3dmet:
  description: 3DMET is a database collecting three-dimensional structures of natural
    metabolites.
  example: B00162
  homepage: http://www.3dmet.dna.affrc.go.jp/
  mappings:
    miriam: 3dmet
    n2t: 3dmet
    prefixcommons: 3DMET
    wikidata: P2796
  name: 3D Metabolites
  pattern: ^B\d{5}$
  preferred_prefix: 3dmet
  uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1
4dn.biosource:
  description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network
    and other reference nucleomics data sets. The 4D Nucleome Network aims to understand
    the principles underlying nuclear organization in space and time, the role nuclear
    organization plays in gene expression and cellular function, and how changes in
    nuclear organization affect normal development as well as various diseases.
  example: 4DNSR73BT2A2
  homepage: https://data.4dnucleome.org/biosources
  mappings:
    cellosaurus: 4DN
    miriam: 4dn
  name: 4D Nucleome Data Portal Biosource
  pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
  preferred_prefix: 4dn.biosource
  synonyms:
  - 4DN
  uri_format: https://data.4dnucleome.org/biosources/$1
4dn.replicate:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database portal containing replicate experiments of different assays
    and samples
  example: 4DNESWX1J3QU
  homepage: https://data.4dnucleome.org/experiment-set-replicates/
  name: 4D Nucleome Data Portal Experiment Replicate
  preferred_prefix: 4dn.replicate
  uri_format: https://data.4dnucleome.org/experiment-set-replicates/$1
aao:
  banana: AAO
  contact:
    email: david.c.blackburn@gmail.com
    github: null
    name: David Blackburn
    orcid: null
  deprecated: true
  description: A structured controlled vocabulary of the anatomy of Amphibians. Note
    that AAO is currently being integrated into Uberon.
  homepage: http://github.com/seger/aao
  mappings:
    obofoundry: AAO
    prefixcommons: AAO
  name: Amphibian gross anatomy
  no_own_terms: true
  preferred_prefix: AAO
  uri_format: http://purl.obolibrary.org/obo/AAO_$1
abcd:
  description: The ABCD (AntiBodies Chemically Defined) database is a manually curated
    depository of sequenced antibodies
  example: AD834
  homepage: https://web.expasy.org/abcd/
  mappings:
    cellosaurus: ABCD
    uniprot: ABCD
  name: AntiBodies Chemically Defined database
  preferred_prefix: abcd
  uri_format: https://web.expasy.org/abcd/ABCD_$1
abs:
  description: The database of Annotated regulatory Binding Sites (from orthologous
    promoters), ABS, is a public database of known binding sites identified in promoters
    of orthologous vertebrate genes that have been manually curated from bibliography.
  example: A0014
  homepage: http://genome.crg.es/datasets/abs2005/
  mappings:
    miriam: abs
    n2t: abs
    prefixcommons: ABS
  name: Annotated Regulatory Binding Sites
  pattern: ^A\d+$
  preferred_prefix: abs
  uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html
ac:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Activity Streams is an open format specification for activity stream
    protocols, which are used to syndicate activities taken in social web applications
    and services, similar to those in Facebook's, Instagram's, and Twitter's. The
    standard provides a general way to represent activities.
  example: Add
  homepage: http://www.w3.org/ns/activitystreams
  name: Activity Streams
  preferred_prefix: ac
  uri_format: http://www.w3.org/ns/activitystreams#$1
aceview.worm:
  description: AceView provides a curated sequence representation of all public mRNA
    sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST
    and Trace). These are aligned on the genome and clustered into a minimal number
    of alternative transcript variants and grouped into genes. In addition, alternative
    features such as promoters, and expression in tissues is recorded. This collection
    references C. elegans genes and expression.
  example: aap-1
  homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm
  mappings:
    miriam: aceview.worm
    n2t: aceview.worm
    prefixcommons: ACEVIEW.WORM
  name: Aceview Worm
  pattern: ^[a-z0-9-]+$
  preferred_prefix: aceview.worm
  uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1
addgene:
  description: Addgene is a non-profit plasmid repository. Addgene facilitates the
    exchange of genetic material between laboratories by offering plasmids and their
    associated cloning data to not-for-profit laboratories around the world.
  example: '50943'
  homepage: http://addgene.org/
  mappings:
    miriam: addgene
    n2t: addgene
  name: Addgene Plasmid Repository
  pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$
  preferred_prefix: addgene
  uri_format: http://addgene.org/$1
adw:
  banana: ADW
  contact:
    email: adw_geeks@umich.edu
    github: null
    name: Animal Diversity Web technical staff
    orcid: null
  deprecated: true
  description: Animal Diversity Web (ADW) is an online database of animal natural
    history, distribution, classification, and conservation biology.
  example: Lycalopex_vetulus
  homepage: http://www.animaldiversity.org
  mappings:
    bioportal: ADW
    miriam: adw
    n2t: adw
    obofoundry: ADW
    prefixcommons: ADW
  name: Animal natural history and life history
  pattern: ^[A-Z_a-z]+$
  preferred_prefix: ADW
  uri_format: https://animaldiversity.org/accounts/$1
aeo:
  banana: AEO
  contact:
    email: J.Bard@ed.ac.uk
    github: null
    name: Jonathan Bard
    orcid: null
  description: AEO is an ontology of anatomical structures that expands CARO, the
    Common Anatomy Reference Ontology
  example: '0001017'
  homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
  license: CC BY 4.0
  mappings:
    bioportal: AEO
    obofoundry: AEO
    ols: aeo
    ontobee: AEO
    prefixcommons: AEO
  name: Anatomical Entity Ontology
  pattern: ^\d{7}$
  preferred_prefix: AEO
  synonyms:
  - AEO_RETIRED
  uri_format: http://purl.obolibrary.org/obo/AEO_$1
  version: '2014-12-05'
aero:
  banana: AERO
  contact:
    email: mcourtot@gmail.com
    github: null
    name: Melanie Courtot
    orcid: null
  deprecated: true
  description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at
    supporting clinicians at the time of data entry, increasing quality and accuracy
    of reported adverse events
  example: '0000125'
  homepage: http://purl.obolibrary.org/obo/aero
  license: CC BY 3.0
  mappings:
    bioportal: AERO
    obofoundry: AERO
    prefixcommons: AERO
  name: Adverse Event Reporting Ontology
  preferred_prefix: AERO
  uri_format: http://purl.obolibrary.org/obo/AERO_$1
affy.probeset:
  description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide)
    microarray probes designed to measure a single gene or a family of genes as a
    unit. Multiple probe sets may be available for each gene under consideration.
  example: 243002_at
  homepage: http://www.affymetrix.com/
  mappings:
    miriam: affy.probeset
    n2t: affy.probeset
    prefixcommons: AFFY.PROBESET
  name: Affymetrix Probeset
  pattern: ^\d{4,}((_[asx])?_at)$
  preferred_prefix: affy.probeset
  providers:
  - code: CURATOR_REVIEW
    description: Bio2RDF
    homepage: http://cu.affymetrix.bio2rdf.org/fct/
    name: Bio2RDF
    uri_format: http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1
  uri_format: https://www.affymetrix.com/LinkServlet?probeset=$1
afo:
  description: Allotrope Merged Ontology Suite
  homepage: https://www.allotrope.org/
  license: CC-BY
  mappings:
    bioportal: AFO
    ols: afo
  name: Allotrope Merged Ontology Suite
  no_own_terms: true
  preferred_prefix: afo
  version: '2019-05-10'
aftol.taxonomy:
  description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated
    to significantly enhancing our understanding of the evolution of the Kingdom Fungi,
    which represents one of the major clades of life. There are roughly 80,000 described
    species of Fungi, but the actual diversity in the group has been estimated to
    be about 1.5 million species.
  example: '959'
  homepage: http://aftol.org/data.php
  mappings:
    miriam: aftol.taxonomy
    n2t: aftol.taxonomy
    prefixcommons: AFTOL.TAXONOMY
  name: Assembling the Fungal Tree of Life - Taxonomy
  pattern: ^\d+$
  preferred_prefix: aftol.taxonomy
  uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1
agricola:
  description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index
    to the collections of the National Agricultural Library, as well as a primary
    public source for world-wide access to agricultural information. The database
    covers materials in all formats and periods, including printed works from as far
    back as the 15th century.
  example: '50018'
  homepage: http://agricola.nal.usda.gov/
  mappings:
    go: AGRICOLA_ID
    miriam: agricola
    n2t: agricola
    prefixcommons: AGRICOLA
  name: Agricultural Online Access
  pattern: ^\d+$
  preferred_prefix: agricola
  synonyms:
  - AGR
  - AGRICOLA_ID
  uri_format: http://ddr.nal.usda.gov/dspace/handle/10113/$1
agro:
  banana: AGRO
  contact:
    email: m.a.laporte@cgiar.org
    github: marieALaporte
    name: "Marie-Ang\xE9lique Laporte"
    orcid: null
  description: AgrO is an ontlogy for representing agronomic practices, techniques,
    variables and related entities
  example: '00020007'
  homepage: https://github.com/AgriculturalSemantics/agro
  license: CC BY 4.0
  mappings:
    bioportal: AGRO
    obofoundry: AGRO
    ols: agro
    ontobee: AGRO
    prefixcommons: AGRO
  name: Agronomy Ontology
  preferred_prefix: AGRO
  uri_format: http://purl.obolibrary.org/obo/AGRO_$1
  version: '2021-11-05'
aism:
  banana: AISM
  contact:
    email: entiminae@gmail.com
    github: null
    name: "Jennifer C. Gir\xF3n"
    orcid: null
  description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
    contains terms used to describe the cuticle - as a single anatomical structure
    - and the skeletal muscle system, to be used in insect biodiversity research.
  example: '0000027'
  homepage: https://github.com/insect-morphology/aism
  license: CC BY 4.0
  mappings:
    bioportal: AISM
    obofoundry: AISM
    ols: aism
    ontobee: AISM
  name: Ontology for the Anatomy of the Insect SkeletoMuscular system
  preferred_prefix: AISM
  uri_format: http://purl.obolibrary.org/obo/AISM_$1
  version: '2021-11-19'
allergome:
  description: Allergome is a repository of data related to all IgE-binding compounds.
    Its purpose is to collect a list of allergenic sources and molecules by using
    the widest selection criteria and sources.
  example: '1948'
  homepage: http://www.allergome.org/
  mappings:
    miriam: allergome
    n2t: allergome
    prefixcommons: ALLERGOME
    uniprot: Allergome
  name: Allergome
  pattern: ^\d+$
  preferred_prefix: allergome
  uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1
alzforum.mutation:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Alzforum mutations is a repository of genes and rare variants associated
    with Alzheimer's disease.
  example: app-d678n-tottori
  homepage: https://www.alzforum.org/mutations
  name: Alzforum Mutations
  preferred_prefix: alzforum.mutation
  synonyms:
  - Alzforum_mut
  uri_format: https://www.alzforum.org/mutations/$1
amoebadb:
  description: AmoebaDB is one of the databases that can be accessed through the EuPathDB
    (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
    the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
    Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
    database built upon the same infrastructure, the EuPathDB portal offers an entry
    point to all these resources, and the opportunity to leverage orthology for searches
    across genera.
  example: EDI_244000
  homepage: http://amoebadb.org/amoeba/
  mappings:
    miriam: amoebadb
    n2t: amoebadb
    prefixcommons: AMOEBADB
  name: AmoebaDB
  pattern: ^EDI_\d+$
  preferred_prefix: amoebadb
  uri_format: https://amoebadb.org/amoeba/app/record/gene/$1
amphx:
  banana: AMPHX
  contact:
    email: hescriva@obs-banyuls.fr
    github: null
    name: Hector Escriva
    orcid: null
  description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
    lanceolatum).
  example: '1000160'
  homepage: https://github.com/EBISPOT/amphx_ontology
  license: CC BY 3.0
  mappings:
    bioportal: AMPHX
    obofoundry: AMPHX
    ols: amphx
    ontobee: AMPHX
  name: The Amphioxus Development and Anatomy Ontology
  preferred_prefix: AMPHX
  uri_format: http://purl.obolibrary.org/obo/AMPHX_$1
  version: '2020-12-18'
antibodyregistry:
  description: The Antibody Registry provides identifiers for antibodies used in publications.
    It lists commercial antibodies from numerous vendors, each assigned with a unique
    identifier. Unlisted antibodies can be submitted by providing the catalog number
    and vendor information.
  example: '493771'
  homepage: http://antibodyregistry.org/
  mappings:
    miriam: antibodyregistry
    n2t: antibodyregistry
    prefixcommons: ANTIBODYREGISTRY
  name: Antibody Registry
  pattern: ^\d{6}$
  preferred_prefix: antibodyregistry
  uri_format: http://antibodyregistry.org/AB_$1
antweb:
  description: AntWeb is a website documenting the known species of ants, with records
    for each species linked to their geographical distribution, life history, and
    includes pictures.
  example: casent0106247
  homepage: http://www.antweb.org/
  mappings:
    miriam: antweb
    n2t: antweb
    ncbi: AntWeb
    prefixcommons: ANTWEB
  name: Ant Database
  pattern: ^casent\d+(\-D\d+)?$
  preferred_prefix: antweb
  uri_format: http://www.antweb.org/specimen.do?name=$1
aop:
  description: International repository of Adverse Outcome Pathways.
  example: '98'
  homepage: https://aopwiki.org/
  mappings:
    miriam: aop
    n2t: aop
    prefixcommons: AOP
  name: AOPWiki
  pattern: ^\d+$
  preferred_prefix: aop
  uri_format: https://aopwiki.org/aops/$1
aop.events:
  description: International repository of Adverse Outcome Pathways.
  example: '3'
  homepage: https://aopwiki.org/
  mappings:
    miriam: aop.events
    n2t: aop.events
    prefixcommons: AOP.EVENTS
  name: AOPWiki (Key Event)
  pattern: ^\d+$
  preferred_prefix: aop.events
  uri_format: https://aopwiki.org/events/$1
aop.relationships:
  description: International repository of Adverse Outcome Pathways.
  example: '5'
  homepage: https://aopwiki.org/
  mappings:
    miriam: aop.relationships
    n2t: aop.relationships
    prefixcommons: AOP.RELATIONSHIPS
  name: AOPWiki (Key Event Relationship)
  pattern: ^\d+$
  preferred_prefix: aop.relationships
  uri_format: https://aopwiki.org/relationships/$1
aop.stressor:
  description: International repository of Adverse Outcome Pathways.
  example: '9'
  homepage: https://aopwiki.org/
  mappings:
    miriam: aop.stressor
    n2t: aop.stressor
    prefixcommons: AOP.STRESSOR
  name: AOPWiki (Stressor)
  pattern: ^\d+$
  preferred_prefix: aop.stressor
  uri_format: https://aopwiki.org/stressors/$1
apd:
  description: The antimicrobial peptide database (APD) provides information on anticancer,
    antiviral, antifungal and antibacterial peptides.
  example: '01001'
  homepage: http://aps.unmc.edu/AP/
  mappings:
    miriam: apd
    n2t: apd
    prefixcommons: APD
  name: Antimicrobial Peptide Database
  pattern: ^\d{5}$
  preferred_prefix: apd
  uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1
aphidbase.transcript:
  description: AphidBase is a centralized bioinformatic resource that was developed
    to facilitate community annotation of the pea aphid genome by the International
    Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed
    to organize and distribute genomic data and annotations for a large international
    community. This collection references the transcript report, which describes genomic
    location, sequence and exon information.
  example: ACYPI000159
  homepage: http://www.aphidbase.com/aphidbase
  mappings:
    miriam: aphidbase.transcript
    n2t: aphidbase.transcript
    prefixcommons: APHIDBASE.TRANSCRIPT
  name: AphidBase Transcript
  pattern: ^ACYPI\d{6}(-RA)?$
  preferred_prefix: aphidbase.transcript
  uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1
apid.interactions:
  description: APID (Agile Protein Interactomes DataServer) provides information on
    the protein interactomes of numerous  organisms, based on the integration of known
    experimentally validated protein-protein physical interactions (PPIs). Interactome
    data includes a report on  quality levels and coverage over the proteomes for
    each organism included. APID integrates PPIs from primary databases of molecular
    interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally
    resolved 3D structures (PDB) where more than two distinct proteins have been identified.
    This collection references protein interactors, through a UniProt identifier.
  example: P01116
  homepage: http://cicblade.dep.usal.es:8080/APID/
  mappings:
    miriam: apid.interactions
    n2t: apid.interactions
    prefixcommons: APID.INTERACTIONS
  name: APID Interactomes
  pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
    0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
  preferred_prefix: apid.interactions
  provides: uniprot
  uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1
apo:
  banana: YPO
  contact:
    email: cherry@genome.stanford.edu
    github: null
    name: Mike Cherry
    orcid: null
  deprecated: true
  description: A structured controlled vocabulary for the phenotypes of Ascomycete
    fungi.
  example: 0000184
  homepage: http://www.yeastgenome.org/
  license: CC BY 4.0
  mappings:
    bioportal: APO
    obofoundry: YPO
    ols: apo
    ontobee: APO
    prefixcommons: YPO
  name: Yeast phenotypes
  pattern: ^\d{7}$
  preferred_prefix: APO
  synonyms:
  - YPO
  uri_format: https://www.yeastgenome.org/observable/APO:$1
  version: '2021-10-07'
apollosv:
  banana: APOLLO_SV
  contact:
    email: MBrochhausen@uams.edu
    github: null
    name: Mathias Brochhausen
    orcid: null
  description: Defines terms and relations necessary for interoperation between epidemic
    models and public health application software that interface with these models
  example: '00000443'
  homepage: https://github.com/ApolloDev/apollo-sv
  license: CC BY 4.0
  mappings:
    bioportal: APOLLO-SV
    obofoundry: APOLLO_SV
    ols: apollo_sv
    ontobee: APOLLO_SV
  name: Apollo Structured Vocabulary
  preferred_prefix: APOLLO_SV
  uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1
  version: 4.1.1
arachnoserver:
  description: ArachnoServer (www.arachnoserver.org) is a manually curated database
    providing information on the sequence, structure and biological activity of protein
    toxins from spider venoms. It include a molecular target ontology designed specifically
    for venom toxins, as well as current and historic taxonomic information.
  example: AS000060
  homepage: http://www.arachnoserver.org/
  mappings:
    miriam: arachnoserver
    n2t: arachnoserver
    prefixcommons: ARACHNOSERVER
    uniprot: ArachnoServer
  name: ArachnoServer
  pattern: ^AS\d{6}$
  preferred_prefix: arachnoserver
  uri_format: http://www.arachnoserver.org/toxincard.html?id=$1
araport:
  description: Website with general information about Arabidopsis and functionalities
    such as a genomic viewer
  example: AT1G01010
  homepage: https://www.araport.org/
  mappings:
    ncbi: Araport
    uniprot: Araport
  name: Arabidopsis Information Portal
  preferred_prefix: araport
  uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1
ardb:
  description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated
    database which characterises genes involved in antibiotic resistance. Each gene
    and resistance type is annotated with information, including resistance profile,
    mechanism of action, ontology, COG and CDD annotations, as well as external links
    to sequence and protein databases. This collection references resistance genes.
  example: CAE46076
  homepage: http://ardb.cbcb.umd.edu/
  mappings:
    miriam: ardb
    n2t: ardb
    prefixcommons: ARDB
  name: Antibiotic Resistance Genes Database
  pattern: ^[A-Z_]{3}[0-9]{4,}$
  preferred_prefix: ardb
  uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1
ark:
  banana: ark
  description: An Archival Resource Key (ARK) is a Uniform Resource Locator (URL)
    that is a multi-purpose persistent identifier for information objects of any type.
