriam":"sgn","n2t":"sgn","ncbi":"SGN","pathguide":"433","prefixcommons":"sgn","re3data":"r3d100012078"},"synonyms":[],"keywords":["cdna/est","expression","genome","genome/gene","method","pathway","phenotype","plant","repository","sequence","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"25428362","doi":"10.1093/nar/gku1195","pmc":"PMC4383978","arxiv":null,"title":"The Sol Genomics Network (SGN)--from genotype to phenotype to breeding","year":2014},{"pubmed":"20935049","doi":"10.1093/nar/gkq866","pmc":"PMC3013765","arxiv":null,"title":"The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl","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":"sgn","mastodon":null,"github_request_issue":null,"logo":"https://solgenomics.net/documents/img/sgn_transparent_logo.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"slm":{"prefix":"slm","name":"SwissLipid","description":"SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.","pattern":"^\\d+$","uri_format":"https://www.swisslipids.org/#/entity/SLM:$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.swisslipids.org/#/","repository":null,"contact":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":"000000341","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/slm/slm.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/slm/slm.obo.gz","download_json":"https://w3id.org/biopragmatics/resources/slm/slm.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":"SLM","banana_peel":null,"deprecated":false,"mappings":{"biocontext":"SWISSLIPID","integbio":"nbdc02026","miriam":"slm","n2t":"swisslipid","ols":"slm","pathguide":"687","re3data":"r3d100012603","togoid":"Swisslipids","uniprot":"DB-0197","wikidata":"P8691"},"synonyms":["swisslipid","swisslipids"],"keywords":["chemical structure","chemistry databases","interaction/pathway","lipid","ontology","protein"],"domain":null,"references":null,"publications":[{"pubmed":"25943471","doi":"10.1093/bioinformatics/btv285","pmc":"PMC4547616","arxiv":null,"title":"The SwissLipids knowledgebase for lipid biology","year":2015}],"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":"SLM","mastodon":null,"github_request_issue":null,"logo":"https://www.swisslipids.org/images/SL_title_swiss.png","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"soybase":{"prefix":"soybase","name":"SoyBase","description":"SoyBase is a repository for curated genetics, genomics and related data resources for soybean.","pattern":"^\\w+(\\-)?\\w+(\\-)?\\w+$","uri_format":"https://legacy.soybase.org/sbt/search/search_results.php?category=SNP&search_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/soy:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://soybase.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"BARC-013845-01256","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":"SOYBASE","integbio":"nbdc01817","miriam":"soybase","n2t":"soybase","ncbi":"SoyBase","pathguide":"44","prefixcommons":"soy","re3data":"r3d100010846"},"synonyms":[],"keywords":["development","dna","expression","genetic variation","genome/gene","image/movie","interaction/pathway","method","obo","ontology/terminology/nomenclature","organism","phenotype","protein","sequence","spider"],"domain":null,"references":null,"publications":[{"pubmed":"20008513","doi":"10.1093/nar/gkp798","pmc":"PMC2808871","arxiv":null,"title":"SoyBase, the USDA-ARS soybean genetics and genomics 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":"soybase","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"spp":{"prefix":"spp","name":"Signaling Pathways Project","description":"The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways.","pattern":"^10.\\w{4}/\\w{10}$","uri_format":"https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.signalingpathways.org/index.jsf","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"02pttbw34","wikidata":null,"gnd":null,"name":"Baylor College of Medicine","partnered":false}],"example":"10.1621/vwN2g2HaX3","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":{"miriam":"spp","re3data":"r3d100013650"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"31672983","doi":"10.1038/s41597-019-0193-4","pmc":"PMC6823428","arxiv":null,"title":"The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways","year":2019}],"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":"spp","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"stitch":{"prefix":"stitch","name":"Search Tool for Interactions of