'0000001': authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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.' identifier: '0000001' name: 'Resources mentioned in "Sharing biological data: why, when, and how"' resources: - biostudies - bmrb - cellimage - ega.dataset - ega.study - emdb - empiar - genbank - geo - idr - insdc.sra - massive - panorama - pdb - peptideatlas.dataset - pride - ssbd.dataset - ssbd.project '0000002': authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 context: semweb description: Resources used in the semantic web, inspired by [this list](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) in BioContext. identifier: '0000002' name: Semantic Web Context resources: - ac - bibo - dc - dcat - dcterms - dctypes - faldo - foaf - idot - oa - oboinowl - oslc - owl - pav - prov - qb - qudt - rdf - rdfs - schema - shacl - shex - skos - skosxl - swrl - vann - void - xsd '0000003': authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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). identifier: '0000003' name: ChEBI Data Sources 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 '0000004': authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions. identifier: '0000004' name: International Classifications of Diseases resources: - icd10 - icd10cm - icd10pcs - icd11 - icd9 - icd9cm - icdo '0000005': authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: This collection contains various brain atlases from the Allen Institute. identifier: '0000005' name: Allen Institute Ontologies resources: - dhba - dmba - hba - mba - pba '0000006': authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 context: spar 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. identifier: '0000006' name: SPAR Ontologies resources: - bido - biro - c4o - cito - datacite - deo - doco - fabio - frapo - pso - puro - pwo - scoro '0000007': authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Prefixes useful in annotating documentation provenance. identifier: '0000007' name: Publication Provenance Prefixes resources: - arxiv - doi - pmc - pubmed 0000008: authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 description: Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project. identifier: 0000008 name: ASKEM Epidemiology Prefixes resources: - bfo - caro - doi - doid - dso - hp - ido - oae - oboinowl - ovae - owl - pmc - pubmed - rdfs - ro - symp - trans - vo 0000009: authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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: - HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460)) - [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries - [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_ - [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_ - [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' identifier: 0000009 name: FHIR External Terminologies resources: - atcc - clinicaltrials - clinvar - cosmic - 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 '0000010': authors: - email: cthoyt@gmail.com github: cthoyt name: Charles Tapley Hoyt orcid: 0000-0003-4423-4370 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: - [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.) - [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC) - [GENCODE](https://www.gencodegenes.org/) (uses GenBank) - [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc) - [STRING](https://string-db.org/) (uses UniProt)' identifier: '0000010' name: Global Biodata Coalition - Global Core Biodata Resources 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 - orphanet - 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