  example: /12345/fk1234
  homepage: http://n2t.net/
  mappings:
    miriam: ark
    n2t: ark
    prefixcommons: ARK
  name: Archival Resource Key
  namespace_in_lui: true
  pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
  preferred_prefix: ark
  uri_format: http://n2t.net/ark:$1
aro:
  banana: ARO
  contact:
    email: mcarthua@mcmaster.ca
    github: agmcarthur
    name: Andrew G. McArthur
    orcid: null
  description: Antibiotic resistance genes and mutations
  example: '1000001'
  homepage: https://github.com/arpcard/aro
  license: CC BY 4.0
  mappings:
    bioportal: ARO
    obofoundry: ARO
    ols: aro
    ontobee: ARO
    prefixcommons: ARO
  name: Antibiotic Resistance Ontology
  pattern: ^\d{7}$
  preferred_prefix: ARO
  uri_format: http://purl.obolibrary.org/obo/ARO_$1
  version: '2019-10-24'
arrayexpress:
  description: ArrayExpress is a public repository for microarray data, which is aimed
    at storing MIAME-compliant data in accordance with Microarray Gene Expression
    Data (MGED) recommendations.
  example: E-MEXP-1712
  homepage: https://www.ebi.ac.uk/arrayexpress/
  mappings:
    cellosaurus: ArrayExpress
    miriam: arrayexpress
    n2t: arrayexpress
    prefixcommons: ARRAYEXPRESS
  name: ArrayExpress
  pattern: ^[AEP]-\w{4}-\d+$
  preferred_prefix: arrayexpress
  providers:
  - code: omicsdi
    description: ArrayExpress through OmicsDI
    homepage: https://www.omicsdi.org/
    name: ArrayExpress through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/arrayexpress-repository/$1
  uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1
arrayexpress.platform:
  description: ArrayExpress is a public repository for microarray data, which is aimed
    at storing MIAME-compliant data in accordance with Microarray Gene Expression
    Data (MGED) recommendations.This collection references the specific platforms
    used in the generation of experimental results.
  example: A-GEOD-50
  homepage: https://www.ebi.ac.uk/arrayexpress/
  mappings:
    miriam: arrayexpress.platform
    n2t: arrayexpress.platform
    prefixcommons: ARRAYEXPRESS.PLATFORM
  name: ArrayExpress Platform
  pattern: ^[AEP]-\w{4}-\d+$
  preferred_prefix: arrayexpress.platform
  uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1
arraymap:
  description: arrayMap is a collection of pre-processed oncogenomic array data sets
    and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation
    commonly found in cancer genomes. arrayMap data is assembled from public repositories
    and supplemented with additional sources, using custom curation pipelines. This
    information has been mapped to multiple editions of the reference human genome.
  example: icdom:8500_3
  homepage: https://www.arraymap.org
  mappings:
    miriam: arraymap
    n2t: arraymap
    prefixcommons: ARRAYMAP
  name: ArrayMap
  pattern: ^[\w\-:,]{3,64}$
  preferred_prefix: arraymap
  uri_format: https://www.arraymap.org/pgx:$1
arxiv:
  description: arXiv is an e-print service in the fields of physics, mathematics,
    non-linear science, computer science, and quantitative biology.
  example: 0807.4956v1
  homepage: https://arxiv.org/
  mappings:
    miriam: arxiv
    n2t: arxiv
    prefixcommons: ARXIV
    scholia: arxiv
  name: arXiv
  pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$
  preferred_prefix: arxiv
  uri_format: https://arxiv.org/abs/$1
asap:
  description: ASAP (a systematic annotation package for community analysis of genomes)
    stores bacterial genome sequence and functional characterization data. It includes
    multiple genome sequences at various stages of analysis, corresponding experimental
    data and access to collections of related genome resources.
  example: ABE-0009634
  homepage: http://asap.ahabs.wisc.edu/asap/home.php
  mappings:
    go: ASAP
    miriam: asap
    n2t: asap
    ncbi: ASAP
    prefixcommons: ASAP
  name: A Systematic Annotation Package for Community Analysis of Genomes
  pattern: ^[A-Za-z0-9-]+$
  preferred_prefix: asap
  uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1
ascl:
  description: The Astrophysics Source Code Library (ASCL) is a free online registry
    for software that have been used in research that has appeared in, or been submitted
    to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics
    Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable
    by using the unique ascl ID assigned to each code. The ascl ID can be used to
    link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).
  example: '1801.012'
  homepage: http://ascl.net/
  mappings:
    miriam: ascl
    n2t: ascl
    prefixcommons: ASCL
  name: Astrophysics Source Code Library
  pattern: ^[0-9\.]+$
  preferred_prefix: ascl
  uri_format: http://ascl.net/$1
asin:
  description: Almost every product on our site has its own ASIN, a unique code we
    use to identify it. For books, the ASIN is the same as the ISBN number, but for
    all other products a new ASIN is created when the item is uploaded to our catalogue.
  example: 0471491039
  homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182
  mappings:
    miriam: asin
    n2t: asin
    prefixcommons: ASIN
  name: Amazon Standard Identification Number
  pattern: ^[0-9]{10}$
  preferred_prefix: asin
  uri_format: https://amzn.com/$1
aspgd.locus:
  description: The Aspergillus Genome Database (AspGD) is a repository for information
    relating to fungi of the genus Aspergillus, which includes organisms of clinical,
    agricultural and industrial importance. AspGD facilitates comparative genomics
    by providing a full-featured genomics viewer, as well as matched and standardized
    sets of genomic information for the sequenced aspergilli. This collection references
    gene information.
  example: ASPL0000349247
  homepage: http://www.aspgd.org/
  mappings:
    go: AspGD_LOCUS
    miriam: aspgd.locus
    n2t: aspgd.locus
    prefixcommons: ASPGD.LOCUS
  name: Aspergillus Genome Database
  pattern: ^[A-Za-z_0-9]+$
  preferred_prefix: aspgd.locus
  uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1
aspgd.protein:
  description: The Aspergillus Genome Database (AspGD) is a repository for information
    relating to fungi of the genus Aspergillus, which includes organisms of clinical,
    agricultural and industrial importance. AspGD facilitates comparative genomics
    by providing a full-featured genomics viewer, as well as matched and standardized
    sets of genomic information for the sequenced aspergilli. This collection references
    protein information.
  example: ASPL0000349247
  homepage: http://www.aspgd.org/
  mappings:
    miriam: aspgd.protein
    n2t: aspgd.protein
    prefixcommons: ASPGD.PROTEIN
  name: AspGD Protein
  pattern: ^[A-Za-z_0-9]+$
  preferred_prefix: aspgd.protein
  uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1
asrp:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis
    small RNA genes.
  example: ASRP1423
  homepage: https://asrp.danforthcenter.org/
  name: Arabidopsis Small RNA Project
  preferred_prefix: asrp
assembly:
  description: A database providing information on the structure of assembled genomes,
    assembly names and other meta-data, statistical reports, and links to genomic
    sequence data.
  example: GCF_000005845.2
  homepage: https://www.ncbi.nlm.nih.gov/
  mappings:
    miriam: assembly
  name: Assembly
  pattern: ^[a-zA-Z0-9_\.]+$
  preferred_prefix: assembly
  uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1
atc:
  description: The Anatomical Therapeutic Chemical (ATC) classification system, divides
    active substances into different groups according to the organ or system on which
    they act and their therapeutic, pharmacological and chemical properties. Drugs
    are classified in groups at five different levels;  Drugs are divided into fourteen
    main groups (1st level), with pharmacological/therapeutic subgroups (2nd level).  The
    3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the
    5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC)
    classification system and the Defined Daily Dose (DDD) is a tool for exchanging
    and comparing data on drug use at international, national or local levels.
  example: A10BA02
  homepage: http://www.whocc.no/atc_ddd_index/
  mappings:
    bioportal: ATC
    miriam: atc
    n2t: atc
    prefixcommons: ATC
    wikidata: P267
  name: Anatomical Therapeutic Chemical Classification System
  pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$
  preferred_prefix: atc
  synonyms:
  - ATC_code
  - ATTC
  uri_format: http://www.whocc.no/atc_ddd_index/?code=$1
atcc:
  description: The American Type Culture Collection (ATCC) is a private, nonprofit
    biological resource center whose mission focuses on the acquisition, authentication,
    production, preservation, development and distribution of standard reference microorganisms,
    cell lines and other materials for research in the life sciences.
  example: '11303'
  homepage: https://www.lgcstandards-atcc.org
  mappings:
    cellosaurus: ATCC
    miriam: atcc
    n2t: atcc
    ncbi: ATCC
    prefixcommons: ATCC
  name: American Type Culture Collection
  pattern: ^([A-Z]+-)?\d+$
  preferred_prefix: atcc
  synonyms:
  - ATCC
  - ATCC number
  - ATCC(dna)
  - ATCC(in host)
  uri_format: https://www.atcc.org/products/$1
atcvet:
  description: The ATCvet system for the classification of veterinary medicines is
    based on the same overall principles as the ATC system for substances used in
    human medicine. In ATCvet systems, preparations are divided into groups, according
    to their therapeutic use. First, they are divided into 15 anatomical groups (1st
    level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic
    use.
  example: QJ51RV02
  homepage: http://www.whocc.no/atcvet/atcvet_index/
  mappings:
    miriam: atcvet
    n2t: atcvet
    prefixcommons: ATCVET
  name: Anatomical Therapeutic Chemical Vetinary
  pattern: ^Q[A-Z0-9]+$
  preferred_prefix: atcvet
  uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1
atfdb.family:
  description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs
    in sequenced animal genomes, as well as collecting the transcription co-factors
    and chromatin remodeling factors of those genomes. This collections refers to
    transcription factor families, and the species in which they are found.
  example: CUT
  homepage: http://www.bioguo.org/AnimalTFDB/family_index.php
  mappings:
    miriam: atfdb.family
    n2t: atfdb.family
    prefixcommons: ATFDB.FAMILY
  name: Animal TFDB Family
  pattern: ^\w+$
  preferred_prefix: atfdb.family
  uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1
ato:
  banana: ATO
  contact:
    email: david.c.blackburn@gmail.com
    github: null
    name: David Blackburn
    orcid: null
  deprecated: true
  homepage: http://www.amphibanat.org
  mappings:
    bioportal: ATO
    obofoundry: ATO
    prefixcommons: ATO
  name: Amphibian taxonomy
  preferred_prefix: ATO
  uri_format: http://purl.obolibrary.org/obo/ATO_$1
atol:
  description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics
    defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide
    a reference ontology of phenotypic traits of farm animals for the international
    scientificand educational - communities, farmers, etc.; - deliver this reference
    ontology in a language which can be used by computers in order to support database
    management, semantic analysis and modeling; - represent traits as generic as possible
    for livestock vertebrates; - make the ATOL ontology as operational as possible
    and closely related to measurement techniques; - structure the ontology in relation
    to animal production.'
  example: '0002233'
  homepage: http://www.atol-ontology.com
  mappings:
    bioportal: ATOL
    ols: atol
  name: Animal Trait Ontology for Livestock
  preferred_prefix: atol
  version: '2018-09-13'
autdb:
  description: AutDB is a curated database for autism research. It is built on information
    extracted from the studies on molecular genetics and biology of Autism Spectrum
    Disorders (ASD). The four modules of AutDB include information on Human Genes,
    Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively.
    It provides an annotated list of ASD candidate genes in the form of reference
    dataset for interrogating molecular mechanisms underlying the disorder.
  example: ADA
  homepage: http://autism.mindspec.org/autdb/
  mappings:
    miriam: autdb
    n2t: autdb
    prefixcommons: AUTDB
  name: AutDB
  pattern: ^[A-Z]+[A-Z-0-9]{2,}$
  preferred_prefix: autdb
  uri_format: http://autism.mindspec.org/GeneDetail/$1
bacdive:
  description: "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed\
    \ strain-linked information on the different aspects of bacterial and archaeal\
    \ biodiversity."
  example: '131392'
  homepage: https://bacdive.dsmz.de/
  mappings:
    miriam: bacdive
    n2t: bacdive
  name: Bacterial Diversity Metadatabase
  pattern: ^[0-9]+$
  preferred_prefix: bacdive
  uri_format: https://bacdive.dsmz.de/strain/$1
bacmap.biog:
  description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
    genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
    prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
    to the level of individual genes and each gene is hyperlinked to a richly annotated
    gene card. All bacterial genome maps are supplemented with separate prophage genome
    maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in
    BacMap contains graphs and tables on a variety of gene and protein statistics.
    Likewise, every bacterial species entry contains a bacterial 'biography' card,
    with taxonomic details, phenotypic details, textual descriptions and images. This
    collection references 'biography' information.
  example: '1050'
  homepage: http://bacmap.wishartlab.com/
  mappings:
    miriam: bacmap.biog
    n2t: bacmap.biog
    prefixcommons: BACMAP.BIOG
  name: BacMap Biography
  pattern: ^\d+$
  preferred_prefix: bacmap.biog
  uri_format: http://bacmap.wishartlab.com/organisms/$1
bacmap.map:
  description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
    genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
    prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
    to the level of individual genes and each gene is hyperlinked to a richly annotated
    gene card. All bacterial genome maps are supplemented with separate prophage genome
    maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in
    BacMap contains graphs and tables on a variety of gene and protein statistics.
    Likewise, every bacterial species entry contains a bacterial 'biography' card,
    with taxonomic details, phenotypic details, textual descriptions and images. This
    collection references genome map information.
  example: AP011135
  homepage: http://bacmap.wishartlab.com/
  mappings:
    miriam: bacmap.map
    n2t: bacmap.map
    prefixcommons: BACMAP.MAP
  name: BacMap Map
  pattern: ^\w+(\_)?\d+(\.\d+)?$
  preferred_prefix: bacmap.map
  uri_format: http://bacmap.wishartlab.com/maps/$1/index.html
bactibase:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Bactibase is a database describing the physical and chemical properties
    of bacteriocins from gram-negative and gram-positive bacteria.
  example: BAC045
  homepage: http://bactibase.hammamilab.org
  name: 'Bactibase: a database dedicated to bacteriocins'
  preferred_prefix: bactibase
  uri_format: http://bactibase.hammamilab.org/$1
bams:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: 'BAMS (Brain Architectural Management System) describes vertebrate
    neuroinformatics data at four levels of organization: expressed molecules, neuron
    types and classes, brain regions, and networks of brain regions.'
  homepage: https://bams1.org
  name: Brain Architecture Knowledge Management System Neuroanatomical Ontology
  preferred_prefix: bams
  references:
  - https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full
bao:
  description: The BioAssay Ontology (BAO) describes chemical biology screening assays
    and their results including high-throughput screening (HTS) data for the purpose
    of categorizing assays and data analysis.
  example: 0002989
  homepage: http://bioassayontology.org
  license: CC BY-SA 4.0
  mappings:
    bioportal: BAO
    miriam: bao
    n2t: bao
    ols: bao
    prefixcommons: BAO
  name: BioAssay Ontology
  pattern: ^\d{7}$
  preferred_prefix: bao
  synonyms:
  - BAO
  uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1
  version: 2.7.2
bcgo:
  banana: BCGO
  contact:
    email: jiezheng@pennmedicine.upenn.edu
    github: zhengj2007
    name: Jie Zheng
    orcid: null
  deprecated: true
  description: An application ontology built for beta cell genomics studies.
  homepage: https://github.com/obi-bcgo/bcgo
  license: CC BY 3.0
  mappings:
    bioportal: BCGO
    cellosaurus: BCGO
    obofoundry: BCGO
    ontobee: BCGO
    prefixcommons: BCGO
  name: Beta Cell Genomics Ontology
  preferred_prefix: BCGO
  uri_format: http://purl.obolibrary.org/obo/BCGO_$1
bcio:
  description: The Behaviour Change Intervention Ontology is an ontology for all aspects
    of human behaviour change interventions and their evaluation.
  example: '040000'
  homepage: https://www.humanbehaviourchange.org/
  mappings:
    bioportal: BCI-O
    ols: bcio
  name: The Behaviour Change Intervention Ontology
  preferred_prefix: bcio
  version: '2020-12-15'
bco:
  banana: BCO
  contact:
    email: rlwalls2008@gmail.com
    github: ramonawalls
    name: Ramona Walls
    orcid: null
  description: An ontology to support the interoperability of biodiversity data, including
    data on museum collections, environmental/metagenomic samples, and ecological
    surveys.
  example: 0000081
  homepage: https://github.com/tucotuco/bco
  license: CC0 1.0
  mappings:
    bioportal: BCO
    obofoundry: BCO
    ols: bco
    ontobee: BCO
    prefixcommons: BCO
  name: Biological Collections Ontology
  preferred_prefix: BCO
  uri_format: http://purl.obolibrary.org/obo/BCO_$1
  version: '2021-11-14'
bdgp.est:
  description: The BDGP EST database collects the expressed sequence tags (ESTs) derived
    from a variety of tissues and developmental stages for Drosophila melanogaster.
    All BDGP ESTs are available at dbEST (NCBI).
  example: EY223054.1
  has_canonical: dbest
  homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html
  mappings:
    miriam: bdgp.est
    n2t: bdgp.est
    ncbi: BDGP_EST
    prefixcommons: BDGP.EST
  name: Berkeley Drosophila Genome Project EST database
  pattern: ^\w+(\.)?(\d+)?$
  preferred_prefix: bdgp.est
  uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
bdgp.insertion:
  description: BDGP gene disruption collection provides a public resource of gene
    disruptions of Drosophila genes using a single transposable element.
  example: KG09531
  homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/
  mappings:
    miriam: bdgp.insertion
    n2t: bdgp.insertion
    prefixcommons: BDGP.INSERTION
  name: BDGP insertion DB
  pattern: ^\w+$
  preferred_prefix: bdgp.insertion
  uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1
bdsc:
  description: The Bloomington Drosophila Stock Center collects, maintains and distributes
    Drosophila melanogaster strains for research.
  example: '33607'
  homepage: https://bdsc.indiana.edu/about/mission.html
  mappings:
    miriam: bdsc
    n2t: bdsc
  name: Bloomington Drosophila Stock Center
  pattern: ^\d+$
  preferred_prefix: bdsc
  uri_format: https://bdsc.indiana.edu/stocks/$1
beetlebase:
  description: BeetleBase is a comprehensive sequence database and community resource
    for Tribolium genetics, genomics and developmental biology. It incorporates information
    about genes, mutants, genetic markers, expressed sequence tags and publications.
  example: TC010103
  homepage: http://beetlebase.org/
  mappings:
    miriam: beetlebase
    n2t: beetlebase
    ncbi: BEETLEBASE
    prefixcommons: BEETLEBASE
  name: Tribolium Genome Database -- Insertion
  pattern: ^TC\d+$
  preferred_prefix: beetlebase
  uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1
begdb:
  description: The Benchmark Energy & Geometry Database (BEGDB) collects results of
    highly accurate quantum mechanics (QM) calculations of molecular structures, energies
    and properties. These data can serve as benchmarks for testing and parameterization
    of other computational methods.
  example: '4214'
  homepage: http://www.begdb.com
  mappings:
    miriam: begdb
    n2t: begdb
    prefixcommons: BEGDB
  name: Benchmark Energy & Geometry Database
  pattern: ^[0-9]+$
  preferred_prefix: begdb
  uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1
bel:
  comment: INDRA uses bel as a catch-all for scomp/sfam
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Biological Expression Language is a domain-specific language for
    describing causal, correlative, and associative relationships between a variety
    of biological agents.
  example: 9-1-1 Complex
  homepage: https://biological-expression-language.github.io/
  name: Biological Expression Language
  preferred_prefix: bel
bfo:
  banana: BFO
  contact:
    email: phismith@buffalo.edu
    github: phismith
    name: Barry Smith
    orcid: null
  description: The upper level ontology upon which OBO Foundry ontologies are built.