Chemicals","description":"STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.","pattern":"^\\w{14}$","uri_format":"http://stitch.embl.de/interactions/$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/stitch:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://stitch.embl.de/","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":"BQJCRHHNABKAKU","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":"STITCH","miriam":"stitch","n2t":"stitch","pathguide":"313","prefixcommons":"stitch","re3data":"r3d100012165"},"synonyms":[],"keywords":["interaction","protein","small molecule"],"domain":null,"references":null,"publications":[{"pubmed":"24293645","doi":"10.1093/nar/gkt1207","pmc":"PMC3964996","arxiv":null,"title":"STITCH 4: integration of protein-chemical interactions with user data","year":2013},{"pubmed":"22075997","doi":"10.1093/nar/gkr1011","pmc":"PMC3245073","arxiv":null,"title":"STITCH 3: zooming in on protein-chemical interactions","year":2011},{"pubmed":"19897548","doi":"10.1093/nar/gkp937","pmc":"PMC2808890","arxiv":null,"title":"STITCH 2: an interaction network database for small molecules and proteins","year":2009},{"pubmed":"18084021","doi":"10.1093/nar/gkm795","pmc":"PMC2238848","arxiv":null,"title":"STITCH: interaction networks of chemicals and proteins","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":"stitch","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"storedb":{"prefix":"storedb","name":"Store DB","description":"STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.","pattern":"^(STUDY|FILE|DATASET)\\d+$","uri_format":"https://www.storedb.org/?$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.storedb.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"STUDY1040","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":"STOREDB","banana_peel":null,"deprecated":false,"mappings":{"biocontext":"STOREDB","integbio":"nbdc02191","miriam":"storedb","n2t":"storedb","re3data":"r3d100011049"},"synonyms":[],"keywords":["bibliography/documents","expression","genetic variation","genome/gene","health/disease","method","organism","repository"],"domain":null,"references":null,"publications":[],"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":"storedb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"strenda":{"prefix":"strenda","name":"Standards for Reporting Enzymology Data","description":"STRENDA stands for “Standards for Reporting Enzymology Data”. For researchers it is essential to be able to compare, evaluate, interpret and reproduce experimental research results published in the literature and databases. Thus, for enzyme research, the STRENDA Commission has established standards for data reporting with the aim to improve the quality of data published in the scientific literature. [from homepage]","pattern":null,"uri_format":"https://beilstein-strenda-db.org/strenda/public/doiQuery.xhtml?doi=10.22011/strenda_db.$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.beilstein-institut.de/en/projects/strenda/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"KTRCXF","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":{"integbio":"nbdc02138","re3data":"r3d100012329","uniprot":"DB-0278"},"synonyms":["strendadb"],"keywords":["bibliography/documents","enzyme and pathway databases","method","protein"],"domain":null,"references":null,"publications":[{"pubmed":"29498804","doi":"10.1111/febs.14427","pmc":null,"arxiv":null,"title":null,"year":null}],"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":"strenda","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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":"2302","integbio":"nbdc00690","miriam":"string","n2t":"string","pathguide":"93","prefixcommons":"string","re3data":"r3d100010604","uniprot":"DB-0141"},"synonyms":[],"keywords":["classification","interaction","interaction/pathway","protein","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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"surechembl":{"prefix":"surechembl","name":"SureChEMBL ID","description":"the chemical compound identifier for the EBI SureChEMBL 'chemical compounds in patents' database","pattern":"^\\d+$","uri_format":"https://www.surechembl.org/chemical/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://www.surechembl.