{"0000001":{"identifier":"0000001","name":"Resources mentioned in \"Sharing biological data: why, when, and how\"","description":"These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible.","resources":["biostudies","bmrb.entry","cellimage","ega.dataset","ega.study","emdb","empiar","genbank","geo","idr","insdc.sra","massive","panorama","pdb","peptideatlas.dataset","pride","ssbd.dataset","ssbd.project"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000002":{"identifier":"0000002","name":"Semantic Web Context","description":"Resources used in the semantic web, drawing from lists in [BioContext](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) and [LinkML](https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/linked_data.curated.yaml) as well as W3C recommendations.","resources":["ac","bibo","dc","dcat","dcterms","dctypes","doap","faldo","foaf","idot","oa","oboinowl","oslc","owl","pav","prov","qb","qudt","rdf","rdfs","schema","sh","shex","skos","skosxl","swrl","vann","void","xsd"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":"semweb","references":null,"keywords":null,"mappings":null},"0000003":{"identifier":"0000003","name":"ChEBI Data Sources","description":"The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx).","resources":["chebi","chemidplus","come","drugbank","ecmdb","eurofir","google.patent","hmdb","kegg.compound","kegg.drug","kegg.glycan","knapsack","lincs.smallmolecule","lipidmaps","metacyc.compound","molbase.sheffield","pdb","pdb-ccd","pesticides","resid","smid","umbbd.compound","webelements","ymdb"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000004":{"identifier":"0000004","name":"International Classifications of Diseases","description":"This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions.","resources":["icd10","icd10cm","icd10pcs","icd11","icd11.code","icd9","icd9cm","icdo"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000005":{"identifier":"0000005","name":"Allen Institute Ontologies","description":"This collection contains various brain atlases from the Allen Institute.","resources":["dhba","dmba","hba","mba","pba"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000006":{"identifier":"0000006","name":"SPAR Ontologies","description":"The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF.","resources":["bido","biro","c4o","cito","datacite","deo","doco","fabio","frapo","mito","pso","puro","pwo","scoro"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":"spar","references":null,"keywords":null,"mappings":null},"0000007":{"identifier":"0000007","name":"Publication Provenance Prefixes","description":"Prefixes useful in annotating documentation provenance.","resources":["arxiv","doi","pmc","pubmed"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000008":{"identifier":"0000008","name":"ASKEM Epidemiology Prefixes","description":"Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project.","resources":["bfo","caro","doi","doid","dso","hp","ido","oae","oboinowl","ovae","owl","pmc","pubmed","rdfs","ro","symp","trans","vo"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000009":{"identifier":"0000009","name":"FHIR External Terminologies","description":"Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated:\n\n- HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460))\n- [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries\n- [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_\n- [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_\n- [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation","resources":["atcc","clinicaltrials","clinvar.variation","cosmic.gene","cpt","cvx","dbsnp","dicom","dsm5","ensembl","hc.din","hc.npn","hgnc","hl7.v2codesystem","hl7.v3codesystem","icd10","icd9","icf","ietf.language","imgt.hla","iso.3166","loinc","lrg","ncit","ndc","ndfrt","nucc.taxonomy","omim","pharmgkb.gene","pubmed","radlex","refseq","rxnorm","snomedct","so","ucum","unii"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000010":{"identifier":"0000010","name":"Global Biodata Coalition - Global Core Biodata Resources","description":"The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)","resources":["agrkb","bacdive","brenda","brenda.ligand","brenda.ligandgroup","bto","chebi","chembl","civic.aid","civic.did","civic.eid","civic.gid","civic.sid","civic.tid","civic.vid","ecocyc","ena.embl","ensembl","eupath","flybase","gbif","gnomad","go","hgnc","interpro","mgi","orpha","orphanet.ordo","panther.family","panther.node","panther.pathway","panther.pthcmp","pdb","pharmgkb.disease","pharmgkb.drug","pharmgkb.gene","pharmgkb.pathways","pmc","pombase","px","reactome","rgd","rhea","sgd","ucsc","uniprot","wormbase","zfin"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000011":{"identifier":"0000011","name":"NDFI4Cat Collection","description":"A collection of ontologies, controlled vocabularies, and schemas relevant for the NDFI4Cat Consortium.