  example: '0000001'
  homepage: http://ifomis.org/bfo/
  license: CC BY 4.0
  mappings:
    bioportal: BFO
    go: BFO
    obofoundry: BFO
    ols: bfo
    ontobee: BFO
    prefixcommons: BFO
  name: Basic Formal Ontology
  pattern: ^\d{7}$
  preferred_prefix: BFO
  uri_format: http://purl.obolibrary.org/obo/BFO_$1
  version: '2019-08-26'
bgee.family:
  description: Bgee is a database of gene expression patterns within particular anatomical
    structures within a species, and between different animal species. This collection
    refers to expression across species.
  example: ENSFM00500000270089
  homepage: http://bgee.unil.ch/bgee/bgee
  mappings:
    miriam: bgee.family
    n2t: bgee.family
    prefixcommons: BGEE.FAMILY
  name: Bgee family
  pattern: ^(ENSFM|ENSGTV:)\d+$
  preferred_prefix: bgee.family
  uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1
bgee.gene:
  description: Bgee is a database to retrieve and compare gene expression patterns
    in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in
    situ hybridization, and EST data). This collection references genes in Bgee.
  example: FBgn0000015
  homepage: https://bgee.org/
  mappings:
    miriam: bgee.gene
    n2t: bgee.gene
    prefixcommons: BGEE.GENE
  name: Bgee gene
  pattern: ^[A-Za-z]+\d+$
  preferred_prefix: bgee.gene
  uri_format: https://bgee.org/?page=gene&gene_id=$1
bgee.organ:
  description: Bgee is a database of gene expression patterns within particular anatomical
    structures within a species, and between different animal species. This collection
    refers to anatomical structures.
  example: EHDAA:2185
  homepage: http://bgee.unil.ch/bgee/bgee
  mappings:
    miriam: bgee.organ
    n2t: bgee.organ
    prefixcommons: BGEE.ORGAN
  name: Bgee organ
  pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$
  preferred_prefix: bgee.organ
  uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1
bgee.stage:
  description: Bgee is a database of gene expression patterns within particular anatomical
    structures within a species, and between different animal species. This collection
    refers to developmental stages.
  example: HsapDO:0000004
  homepage: http://bgee.unil.ch/bgee/bgee
  mappings:
    miriam: bgee.stage
    n2t: bgee.stage
    prefixcommons: BGEE.STAGE
  name: Bgee stage
  pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$
  preferred_prefix: bgee.stage
  uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1
bigg.compartment:
  description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
    structured genome-scale metabolic network reconstructions. It more published genome-scale
    metabolic networks into a single database with a set of stardized identifiers
    called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
    and metabolites are linked to many external databases (KEGG, PubChem, and many
    more). This collection references model compartments.
  example: c
  homepage: http://bigg.ucsd.edu/compartments/
  mappings:
    miriam: bigg.compartment
    n2t: bigg.compartment
    prefixcommons: BIGG.COMPARTMENT
  name: BiGG Compartment
  pattern: ^[a-z_A-Z]+$
  preferred_prefix: bigg.compartment
  uri_format: http://bigg.ucsd.edu/compartments/$1
bigg.metabolite:
  description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
    structured genome-scale metabolic network reconstructions. It more published genome-scale
    metabolic networks into a single database with a set of stardized identifiers
    called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
    and metabolites are linked to many external databases (KEGG, PubChem, and many
    more). This collection references individual metabolotes.
  example: 12dgr161
  homepage: http://bigg.ucsd.edu/universal/metabolites
  mappings:
    miriam: bigg.metabolite
    n2t: bigg.metabolite
    prefixcommons: BIGG.METABOLITE
  name: BiGG Metabolite
  pattern: ^[a-z_A-Z0-9]+$
  preferred_prefix: bigg.metabolite
  uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1
bigg.model:
  description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
    structured genome-scale metabolic network reconstructions. It more published genome-scale
    metabolic networks into a single database with a set of stardized identifiers
    called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
    and metabolites are linked to many external databases (KEGG, PubChem, and many
    more). This collection references individual models.
  example: iECABU_c1320
  homepage: http://bigg.ucsd.edu/models
  mappings:
    miriam: bigg.model
    n2t: bigg.model
    prefixcommons: BIGG.MODEL
  name: BiGG Model
  pattern: ^[a-z_A-Z0-9]+$
  preferred_prefix: bigg.model
  uri_format: http://bigg.ucsd.edu/models/$1
bigg.reaction:
  description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
    structured genome-scale metabolic network reconstructions. It more published genome-scale
    metabolic networks into a single database with a set of stardized identifiers
    called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
    and metabolites are linked to many external databases (KEGG, PubChem, and many
    more). This collection references reactions.
  example: 13GS
  homepage: http://bigg.ucsd.edu/universal/reactions
  mappings:
    miriam: bigg.reaction
    n2t: bigg.reaction
    prefixcommons: BIGG.REACTION
  name: BiGG Reaction
  pattern: ^[a-z_A-Z0-9]+$
  preferred_prefix: bigg.reaction
  uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1
bila:
  banana: BILA
  deprecated: true
  mappings:
    obofoundry: BILA
    prefixcommons: BILA
  name: Bilateria anatomy
  preferred_prefix: BILA
  uri_format: http://purl.obolibrary.org/obo/BILA_$1
bindingdb:
  description: BindingDB is the first public database of protein-small molecule affinity
    data.
  example: e999
  homepage: https://www.bindingdb.org
  mappings:
    miriam: bindingdb
    n2t: bindingdb
    prefixcommons: BINDINGDB
    uniprot: BindingDB
  name: BindingDB
  pattern: ^\w\d+$
  preferred_prefix: bindingdb
  uri_format: http://www.bindingdb.org/compact/$1
biocarta.pathway:
  description: BioCarta is a supplier and distributor of characterized reagents and
    assays for biopharmaceutical and academic research. It catalogs community produced
    online maps depicting molecular relationships from areas of active research, generating
    classical pathways as well as suggestions for new pathways. This collections references
    pathway maps.
  example: h_aktPathway
  homepage: https://www.biocarta.com/
  mappings:
    miriam: biocarta.pathway
    n2t: biocarta.pathway
    prefixcommons: BIOCARTA.PATHWAY
  name: BioCarta Pathway
  pattern: ^([hm]\_)?\w+Pathway$
  preferred_prefix: biocarta.pathway
  uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1
biocatalogue.service:
  description: The BioCatalogue provides a common interface for registering, browsing
    and annotating Web Services to the Life Science community. Registered services
    are monitored, allowing the identification of service problems and changes and
    the filtering-out of unavailable or unreliable resources. BioCatalogue is free
    to use, for all.
  example: '614'
  homepage: https://www.biocatalogue.org/
  mappings:
    miriam: biocatalogue.service
    n2t: biocatalogue.service
    prefixcommons: BIOCATALOGUE.SERVICE
  name: BioCatalogue Service
  pattern: ^\d+$
  preferred_prefix: biocatalogue.service
  uri_format: https://www.biocatalogue.org/services/$1
biocyc:
  description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides
    an electronic reference source on the genomes and metabolic pathways of sequenced
    organisms.
  example: ECOLI:CYT-D-UBIOX-CPLX
  homepage: http://biocyc.org
  mappings:
    go: BioCyc
    miriam: biocyc
    n2t: biocyc
    prefixcommons: BIOCYC
    uniprot: BioCyc
  name: BioCyc collection of metabolic pathway databases
  pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$
  preferred_prefix: biocyc
  uri_format: http://biocyc.org/getid?id=$1
biogrid:
  description: BioGRID is a database of physical and genetic interactions in Saccharomyces
    cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
    Schizosaccharomyces pombe.
  example: '31623'
  homepage: http://thebiogrid.org/
  mappings:
    miriam: biogrid
    n2t: biogrid
    prefixcommons: BIOGRID
    uniprot: BioGRID
  name: BioGRID
  pattern: ^\d+$
  preferred_prefix: biogrid
  uri_format: http://thebiogrid.org/$1
biogrid.interaction:
  contact:
    email: md.tyers@umontreal.ca
    github: null
    name: Mike Tyers
    orcid: 0000-0002-9713-9994
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: BioGRID is a database of physical and genetic interactions in Saccharomyces
    cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
    Schizosaccharomyces pombe.
  example: '2649230'
  homepage: https://thebiogrid.org/
  name: BioGRID Interactions
  part_of: biogrid
  pattern: ^\d+$
  preferred_prefix: biogrid.interaction
  uri_format: https://thebiogrid.org/interaction/$1
biolegend:
  description: BioLegend is a life sciences supply vendor.
  example: '3403'
  homepage: https://www.biolegend.com
  name: BioLegend
  preferred_prefix: biolegend
  uri_format: https://www.biolegend.com/Default.aspx?ID=6664&productid=$1
biolink:
  description: A high level datamodel of biological entities (genes, diseases, phenotypes,
    pathways, individuals, substances, etc) and their associations.
  example: Gene
  homepage: https://biolink.github.io/biolink-model/
  mappings:
    biolink: biolink
    miriam: biolink
  name: BioLink Model
  pattern: ^\S+$
  preferred_prefix: biolink
  uri_format: https://w3id.org/biolink/vocab/$1
biominder:
  description: Database of the dielectric properties of biological tissues.
  example: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3
  homepage: https://datalab.rwth-aachen.de/MINDER
  mappings:
    miriam: biominder
    n2t: biominder
    prefixcommons: BIOMINDER
  name: Bio-MINDER Tissue Database
  pattern: ^[a-z0-9\-]+$
  preferred_prefix: biominder
  uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1
biomodels.db:
  description: BioModels Database is a data resource that allows biologists to store,
    search and retrieve published mathematical models of biological interests.
  example: BIOMD0000000048
  homepage: https://www.ebi.ac.uk/biomodels/
  mappings:
    go: BIOMD
    miriam: biomodels.db
    n2t: biomodels.db
    prefixcommons: BIOMODELS.DB
  name: BioModels Database
  pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
  preferred_prefix: biomodels.db
  providers:
  - code: CURATOR_REVIEW
    description: Caltech mirror
    homepage: http://biomodels.caltech.edu/
    name: Caltech mirror
    uri_format: http://biomodels.caltech.edu/$1
  - code: omicsdi
    description: BioModels through OmicsDI
    homepage: https://www.omicsdi.org/
    name: BioModels through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/biomodels/$1
  synonyms:
  - BIOMD
  uri_format: https://www.ebi.ac.uk/biomodels/$1
biomodels.kisao:
  banana: KISAO
  contact:
    email: karr@mssm.edu
    github: jonrkarr
    name: Jonathan Karr
    orcid: null
  description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that
    describes simulation algorithms and methods used for biological kinetic models,
    and the relationships between them. This provides a means to unambiguously refer
    to simulation algorithms when describing a simulation experiment.
  example: KISAO_0000057
  homepage: http://co.mbine.org/standards/kisao
  license: Artistic License 2.0
  mappings:
    bioportal: KISAO
    miriam: biomodels.kisao
    n2t: biomodels.kisao
    obofoundry: KISAO
    ols: kisao
    ontobee: KISAO
    prefixcommons: KISAO
  name: Kinetic Simulation Algorithm Ontology
  pattern: ^KISAO_\d+$
  preferred_prefix: biomodels.kisao
  synonyms:
  - kisao
  uri_format: http://purl.obolibrary.org/obo/KISAO_$1
  version: '2.30'
biomodels.teddy:
  description: The Terminology for Description of Dynamics (TEDDY) is an ontology
    for dynamical behaviours, observable dynamical phenomena, and control elements
    of bio-models and biological systems in Systems Biology and Synthetic Biology.
  example: '0000066'
  homepage: http://teddyontology.sourceforge.net/
  mappings:
    bioportal: TEDDY
    miriam: biomodels.teddy
    n2t: biomodels.teddy
    ols: teddy
    prefixcommons: BIOMODELS.TEDDY
  name: Terminology for Description of Dynamics
  pattern: ^\d+$
  preferred_prefix: biomodels.teddy
  synonyms:
  - teddy
  uri_format: https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1
  version: '2014-04-24'
biomodels.vocabulary:
  description: Vocabulary used in the RDF representation of SBML models.
  example: rateRule
  homepage: http://biomodels.net/rdf/vocabulary.rdf
  mappings:
    miriam: biomodels.vocabulary
    n2t: biomodels.vocabulary
    prefixcommons: BIOMODELS.VOCABULARY
  name: SBML RDF Vocabulary
  pattern: ^[A-Za-z]+$
  preferred_prefix: biomodels.vocabulary
  uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1
bionumbers:
  description: BioNumbers is a database of key numberical information that may be
    used in molecular biology. Along with the numbers, it contains references to the
    original literature, useful comments, and related numeric data.
  example: '104674'
  homepage: https://bionumbers.hms.harvard.edu
  mappings:
    miriam: bionumbers
    n2t: bionumbers
    prefixcommons: BIONUMBERS
  name: BioNumbers
  pattern: ^\d+$
  preferred_prefix: bionumbers
  uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1
bioportal:
  description: "BioPortal is an open repository of biomedical ontologies that provides\
    \ access via Web services and Web browsers to ontologies developed in OWL, RDF,\
    \ OBO format and Prot\xE9g\xE9 frames. BioPortal functionality includes the ability\
    \ to browse, search and visualize ontologies."
  example: '1046'
  homepage: http://bioportal.bioontology.org/
  mappings:
    miriam: bioportal
    n2t: bioportal
    prefixcommons: BIOPORTAL
  name: BioPortal
  pattern: ^\d+$
  preferred_prefix: bioportal
  uri_format: http://bioportal.bioontology.org/ontologies/$1
bioproject:
  description: "BioProject provides an organizational framework to access metadata\
    \ about research projects and the data from the projects that are deposited into\
    \ different databases. It provides information about a project\u2019s scope, material,\
    \ objectives, funding source and general relevance categories."
  example: PRJDB3
  homepage: http://trace.ddbj.nig.ac.jp/bioproject/
  mappings:
    miriam: bioproject
    n2t: bioproject
    prefixcommons: BIOPROJECT
  name: BioProject
  pattern: ^PRJ[DEN][A-Z]\d+$
  preferred_prefix: bioproject
  providers:
  - code: ncbi
    description: BioProject at NCBI
    homepage: https://www.ncbi.nlm.nih.gov/bioproject
    name: BioProject at NCBI
    uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1
  - code: ebi
    description: BioProject at European Nucleotide Archive (ENA)
    homepage: https://www.ebi.ac.uk/ena/
    name: BioProject at European Nucleotide Archive (ENA)
    uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
  uri_format: https://www.ncbi.nlm.nih.gov/bioproject/?term=$1
bioregistry:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Bioregistry is integrative meta-registry of biological databases,
    ontologies, and nomenclatures that is backed by an open database.
  example: bioregistry
  homepage: https://bioregistry.io
  name: Bioregistry
  preferred_prefix: bioregistry
  uri_format: https://bioregistry.io/registry/$1
bioregistry.collection:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Manually curated collections of resources stored in the bioregistry
  example: '0000001'
  homepage: https://bioregistry.io/collection
  name: Bioregistry Collections
  pattern: ^\d{7}$
  preferred_prefix: bioregistry.collection
  uri_format: https://bioregistry.io/collection/$1
bioregistry.schema:
  contact:
    email: cthoyt@gmail.com
    github: cthoyt
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Schema for the export of the Bioregistry as RDF
  example: '0000001'
  homepage: https://bioregistry.io/schema
  name: Bioregistry Schema
  pattern: ^\d{7}$
  preferred_prefix: bioregistry.schema
  uri_format: https://bioregistry.io/schema/#$1
biorxiv:
  description: The bioRxiv is a preprint server for biology
  example: 2021.07.23.453588
  homepage: https://biorxiv.org
  mappings:
    go: bioRxiv
    scholia: biorxiv
  name: bioRxiv
  preferred_prefix: biorxiv
  uri_format: https://www.biorxiv.org/content/$1
biosample:
  description: The BioSample Database stores information about biological samples
    used in molecular experiments, such as sequencing, gene expression or proteomics.
    It includes reference samples, such as cell lines, which are repeatedly used in
    experiments. Accession numbers for the reference samples will be exchanged with
    a similar database at NCBI, and DDBJ (Japan). Record access may be affected due
    to different release cycles and inter-institutional synchronisation.
  example: SAMEA2397676
  homepage: https://www.ebi.ac.uk/biosamples/
  mappings:
    cellosaurus: BioSample
    miriam: biosample
    n2t: biosample
    prefixcommons: BIOSAMPLE
  name: BioSample
  pattern: ^SAM[NED](\w)?\d+$
  preferred_prefix: biosample
  providers:
  - code: ncbi
    description: BioSample at NCBI
    homepage: http://www.ncbi.nlm.nih.gov/biosample
    name: BioSample at NCBI
    uri_format: http://www.ncbi.nlm.nih.gov/biosample?term=$1
  - code: CURATOR_REVIEW
    description: BioSample at DNA Data Bank of Japan
    homepage: http://trace.ddbj.nig.ac.jp/biosample/
    name: BioSample at DNA Data Bank of Japan
    uri_format: http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1
  uri_format: https://www.ebi.ac.uk/biosamples/sample/$1
biosimulations:
  description: BioSimulations is an open repository of simulation projects, including
    simulation experiments, their results, and data visualizations of their results.
    BioSimulations supports a broad range of model languages, modeling frameworks,
    simulation algorithms, and simulation software tools.
  example: Yeast-cell-cycle-Irons-J-Theor-Biol-2009
  homepage: https://icahn.mssm.edu/
  mappings:
    miriam: biosimulations
  name: biosimulations
  pattern: ^[a-zA-Z0-9_-]{3,}$
  preferred_prefix: biosimulations
  uri_format: https://biosimulations.org/projects/$1
biosimulators:
  description: BioSimulators is a registry of containerized simulation tools that
    support a common interface. The containers in BioSimulators support a range of
    modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete
    kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats
    (e.g., BGNL, SBML, SED-ML).
  example: vcell
  homepage: https://biosimulators.org/
  mappings:
    miriam: biosimulators
  name: BioSimulators
  pattern: ^[a-zA-Z0-9-_]+$
  preferred_prefix: biosimulators
  uri_format: https://biosimulators.org/simulators/$1
biostudies:
  description: The BioStudies database holds descriptions of biological studies, links
    to data from these studies in other databases at EMBL-EBI or outside, as well
    as data that do not fit in the structured archives at EMBL-EBI. The database can
    accept a wide range of types of studies described via a simple format. It also
    enables manuscript authors to submit supplementary information and link to it
    from the publication.
  example: S-EPMC6266652
  homepage: https://www.ebi.ac.uk/biostudies/
  mappings:
    fairsharing: biodbcore-000989
    miriam: biostudies
    n2t: biostudies
  name: BioStudies database
  pattern: ^S-[A-Z]{4}[A-Z\d\-]+$
  preferred_prefix: biostudies
  uri_format: https://www.ebi.ac.uk/biostudies/studies/$1
biosystems:
  description: The NCBI BioSystems database centralizes and cross-links existing biological
    systems databases, increasing their utility and target audience by integrating
    their pathways and systems into NCBI resources.
  example: '001'
  homepage: https://www.ncbi.nlm.nih.gov/biosystems/
  mappings:
    miriam: biosystems
    n2t: biosystems
    prefixcommons: BIOSYSTEMS
  name: BioSystems
  pattern: ^\d+$
  preferred_prefix: biosystems
  uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1
biotools:
  description: BioTools is a registry of databases and software with tools, services,
    and workflows for biological and biomedical research.
  example: uniprotkb
  homepage: https://bio.tools/
  mappings:
    miriam: biotools
    n2t: biotools
    prefixcommons: BIOTOOLS
  name: BioTools
  pattern: ^[A-Za-z0-9\_]*$
  preferred_prefix: biotools
  uri_format: https://bio.tools/$1
biozil:
  description: Redistributor of bilogics and biomedical supplies
  example: ls-c35719-120
  homepage: https://www.biozol.de/en
  name: BIOZIL
  preferred_prefix: biozil
  uri_format: https://www.biozol.de/en/product/$1
birnlex:
  comment: Part of the NeuroLex namespace now
  description: The BIRN Project lexicon will provide entities for data and database
    annotation for the BIRN project, covering anatomy, disease, data collection, project
    management and experimental design.
  example: birnlex_2023
  homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX
  mappings:
    bioportal: BIRNLEX
  name: Biomedical Informatics Research Network Lexicon
  preferred_prefix: birnlex
bitterdb.cpd:
  description: BitterDB is a database of compounds reported to taste bitter to humans.