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"17951640","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"re3data":"r3d100011037","wikidata":"P2877"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"surechembl","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"swiss-model":{"prefix":"swiss-model","name":"SWISS-MODEL Repository","description":"The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences.","pattern":"^\\w+$","uri_format":"https://swissmodel.expasy.org/repository/uniprot/$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/swissmodel:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://swissmodel.expasy.org","repository":null,"contact":{"name":"Torsten Schwede","orcid":"0000-0003-2715-335X","email":"torsten.schwede@unibas.ch","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"P23298","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":"SWISS-MODEL","miriam":"swiss-model","n2t":"swiss-model","prefixcommons":"swissmodel","re3data":"r3d100010605"},"synonyms":[],"keywords":["protein","structure"],"domain":null,"references":null,"publications":[{"pubmed":"27899672","doi":"10.1093/nar/gkw1132","pmc":"PMC5210589","arxiv":null,"title":"The SWISS-MODEL Repository-new features and functionality","year":2016},{"pubmed":"24782522","doi":"10.1093/nar/gku340","pmc":"PMC4086089","arxiv":null,"title":"SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information","year":2014},{"pubmed":"18931379","doi":"10.1093/nar/gkn750","pmc":"PMC2686475","arxiv":null,"title":"The SWISS-MODEL Repository and associated resources","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":"swiss-model","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"synapse":{"prefix":"synapse","name":"Synapse Data Repository","description":"Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.","pattern":"^[0-9]*\\.*[0-9]*$","uri_format":"https://www.synapse.org/Synapse:syn$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://sagebionetworks.org","repository":null,"contact":{"name":"Kevin Boske","orcid":"0000-0002-3278-5207","email":"kevin.boske@sagebase.org","github":"kevinboske","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"049ncjx51","wikidata":null,"gnd":null,"name":"Sage Bionetworks","partnered":false}],"example":"41455251.1","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":{"integbio":"nbdc02162","miriam":"synapse","re3data":"r3d100011894","wikidata.entity":"Q56328412"},"synonyms":["syn"],"keywords":["bibliography/documents","method","repository"],"domain":null,"references":null,"publications":[{"pubmed":"24071850","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":"synapse","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":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":"2662","miriam":"t3db","n2t":"t3db","pathguide":"326","prefixcommons":"t3db","re3data":"r3d100012189"},"synonyms":[],"keywords":["molecule","protein"],"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":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"topfind":{"prefix":"topfind","name":"TopFind","description":"TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.","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])$","uri_format":"http://clipserve.clip.ubc.ca/topfind/proteins/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://topfind.clip.msl.ubc.ca","repository":null,"contact":{"name":"Christopher M. Overall","orcid":"0000-0001-5844-2731","email":"chris.overall@ubc.ca","github":null,"wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"Q9UKQ2","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":"TOPFIND","miriam":"topfind","n2t":"topfind","re3data":"r3d100012721"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"25332401","doi":"10.1093/nar/gku1012","pmc":"PMC4383881","arxiv":null,"title":"Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events","year":2014},{"pubmed":"22102574","doi":"10.1093/nar/gkr1025","pmc":"PMC3244998","arxiv":null,"title":"TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function","year":2011},{"pubmed":"21822272","doi":"10.1038/nmeth.1669","pmc":null,"arxiv":null,"title":"TopFIND, a knowledgebase linking protein termini with function","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":"topfind","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"treebase":{"prefix":"treebase","name":"TreeBASE","description":"TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.","pattern":"^TB[1,2]?:[A-Z][a-z]?