\n\nThis collection was originally based on the metadata landscape of the ontologies in this list can be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat).\n\nOntoCompChem and OntoKin appear on the NFDI4Cat list but have not yet been registered in the Bioregistry because the resources are missing/incomplete such that they do not meet minimum Bioregistry metadata standards. These might be added in the future if additional metadata can be found.","resources":["afo","bao","bfo","cao","chebi","cheminf","chmo","dolce","edam","emmo","emmo.cif","envo","iso15926","m4i","mop","ms","obi","om","ontocape","osmo","rex","rxno","sbo","voc4cat","worldavatar.compchem","worldavatar.kin"],"contributors":[{"name":" Hendrik Borgelt","orcid":"0000-0001-5886-7860","email":"hendrik.borgelt@tu-dortmund.de","github":"HendrikBorgelt","wikidata":null},{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":[{"name":" Hendrik Borgelt","orcid":"0000-0001-5886-7860","email":"hendrik.borgelt@tu-dortmund.de","github":"HendrikBorgelt","wikidata":null},{"name":"Alexander Behr","orcid":"0000-0003-4620-8248","email":"alexander.behr@tu-dortmund.de","github":"Amberlamps","wikidata":null},{"name":"David Linke","orcid":"0000-0002-5898-1820","email":"david.linke@catalysis.de","github":"dalito","wikidata":null}],"logo":"https://www.nfdi.de/wp-content/uploads/2021/06/Logo_Ohne-BG.png","organizations":[{"ror":"01k9z4a50","wikidata":"Q98380342","name":"NFDI4Cat","partnered":false},{"ror":"05qj6w324","wikidata":"Q61658497","name":"NFDI","partnered":false}],"context":null,"references":["https://nfdi4cat.org/services/ontologie-sammlung/","https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1","https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat"],"keywords":null,"mappings":[{"prefix":"tib.collection","identifier":"nfdi4cat"}]},"0000012":{"identifier":"0000012","name":"Clinical Trial Registries","description":"A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)","resources":["anzctr","chictr","clinicaltrials","ctis","ctri","drks","euclinicaltrials","hc.trial","irct","isrctn","itmctr","jrct","kcris","lbctr","pactr","phrr","rebec","repec","rpcec","slctr","snctp","tctr","uminctr"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000013":{"identifier":"0000013","name":"Software Package Repositories","description":"These resources represent software repositories","resources":["cran","crates","npm","packagist","pypi","rubygems"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000014":{"identifier":"0000014","name":"NFDI4Chem Collection","description":"A collection of ontologies relevant within the [NFDI4Chem project](https://www.nfdi4chem.de/) that is mostly based on the overview paper [Ontologies4Chem: the landscape of ontologies in chemistry](https://doi.org/10.1515/pac-2021-2007).\n\nNFDI4Chem deploys a [custom instance](https://terminology.nfdi4chem.de/ts/) of the Ontology Lookup Service (OLS), called NFDI4Chem Terminology Services (TS), that provides the ontologies in this list. This list contains ontologies that cover various domains of chemistry (e.g. ChEBI, CHMO, and RXNO), those that are dependencies of these chemistry specific ontologies (e.g. BFO, RO, IAO, and OBI) as well as those ontologies, which where indexed in the NFDI4Chem TS for interoperability research purposes (e.g. PROV-O, SOSA, and OBOE).","resources":["afo","bfo","bto",{"prefix":"chebi","comment":"Used in YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB"},"cheminf","chemrof","chiro","chmo","duo","edam","efo","enm","envo","fair","fix","gainesville.core","iao","mod","mop","ms","ncit","nmr","obi","oboe","om","ontorxn","pato","proco","prov","reproduceme","rex","ro","rxno","sepio","sio","sosa","ssn","ssn.system","suprabank.additive","suprabank.buffer","suprabank.interaction","suprabank.molecule","suprabank.solvent","swo","time","uo","vibso","voc4cat","worldavatar.compchem","worldavatar.kin","worldavatar.os"],"contributors":[{"name":" Philip