    The compounds can be searched by name, chemical structure, similarity to other
    bitter compounds, association with a particular human bitter taste receptor, and
    so on. The database also contains information on mutations in bitter taste receptors
    that were shown to influence receptor activation by bitter compounds. The aim
    of BitterDB is to facilitate studying the chemical features associated with bitterness.
    This collection references compounds.
  example: '46'
  homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
  mappings:
    miriam: bitterdb.cpd
    n2t: bitterdb.cpd
    prefixcommons: BITTERDB.CPD
  name: BitterDB Compound
  pattern: ^\d+$
  preferred_prefix: bitterdb.cpd
  uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1
bitterdb.rec:
  description: BitterDB is a database of compounds reported to taste bitter to humans.
    The compounds can be searched by name, chemical structure, similarity to other
    bitter compounds, association with a particular human bitter taste receptor, and
    so on. The database also contains information on mutations in bitter taste receptors
    that were shown to influence receptor activation by bitter compounds. The aim
    of BitterDB is to facilitate studying the chemical features associated with bitterness.
    This collection references receptors.
  example: '1'
  homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
  mappings:
    miriam: bitterdb.rec
    n2t: bitterdb.rec
    prefixcommons: BITTERDB.REC
  name: BitterDB Receptor
  pattern: ^\d+$
  preferred_prefix: bitterdb.rec
  uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1
bmrb:
  description: BMRB collects, annotates, archives, and disseminates (worldwide in
    the public domain) the important spectral and quantitative data derived from NMR
    spectroscopic investigations of biological macromolecules and metabolites. The
    goal is to empower scientists in their analysis of the structure, dynamics, and
    chemistry of biological systems and to support further development of the field
    of biomolecular NMR spectroscopy.
  example: '15000'
  homepage: http://www.bmrb.wisc.edu/
  mappings:
    fairsharing: FAIRsharing.p06nme
    miriam: bmrb
    uniprot: BMRB
  name: Biological Magnetic Resonance Data Bank
  pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$
  preferred_prefix: bmrb
  uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html
bmrb.restraint:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NMR Restraints Grid contains the original NMR data as collected
    for over 2500 protein and nucleic acid structures with corresponding PDB entries.
    In addition to the original restraints, most of the distance, dihedral angle and
    RDC restraint data (>85%) were parsed, and those in over 500 entries were converted
    and filtered. The converted and filtered data sets constitute the DOCR and FRED
    databases respectively.
  example: '28789'
  homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
  name: NMR Restraints Grid
  preferred_prefix: bmrb.restraint
  uri_format: https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1
bold.taxonomy:
  description: The Barcode of Life Data System (BOLD) is an informatics workbench
    aiding the acquisition, storage, analysis and publication of DNA barcode records.
    The associated taxonomy browser shows the progress of DNA barcoding and provides
    sample collection site distribution, and taxon occurence information.
  example: '27267'
  homepage: http://www.boldsystems.org/
  mappings:
    miriam: bold.taxonomy
    n2t: bold.taxonomy
    ncbi: BOLD
    prefixcommons: BOLD.TAXONOMY
  name: Barcode of Life database
  pattern: ^\d+$
  preferred_prefix: bold.taxonomy
  uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1
bootstrep:
  banana: BOOTSTREP
  contact:
    email: vlee@ebi.ac.uk
    github: null
    name: Vivian Lee
    orcid: null
  deprecated: true
  homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html
  mappings:
    obofoundry: BOOTSTREP
    prefixcommons: BOOTSTREP
  name: Gene Regulation Ontology
  preferred_prefix: BOOTSTREP
  uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1
bpdb:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Database of biopesticides maintained by the University of Hertfordshire '
  example: '2404'
  homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm
  name: Bio-Pesticides DataBase
  preferred_prefix: bpdb
  uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm
brenda:
  description: BRENDA is a collection of enzyme functional data available to the scientific
    community. Data on enzyme function are extracted directly from the primary literature
    The database covers information on classification and nomenclature, reaction and
    specificity, functional parameters, occurrence, enzyme structure and stability,
    mutants and enzyme engineering, preparation and isolation, the application of
    enzymes, and ligand-related data.
  example: 1.1.1.1
  homepage: https://www.brenda-enzymes.org/
  mappings:
    go: BRENDA
    miriam: brenda
    n2t: brenda
    prefixcommons: BRENDA
    uniprot: BRENDA
  name: BRENDA, The Comprehensive Enzyme Information System
  pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
  preferred_prefix: brenda
  uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1
broad:
  description: Magnaporthe grisea, the causal agent of rice blast disease, is one
    of the most devasting threats to food security worldwide and is a model organism
    for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe
    comparative genomics database provides accesses to multiple fungal genomes from
    the Magnaporthaceae family to facilitate the comparative analysis. As part of
    the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes
    the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies
    of Gaeumannomyces graminis var. tritici and M. poae.
  example: S7000002168151102
  homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/
  mappings:
    miriam: broad
    n2t: broad
    prefixcommons: BROAD
  name: Broad Fungal Genome Initiative
  pattern: ^S\d+$
  preferred_prefix: broad
  uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1
bs:
  comment: An alernative vocabulary that has been aligned and integrated in Sequence
    Ontology (SO).
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: SO is a collaborative ontology project for the definition of sequence
    features used in biological sequence annotation. It is part of the Open Biomedical
    Ontologies library.
  example: '00042'
  homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies
  name: Biosapiens Protein Feature Ontology
  pattern: ^\d+$
  preferred_prefix: bs
bspo:
  banana: BSPO
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: null
  description: An ontology for respresenting spatial concepts, anatomical axes, gradients,
    regions, planes, sides and surfaces. These concepts can be used at multiple biological
    scales and in a diversity of taxa, including plants, animals and fungi. The BSPO
    is used to provide a source of anatomical location descriptors for logically defining
    anatomical entity classes in anatomy ontologies.
  example: 0000029
  homepage: https://github.com/obophenotype/biological-spatial-ontology
  license: CC BY 3.0
  mappings:
    bioportal: BSPO
    obofoundry: BSPO
    ols: bspo
    ontobee: BSPO
    prefixcommons: BSPO
  name: Biological Spatial Ontology
  pattern: ^\d{7}$
  preferred_prefix: BSPO
  uri_format: http://purl.obolibrary.org/obo/BSPO_$1
  version: '2021-10-13'
bto:
  banana: BTO
  contact:
    email: a.chang@tu-bs.de
    github: null
    name: Antje Chang
    orcid: null
  description: The Brenda tissue ontology is a structured controlled vocabulary eastablished
    to identify the source of an enzyme cited in the Brenda enzyme database. It comprises
    terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular
    organisms.
  example: 0000590
  homepage: http://www.brenda-enzymes.org
  license: CC BY 4.0
  mappings:
    bioportal: BTO
    cellosaurus: BTO
    go: BTO
    miriam: bto
    n2t: bto
    obofoundry: BTO
    ols: bto
    ontobee: BTO
    prefixcommons: BTO
    wikidata: P5501
  name: BRENDA tissue / enzyme source
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: BTO
  synonyms:
  - BTO
  uri_format: https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1
  version: '2021-10-26'
bugbase.expt:
  description: BugBase is a MIAME-compliant microbial gene expression and comparative
    genomic database. It stores experimental annotation and multiple raw and analysed
    data formats, as well as protocols for bacterial microarray designs. This collection
    references microarray experiments.
  example: '288'
  homepage: http://bugs.sgul.ac.uk/E-BUGS
  mappings:
    miriam: bugbase.expt
    n2t: bugbase.expt
    prefixcommons: BUGBASE.EXPT
  name: BugBase Expt
  pattern: ^\d+$
  preferred_prefix: bugbase.expt
  uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view
bugbase.protocol:
  description: BugBase is a MIAME-compliant microbial gene expression and comparative
    genomic database. It stores experimental annotation and multiple raw and analysed
    data formats, as well as protocols for bacterial microarray designs. This collection
    references design protocols.
  example: '67'
  homepage: http://bugs.sgul.ac.uk/E-BUGS
  mappings:
    miriam: bugbase.protocol
    n2t: bugbase.protocol
    prefixcommons: BUGBASE.PROTOCOL
  name: BugBase Protocol
  pattern: ^\d+$
  preferred_prefix: bugbase.protocol
  uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view
bykdb:
  description: The bacterial tyrosine kinase database (BYKdb) that collects sequences
    of putative and authentic bacterial tyrosine kinases,  providing structural and
    functional information.
  example: A0A009E7X8
  homepage: https://bykdb.ibcp.fr/BYKdb/
  mappings:
    miriam: bykdb
    n2t: bykdb
    prefixcommons: BYKDB
  name: Bacterial Tyrosine Kinase Database
  pattern: ^[A-Z0-9]+$
  preferred_prefix: bykdb
  uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html
cabri:
  description: CABRI (Common Access to Biotechnological Resources and Information)
    is an online service where users can search a number of European Biological Resource
    Centre catalogues. It lists the availability of a particular organism or genetic
    resource and defines the set of technical specifications and procedures which
    should be used to handle it.
  example: dsmz_mutz-id:ACC 291
  homepage: http://www.cabri.org/
  mappings:
    miriam: cabri
    n2t: cabri
    ncbi: CABRI
    prefixcommons: CABRI
  name: Common Access to Biological Resources and Information Project
  pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$
  preferred_prefix: cabri
  providers:
  - code: CURATOR_REVIEW
    description: CABRI Cell Lines catalogue in Brussels (SRS)
    homepage: http://www.be.cabri.org/
    name: CABRI Cell Lines catalogue in Brussels (SRS)
    uri_format: http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]
  uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]
cadsr:
  description: The US National Cancer Institute (NCI) maintains and administers data
    elements, forms, models, and components of these items in a metadata registry
    referred to as the Cancer Data Standards Registry and Repository, or caDSR.
  example: '3771992'
  homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki
  mappings:
    miriam: cadsr
    n2t: cadsr
  name: Cancer Data Standards Registry and Repository
  pattern: ^[0-9]*$
  preferred_prefix: cadsr
  uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]
caloha:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This is a code repository for the SIB - Swiss Institute of Bioinformatics
    CALIPHO group neXtProt project, which is a comprehensive human-centric discovery
    platform, that offers a integration of and navigation through protein-related
    data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies
    to help uncover the function of uncharacterized human proteins.
  example: '0001'
  homepage: https://github.com/calipho-sib/controlled-vocabulary
  name: CALIPHO Group Ontology of Human Anatomy
  pattern: ^\d+$
  preferred_prefix: caloha
  references:
  - https://twitter.com/neXtProt_news/status/1350105997633867781
cameo:
  description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community
    project is to continuously evaluate the accuracy and reliability of protein structure
    prediction servers, offering scores on  tertiary and quaternary structure prediction,
    model quality estimation, accessible surface area prediction, ligand binding site
    residue prediction and contact prediction services in a fully automated manner.
    These predictions are regularly compared against reference structures from PDB.
  example: 2019-08-03_00000089_1
  homepage: https://cameo3d.org
  mappings:
    miriam: cameo
    n2t: cameo
    prefixcommons: CAMEO
  name: Continuous Automated Model Evaluation
  pattern: ^[0-9\-_]+$
  preferred_prefix: cameo
  uri_format: https://www.cameo3d.org/sp/targets/target/$1
caps:
  description: CAPS-DB is a structural classification of helix-cappings or caps compiled
    from protein structures. The regions of the polypeptide chain immediately preceding
    or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps
    extracted from protein structures have been structurally classified based on geometry
    and conformation and organized in a tree-like hierarchical classification where
    the different levels correspond to different properties of the caps.
  example: '434'
  homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home
  mappings:
    miriam: caps
    n2t: caps
    prefixcommons: CAPS
  name: CAPS-DB
  pattern: ^\d+$
  preferred_prefix: caps
  uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1
caro:
  banana: CARO
  contact:
    email: haendel@ohsu.edu
    github: mellybelly
    name: Melissa Haendel
    orcid: null
  description: An upper level ontology to facilitate interoperability between existing
    anatomy ontologies for different species
  example: '0000000'
  homepage: https://github.com/obophenotype/caro/
  license: CC BY 3.0
  mappings:
    bioportal: CARO
    go: CARO
    obofoundry: CARO
    ols: caro
    ontobee: CARO
    prefixcommons: CARO
  name: Common Anatomy Reference Ontology
  preferred_prefix: CARO
  uri_format: http://purl.obolibrary.org/obo/CARO_$1
  version: '2019-05-24'
cas:
  description: CAS (Chemical Abstracts Service) is a division of the American Chemical
    Society and is the producer of comprehensive databases of chemical information.
  example: 50-00-0
  homepage: https://commonchemistry.cas.org/
  mappings:
    cheminf: '000446'
    go: CAS
    miriam: cas
    n2t: cas
    prefixcommons: CAS
    scholia: cas
    wikidata: P231
  name: CAS Chemical Registry
  pattern: ^\d{1,7}\-\d{2}\-\d$
  preferred_prefix: cas
  providers:
  - code: 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/
    name: Scholia
    uri_format: https://scholia.toolforge.org/cas/$1
  synonyms:
  - CASID
  - CAS_RN
  - SECONDARY_CAS_RN
  - cas_id
  uri_format: https://commonchemistry.cas.org/detail?ref=$1
cath:
  description: CATH is a classification of protein structural domains. We group protein
    domains into superfamilies when there is sufficient evidence they have diverged
    from a common ancestor. CATH can be used to predict structural and functional
    information directly from protein sequence.
  example: 1.10.8.10
  homepage: http://www.cathdb.info
  mappings:
    miriam: cath
    n2t: cath
    prefixcommons: CATH
  name: CATH Protein Structural Domain Superfamily
  pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$
  preferred_prefix: cath
  uri_format: http://www.cathdb.info/cathnode/$1
cath.domain:
  description: The CATH database is a hierarchical domain classification of protein
    structures in the Protein Data Bank. Protein structures are classified using a
    combination of automated and manual procedures. There are four major levels in
    this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
    Architecture (classification based on overall shape), Topology (fold family) and
    Homologous superfamily (protein domains which are thought to share a common ancestor).
    This colelction is concerned with CATH domains.
  example: 1cukA01
  homepage: http://www.cathdb.info/
  mappings:
    miriam: cath.domain
    n2t: cath.domain
    prefixcommons: CATH.DOMAIN
  name: CATH domain
  pattern: ^\w+$
  preferred_prefix: cath.domain
  uri_format: http://www.cathdb.info/domain/$1
cath.superfamily:
  description: The CATH database is a hierarchical domain classification of protein
    structures in the Protein Data Bank. Protein structures are classified using a
    combination of automated and manual procedures. There are four major levels in
    this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
    Architecture (classification based on overall shape), Topology (fold family) and  Homologous
    superfamily (protein domains which are thought to share a common ancestor). This
    colelction is concerned with superfamily classification.
  example: 1.10.10.200
  homepage: http://www.cathdb.info/
  mappings:
    miriam: cath.superfamily
    n2t: cath.superfamily
    prefixcommons: CATH.SUPERFAMILY
  name: CATH superfamily
  part_of: cath
  pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
  preferred_prefix: cath.superfamily
  uri_format: http://www.cathdb.info/cathnode/$1
cattleqtldb:
  description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
    designed to house publicly all available QTL and single-nucleotide polymorphism/gene
    association data on livestock animal species. This collection references cattle
    QTLs.
  example: '4685'
  homepage: https://www.animalgenome.org/QTLdb
  mappings:
    miriam: cattleqtldb
    n2t: cattleqtldb
    prefixcommons: CATTLEQTLDB
  name: Animal Genome Cattle QTL
  part_of: qtldb
  pattern: ^\d+$
  preferred_prefix: cattleqtldb
  uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
cazy:
  description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized
    in enzymes that build and breakdown complex carbohydrates and glycoconjugates.
    These enzymes are classified into families based on structural features.
  example: GT10
  homepage: http://www.cazy.org/
  mappings:
    go: CAZY
    miriam: cazy
    n2t: cazy
    prefixcommons: CAZY
    uniprot: CAZy
  name: Carbohydrate Active EnZYmes
  pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$
  preferred_prefix: cazy
  uri_format: http://www.cazy.org/$1.html
cba:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological
    Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available
    in MEDLINE.'
  example: '375364'
  homepage: http://www.cba.ac.cn
  name: Chinese Biological Abstracts
  preferred_prefix: cba
  uri_format: https://europepmc.org/article/CBA/$1
cbioportal:
  description: The cBioPortal for Cancer Genomics provides visualization, analysis
    and download of large-scale cancer genomics data sets.
  example: laml_tcga_pub
  homepage: http://www.cbioportal.org
  mappings:
    miriam: cbioportal
    n2t: cbioportal
  name: The cBioPortal for Cancer Genomics
  pattern: ^[a-z0-9\_]+$
  preferred_prefix: cbioportal
  uri_format: https://www.cbioportal.org/study/summary?id=$1
ccdc:
  description: The Cambridge Crystallographic Data Centre (CCDC) develops and maintains
    the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule
    crystal structure data. A CCDC Number is a unique identifier assigned to a dataset
    deposited with the CCDC.
  example: '1829126'
  homepage: https://www.ccdc.cam.ac.uk/
  mappings:
    miriam: ccdc
  name: CCDC Number
  pattern: ^\d{6,7}$
  preferred_prefix: ccdc
  uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG
ccds:
  description: The Consensus CDS (CCDS) project is a collaborative effort to identify
    a core set of human and mouse protein coding regions that are consistently annotated
    and of high quality. The CCDS set is calculated following coordinated whole genome
    annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal
    is to support convergence towards a standard set of gene annotations.
  example: CCDS13573.1
  homepage: http://www.ncbi.nlm.nih.gov/CCDS/
  mappings:
    miriam: ccds
    n2t: ccds
    prefixcommons: CCDS
    uniprot: CCDS
  name: Consensus CDS
  pattern: ^CCDS\d+\.\d+$
  preferred_prefix: ccds
  uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1
ccle:
  description: Datasets around different cancer cell lines generated by the Broad
    Institute and Novartis
  example: BT20_BREAST
  homepage: https://www.cbioportal.org/study/summary?id=ccle_broad_2019
  mappings:
    cellosaurus: CCLE
  name: Cancer Cell Line Encyclopedia (CCLE) Cells
  preferred_prefix: ccle
  synonyms:
  - ccle.cell
  uri_format: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1
cco:
  banana: CCO
  description: The Cell Cycle Ontology is an application ontology that captures and
    integrates detailed knowledge on the cell cycle process.
  example: '0000003'
  homepage: http://www.semantic-systems-biology.org/apo
  mappings:
    bioportal: CCO
    miriam: cco
    n2t: cco
    ols: cco
    prefixcommons: CCO
  name: Cell Cycle Ontology
  namespace_in_lui: true
  pattern: ^\w+$
  preferred_prefix: cco
  uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1
  version: '2016-03-23'
cdao:
  banana: CDAO
  contact:
    email: balhoff@renci.org
    github: balhoff
    name: Jim Balhoff
    orcid: null
  description: The Comparative Data Analysis Ontology (CDAO) provides a framework
    for understanding data in the context of evolutionary-comparative analysis.  This
    comparative approach is used commonly in bioinformatics and other areas of biology
    to draw inferences from a comparison of differently evolved versions of something,
    such as differently evolved versions of a protein.  In this kind of analysis,
    the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic
    Units).  The OTUs can represent biological species, but also may be drawn from
    higher or lower in a biological hierarchy, anywhere from molecules to communities.  The
    features to be compared among OTUs are rendered in an entity-attribute-value model
    sometimes referred to as the 'character-state data model'.  For a given character,
    such as 'beak length', each OTU has a state, such as 'short' or 'long'.  The differences
    between states are understood to emerge by a historical process of evolutionary
    transitions in state, represented by a model (or rules) of transitions along with
    a phylogenetic tree.  CDAO provides the framework for representing OTUs, trees,
    transformations, and characters.  The representation of characters and transformations
    may depend on imported ontologies for a specific type of character.
