'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, 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.
  identifier: '0000002'
  name: Semantic Web Context
  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
'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
'0000011':
  authors:
  - email: hendrik.borgelt@tu-dortmund.de
    github: HendrikBorgelt
    name: ' Hendrik Borgelt'
    orcid: 0000-0001-5886-7860
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'A collection of ontologies relevant for chemistry.


    The NFDI program deploys a [custom instance](https://terminology.tib.eu/ts/ontologies?collection=NFDI4CAT&and=false&page=1)
    of the Ontology Lookup Service (OLS) that provides the ontologies in this list.


    A further analysis of the metadata landscape of the ontologies in this list can
    be found [here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat).


    OntoCompChem 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.'
  identifier: '0000011'
  name: NDFI4Cat Collection
  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
  resources:
  - afo
  - bfo
  - cao
  - chebi
  - cheminf
  - chmo
  - dolce
  - emmo
  - emmo.cif
  - iso15926
  - nfdi4chem.ontocape
  - nfdi4chem.osmo
  - rex
  - rxno
  - sbo
  - voc4cat
'0000012':
  authors:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A collection of clinical trial registries appearing in the World Health
    Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)
  identifier: '0000012'
  name: Clinical Trial Registries
  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
'0000013':
  authors:
  - email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: These resources represent software repositories
  identifier: '0000013'
  name: Software Package Repositories
  resources:
  - cran
  - crates
  - npm
  - packagist
  - pypi
  - rubygems