Strömert","orcid":"0000-0002-1595-3213","email":"philip.stroemert@tib.eu","github":"StroemPhi","wikidata":null},{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":[{"name":" Philip Strömert","orcid":"0000-0002-1595-3213","email":"philip.stroemert@tib.eu","github":"StroemPhi","wikidata":null}],"logo":"https://nfdi4chem.de/wp-content/themes/wptheme/assets/img/logo.svg","organizations":[{"ror":"05wwzbv21","wikidata":"Q96678459","name":"NFDI4Chem","partnered":false},{"ror":"05qj6w324","wikidata":"Q61658497","name":"NFDI","partnered":false}],"context":null,"references":["https://terminology.nfdi4chem.de/ts/","https://doi.org/10.1515/pac-2021-2007"],"keywords":["chemistry"],"mappings":[{"prefix":"tib.collection","identifier":"nfdi4chem"}]},"0000015":{"identifier":"0000015","name":"Biocuration Conference 2025 Collection","description":"A collection of resources added during Biocuration 2025 in Kansas City, 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portals","resources":["ado","agrkb","anzctr","arrayexpress","arxiv","atc","atcc","bacdive","bfo","bgee.gene","biocyc","biogrid","bioportal","bioproject","biorxiv","biosample","biostudies","bmrb.entry","brenda","brenda.ligand","brenda.ligandgroup","bto","cath","cbioportal","cdd","cellimage","cellxgene.collection","chebi","chembl","chembl.compound","chemspider","civic.aid","civic.did","civic.eid","civic.gid","civic.sid","civic.tid","civic.vid","clinicaltrials","clinvar.record","clinvar.variation","complexportal","cosmic.cell","cosmic.gene","cpt","ctd.chemical","ctri","cvx","dbgap","dbsnp","decipher","depmap","dhba","disprot","dmba","doi","doid","drks","drugbank","drugcentral","duo","ec","ecacc","edam","ega.dataset","ega.study","emdb","empiar","ena.embl","ensembl","ensembl.metazoa","ensembl.plant","euclinicaltrials","eupath","exac.variant","fairsharing","flybase","fma","funderregistry","gard","gbif","gdc","genecards.gene","geo","go","gramene.gene","gramene.growthstage","gramene.protein","gtdb","hba","hc.trial","hgnc","hl7.v2codesystem","hmdb","icd10","icd9","icdc","icf","idr","imgt.hla","inchi","inchikey","insdc","insdc.sra","intact","interpro","iso.3166","isrctn","itis","jaxmice","kegg","kegg.compound","kegg.disease","kegg.drug","kegg.glycan","kegg.pathway","kegg.reaction","loinc","massive","mba","mesh","metabolights","metacyc.compound","mgi","mir","mirbase","mondo","ncbigene","ncbiprotein","ncbitaxon","ncit","ndc","ndfrt","nextprot","nihreporter.project","nord","omim","omop","orcid","orpha","orphanet.ordo","osf","panther.family","panther.pathway","panther.pthcmp","pba","pdb","pdb-ccd","pdb.ligand","pdc.study","peco","peptideatlas.dataset","pfam","pfam.clan","pharmgkb.disease","pharmgkb.drug","pharmgkb.gene","pharmgkb.pathways","pmc","pombase","pride.project","pubchem.compound","pubmed","px","radlex","reactome","rebec","refseq","rfam","rfc","rgd","rhea","rnacentral","ror","rrid","rrrc","rxnorm","scop","sgd","signor","snomedct","so","ssbd.dataset","ssbd.project","stitch","string","tao","tcdb","uberon","unii","uniparc","uniprot","uniprot.isoform","uniprot.proteome","uniref","wikidata","wikigenes","wikipathways","wormbase","xenbase","zenodo.record","zfin","zinc"],"contributors":[{"name":"Robert Allaway","orcid":"0000-0003-3573-3565","email":"robert.j.allaway@gmail.com","github":"allaway","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000017":{"identifier":"0000017","name":"DALIA Resources","description":"Prefixes relevant for the [Data Literacy Alliance (DALIA)](https://dalia.education/en) project","resources":["ans.educationlevel","bibframe","bibo","bmbf.glossary","ceds.element","citedcat","codata.rdmt","dai.thesauri","datacite","dbpedia.resource","dcterms","emmo","fabio","iana.mediatype","isced1997","isced2011","loc.fdd","m4i","marc21","modalia","nfdi4dso","owl","prov","sage.socialsciencethesaurus","schema","sio","spdx","spdx.term","t4fs","unesco.thesaurus","wdrs","wikidata"],"contributors":[{"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","email":"cthoyt@gmail.com","github":"cthoyt","wikidata":null}],"maintainers":null,"logo":null,"organizations":null,"context":null,"references":null,"keywords":null,"mappings":null},"0000018":{"identifier":"0000018","name":"Resources for modeling Open Educational Resources","description":"The prefixes appearing in this collection correspond resources whose entities could appear as values for target groups, media types, educational levels, and other fields in OER data models. 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