  example: '0000072'
  homepage: https://github.com/evoinfo/cdao
  license: CC0 1.0
  mappings:
    bioportal: CDAO
    obofoundry: CDAO
    ols: cdao
    ontobee: CDAO
    prefixcommons: CDAO
  name: Comparative Data Analysis Ontology
  preferred_prefix: CDAO
  uri_format: http://purl.obolibrary.org/obo/CDAO_$1
  version: '2019-06-26'
cdd:
  description: The Conserved Domain Database (CDD) is a collection of multiple sequence
    alignments and derived database search models, which represent protein domains
    conserved in molecular evolution.
  example: cd00400
  homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd
  mappings:
    go: CDD
    miriam: cdd
    n2t: cdd
    ncbi: CDD
    prefixcommons: CDD
    uniprot: CDD
  name: Conserved Domain Database at NCBI
  pattern: ^(cd)?\d{5}$
  preferred_prefix: cdd
  uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
cdno:
  banana: CDNO
  contact:
    email: l.andres.hernandez.18@student.scu.edu.au
    github: LilyAndres
    name: Liliana Andres Hernandez
    orcid: null
  description: None
  example: '0000013'
  homepage: https://github.com/Southern-Cross-Plant-Science/cdno
  license: CC BY 3.0
  mappings:
    obofoundry: CDNO
    ols: cdno
    ontobee: CDNO
  name: Compositional Dietary Nutrition Ontology
  preferred_prefix: CDNO
  uri_format: http://purl.obolibrary.org/obo/CDNO_$1
  version: '2021-10-20'
cdpd:
  description: The Canadian Drug Product Database (DPD) contains product specific
    information on drugs approved for use in Canada, and includes human pharmaceutical
    and biological drugs, veterinary drugs and disinfectant products. This information
    includes 'brand name', 'route of administration' and a Canadian 'Drug Identification
    Number' (DIN).
  example: '63250'
  homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp
  mappings:
    miriam: cdpd
    n2t: cdpd
    prefixcommons: CDPD
  name: Canadian Drug Product Database
  pattern: ^\d+$
  preferred_prefix: cdpd
  uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1
cellbank.australia:
  description: CellBank Australia collects novel cell lines, developed by Australian
    researchers, submits these cell lines to rigorous testing to confirm their integrity,
    and then distributes the cell lines to researchers throughout the world.
  example: ab-1-ha
  homepage: http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/
  mappings:
    cellosaurus: CBA
  name: CellBank Australia
  preferred_prefix: cellbank.australia
  uri_format: https://www.cellbankaustralia.com/$1.html
cellimage:
  description: "The Cell: An Image Library\u2122 is a freely accessible, public repository\
    \ of reviewed and annotated images, videos, and animations of cells from a variety\
    \ of organisms, showcasing cell architecture, intracellular functionalities, and\
    \ both normal and abnormal processes."
  example: '24801'
  homepage: http://cellimagelibrary.org/
  mappings:
    fairsharing: FAIRsharing.8t18te
    miriam: cellimage
    n2t: cellimage
    prefixcommons: CELLIMAGE
  name: Cell Image Library
  pattern: ^\d+$
  preferred_prefix: cellimage
  uri_format: http://cellimagelibrary.org/images/$1
cellosaurus:
  description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts
    to describe all cell lines used in biomedical research. Its scope includes: Immortalized
    cell lines; naturally immortal cell lines (example: stem cell lines); finite life
    cell lines when those are distributed and used widely; vertebrate cell line with
    an emphasis on human, mouse and rat cell lines; and invertebrate (insects and
    ticks) cell lines. Its scope does not include primary cell lines (with the exception
    of the finite life cell lines described above) and plant cell lines.'
  example: CVCL_0440
  homepage: https://web.expasy.org/cellosaurus/
  mappings:
    miriam: cellosaurus
    n2t: cellosaurus
    prefixcommons: CELLOSAURUS
    wikidata: P3289
  name: Cellosaurus ID
  pattern: ^CVCL_[A-Z0-9]{4}$
  preferred_prefix: cellosaurus
  synonyms:
  - CVCL
  uri_format: https://web.expasy.org/cellosaurus/$1
cellrepo:
  description: The Cell Version Control Repository is the single worldwide version
    control repository for engineered and natural cell lines
  example: '82'
  homepage: https://cellrepo.ico2s.org/
  mappings:
    miriam: cellrepo
  name: Cell Version Control Repository
  pattern: ^[0-9]+$
  preferred_prefix: cellrepo
  uri_format: https://cellrepo.ico2s.org/repositories/$1
ceph:
  banana: CEPH
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: null
  description: An anatomical and developmental ontology for cephalopods
  example: 0000109
  homepage: https://github.com/obophenotype/cephalopod-ontology
  license: CC BY 3.0
  mappings:
    bioportal: CEPH
    obofoundry: CEPH
    ols: ceph
    ontobee: CEPH
    prefixcommons: CEPH
  name: Cephalopod Ontology
  pattern: ^\d{7}$
  preferred_prefix: CEPH
  uri_format: http://purl.obolibrary.org/obo/CEPH_$1
  version: '2016-01-12'
cgd:
  description: The Candida Genome Database (CGD) provides access to genomic sequence
    data and manually curated functional information about genes and proteins of the
    human pathogen Candida albicans. It collects gene names and aliases, and assigns
    gene ontology terms to describe the molecular function, biological process, and
    subcellular localization of gene products.
  example: CAL0003079
  homepage: http://www.candidagenome.org/
  mappings:
    go: CGD
    miriam: cgd
    n2t: cgd
    ncbi: CGD
    prefixcommons: CGD
    uniprot: CGD
  name: Candida Genome Database
  pattern: ^CAL\d{7}$
  preferred_prefix: cgd
  uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
cgnc:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Nomenclature Consortium around Chicken genes (analogous to the HGNC
    for humans)
  example: '10087'
  homepage: http://birdgenenames.org/cgnc/
  name: Chicken Gene Nomenclature Consortium
  preferred_prefix: cgnc
  synonyms:
  - BirdBase
  - CGNC
  uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1
cgsc:
  description: The CGSC Database of E. coli genetic information includes genotypes
    and reference information for the strains in the CGSC collection, the names, synonyms,
    properties, and map position for genes, gene product information, and information
    on specific mutations and references to primary literature.
  example: '74'
  homepage: http://cgsc.biology.yale.edu/index.php
  mappings:
    go: CGSC
    miriam: cgsc
    n2t: cgsc
    prefixcommons: CGSC
  name: Coli Genetic Stock Center
  pattern: ^\d+$
  preferred_prefix: cgsc
  uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1
charprot:
  description: CharProt is a database of biochemically characterized proteins designed
    to support automated annotation pipelines. Entries are annotated with gene name,
    symbol and various controlled vocabulary terms, including Gene Ontology terms,
    Enzyme Commission number and TransportDB accession.
  example: CH_001923
  homepage: http://www.jcvi.org/charprotdb
  mappings:
    miriam: charprot
    n2t: charprot
    prefixcommons: CHARPROT
  name: CharProt
  pattern: ^CH_\d+$
  preferred_prefix: charprot
  uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1
chebi:
  banana: CHEBI
  contact:
    email: amalik@ebi.ac.uk
    github: amalik01
    name: Adnan Malik
    orcid: null
  description: Chemical Entities of Biological Interest (ChEBI) is a freely available
    dictionary of molecular entities focused on 'small' chemical compounds.
  example: '24867'
  homepage: http://www.ebi.ac.uk/chebi
  license: CC BY 4.0
  mappings:
    bioportal: CHEBI
    cellosaurus: ChEBI
    cheminf: '000407'
    go: CHEBI
    miriam: chebi
    n2t: chebi
    obofoundry: CHEBI
    ols: chebi
    ontobee: CHEBI
    prefixcommons: CHEBI
    wikidata: P683
  name: Chemical Entities of Biological Interest
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: CHEBI
  providers:
  - code: chebi-img
    description: Image server from chebi
    homepage: https://www.ebi.ac.uk/chebi/
    name: ChEBI
    uri_format: https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=$1
  synonyms:
  - CHEBI
  - CHEBIID
  - ChEBI
  uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
  version: '205'
chembl:
  description: ChEMBL is a database of bioactive compounds, their quantitative properties
    and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
    abstracted and curated from the primary scientific literature.
  example: CHEMBL4303805
  homepage: https://www.ebi.ac.uk/chembl
  mappings:
    cheminf: '000412'
    miriam: chembl
    uniprot: ChEMBL
  name: ChEMBL
  pattern: ^CHEMBL\d+$
  preferred_prefix: chembl
  synonyms:
  - ChEMBL
  - ChEMBL_ID
  - chembl
  uri_format: https://www.ebi.ac.uk/chembl/entity/$1
chembl.compound:
  description: ChEMBL is a database of bioactive compounds, their quantitative properties
    and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
    abstracted and curated from the primary scientific literature.
  example: CHEMBL465070
  homepage: https://www.ebi.ac.uk/chembldb/
  mappings:
    miriam: chembl.compound
    n2t: chembl.compound
    prefixcommons: CHEMBL.COMPOUND
    wikidata: P592
  name: ChEMBL ID
  part_of: chembl
  pattern: ^CHEMBL\d+$
  preferred_prefix: chembl.compound
  providers:
  - code: CURATOR_REVIEW
    description: ChEMBL compound RDF
    homepage: https://github.com/egonw/chembl.rdf
    name: ChEMBL compound RDF
    uri_format: http://linkedchemistry.info/chembl/chemblid/$1
  - code: CURATOR_REVIEW
    description: ChEMBL compound RDF through EBI RDF Platform
    homepage: https://www.ebi.ac.uk/rdf/services/chembl/
    name: ChEMBL compound RDF through EBI RDF Platform
    uri_format: https://rdf.ebi.ac.uk/resource/chembl/molecule/$1
  uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1
chembl.target:
  description: ChEMBL is a database of bioactive compounds, their quantitative properties
    and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
    abstracted and curated from the primary scientific literature.
  example: CHEMBL3467
  homepage: https://www.ebi.ac.uk/chembldb/
  mappings:
    miriam: chembl.target
    n2t: chembl.target
    prefixcommons: CHEMBL.TARGET
  name: ChEMBL target
  part_of: chembl
  pattern: ^CHEMBL\d+$
  preferred_prefix: chembl.target
  providers:
  - code: CURATOR_REVIEW
    description: ChEMBL target RDF
    homepage: https://github.com/egonw/chembl.rdf
    name: ChEMBL target RDF
    uri_format: http://linkedchemistry.info/chembl/chemblid/$1
  - code: CURATOR_REVIEW
    description: ChEMBL target RDF through EBI RDF Platform
    homepage: https://rdf.ebi.ac.uk/resource/chembl/
    name: ChEMBL target RDF through EBI RDF Platform
    uri_format: https://rdf.ebi.ac.uk/resource/chembl/target/$1
  uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1
chemdb:
  description: ChemDB is a chemical database containing commercially available small
    molecules, important for use as synthetic building blocks, probes in systems biology
    and as leads for the discovery of drugs and other useful compounds.
  example: '3966782'
  homepage: http://cdb.ics.uci.edu/
  mappings:
    miriam: chemdb
    n2t: chemdb
    prefixcommons: CHEMDB
  name: ChemDB
  pattern: ^\d+$
  preferred_prefix: chemdb
  uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1
chemidplus:
  description: ChemIDplus is a web-based search system that provides access to structure
    and nomenclature authority files used for the identification of chemical substances
    cited in National Library of Medicine (NLM) databases. It also provides structure
    searching and direct links to many biomedical resources at NLM and on the Internet
    for chemicals of interest.
  example: 57-27-2
  homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp
  mappings:
    miriam: chemidplus
    n2t: chemidplus
    prefixcommons: CHEMIDPLUS
  name: ChemIDplus
  pattern: ^\d+\-\d+\-\d+$
  preferred_prefix: chemidplus
  synonyms:
  - ChemIDplus
  uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1
cheminf:
  banana: CHEMINF
  contact:
    email: egon.willighagen@gmail.com
    github: egonw
    name: Egon Willighagen
    orcid: null
  description: Includes terms for the descriptors commonly used in cheminformatics
    software applications and the algorithms which generate them.
  example: '000410'
  homepage: https://github.com/semanticchemistry/semanticchemistry
  license: CC BY 4.0
  mappings:
    bioportal: CHEMINF
    obofoundry: CHEMINF
    ols: cheminf
    ontobee: CHEMINF
    prefixcommons: CHEMINF
  name: Chemical Information Ontology
  preferred_prefix: CHEMINF
  uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1
  version: '2.0'
chemspider:
  description: ChemSpider is a collection of compound data from across the web, which
    aggregates chemical structures and their associated information into a single
    searchable repository entry. These entries are supplemented with additional properties,
    related information and links back to original data sources.
  example: '56586'
  homepage: http://www.chemspider.com/
  mappings:
    cheminf: '000405'
    miriam: chemspider
    n2t: chemspider
    prefixcommons: CHEMSPIDER
    wikidata: P661
  name: ChemSpider ID
  pattern: ^\d+$
  preferred_prefix: chemspider
  synonyms:
  - Chemspider
  uri_format: http://www.chemspider.com/Chemical-Structure.$1.html
chickenqtldb:
  description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
    designed to house publicly all available QTL and single-nucleotide polymorphism/gene
    association data on livestock animal species. This collection references chicken
    QTLs.
  example: '14362'
  homepage: https://www.animalgenome.org/QTLdb
  mappings:
    miriam: chickenqtldb
    n2t: chickenqtldb
    prefixcommons: CHICKENQTLDB
  name: Animal Genome Chicken QTL
  part_of: qtldb
  pattern: ^\d+$
  preferred_prefix: chickenqtldb
  uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
chiro:
  banana: CHIRO
  contact:
    email: vasilevs@ohsu.edu
    github: nicolevasilevsky
    name: Nicole Vasilevsky
    orcid: null
  description: CHEBI provides a distinct role hierarchy. Chemicals in the structural
    hierarchy are connected via a 'has role' relation. CHIRO provides links from these
    roles to useful other classes in other ontologies. This will allow direct connection
    between chemical structures (small molecules, drugs) and what they do. This could
    be formalized using 'capable of', in the same way Uberon and the Cell Ontology
    link structures to processes.
  homepage: https://github.com/obophenotype/chiro
  license: CC0 1.0
  mappings:
    bioportal: CHIRO
    obofoundry: CHIRO
    ols: chiro
    ontobee: CHIRO
  name: ChEBI Integrated Role Ontology
  no_own_terms: true
  preferred_prefix: CHIRO
  uri_format: http://purl.obolibrary.org/obo/CHIRO_$1
  version: '2015-11-23'
chmo:
  banana: CHMO
  contact:
    email: batchelorc@rsc.org
    github: batchelorc
    name: Colin Batchelor
    orcid: null
  description: CHMO, the chemical methods ontology, describes methods used to collect
    data in chemical experiments, such as mass spectrometry and electron microscopy
    prepare and separate material for further analysis, such as sample ionisation,
    chromatography, and electrophoresis synthesise materials, such as epitaxy and
    continuous vapour deposition It also describes the instruments used in these experiments,
    such as mass spectrometers and chromatography columns. It is intended to be complementary
    to the Ontology for Biomedical Investigations (OBI).
  example: 0002902
  homepage: https://github.com/rsc-ontologies/rsc-cmo
  license: CC BY 4.0
  mappings:
    bioportal: CHMO
    obofoundry: CHMO
    ols: chmo
    ontobee: CHMO
    prefixcommons: CHMO
  name: Chemical Methods Ontology
  pattern: ^\d{7}$
  preferred_prefix: CHMO
  uri_format: http://purl.obolibrary.org/obo/CHMO_$1
  version: '2019-11-14'
cido:
  banana: CIDO
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqun Oliver He
    orcid: null
  description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven
    open-source biomedical ontology in the area of coronavirus infectious disease.
    The CIDO is developed to provide standardized human- and computer-interpretable
    annotation and representation of various coronavirus infectious diseases, including
    their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.
  example: '0000005'
  homepage: https://github.com/cido-ontology/cido
  license: CC BY 4.0
  mappings:
    bioportal: CIDO
    obofoundry: CIDO
    ols: cido
    ontobee: CIDO
  name: Coronavirus Infectious Disease Ontology
  preferred_prefix: CIDO
  uri_format: http://purl.obolibrary.org/obo/CIDO_$1
  version: 1.0.259
cio:
  banana: CIO
  contact:
    email: frederic.bastian@unil.ch
    github: fbastian
    name: "Fr\xE9d\xE9ric Bastian"
    orcid: null
  description: An ontology to capture confidence information about annotations.
  example: '0000040'
  homepage: https://github.com/BgeeDB/confidence-information-ontology
  license: CC0 1.0
  mappings:
    bioportal: CIO
    obofoundry: CIO
    ols: cio
    ontobee: CIO
    prefixcommons: CIO
  name: Confidence Information Ontology
  pattern: ^\d{7}$
  preferred_prefix: CIO
  uri_format: http://purl.obolibrary.org/obo/CIO_$1
  version: '2015-03-10'
citexplore:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: One of the precursors to the EuropePMC project. Now EuropePMC is able
    to resolve CiteXplore codes.
  example: C6155
  homepage: https://www.ebi.ac.uk/citexplore/
  name: CiteXplore
  preferred_prefix: citexplore
  references:
  - https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/
  synonyms:
  - CTX
  uri_format: https://europepmc.org/article/CTX/$1
civic.aid:
  description: 'A CIViC assertion classifies the clinical significance of a variant-disease
    relationship under recognized guidelines. The CIViC Assertion (AID) summarizes
    a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic,
    prognostic or predisposing clinical information for a variant in a specific cancer
    context. CIViC currently has two main types of Assertions: those based on variants
    of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic)
    and those based on variants of primarily germline origin (predisposing). When
    the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence
    Items (EIDs) in CIViC sufficiently cover what is known for a particular variant
    and cancer type, then a corresponding assertion be created in CIViC.'
  example: '3'
  homepage: https://civicdb.org/
  mappings:
    miriam: civic.aid
  name: CIViC Assertion
  pattern: ^[0-9]+$
  preferred_prefix: civic.aid
  uri_format: https://civicdb.org/links/assertions/$1
civic.eid:
  description: "Evidence Items are the central building block of the Clinical Interpretation\
    \ of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a\
    \ piece of information that has been manually curated from trustable medical literature\
    \ about a Variant or genomic \u2018event\u2019 that has implications in cancer\
    \ Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive\
    \ response to therapy, Oncogenicity or protein Function. For example, an Evidence\
    \ Item might describe a line of evidence supporting the notion that tumors with\
    \ a somatic BRAF V600 mutation generally respond well to the drug dabrafenib.\
    \ A Variant may be a single nucleotide substitution, a small insertion or deletion,\
    \ an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g.\
    \ over-expression), etc. Each clinical Evidence statement corresponds to a single\
    \ citable Source (a publication or conference abstract)."
  example: '1199'
  homepage: https://civicdb.org/
  mappings:
    miriam: civic.eid
  name: CIViC Evidence
  pattern: ^[0-9]+$
  preferred_prefix: civic.eid
  uri_format: https://civicdb.org/links/evidence/$1
cl:
  banana: CL
  contact:
    email: addiehl@buffalo.edu
    github: addiehl
    name: Alexander Diehl
    orcid: null
  description: The Cell Ontology is designed as a structured controlled vocabulary
    for cell types. The ontology was constructed for use by the model organism and
    other bioinformatics databases, incorporating cell types from prokaryotes to mammals,
    and includes plants and fungi.