\\d+$","uri_format":"http://purl.org/phylo/treebase/phylows/study/$1?format=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/treebase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://treebase.org/","repository":null,"contact":{"name":"Rutger Vos","orcid":"0000-0001-9254-7318","email":"rutgeraldo@gmail.com","github":"rvosa","wikidata":null},"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"TB2:S1000","example_extras":[],"example_decoys":null,"license":"BSD-3-Clause","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":"TREEBASE","integbio":"nbdc01882","miriam":"treebase","n2t":"treebase","prefixcommons":"treebase","re3data":"r3d100010170"},"synonyms":[],"keywords":["classification","organism","sequence","taxonomy"],"domain":null,"references":null,"publications":[{"pubmed":"19426482","doi":"10.1186/1471-2148-9-93","pmc":"PMC2685121","arxiv":null,"title":"Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment","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":"treebase","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"trichdb":{"prefix":"trichdb","name":"TrichDB","description":"TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","pattern":"^\\w+$","uri_format":"http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://trichdb.org/trichdb/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"TVAG_386080","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":"TRICHDB","integbio":"nbdc01785","miriam":"trichdb","n2t":"trichdb","re3data":"r3d100012461"},"synonyms":[],"keywords":["cdna/est","expression","genome/gene","health/disease","ontology/terminology/nomenclature","organism","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"18824479","doi":"10.1093/nar/gkn631","pmc":"PMC2686445","arxiv":null,"title":"GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis","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":"trichdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"tritrypdb":{"prefix":"tritrypdb","name":"TriTrypDB","description":"TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.","pattern":"^\\w+(\\.)?\\w+(\\.)?\\w+$","uri_format":"http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://tritrypdb.org/tritrypdb/","repository":null,"contact":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":"Tb927.8.620","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":"TRITRYPDB","go":"TriTrypDB","integbio":"nbdc01786","miriam":"tritrypdb","n2t":"tritrypdb","re3data":"r3d100011479"},"synonyms":[],"keywords":["cdna/est","expression","genome/gene","health/disease","ontology/terminology/nomenclature","organism","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"19843604","doi":"10.1093/nar/gkp851","pmc":"PMC2808979","arxiv":null,"title":"TriTrypDB: a functional genomic resource for the Trypanosomatidae","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":"tritrypdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"unigene":{"prefix":"unigene","name":"UniGene","description":"A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.","pattern":"^\\d+$","uri_format":"http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$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/unigene:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.ncbi.nlm.nih.gov/unigene","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":"4900","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":"UNIGENE","integbio":"nbdc00220","miriam":"unigene","n2t":"unigene","prefixcommons":"unigene","re3data":"r3d100010774"},"synonyms":[],"keywords":["cdna/est","dna","expression","gene","gene expression","protein","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"8849440","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"7670480","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"12519941","doi":"10.1093/nar/gkg033","pmc":"PMC165480","arxiv":null,"title":"Database resources of the National Center for Biotechnology","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":"unigene","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2392","go":"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?(-\\d+)?(#PRO_\\d+)?$","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":[],"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/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":{"aberowl":"UP","biocontext":"UniProtKB","biolink":"UniProtKB","cellosaurus":"UniProtKB","edam":"3021","fairsharing":"FAIRsharing.wf28wm","go":"UniProtKB","integbio":"nbdc00221","miriam":"uniprot","n2t":"uniprot","ncbi":"UniProt","prefixcommons":"uniprot","re3data":"r3d100011521","togoid":"Uniprot","wikidata":"P352"},"synonyms":["SwissProt","UP","UniProt","UniProtKB","Uniprot ID","uniprot/swiss-prot"],"keywords":["biology","ontology","protein","repository","sequence","taxonomic classification"],"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":"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2346","miriam":"uniref","prefixcommons":"uniref","re3data":"r3d100011518"},"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":"uniref","mastodon":null,"github_request_issue":null,"logo":"https://www.uniprot.org/uniprot-logo.img.0df091.svg","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"2390","integbio":"nbdc01905","miriam":"unite","n2t":"unite","ncbi":"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"vectorbase":{"prefix":"vectorbase","name":"VectorBase","description":"VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.","pattern":"^\\D{4}\\d{6}(\\-\\D{2})?