  example: '0000062'
  homepage: https://obophenotype.github.io/cell-ontology/
  license: CC BY 4.0
  mappings:
    bioportal: CL
    go: CL
    miriam: cl
    n2t: cl
    obofoundry: CL
    ols: cl
    ontobee: CL
    prefixcommons: CL
    wikidata: P7963
  name: Cell Ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: CL
  uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1
  version: '2021-11-25'
clao:
  banana: CLAO
  contact:
    email: lagonzalezmo@unal.edu.co
    github: luis-gonzalez-m
    name: "Luis Gonz\xE1lez-Monta\xF1a"
    orcid: null
  description: 'CLAO is an ontology of anatomical terms employed in morphological
    descriptions for the Class Collembola (Arthropoda: Hexapoda).'
  example: 0000088
  homepage: https://github.com/luis-gonzalez-m/Collembola
  license: CC0 1.0
  mappings:
    bioportal: CLAO
    obofoundry: CLAO
    ols: clao
    ontobee: CLAO
  name: Collembola Anatomy Ontology
  preferred_prefix: CLAO
  uri_format: http://purl.obolibrary.org/obo/CLAO_$1
  version: '2021-09-27'
classyfire:
  description: ClassyFire is a web-based application for automated structural classification
    of chemical entities. This application uses a rule-based approach that relies
    on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire
    provides a hierarchical chemical classification of chemical entities (mostly small
    molecules and short peptide sequences), as well as a structure-based textual description,
    based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes
    of organic and inorganic compounds. Moreover, ClassyFire allows for text-based
    search via its web interface. It can be accessed via the web interface or via
    the ClassyFire API.
  example: C0004828
  homepage: http://classyfire.wishartlab.com/
  mappings:
    miriam: classyfire
  name: ClassyFire
  pattern: ^C[0-9]{7}$
  preferred_prefix: classyfire
  uri_format: http://classyfire.wishartlab.com/tax_nodes/$1
cldb:
  description: The Cell Line Data Base (CLDB) is a reference information source for
    human and animal cell lines. It provides the characteristics of the cell lines
    and their availability through  distributors, allowing cell line requests to be
    made from collections and laboratories.
  example: cl3603
  homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html
  mappings:
    cellosaurus: CLDB
    miriam: cldb
    n2t: cldb
    prefixcommons: CLDB
  name: Cell Line Database
  pattern: ^(cl|tum)\d+$
  preferred_prefix: cldb
  uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html
clingene:
  description: The allele registry provides and maintains identifiers for genetic
    variants
  example: CA981206459
  homepage: https://reg.clinicalgenome.org
  mappings:
    biolink: CAID
  name: ClinGen Allele Registry
  preferred_prefix: clingene
  uri_format: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1
clinicaltrials:
  description: ClinicalTrials.gov provides free access to information on clinical
    studies for a wide range of diseases and conditions. Studies listed in the database
    are conducted in 175 countries
  example: NCT00222573
  homepage: https://clinicaltrials.gov/
  mappings:
    miriam: clinicaltrials
    n2t: clinicaltrials
    prefixcommons: CLINICALTRIALS
  name: ClinicalTrials.gov
  pattern: ^NCT\d{8}$
  preferred_prefix: clinicaltrials
  uri_format: https://clinicaltrials.gov/ct2/show/$1
clinvar:
  description: ClinVar archives reports of relationships among medically important
    variants and phenotypes. It records human variation, interpretations of the relationship
    specific variations to human health, and supporting evidence for each interpretation.
    Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
    of the same variation and condition from one or more submitters. Submissions for
    individual variation/phenotype combinations (SCV identifier) are also collected
    and made available separately. This collection references the Variant identifier.
  example: '12345'
  homepage: http://www.ncbi.nlm.nih.gov/clinvar/
  mappings:
    biolink: CLINVAR
    cellosaurus: ClinVar
    miriam: clinvar
    n2t: clinvar
    prefixcommons: ClinVar
    wikidata: P1929
  name: ClinVar Variation ID
  pattern: ^\d+$
  preferred_prefix: clinvar
  uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1
clinvar.record:
  description: ClinVar archives reports of relationships among medically important
    variants and phenotypes. It records human variation, interpretations of the relationship
    specific variations to human health, and supporting evidence for each interpretation.
    Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
    of  the same variation and condition from one or more submitters. Submissions
    for individual variation/phenotype combinations (SCV identifier) are also collected
    and made available separately. This collection references the Record Report, based
    on RCV accession.
  example: RCV000033555.3
  homepage: http://www.ncbi.nlm.nih.gov/clinvar/
  mappings:
    miriam: clinvar.record
    n2t: clinvar.record
    prefixcommons: CLINVAR.RECORD
  name: ClinVar Record
  pattern: ^RCV\d+(\.\d+)?$
  preferred_prefix: clinvar.record
  uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1
clinvar.submission:
  description: ClinVar archives reports of relationships among medically important
    variants and phenotypes. It records human variation, interpretations of the relationship
    specific variations to human health, and supporting evidence for each interpretation.
    Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
    of the same variation and condition from one or more submitters. Submissions for
    individual variation/phenotype combinations (SCV identifier) are also collected
    and made available separately. This collection references submissions, and is
    based on SCV accession.
  example: SCV000151292
  homepage: http://www.ncbi.nlm.nih.gov/clinvar/
  mappings:
    miriam: clinvar.submission
    n2t: clinvar.submission
    prefixcommons: CLINVAR.SUBMISSION
  name: ClinVar Submission
  pattern: ^SCV\d+(\.\d+)?$
  preferred_prefix: clinvar.submission
  uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1
clinvar.submitter:
  description: ClinVar archives reports of relationships among medically important
    variants and phenotypes. It records human variation, interpretations of the relationship
    specific variations to human health, and supporting evidence for each interpretation.
    Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
    of the same variation and condition from one or more submitters (Submitter IDs).
    Submissions for individual variation/phenotype combinations (SCV identifier) are
    also collected and made available separately. This collection references submitters
    (submitter ids) that submit the submissions (SCVs).
  example: '26957'
  homepage: https://www.ncbi.nlm.nih.gov/clinvar/
  mappings:
    miriam: clinvar.submitter
  name: ClinVar Submitter
  pattern: ^\d+$
  preferred_prefix: clinvar.submitter
  uri_format: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1
clo:
  banana: CLO
  contact:
    email: siiraa@umich.edu
    github: null
    name: Sirarat Sarntivijai
    orcid: null
  description: The Cell Line Ontology (CLO) is a community-based ontology of cell
    lines. The CLO is developed to unify publicly available cell line entry data from
    multiple sources to a standardized logically defined format based on consensus
    design patterns.
  example: 0000091
  homepage: http://www.clo-ontology.org
  license: CC BY 3.0
  mappings:
    bioportal: CLO
    cellosaurus: CLO
    obofoundry: CLO
    ols: clo
    ontobee: CLO
    prefixcommons: CLO
    wikidata: P2158
  name: Cell Line Ontology
  preferred_prefix: CLO
  synonyms:
  - CLO
  uri_format: http://purl.obolibrary.org/obo/CLO_$1
  version: 2.1.162
clyh:
  banana: CLYH
  contact:
    email: lucas.leclere@obs-vlfr.fr
    github: L-Leclere
    name: Lucas Leclere
    orcid: null
  description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish
    - of the cnidarian hydrozoan species, Clytia hemiphaerica.
  example: '1000100'
  homepage: https://github.com/EBISPOT/clyh_ontology
  license: CC BY 3.0
  mappings:
    bioportal: CLYH
    obofoundry: CLYH
    ols: clyh
    ontobee: CLYH
  name: Clytia hemisphaerica Development and Anatomy Ontology
  preferred_prefix: CLYH
  uri_format: http://purl.obolibrary.org/obo/CLYH_$1
  version: '2020-05-29'
cmf:
  banana: CMF
  contact:
    email: engelsta@ohsu.edu
    github: null
    name: Mark Engelstad
    orcid: null
  deprecated: true
  description: This ontology represents the clinical findings and procedures used
    in the oral and maxillo-facial surgical domain
  homepage: https://code.google.com/p/craniomaxillofacial-ontology/
  mappings:
    obofoundry: CMF
    prefixcommons: CMF
  name: CranioMaxilloFacial ontology
  preferred_prefix: CMF
  uri_format: http://purl.obolibrary.org/obo/CMF_$1
cmo:
  banana: CMO
  contact:
    email: shimoyama@mcw.edu
    github: null
    name: Mary Shimoyama
    orcid: null
  description: Morphological and physiological measurement records generated from
    clinical and model organism research and health programs.
  example: '0001350'
  homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
  license: CC0 1.0
  mappings:
    bioportal: CMO
    obofoundry: CMO
    ols: cmo
    ontobee: CMO
    prefixcommons: CMO
  name: Clinical measurement ontology
  pattern: ^\d{7}$
  preferred_prefix: CMO
  uri_format: http://purl.obolibrary.org/obo/CMO_$1
  version: '2019-02-19'
cmpo:
  description: CMPO is a species neutral ontology for describing general phenotypic
    observations relating to the whole cell, cellular components, cellular processes
    and cell populations.
  example: '0000435'
  homepage: http://www.ebi.ac.uk/cmpo
  mappings:
    bioportal: CMPO
    ols: cmpo
  name: Cellular Microscopy Phenotype Ontology
  preferred_prefix: cmpo
  version: '2017-12-19'
co_320:
  description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based
    on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping
    Network variables
  example: 0000618
  homepage: https://cropontology.org/ontology/CO_320/Rice
  mappings:
    ols: co_320
  name: Rice ontology
  preferred_prefix: co_320
  uri_format: https://www.cropontology.org/rdf/CO_320:$1
  version: '2019-10-09'
co_321:
  description: July 2018
  example: 0000449
  homepage: https://cropontology.org/ontology/CO_321/Wheat
  mappings:
    ols: co_321
  name: Wheat ontology
  preferred_prefix: co_321
  uri_format: https://www.cropontology.org/rdf/CO_321:$1
  version: '2019-10-09'
co_322:
  description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016
  example: '0000773'
  homepage: https://cropontology.org/ontology/CO_322/Maize
  mappings:
    ols: co_322
  name: Maize ontology
  preferred_prefix: co_322
  uri_format: https://www.cropontology.org/rdf/CO_322:$1
  version: '2019-10-09'
co_323:
  description: ICARDA - TDv5 - Sept 2018
  example: '0000252'
  homepage: https://cropontology.org/ontology/CO_323/Barley
  mappings:
    ols: co_323
  name: Barley ontology
  preferred_prefix: co_323
  uri_format: https://www.cropontology.org/rdf/CO_323:$1
  version: '2019-11-20'
co_324:
  description: Sorghum TDv5 - Oct 2019
  example: '0000111'
  homepage: https://cropontology.org/ontology/CO_324/Sorghum
  mappings:
    ols: co_324
  name: Sorghum ontology
  preferred_prefix: co_324
  uri_format: https://www.cropontology.org/rdf/CO_324:$1
  version: '2019-10-09'
co_325:
  description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019
  example: 0000519
  homepage: https://cropontology.org/ontology/CO_325/Banana
  mappings:
    ols: co_325
  name: Banana ontology
  preferred_prefix: co_325
  uri_format: https://www.cropontology.org/rdf/CO_325:$1
  version: '2019-10-09'
co_326:
  description: Draft version
  example: '0000254'
  homepage: https://cropontology.org/ontology/CO_326/Coconut
  mappings:
    ols: co_326
  name: Coconut ontology
  preferred_prefix: co_326
co_327:
  description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April
    2016
  example: 0000095
  homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet
  license: CC BY 4.0
  mappings:
    ols: co_327
  name: Pearl millet ontology
  preferred_prefix: co_327
  uri_format: https://www.cropontology.org/rdf/CO_327:$1
  version: '2019-10-09'
co_330:
  description: CIP - potato ontology - december 2018
  example: '0000106'
  homepage: https://cropontology.org/ontology/CO_330/Potato
  mappings:
    ols: co_330
  name: Potato ontology
  preferred_prefix: co_330
  uri_format: https://www.cropontology.org/rdf/CO_330:$1
  version: '2019-10-09'
co_331:
  description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019
  example: 0000088
  homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato
  license: CC BY 4.0
  mappings:
    ols: co_331
  name: Sweet Potato ontology
  preferred_prefix: co_331
  uri_format: https://www.cropontology.org/rdf/CO_331:$1
  version: '2019-10-09'
co_333:
  description: 'This ontology was built as part of the AKER project. It describes
    variables used in beet phenotyping (experimental properties and measurement scale)
    for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez).
    Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez)
    - First submission in November 2017.'
  example: '3000045'
  homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology
  license: CC BY 4.0
  mappings:
    ols: co_333
  name: Beet Ontology ontology
  preferred_prefix: co_333
  uri_format: https://www.cropontology.org/rdf/CO_333:$1
  version: '2019-01-23'
co_334:
  description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated
    in February 2016
  example: '0000070'
  homepage: https://cropontology.org/ontology/CO_334/Cassava
  mappings:
    ols: co_334
  name: Cassava ontology
  preferred_prefix: co_334
  uri_format: https://www.cropontology.org/rdf/CO_334:$1
  version: '2019-10-09'
co_335:
  description: CIAT Common bean trait dictionary - version August 2014
  example: 0000189
  homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean
  license: CC BY 4.0
  mappings:
    ols: co_335
  name: Common Bean ontology
  preferred_prefix: co_335
  uri_format: https://www.cropontology.org/rdf/CO_335:$1
  version: '2019-10-09'
co_336:
  description: Soybean Trait Dictionary in template v5 - IITA - July 2015
  example: 0000339
  homepage: https://cropontology.org/ontology/CO_336/Soybean
  mappings:
    ols: co_336
  name: Soybean ontology
  preferred_prefix: co_336
  uri_format: https://www.cropontology.org/rdf/CO_336:$1
co_337:
  description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept
    2015
  example: '0000054'
  homepage: https://cropontology.org/ontology/CO_337/Groundnut
  mappings:
    ols: co_337
  name: Groundnut ontology
  preferred_prefix: co_337
  uri_format: https://www.cropontology.org/rdf/CO_337:$1
  version: '2019-10-09'
co_338:
  description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015
  example: 0000138
  homepage: https://cropontology.org/ontology/CO_338/Chickpea
  mappings:
    ols: co_338
  name: Chickpea ontology
  preferred_prefix: co_338
  uri_format: https://www.cropontology.org/rdf/CO_338:$1
  version: '2019-10-09'
co_339:
  description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015
  example: '0000032'
  homepage: https://cropontology.org/ontology/CO_339/Lentil
  mappings:
    ols: co_339
  name: Lentil ontology
  preferred_prefix: co_339
  uri_format: https://www.cropontology.org/rdf/CO_339:$1
  version: '2019-10-09'
co_340:
  description: Cowpea Trait Dictionary in template v5 - IITA - August 2015
  example: 0000639
  homepage: https://cropontology.org/ontology/CO_340/Cowpea
  mappings:
    ols: co_340
  name: Cowpea ontology
  preferred_prefix: co_340
  uri_format: https://www.cropontology.org/rdf/CO_340:$1
  version: '2019-10-09'
co_341:
  description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015
  example: '0000140'
  homepage: https://cropontology.org/ontology/CO_341/Pigeonpea
  mappings:
    ols: co_341
  name: Pigeonpea ontology
  preferred_prefix: co_341
  uri_format: https://www.cropontology.org/rdf/CO_341:$1
  version: '2019-11-18'
co_343:
  description: version 2019 - pvs
  example: '0100010'
  homepage: https://cropontology.org/ontology/CO_343/Yam
  mappings:
    ols: co_343
  name: Yam ontology
  preferred_prefix: co_343
  uri_format: https://www.cropontology.org/rdf/CO_343:$1
  version: '2019-10-09'
co_345:
  description: Brachiaria (forages) ontology TD v5 - Version Oct 2016
  example: '0000127'
  homepage: https://cropontology.org/ontology/CO_345/Brachiaria
  mappings:
    ols: co_345
  name: Brachiaria ontology
  preferred_prefix: co_345
  uri_format: https://www.cropontology.org/rdf/CO_345:$1
  version: '2019-10-09'
co_346:
  description: oct 2016
  example: 0000199
  homepage: https://cropontology.org/ontology/CO_346/Mungbean
  mappings:
    ols: co_346
  name: Mungbean ontology
  preferred_prefix: co_346
  uri_format: https://www.cropontology.org/rdf/CO_346:$1
  version: '2019-10-09'
co_347:
  description: 'March 2017 version '
  example: 0000108
  homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean
  license: CC BY 4.0
  mappings:
    ols: co_347
  name: Castor bean ontology
  preferred_prefix: co_347
  uri_format: https://www.cropontology.org/rdf/CO_347:$1
  version: '2019-10-09'
co_348:
  description: Brassica Trait Ontology (BRaTO) hosts trait information to describe
    brassica crop data. Terms are collected from various projects including OREGIN,
    RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute
    (UK), Southern Cross University (Australia) and INRA (France).
  example: '1100107'
  homepage: https://cropontology.org/ontology/CO_348/Brassica
  mappings:
    ols: co_348
  name: Brassica ontology
  preferred_prefix: co_348
  uri_format: https://www.cropontology.org/rdf/CO_348:$1
  version: '2019-11-29'
co_350:
  description: Oat trait dictionary started by Oat Global (http://oatglobal.org/)
    and improved by NIAB and PepsiCo
  example: '0000215'
  homepage: https://cropontology.org/ontology/CO_350/Oat
  mappings:
    ols: co_350
  name: Oat ontology
  preferred_prefix: co_350
  uri_format: https://www.cropontology.org/rdf/CO_350:$1
  version: '2019-10-09'
co_356:
  description: Grape Ontology including OIV and bioversity descriptors. INRA July
    2017
  example: '4000027'
  homepage: https://cropontology.org/ontology/CO_356/Vitis
  mappings:
    ols: co_356
  name: Vitis ontology
  preferred_prefix: co_356
  uri_format: https://www.cropontology.org/rdf/CO_356:$1
  version: '2019-11-29'
co_357:
  description: 'This ontology lists all variables used for woody plant observations.