$","uri_format":"https://vectorbase.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/vectorbase:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"vectorbase.alt1","name":"Vectorbase Alt. 1","description":"An alternate provider based on the search functionality","homepage":"https://www.vectorbase.org","contact":null,"uri_format":"https://www.vectorbase.org/search/site/$1?&site=\"Genome\"","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"vectorbase.alt2","name":"Vectorbase Alt. 2","description":"An alternate provider based on the app structure","homepage":"https://www.vectorbase.org","contact":null,"uri_format":"https://vectorbase.org/vectorbase/app/record/gene/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://www.vectorbase.org/","repository":null,"contact":{"name":"David Starns","orcid":"0000-0001-6583-9067","email":"d.e.starns@liv.ac.uk","github":"obsidian83","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":"ISCW007415","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":"VECTORBASE","integbio":"nbdc01909","miriam":"vectorbase","n2t":"vectorbase","ncbi":"VectorBase","prefixcommons":"vectorbase","re3data":"r3d100010880"},"synonyms":[],"keywords":["environment","expression","gene","genome","genome/gene","localization","organism","protein","sequence"],"domain":null,"references":null,"publications":[{"pubmed":"25510499","doi":"10.1093/nar/gku1117","pmc":"PMC4383932","arxiv":null,"title":"VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases","year":2014},{"pubmed":"19028744","doi":"10.1093/nar/gkn857","pmc":"PMC2686483","arxiv":null,"title":"VectorBase: a data resource for invertebrate vector genomics","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":"vectorbase","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"vega":{"prefix":"vega","name":"Vertebrate Genome Annotation Database","description":"A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.","pattern":null,"uri_format":"https://bioregistry.io/vega:$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/vega:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"https://vega.archive.ensembl.org/index.html","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"OTTHUMG00000169812","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":{"prefixcommons":"vega","re3data":"r3d100012575"},"synonyms":["VEGA"],"keywords":["genome"],"domain":null,"references":null,"publications":[{"pubmed":"24316575","doi":"10.1093/nar/gkt1241","pmc":"PMC3964964","arxiv":null,"title":"The Vertebrate Genome Annotation browser 10 years on","year":2013},{"pubmed":"18003653","doi":"10.1093/nar/gkm987","pmc":"PMC2238886","arxiv":null,"title":"The vertebrate genome annotation (Vega) database","year":2007}],"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":"vega","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"vegbank":{"prefix":"vegbank","name":"VegBank","description":"VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited.","pattern":"^((VB\\.)?(?i:ds|cc|ob|pc|to|py)\\..*|doi:10\\.82902\\/.*)$","uri_format":"https://vegbank.org/cite/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://vegbank.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"0146z4r19","wikidata":null,"gnd":null,"name":"National Center for Ecological Analysis and Synthesis","partnered":false}],"example":"VB.Ob.3736.GRSM125","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"miriam":"vegbank","re3data":"r3d100010153"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"vegbank","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"vfb":{"prefix":"vfb","name":"Virtual Fly Brain","description":"An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.","pattern":"^[0-9a-zA-Z]{8}$","uri_format":"http://virtualflybrain.org/reports/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://VirtualFlyBrain.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":[{"ror":"013meh722","wikidata":null,"gnd":null,"name":"The University of Cambridge","partnered":false}],"example":"00000001","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":{"miriam":"vfb","n2t":"vfb","re3data":"r3d100011373"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"22676296","doi":"10.1186/1471-2105-13-122","pmc":"PMC3412715","arxiv":null,"title":"Web tools for large-scale 3D biological images and atlases","year":2012},{"pubmed":"22402613","doi":"10.1093/bioinformatics/bts113","pmc":null,"arxiv":null,"title":"A strategy for building neuroanatomy ontologies","year":2012},{"pubmed":"22180411","doi":"10.1093/bioinformatics/btr677","pmc":null,"arxiv":null,"title":"The Virtual Fly Brain browser and query interface","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":"vfb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"viperdb":{"prefix":"viperdb","name":"VIPERdb","description":"VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.","pattern":null,"uri_format":"https://viperdb.org/Info_Page.php?VDB=$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/viperdb:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://viperdb.scripps.edu/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"2c6s","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":"pdb","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":{"integbio":"nbdc00835","prefixcommons":"viperdb","re3data":"r3d100012362"},"synonyms":[],"keywords":["3d structure","image/movie","protein","rna","sequence","small molecule","structure"],"domain":null,"references":null,"publications":[{"pubmed":"18981051","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":"viperdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"vipr":{"prefix":"vipr","name":"ViPR Strain","description":"The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.","pattern":"^[A-Za-z 0-9]+$","uri_format":"http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.viprbrc.org/brc/home.do?decorator=vipr","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, Maryland","partnered":false}],"example":"BeAn 70563","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":"VIPR","miriam":"vipr","n2t":"vipr","ncbi":"ViPR","re3data":"r3d100011931"},"synonyms":[],"keywords":["immunology"],"domain":null,"references":null,"publications":[{"pubmed":"23202522","doi":"10.3390/v4113209","pmc":"PMC3509690","arxiv":null,"title":"Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community","year":2012},{"pubmed":"22006842","doi":"10.1093/nar/gkr859","pmc":"PMC3245011","arxiv":null,"title":"ViPR: an open bioinformatics database and analysis resource for virology research","year":2011},{"pubmed":null,"doi":"10.1016/b978-0-12-809633-8.20995-3","pmc":"PMC7173540","arxiv":null,"title":"Database and Analytical Resources for Viral Research Community","year":2021},{"pubmed":null,"doi":"10.1016/b978-0-12-801238-3.95728-3","pmc":"PMC7157461","arxiv":null,"title":"Virus Databases ☆","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":"vipr","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"viralzone":{"prefix":"viralzone","name":"ViralZone","description":"ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.","pattern":"^\\d+$","uri_format":"https://viralzone.expasy.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/vz:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null},{"code":"viralzone.alt1","name":"Viralzone Alt 1.","description":"Alternate view","homepage":"http://viralzone.expasy.org","contact":null,"uri_format":"http://viralzone.expasy.org/all_by_protein/$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.expasy.org/viralzone/","repository":null,"contact":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":"992","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":"VIRALZONE","go":"VZ","integbio":"nbdc02226","miriam":"viralzone","n2t":"viralzone","prefixcommons":"vz","re3data":"r3d100013314","wikidata.entity":"Q15674507"},"synonyms":["vz"],"keywords":["expression","genome/gene","health/disease","organism","sequence","taxonomy","virus"],"domain":null,"references":null,"publications":[{"pubmed":"23193299","doi":"10.1093/nar/gks1220","pmc":"PMC3531065","arxiv":null,"title":"ViralZone: recent updates to the virus knowledge resource","year":2012},{"pubmed":"20947564","doi":"10.1093/nar/gkq901","pmc":"PMC3013774","arxiv":null,"title":"ViralZone: a knowledge resource to understand virus diversity","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":"viralzone","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"3952","fairsharing":"FAIRsharing.g7b4rj","integbio":"nbdc02116","miriam":"wikipathways","n2t":"wikipathways","ols":"wikipathways","pathguide":"237","prefixcommons":"wikipathways","re3data":"r3d100013316","togoid":"Wikipathways","wikidata":"P2410","wikidata.entity":"Q7999828"},"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"],"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"WBVocab","edam":"1805","go":"WB_REF","integbio":"nbdc00740","miriam":"wb","n2t":"wb","ncbi":"WormBase","pathguide":"426","prefixcommons":"wormbase","re3data":"r3d100010424","rrid":"WB-STRAIN:WBStrain","uniprot":"DB-0110","wikidata":"P3860"},"synonyms":["WB","WB_REF","wb","wormbase"],"keywords":["anatomy","bibliography/documents","bioresource","blast","c elegans","catalog","cdna/est","database","expression","faseb list","gene","gene expression","gene function","gene mapping","gene prediction","geneotype","genetic variation","genome","genome/gene","genomic sequence","genomics","health/disease","image/movie","ontology/terminology/nomenclature","organism","organism-specific databases","ortholog","orthology assignment","phenotype","protein","repository","roundworm","sequence","transposon family","wormmart"],"domain":null,"references":null,"publications":[{"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":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":"Xenbase","edam":"2738","go":"Xenbase","miriam":"xenbase","n2t":"xenbase","ncbi":"Xenbase","prefixcommons":"xenbase","re3data":"r3d100011331","uniprot":"DB-0129"},"synonyms":["Xenbase"],"keywords":["expression","genome","organism-specific databases"],"domain":null,"references":null,"publications":[{"pubmed":"36755307","doi":"10.1093/genetics/iyad018","pmc":null,"arxiv":null,"title":null,"year":null},{"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":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"ymdb":{"prefix":"ymdb","name":"Yeast Metabolome Database","description":"The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast).","pattern":"^YMDB\\d+$","uri_format":"http://www.ymdb.ca/compounds/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"http://www.ymdb.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":"YMDB00001","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":{"pathguide":"388","re3data":"r3d100012733"},"synonyms":[],"keywords":[],"domain":null,"references":null,"publications":[{"pubmed":"22064855","doi":"10.1093/nar/gkr916","pmc":"PMC3245085","arxiv":null,"title":"YMDB: the Yeast Metabolome Database","year":2011}],"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":"ymdb","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"yrcpdr":{"prefix":"yrcpdr","name":"YRC PDR","description":"The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.","pattern":"^\\d+$","uri_format":"http://yeastrc.org/pdr/viewProtein.do?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/yrc:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://www.yeastrc.org/pdr/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"2673500","example_extras":[],"example_decoys":null,"license":null,"version":null,"part_of":null,"part_of_database":null,"provides":null,"download_owl":null,"download_obo":null,"download_json":null,"download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"YRCPDR","miriam":"yrcpdr","n2t":"yrcpdr","prefixcommons":"yrc","re3data":"r3d100010975"},"synonyms":[],"keywords":["protein"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":null,"contributor_extras":null,"reviewer":null,"reviewer_extras":null,"proprietary":null,"has_canonical":null,"preferred_prefix":"yrcpdr","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"zenodo.record":{"prefix":"zenodo.record","name":"Zenodo","description":"Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts.","pattern":"^\\d+$","uri_format":"https://zenodo.org/record/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[],"homepage":"https://zenodo.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"4390079","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":{"integbio":"nbdc02187","re3data":"r3d100010468","wikidata":"P4901"},"synonyms":["zenodo"],"keywords":["bibliography/documents","health/disease","repository"],"domain":null,"references":null,"publications":[],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"no_own_terms":null,"comment":null,"contributor":{"name":"Benjamin M. Gyori","orcid":"0000-0001-9439-5346","email":"benjamin_gyori@hms.harvard.edu","github":"bgyori","wikidata":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":"zenodo.record","mastodon":null,"github_request_issue":454,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"zfin":{"prefix":"zfin","name":"Zebrafish Information Network Gene","description":"ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.","pattern":"^ZDB\\-\\w+\\-\\d+\\-\\d+$","uri_format":"http://zfin.org/$1","uri_format_resolvable":null,"rdf_uri_format":null,"providers":[{"code":"agr","name":"ZFIN through the Alliance of Genome Resources","description":"ZFIN through the Alliance of Genome Resources","homepage":"https://www.alliancegenome.org","contact":null,"uri_format":"https://test.alliancegenome.org/gene/ZFIN:$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/zfin:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://zfin.org","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"ZDB-GENE-041118-11","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/zfin/zfin.owl.gz","download_obo":"https://w3id.org/biopragmatics/resources/zfin/zfin.obo","download_json":"https://w3id.org/biopragmatics/resources/zfin/zfin.json.gz","download_rdf":null,"download_skos":null,"download_jskos":null,"banana":null,"banana_peel":null,"deprecated":false,"mappings":{"biocontext":"ZFIN","go":"ZFIN","integbio":"nbdc00746","miriam":"zfin","n2t":"zfin","ncbi":"ZFIN","prefixcommons":"zfin","re3data":"r3d100010421","rrid":"ZIRC","uniprot":"DB-0113","wikidata":"P3870"},"synonyms":["ZFIN"],"keywords":["adult","antibody","bibliography/documents","bioresource","cdna","cdna/est","embryo","expressed sequence tag","expression","fish","gene","genetic variation","genome","genome/gene","ontology","ontology/terminology/nomenclature","organism","organism-specific databases","pathology","protein","repository","research","sequence","zebrafish","zebrafish line"],"domain":null,"references":null,"publications":[{"pubmed":"9891346","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"9441953","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"35166825","doi":"10.1093/genetics/iyac016","pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"30407545","doi":"10.1093/nar/gky1090","pmc":"PMC6323962","arxiv":null,"title":"The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources","year":2019},{"pubmed":"23074187","doi":"10.1093/nar/gks938","pmc":null,"arxiv":null,"title":"ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics","year":null},{"pubmed":"21924170","doi":"10.1016/b978-0-12-374814-0.00017-3","pmc":null,"arxiv":null,"title":"Data extraction, transformation, and dissemination through ZFIN","year":null},{"pubmed":"21036866","doi":"10.1093/nar/gkq1077","pmc":null,"arxiv":null,"title":"ZFIN: enhancements and updates to the Zebrafish Model Organism Database","year":null},{"pubmed":"20836073","doi":"10.1002/0471250953.bi0118s31.","pmc":null,"arxiv":null,"title":"Exploring zebrafish genomic, functional and phenotypic data using ZFIN","year":null},{"pubmed":"17991680","doi":"10.1093/nar/gkm956","pmc":"PMC2238839","arxiv":null,"title":"The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes","year":2007},{"pubmed":"16381936","doi":"10.1093/nar/gkj086","pmc":null,"arxiv":null,"title":"The Zebrafish Information Network: the zebrafish model organism database","year":null},{"pubmed":"12519991","doi":"10.1093/nar/gkg027","pmc":null,"arxiv":null,"title":"The Zebrafish Information Network (ZFIN): the zebrafish model organism database","year":null},{"pubmed":"11125057","doi":null,"pmc":null,"arxiv":null,"title":null,"year":null},{"pubmed":"10354586","doi":"10.1016/s0168-9525(99)01741-2","pmc":null,"arxiv":null,"title":"Zebrafish in the Net","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":"zfin","mastodon":null,"github_request_issue":null,"logo":"https://zfin.org/images/zfinlogo_lg.gif","miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null},"zinc":{"prefix":"zinc","name":"ZINC is not Commercial","description":"ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.","pattern":"^(ZINC)?\\d+$","uri_format":"http://zinc15.docking.org/substances/$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/zinc:$1","first_party":null,"publications":null,"example":null,"status":null,"organization":null}],"homepage":"http://zinc15.docking.org/","repository":null,"contact":null,"contact_extras":null,"contact_group_email":null,"contact_page":null,"owners":null,"example":"ZINC1084","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":"ZINC","miriam":"zinc","n2t":"zinc","prefixcommons":"zinc","re3data":"r3d100010372","wikidata":"P2084"},"synonyms":[],"keywords":["chemical"],"domain":null,"references":null,"publications":[{"pubmed":"26479676","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":"zinc","mastodon":null,"github_request_issue":null,"logo":null,"miriam":null,"n2t":null,"prefixcommons":null,"wikidata":null,"wikidata_entity":null,"go":null,"obofoundry":null,"bioportal":null,"ecoportal":null,"agroportal":null,"cropoct":null,"ols":null,"aberowl":null,"ncbi":null,"uniprot":null,"biolink":null,"cellosaurus":null,"ontobee":null,"cheminf":null,"fairsharing":null,"biocontext":null,"edam":null,"re3data":null,"hl7":null,"bartoc":null,"rrid":null,"lov":null,"zazuko":null,"togoid":null,"integbio":null,"pathguide":null,"tib":null,"biodivportal":null}}