    Terms are collected from various sources (past and ongoing projects at national
    and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET)
    - Version 2 submitted on Jun 2020 by INRAE.'
  example: '1000290'
  homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology
  license: CC BY 4.0
  mappings:
    ols: co_357
  name: Woody Plant Ontology ontology
  preferred_prefix: co_357
  uri_format: https://www.cropontology.org/rdf/CO_357:$1
  version: '2019-11-18'
co_358:
  description: Cotton ontology from CottonGen database - June 2019
  example: 0000139
  homepage: https://cropontology.org/ontology/CO_358/Cotton
  mappings:
    ols: co_358
  name: Cotton ontology
  preferred_prefix: co_358
  uri_format: https://www.cropontology.org/rdf/CO_358:$1
  version: '2020-01-03'
co_359:
  description: December 2019
  example: 0000947
  homepage: https://cropontology.org/ontology/CO_359/Sunflower
  mappings:
    ols: co_359
  name: Sunflower ontology
  preferred_prefix: co_359
  uri_format: https://www.cropontology.org/rdf/CO_359:$1
co_360:
  description: Sugar Kelp trait ontology
  example: '0000071'
  homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait
  license: CC BY 4.0
  mappings:
    ols: co_360
  name: Sugar Kelp trait ontology
  preferred_prefix: co_360
  uri_format: https://www.cropontology.org/rdf/CO_360:$1
  version: '2019-06-26'
co_365:
  description: developed by ICARDA - Dec 2018
  example: '0000205'
  homepage: https://cropontology.org/ontology/CO_365/Fababean
  mappings:
    ols: co_365
  name: Fababean ontology
  preferred_prefix: co_365
  uri_format: https://www.cropontology.org/rdf/CO_365:$1
  version: '2019-10-15'
co_366:
  description: version Dec 2019
  example: '0000072'
  homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut
  license: CC BY 4.0
  mappings:
    ols: co_366
  name: Bambara groundnut ontology
  preferred_prefix: co_366
  uri_format: https://www.cropontology.org/rdf/CO_366:$1
  version: '2019-12-23'
cob:
  banana: COB
  contact:
    email: bpeters@lji.org
    github: bpeters42
    name: Bjoern Peters
    orcid: null
  description: COB brings together key terms from a wide range of OBO projects to
    improve interoperability.
  example: 0000080
  homepage: https://github.com/OBOFoundry/COB
  license: CC0 1.0
  mappings:
    bioportal: COB
    obofoundry: COB
    ols: cob
    ontobee: COB
  name: Core Ontology for Biology and Biomedicine
  preferred_prefix: COB
  uri_format: http://purl.obolibrary.org/obo/COB_$1
  version: '2021-09-13'
coconut:
  comment: '@mSorok is the dev of the resource, hope I got it right!'
  contributor:
    email: null
    github: null
    name: Adriano Rutz
    orcid: 0000-0003-0443-9902
  description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source
    project for Natural Products (NPs) storage, search and analysis. It gathers data
    from over 50 open NP resources and is available free of charge and without any
    restriction. Each entry corresponds to a "flat" NP structure, and is associated,
    when available, to their known stereochemical forms, literature, organisms that
    produce them, natural geographical presence and diverse pre-computed molecular
    properties.
  example: CNP0171505
  homepage: https://coconut.naturalproducts.net
  name: COlleCtion of Open Natural ProdUcTs
  pattern: ^CNP\d{7}$
  preferred_prefix: coconut
  reviewer:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://coconut.naturalproducts.net/compound/coconut_id/$1
cog:
  contact:
    email: cogs@ncbi.nlm.nih.gov
    github: null
    name: Michael Y Galperin
    orcid: 0000-0002-2265-5572
  description: 'COGs stands for Clusters of Orthologous Genes. The database was initially
    created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most
    recently in 2014 (Galperin et al., PMID: 25428365). The current update includes
    complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.
    The new features include ~250 updated COG annotations with corresponding references
    and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity,
    sporulation, and photosynthesis, and the lists of COGs grouped by pathways and
    functional systems.'
  example: COG0001
  homepage: https://www.ncbi.nlm.nih.gov/research/cog/
  mappings:
    biolink: COG
    go: COG_Cluster
  name: Cluster of orthologous genes
  pattern: ^COG\d+$
  preferred_prefix: cog
  synonyms:
  - COG_Cluster
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1
cog.category:
  contact:
    email: cogs@ncbi.nlm.nih.gov
    github: null
    name: Michael Y Galperin
    orcid: 0000-0002-2265-5572
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Higher-level classifications of COG Pathways
  example: K
  homepage: https://www.ncbi.nlm.nih.gov/research/cog/
  name: COG Categories
  part_of: cog
  preferred_prefix: cog.category
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1
cog.pathway:
  contact:
    email: cogs@ncbi.nlm.nih.gov
    github: null
    name: Michael Y Galperin
    orcid: 0000-0002-2265-5572
  description: Database of Clusters of Orthologous Genes grouped by pathways and functional
    systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that
    map into 1,234 genera.
  example: NAD%20biosynthesis
  homepage: https://www.ncbi.nlm.nih.gov/research/cog/pathways
  mappings:
    go: COG_Pathway
  name: COG Pathways
  part_of: cog
  preferred_prefix: cog.pathway
  uri_format: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1
cohd:
  comment: not really sure where the source is. this also links to a system called
    athena. I was not able to figure out what COHD stands for.
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: MIMIC-III is a dataset comprising health-related data associated with
    over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess
    Medical Center between 2001 and 2012
  homepage: https://github.com/MIT-LCP/mimic-omop
  name: MIMIC III Database
  no_own_terms: true
  preferred_prefix: cohd
combine.specifications:
  description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative
    to coordinate the development of the various community standards and formats for
    computational models, initially in Systems Biology and related fields. This collection
    pertains to specifications of the standard formats developed by the Computational
    Modeling in Biology Network.
  example: sbgn.er.level-1.version-1.2
  homepage: https://co.mbine.org/standards/
  mappings:
    miriam: combine.specifications
    n2t: combine.specifications
    prefixcommons: COMBINE.SPECIFICATIONS
  name: COMBINE specifications
  pattern: ^\w+(\-|\.|\w)*$
  preferred_prefix: combine.specifications
  uri_format: https://co.mbine.org/specifications/$1
come:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for
    bioinorganic and other small molecule centres in complex proteins, using a classification
    system based on the concept of a bioinorganic motif.
  example: MOL000160
  homepage: https://www.flymine.org/come
  name: The Bioinorganic Motif Database
  preferred_prefix: come
  uri_format: https://www.flymine.org/come/entry?gn=$1
complexportal:
  description: A database that describes manually curated macromolecular complexes
    and provides links to details about these complexes in other databases.
  example: CPX-263
  homepage: https://www.ebi.ac.uk/complexportal
  mappings:
    go: ComplexPortal
    miriam: complexportal
    n2t: complexportal
    prefixcommons: COMPLEXPORTAL
    uniprot: ComplexPortal
    wikidata: P7718
  name: Complex Portal accession ID
  pattern: ^CPX-[0-9]+$
  preferred_prefix: complexportal
  synonyms:
  - ComplexPortal
  uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
comptox:
  description: The Chemistry Dashboard is a part of a suite of databases and web applications
    developed by the US Environmental Protection Agency's Chemical Safety for Sustainability
    Research Program. These databases and apps support EPA's computational toxicology
    research efforts to develop innovative methods to change how chemicals are currently
    evaluated for potential health risks.
  example: DTXSID2021028
  homepage: https://comptox.epa.gov/dashboard
  mappings:
    miriam: comptox
    n2t: comptox
    prefixcommons: COMPTOX
  name: CompTox Chemistry Dashboard
  pattern: ^DTXSID\d+$
  preferred_prefix: comptox
  uri_format: https://comptox.epa.gov/dashboard/$1
compulyeast:
  description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis
    federated database. This collection references a subset of Uniprot, and contains
    general information about the protein record.
  example: O08709
  homepage: http://compluyeast2dpage.dacya.ucm.es/
  mappings:
    miriam: compulyeast
    n2t: compulyeast
    prefixcommons: COMPULYEAST
  name: Compluyeast-2D-DB
  pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
    0-9][A-Z, 0-9][0-9])$
  preferred_prefix: compulyeast
  uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1
conoserver:
  description: ConoServer is a database specialized in the sequence and structures
    of conopeptides, which are peptides expressed by carnivorous marine cone snails.
  example: '2639'
  homepage: http://www.conoserver.org/
  mappings:
    miriam: conoserver
    n2t: conoserver
    prefixcommons: CONOSERVER
    uniprot: ConoServer
  name: ConoServer
  pattern: ^\d+$
  preferred_prefix: conoserver
  uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1
conso:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: An ontology describing phenomena encountered in the literature surrounding
    neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's
    disease, tauopathies, and related protein aggregation diseases.
  example: CONSO00010
  homepage: https://pharmacome.github.io/conso/
  name: Curation of Neurodegeneration Supporting Ontology
  pattern: ^CONSO\d{5}$
  preferred_prefix: conso
  uri_format: https://pharmacome.github.io/conso/$1
coriell:
  description: The Coriell Cell Repositories provide essential research reagents to
    the scientific community by establishing, verifying, maintaining, and distributing
    cell cultures and DNA derived from cell cultures. These collections, supported
    by funds from the National Institutes of Health (NIH) and several foundations,
    are extensively utilized by research scientists around the world.
  example: GM17027
  homepage: http://ccr.coriell.org/
  mappings:
    cellosaurus: Coriell
    go: CORIELL
    miriam: coriell
    n2t: coriell
    prefixcommons: Coriell
  name: Coriell Institute for Medical Research
  pattern: ^[A-Z]{2}\d+$
  preferred_prefix: coriell
  uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1
corrdb:
  description: A genetic correlation is the proportion of shared variance between
    two traits that is due to genetic causes; a phenotypic correlation is the degree
    to which two traits co-vary among individuals in a population. In the genomics
    era, while gene expression, genetic association, and network analysis provide
    unprecedented means to decode the genetic basis of complex phenotypes, it is important
    to recognize the possible effects genetic progress in one trait can have on other
    traits. This database is designed to collect all published livestock genetic/phenotypic
    trait correlation data, aimed at facilitating genetic network analysis or systems
    biology studies.
  example: '37232'
  homepage: https://www.animalgenome.org
  mappings:
    miriam: corrdb
  name: CorrDB
  pattern: ^[0-9]+$
  preferred_prefix: corrdb
  uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1
corum:
  description: The CORUM database provides a resource of manually annotated protein
    complexes from mammalian organisms. Annotation includes protein complex function,
    localization, subunit composition, literature references and more. All information
    is obtained from individual experiments published in scientific articles, data
    from high-throughput experiments is excluded.
  example: '100'
  homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/
  mappings:
    go: CORUM
    miriam: corum
    n2t: corum
    prefixcommons: CORUM
    uniprot: CORUM
  name: CORUM - the Comprehensive Resource of Mammalian protein complexes
  pattern: ^\d+$
  preferred_prefix: corum
  uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1
cosmic:
  description: COSMIC is a comprehensive global resource for information on somatic
    mutations in human cancer, combining curation of the scientific literature with
    tumor resequencing data from the Cancer Genome Project at the Sanger Institute,
    U.K. This collection references genes.
  example: BRAF
  homepage: http://cancer.sanger.ac.uk/cosmic/
  mappings:
    cellosaurus: Cosmic
    miriam: cosmic
    n2t: cosmic
    prefixcommons: COSMIC
  name: COSMIC Gene
  pattern: ^[A-Z0-9]+$
  preferred_prefix: cosmic
  uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1
cosmic.cell:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's
    largest and most comprehensive resource for exploring the impact of somatic mutations
    in human cancer
  example: '906801'
  homepage: https://cancer.sanger.ac.uk/cell_lines/
  name: COSMIC Cell Lines
  preferred_prefix: cosmic.cell
  uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1
covid19:
  description: Curated contextual database gathering samples related to SARS-CoV-2
    virus and covid-19 disease.
  example: SFB_COVID19_MW286762
  homepage: https://covid19.sfb.uit.no
  mappings:
    bioportal: COVID-19
    miriam: covid19
  name: COVID-19 Ontology
  pattern: ^\w+_COVID19_[-\w]+$
  preferred_prefix: covid19
  uri_format: https://covid19.sfb.uit.no/api/records/$1
covoc:
  description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related
    to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity,
    gene and gene products, barrier gestures, treatments and more.
  example: '0010034'
  homepage: https://github.com/EBISPOT/covoc
  license: CC BY 4.0
  mappings:
    ols: covoc
  name: CoVoc Coronavirus Vocabulary
  preferred_prefix: covoc
  version: '2020-08-28'
cp:
  comment: Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Cellular Phenotypes
  preferred_prefix: cp
cpc:
  description: The Cooperative Patent Classification (CPC) is a patent classification
    system, developed jointly by the European Patent Office (EPO) and the United States
    Patent and Trademark Office (USPTO). It is based on the previous European classification
    system (ECLA), which itself was a version of the International Patent Classification
    (IPC) system. The CPC patent classification system has been used by EPO and USPTO
    since 1st January, 2013.
  example: A01M1/026
  homepage: https://worldwide.espacenet.com/classification
  mappings:
    miriam: cpc
    n2t: cpc
    prefixcommons: CPC
  name: Cooperative Patent Classification
  pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H,
    Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$
  preferred_prefix: cpc
  uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1
cpga:
  banana: GRO
  contact:
    email: po-discuss@plantontology.org
    github: null
    name: Plant Ontology Administrators
    orcid: null
  deprecated: true
  homepage: http://www.gramene.org/plant_ontology/
  mappings:
    bioportal: GRO-CPGA
    obofoundry: GRO
    prefixcommons: gro.cpga
  name: Cereal Plant Gross Anatomy
  preferred_prefix: GRO
  uri_format: http://purl.obolibrary.org/obo/GRO_$1
crisprdb:
  description: Repeated CRISPR ("clustered regularly interspaced short palindromic
    repeats") elements found in archaebacteria and eubacteria are believed to defend
    against viral infection, potentially targeting invading DNA for degradation. CRISPRdb
    is a database that stores information on CRISPRs that are automatically extracted
    from newly released genome sequence data.
  example: '551115'
  homepage: http://crispr.i2bc.paris-saclay.fr/
  mappings:
    miriam: crisprdb
    n2t: crisprdb
    prefixcommons: CRISPRDB
  name: CRISPRdb
  pattern: ^[0-9]+$
  preferred_prefix: crisprdb
  uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1
cro:
  banana: CRO
  contact:
    email: whimar@ohsu.edu
    github: marijane
    name: Marijane White
    orcid: null
  description: A classification of the diverse roles performed in the work leading
    to a published research output in the sciences. Its purpose to provide transparency
    in contributions to scholarly published work, to enable improved systems of attribution,
    credit, and accountability.
  example: 0000038
  homepage: https://github.com/data2health/contributor-role-ontology
  license: CC BY 2.0
  mappings:
    bioportal: CRO
    obofoundry: CRO
    ols: cro
    ontobee: CRO
    prefixcommons: CRO
  name: Contributor Role Ontology
  pattern: ^\d{7}$
  preferred_prefix: CRO
  uri_format: http://purl.obolibrary.org/obo/CRO_$1
  version: '2019-12-11'
cryoem:
  description: Ontology that describes data types and image processing operations
    in Cryo Electron Microscopy of Single Particles
  example: '0000052'
  homepage: http://scipion.i2pc.es/ontology/cryoem
  license: CC BY 3.0
  mappings:
    bioportal: CRYOEM
    ols: cryoem
  name: Cryo Electron Microscopy ontology
  preferred_prefix: cryoem
  version: '2021-03-09'
cryptodb:
  description: CryptoDB is one of the databases that can be accessed through the EuPathDB
    (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
    the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
    Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
    database built upon the same infrastructure, the EuPathDB portal offers an entry
    point to all these resources, and the opportunity to leverage orthology for searches
    across genera.
  example: cgd7_230
  homepage: https://cryptodb.org/cryptodb/
  mappings:
    miriam: cryptodb
    n2t: cryptodb
    prefixcommons: CRYPTODB
  name: CryptoDB
  pattern: ^\w+$
  preferred_prefix: cryptodb
  uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1
csa:
  description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
    sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
    for catalytic residues which includes only those residues thought to be directly
    involved in some aspect of the reaction catalysed by an enzyme.
  example: 1a05
  homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/
  mappings:
    miriam: csa
    n2t: csa
    prefixcommons: CSA
  name: Catalytic Site Atlas
  pattern: ^[0-9][A-Za-z0-9]{3}$
  preferred_prefix: csa
  uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1
csd:
  description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive
    collection of small-molecule crystal structures. Entries curated into the CSD
    are identified by a CSD Refcode.
  example: PELNAW
  homepage: https://www.ccdc.cam.ac.uk/
  mappings:
    miriam: csd
  name: Cambridge Structural Database
  pattern: ^[A-Z]{6}(\d{2})?$
  preferred_prefix: csd
  uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG
csp:
  deprecated: true
  example: 2004-2820
  homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm
  mappings:
    bioportal: CRISP
  name: Computer Retrieval of Information on Science Projects (CRISP) Thesaurus
  preferred_prefix: csp
  synonyms:
  - CRISP Thesaurus
  - CRISP Thesaurus, 2006
  - CSP2005
cst:
  description: Cell Signaling Technology is a commercial organisation which provides
    a pathway portal to showcase their phospho-antibody products. This collection
    references pathways.
  example: Akt_PKB
  homepage: http://www.cellsignal.com/pathways/index.html
  mappings:
    bioportal: CST
    miriam: cst
    n2t: cst
    prefixcommons: CST
  name: Cancer Staging Terms
  pattern: ^[A-Za-z0-9_-]+$
  preferred_prefix: cst
  uri_format: http://www.cellsignal.com/reference/pathway/$1.html
cst.ab:
  description: Cell Signaling Technology is a commercial organisation which provides
    a pathway portal to showcase their phospho-antibody products. This collection
    references antibody products.
  example: '3305'
  homepage: http://www.cellsignal.com/catalog/index.html
  mappings:
    miriam: cst.ab
    n2t: cst.ab
    prefixcommons: CST.AB
  name: Cell Signaling Technology Antibody
  pattern: ^\d+$
  preferred_prefix: cst.ab
  uri_format: http://www.cellsignal.com/products/$1.html
ctd.chemical:
  description: The Comparative Toxicogenomics Database (CTD) presents scientifically
    reviewed and curated information on chemicals, relevant genes and proteins, and
    their interactions in vertebrates and invertebrates. It integrates sequence, reference,
    species, microarray, and general toxicology information to provide a unique centralized
    resource for toxicogenomic research. The database also provides visualization
    capabilities that enable cross-species comparisons of gene and protein sequences.
  example: D001151
  homepage: http://ctdbase.org/
  mappings:
    biolink: CTD.CHEMICAL
    miriam: ctd.chemical
    n2t: ctd.chemical
    prefixcommons: CTD.CHEMICAL
  name: CTD Chemical
  part_of: ctd
  pattern: ^[CD]\d+$
  preferred_prefix: ctd.chemical
  provides: mesh
  uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1
ctd.disease:
  description: The Comparative Toxicogenomics Database (CTD) presents scientifically
    reviewed and curated information on chemicals, relevant genes and proteins, and
    their interactions in vertebrates and invertebrates. It integrates sequence, reference,
    species, microarray, and general toxicology information to provide a unique centralized
    resource for toxicogenomic research. The database also provides visualization
    capabilities that enable cross-species comparisons of gene and protein sequences.
  example: D053716
  homepage: http://ctdbase.org/
  mappings:
    biolink: CTD.DISEASE
    miriam: ctd.disease
    n2t: ctd.disease
    prefixcommons: CTD.DISEASE
  name: CTD Disease
  part_of: ctd
  pattern: ^D\d+$
  preferred_prefix: ctd.disease
  provides: mesh
  uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1
ctd.gene:
  description: The Comparative Toxicogenomics Database (CTD) presents scientifically
    reviewed and curated information on chemicals, relevant genes and proteins, and
    their interactions in vertebrates and invertebrates. It integrates sequence, reference,
    species, microarray, and general toxicology information to provide a unique centralized
    resource for toxicogenomic research. The database also provides visualization
    capabilities that enable cross-species comparisons of gene and protein sequences.
  example: '101'
  homepage: http://ctdbase.org/
  mappings:
    biolink: CTD.GENE
    miriam: ctd.gene
    n2t: ctd.gene
    prefixcommons: CTD.GENE
  name: CTD Gene
  part_of: ctd
  pattern: ^\d+$
  preferred_prefix: ctd.gene
  provides: ncbigene
  uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1
cteno:
  banana: CTENO
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: null
  description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
  example: '0000047'
  homepage: https://github.com/obophenotype/ctenophore-ontology
  license: CC BY 3.0
  mappings:
    bioportal: CTENO
    obofoundry: CTENO
    ols: cteno
    ontobee: CTENO
    prefixcommons: CTENO
  name: Ctenophore Ontology
  pattern: ^\d{7}$
  preferred_prefix: CTENO
  uri_format: http://purl.obolibrary.org/obo/CTENO_$1
  version: '2016-10-19'
cto:
  banana: CTO
  contact:
    email: alpha.tom.kodamullil@scai.fraunhofer.de
    github: akodamullil
    name: Dr. Alpha Tom Kodamullil
    orcid: null
  description: The core Ontology of Clinical Trials (CTO) will serve as a structured
    resource integrating basic terms and concepts in the context of clinical trials.
    Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to
    generate extended versions for specific applications such as annotation of variables
    in study documents from clinical trials.
  example: '0000022'
  homepage: https://github.com/ClinicalTrialOntology/CTO/
  license: CC BY 4.0
  mappings:
    bioportal: CTO
    obofoundry: CTO
    ols: cto
    ontobee: CTO
  name: 'CTO: Core Ontology of Clinical Trials'
  preferred_prefix: CTO
  uri_format: http://purl.obolibrary.org/obo/CTO_$1
  version: 1.0.0
cubedb:
  comment: website down as of 2021-10-04
  deprecated: true
  description: Cube-DB is a database of pre-evaluated results for detection of functional
    divergence in human/vertebrate protein families. It analyzes comparable taxonomical
    samples for all paralogues under consideration, storing functional specialisation
    at the level of residues. The data are presented as a table of per-residue scores,
    and mapped onto related structures where available.
  example: AKR
  homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html
  mappings:
    miriam: cubedb
    n2t: cubedb
    prefixcommons: CUBEDB
  name: Cube db
  pattern: ^[A-Za-z_0-9]+$
  preferred_prefix: cubedb
  uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/
cvdo:
  banana: CVDO
  contact:
    email: paul.fabry@usherbrooke.ca
    github: null
    name: Paul Fabry
    orcid: null
  description: An ontology to describe entities related to cardiovascular diseases
  example: '0000546'
  homepage: https://github.com/OpenLHS/CVDO
  license: CC BY 4.0
  mappings:
    bioportal: CVDO
    obofoundry: CVDO
    ols: cvdo
    ontobee: CVDO
    prefixcommons: CVDO
  name: Cardiovascular Disease Ontology
  preferred_prefix: CVDO
  uri_format: http://purl.obolibrary.org/obo/CVDO_$1
  version: '2020-03-05'
d1id:
  description: DataONE provides infrastructure facilitating long-term access to scientific
    research data of relevance to the earth sciences.
  example: 00030692-0FE1-4A1B-955E-A2E55D659267
  homepage: https://www.dataone.org
  mappings:
    miriam: d1id
    n2t: d1id
    prefixcommons: D1ID
  name: DataONE
  pattern: ^\S+$
  preferred_prefix: d1id
  uri_format: https://cn.dataone.org/cn/v2/resolve/{$1}
dailymed:
  description: DailyMed provides information about marketed drugs. This information
    includes FDA labels (package inserts). The Web site provides a standard, comprehensive,
    up-to-date, look-up and download resource of medication content and labeling as
    found in medication package inserts. Drug labeling is the most recent submitted
    to the Food and Drug Administration (FDA) and currently in use; it may include,
    for example, strengthened warnings undergoing FDA review or minor editorial changes.
    These labels have been reformatted to make them easier to read.
  example: 973a9333-fec7-46dd-8eb5-25738f06ee54
  homepage: https://dailymed.nlm.nih.gov/dailymed/
  mappings:
    miriam: dailymed
    n2t: dailymed
    prefixcommons: DAILYMED
  name: DailyMed
  pattern: ^[A-Za-z0-9-]+$
  preferred_prefix: dailymed
  uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1
dandi:
  description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate
    data using community data standards such as NWB and BIDS, and to make data and
    software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable,
    and Reusable).

    DANDI references electrical and optical cellular neurophysiology recordings and
    associated MRI and/or optical imaging data.

    These data will help scientists uncover and understand cellular level mechanisms
    of brain function. Scientists will study the formation of neural networks, how
    cells and networks enable functions such as learning and memory, and how these
    functions are disrupted in neurological disorders.'
  example: '000017'
  homepage: https://dandiarchive.org/
  mappings:
    miriam: dandi
  name: 'DANDI: Distributed Archives for Neurophysiology Data Integration'
  pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$
  preferred_prefix: dandi
  uri_format: https://dandiarchive.org/dandiset/$1
darc:
  description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM
    (electron microscopy) data and atomic coordinates of ribosomal particles from
    the PDB, which are aligned within a common coordinate system. The aligned coordinate
    system simplifies direct visualization of conformational changes in the ribosome,
    such as subunit rotation and head-swiveling, as well as direct comparison of bound
    ligands, such as antibiotics or translation factors.
  example: '1250'
  homepage: http://darcsite.genzentrum.lmu.de/darc/index.php
  mappings:
    miriam: darc
    n2t: darc
    prefixcommons: DARC
  name: Database of Aligned Ribosomal Complexes
  pattern: ^\d+$
  preferred_prefix: darc
  uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1
dashr:
  description: DASHR reports the annotation, expression and evidence for specific
    RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor
    and mature sncRNA products across different human tissues and cell types. DASHR
    integrates information from multiple existing annotation resources for small non-coding
    RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs),
    nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs),
    and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human
    tissues and cell types and were generated for studying or profiling small non-coding
    RNAs. This collection references RNA records.
  example: hsa-mir-200a
  homepage: http://lisanwanglab.org/DASHR/
  mappings:
    miriam: dashr
    n2t: dashr
    prefixcommons: DASHR
  name: Database of small human noncoding RNAs
  pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
  preferred_prefix: dashr
  uri_format: http://lisanwanglab.org/DASHR/entry/$1
dashr.expression:
  description: DASHR reports the annotation, expression and evidence for specific
    RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor
    and mature sncRNA products across different human tissues and cell types. DASHR
    integrates information from multiple existing annotation resources for small non-coding
    RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs),
    nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs),
    and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human
    tissues and cell types and were generated for studying or profiling small non-coding
    RNAs. This collection references RNA expression.
  example: hsa-mir-200a
  homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0
  mappings:
    miriam: dashr.expression
    n2t: dashr.expression
    prefixcommons: DASHR.EXPRESSION
  name: DASHR expression
  pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
  preferred_prefix: dashr.expression
  uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable
datanator.gene:
  description: Datanator is an integrated database of genomic and biochemical data
    designed to help investigators find data about specific molecules and reactions
    in specific organisms and specific environments for meta-analyses and mechanistic
    models. Datanator currently includes metabolite concentrations, RNA modifications
    and half-lives, protein abundances and modifications, and reaction kinetics integrated
    from several databases and numerous publications. The Datanator website and REST
    API provide tools for extracting clouds of data about specific molecules and reactions
    in specific organisms and specific environments, as well as data about similar
    molecules and reactions in taxonomically similar organisms.
  example: K00973
  homepage: https://datanator.info/
  mappings:
    miriam: datanator.gene
  name: Datanator Gene
  part_of: datanator
  pattern: ^K[0-9]+$
  preferred_prefix: datanator.gene
  uri_format: https://www.datanator.info/gene/$1
datanator.metabolite:
  description: Datanator is an integrated database of genomic and biochemical data
    designed to help investigators find data about specific molecules and reactions
    in specific organisms and specific environments for meta-analyses and mechanistic
    models. Datanator currently includes metabolite concentrations, RNA modifications
    and half-lives, protein abundances and modifications, and reaction kinetics integrated
    from several databases and numerous publications. The Datanator website and REST
    API provide tools for extracting clouds of data about specific molecules and reactions
    in specific organisms and specific environments, as well as data about similar
    molecules and reactions in taxonomically similar organisms.
  example: OUYCCCASQSFEME-MRVPVSSYSA-N
  homepage: https://datanator.info/
  mappings:
    miriam: datanator.metabolite
  name: Datanator Metabolite
  part_of: datanator
  pattern: ^[A-Z\-]+$
  preferred_prefix: datanator.metabolite
  uri_format: https://www.datanator.info/metabolite/$1
datanator.reaction:
  description: "\tDatanator is an integrated database of genomic and biochemical data\
    \ designed to help investigators find data about specific molecules and reactions\
    \ in specific organisms and specific environments for meta-analyses and mechanistic\
    \ models. Datanator currently includes metabolite concentrations, RNA modifications\
    \ and half-lives, protein abundances and modifications, and reaction kinetics\
    \ integrated from several databases and numerous publications. The Datanator website\
    \ and REST API provide tools for extracting clouds of data about specific molecules\
    \ and reactions in specific organisms and specific environments, as well as data\
    \ about similar molecules and reactions in taxonomically similar organisms."
  example: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N
  homepage: https://icahn.mssm.edu/
  mappings:
    miriam: datanator.reaction
  name: Datanator Reaction
  pattern: ^.*?--%3E.*?$
  preferred_prefix: datanator.reaction
  uri_format: https://datanator.info/reaction/$1
datf:
  deprecated: true
  description: DATF contains known and predicted Arabidopsis transcription factors
    (1827 genes in 56 families) with the unique information of 1177 cloned sequences
    and many other features including 3D structure templates, EST expression information,
    transcription factor binding sites and nuclear location signals.
  example: AT1G01030.1
  homepage: http://datf.cbi.pku.edu.cn/
  mappings:
    miriam: datf
    n2t: datf
    prefixcommons: DATF
  name: Database of Arabidopsis Transcription Factors
  pattern: ^AT[1-5]G\d{5}(\.\d+)?$
  preferred_prefix: datf
  uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1
dbd:
  description: The DBD (transcription factor database) provides genome-wide transcription
    factor predictions for organisms across the tree of life. The prediction method
    identifies sequence-specific DNA-binding transcription factors through homology
    using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY.
    It does not include basal transcription factors or chromatin-associated proteins.
  example: '0045310'
  homepage: http://www.transcriptionfactor.org/
  mappings:
    miriam: dbd
    n2t: dbd
    prefixcommons: DBD
  name: Transcription Factor Database
  pattern: ^\d+$
  preferred_prefix: dbd
  uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD
dbest:
  description: The dbEST contains sequence data and other information on "single-pass"
    cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
  example: BP100000
  homepage: https://www.ncbi.nlm.nih.gov/nucest
  mappings:
    miriam: dbest
    n2t: dbest
    ncbi: dbEST
    prefixcommons: DBEST
  name: EST database maintained at the NCBI.
  pattern: ^([A-Z]+)?\d+(\.\d+)?$
  preferred_prefix: dbest
  providers:
  - code: ebi
    description: dbEST through European Nucleotide Archive (ENA)
    homepage: https://www.ebi.ac.uk/ena
    name: dbEST through European Nucleotide Archive (ENA)
    uri_format: https://www.ebi.ac.uk/ena/data/view/$1
  - code: CURATOR_REVIEW
    description: dbEST through DNA Data Bank of Japan (DDBJ)
    homepage: http://www.ddbj.nig.ac.jp/
    name: dbEST through DNA Data Bank of Japan (DDBJ)
    uri_format: http://getentry.ddbj.nig.ac.jp/getentry/na/$1
  uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
dbg2introns:
  description: The Database for Bacterial Group II Introns  provides a catalogue of
    full-length, non-redundant group II introns present in bacterial DNA sequences
    in GenBank.
  example: Cu.me.I1
  homepage: http://webapps2.ucalgary.ca/~groupii/
  mappings:
    miriam: dbg2introns
    n2t: dbg2introns
    prefixcommons: DBG2INTRONS
  name: DBG2 Introns
  pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
  preferred_prefix: dbg2introns
  uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1
dbgap:
  description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes
    the results of studies that have investigated the interaction of genotype and
    phenotype.
  example: phs000768.v2.p1
  homepage: https://www.ncbi.nlm.nih.gov/projects/gap
  mappings:
    miriam: dbgap
    n2t: dbgap
    prefixcommons: DBGAP
  name: Database of Genotypes and Phenotypes
  pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$
  preferred_prefix: dbgap
  uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1
dbmhc:
  deprecated: true
  example: '48439'
  homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/
  mappings:
    cellosaurus: dbMHC
  name: Database of human Major Histocompatibility Complex
  preferred_prefix: dbmhc
dbprobe:
  description: The NCBI Probe Database is a public registry of nucleic acid reagents
    designed for use in a wide variety of biomedical research applications, together
    with information on reagent distributors, probe effectiveness, and computed sequence
    similarities.
  example: '1000000'
  homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe
  mappings:
    miriam: dbprobe
    n2t: dbprobe
    ncbi: dbProbe
    prefixcommons: DBPROBE
  name: NCBI Probe database Public registry of nucleic acid reagents
  pattern: ^\d+$
  preferred_prefix: dbprobe
  uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1
dbsnp:
  description: The dbSNP database is a repository for both single base nucleotide
    subsitutions and short deletion and insertion polymorphisms.
  example: rs121909098
  homepage: https://www.ncbi.nlm.nih.gov/snp/
  mappings:
    cellosaurus: dbSNP
    go: dbSNP
    miriam: dbsnp
    n2t: dbsnp
    ncbi: dbSNP
    prefixcommons: dbSNP
    uniprot: dbSNP
  name: NCBI dbSNP
  pattern: ^rs\d+$
  preferred_prefix: dbsnp
  providers:
  - code: sib
    description: SNP2TFBS
    homepage: https://ccg.epfl.ch/snp2tfbs/
    name: SNP2TFBS
    uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1
  uri_format: https://www.ncbi.nlm.nih.gov/snp/$1
dc:
  deprecated: true
  example: 0000598
  mappings:
    bioportal: DC
    prefixcommons: dc
  name: Disease Class
  preferred_prefix: dc
  uri_format: http://purl.org/dc/elements/1.1/$1
dc_cl:
  banana: DC_CL
  contact:
    email: Lindsay.Cowell@utsouthwestern.edu
    github: null
    name: Lindsay Cowell
    orcid: null
  deprecated: true
  homepage: http://www.dukeontologygroup.org/Projects.html
  mappings:
    obofoundry: DC_CL
    prefixcommons: DC_CL
  name: Dendritic cell
  preferred_prefix: DC_CL
  uri_format: http://purl.obolibrary.org/obo/DC_CL_$1
dcat:
  description: DCAT is an RDF vocabulary designed to facilitate interoperability between
    data catalogs published on the Web
  example: Dataset
  homepage: https://www.w3.org/ns/dcat
  mappings:
    biolink: dcat
    bioportal: DCAT
    prefixcommons: dcat
  name: Data Catalog
  preferred_prefix: dcat
  uri_format: http://www.w3.org/ns/dcat#$1
dcterms:
  description: This document is an up-to-date specification of all metadata terms
    maintained by the Dublin Core Metadata Initiative, including properties, vocabulary
    encoding schemes, syntax encoding schemes, and classes.
  example: title
  homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
  mappings:
    biolink: dct
    bioportal: DCTERMS
    prefixcommons: dcterms
  name: Dublin Core Metadata Vocabulary
  preferred_prefix: dcterms
  synonyms:
  - dc.terms
  uri_format: https://dublincore.org/specifications/dublin-core/dcmi-terms/#$1
dctypes:
  description: This document is an up-to-date specification of all metadata terms
    maintained by the Dublin Core Metadata Initiative, including properties, vocabulary
    encoding schemes, syntax encoding schemes, and classes.
  example: Collection
  homepage: https://dublincore.org/specifications/dublin-core/dcmi-terms/
  mappings:
    prefixcommons: dctypes
  name: Dublin Core Types
  preferred_prefix: dctypes
  uri_format: http://purl.org/dc/dcmitype/$1
ddanat:
  banana: DDANAT
  contact:
    email: pfey@northwestern.edu
    github: pfey03
    name: Petra Fey
    orcid: null
  description: A structured controlled vocabulary of the anatomy of the slime-mold
    Dictyostelium discoideum
  example: '0000006'
  homepage: http://dictybase.org/
  license: CC0 1.0
  mappings:
    bioportal: DDANAT
    go: DDANAT
    obofoundry: DDANAT
    ols: ddanat
    ontobee: DDANAT
    prefixcommons: DDANAT
  name: Dictyostelium discoideum anatomy
  pattern: ^\d{7}$
  preferred_prefix: DDANAT
  uri_format: http://purl.obolibrary.org/obo/DDANAT_$1
  version: '2020-04-13'
ddpheno:
  banana: DDPHENO
  contact:
    email: pfey@northwestern.edu
    github: pfey03
    name: Petra Fey
    orcid: null
  description: A structured controlled vocabulary of phenotypes of the slime-mould
    Dictyostelium discoideum.
  example: '0001417'
  homepage: http://dictybase.org/
  license: CC0 1.0
  mappings:
    bioportal: DDPHENO
    obofoundry: DDPHENO
    ols: ddpheno
    ontobee: DDPHENO
    prefixcommons: DDPHENO
  name: Dictyostelium discoideum phenotype ontology
  pattern: ^\d{7}$
  preferred_prefix: DDPHENO
  uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1
  version: '2020-06-19'
degradome:
  description: The Degradome Database contains information on the complete set of
    predicted proteases present in a a variety of mammalian species that have been
    subjected to whole genome sequencing. Each protease sequence is curated and, when
    necessary, cloned and sequenced.
  example: Ax1
  homepage: http://degradome.uniovi.es/
  mappings:
    miriam: degradome
    n2t: degradome
    prefixcommons: DEGRADOME
  name: Degradome Database
  pattern: ^[AMCST][0-9x][0-9]$
  preferred_prefix: degradome
  uri_format: http://degradome.uniovi.es/cgi-bin/protease/$1
depmap:
  description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE
    Cells.
  example: ACH-000001
  homepage: https://depmap.org/portal
  mappings:
    cellosaurus: DepMap
  name: DepMap Cell Lines
  pattern: ^ACH-\d+$
  preferred_prefix: depmap
  uri_format: https://depmap.org/portal/cell_line/$1
depod:
  description: The human DEPhOsphorylation Database (DEPOD) contains information on
    known human active phosphatases and their experimentally verified protein and
    nonprotein substrates. Reliability scores are provided for dephosphorylation interactions,
    according to the type of assay used, as well as the number of laboratories that
    have confirmed such interaction. Phosphatase and substrate entries are listed
    along with the dephosphorylation site, bioassay type, and original literature,
    and contain links to other resources.
  example: PTPN1
  homepage: http://www.depod.bioss.uni-freiburg.de
  mappings:
    miriam: depod
    n2t: depod
    prefixcommons: DEPOD
    uniprot: DEPOD
  name: Human Dephosphorylation Database
  pattern: ^[A-Z0-9]+$
  preferred_prefix: depod
  provides: hgnc.symbol
  uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1
dermo:
  description: DermO is an ontology with broad coverage of the domain of dermatologic
    disease and we demonstrate here its utility for text mining and investigation
    of phenotypic relationships between dermatologic disorders
  example: '0000000'
  homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x
  mappings:
    bioportal: DERMO
  name: Human Dermatological Disease Ontology
  preferred_prefix: dermo
dev.ga4ghdos:
  description: Assists in resolving data across cloud resources.
  example: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00
  homepage: http://github.com/ga4gh/data-object-service-schemas
  mappings:
    miriam: dev.ga4ghdos
    n2t: dev.ga4ghdos
    prefixcommons: DEV.GA4GHDOS
  name: Development Data Object Service
  pattern: ^[a-zA-Z0-9\-:#\.]+$
  preferred_prefix: dev.ga4ghdos
  uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1
dg.4503:
  description: Full implementation of the DRS 1.1 standard with support for persistent
    identifiers. Open source DRS server that follows the Gen3 implementation. Gen3
    is a GA4GH compliant open source platform for developing framework services and
    data commons. Data commons accelerate and democratize the process of scientific
    discovery, especially over large or complex datasets. Gen3 is maintained by the
    Center for Translational Data Science at the University of Chicago. https://gen3.org
  example: 0000ffeb-36e0-4a29-b21d-84423bda979d
  homepage: https://gen3.biodatacatalyst.nhlbi.nih.gov
  mappings:
    miriam: dg.4503
  name: BioData Catalyst
  pattern: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
  preferred_prefix: dg.4503
  uri_format: https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1
dg.4dfc:
  description: DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant
    open source platform for developing framework services and data commons. Data
    commons accelerate and democratize the process of scientific discovery, especially
    over large or complex datasets. Gen3 is maintained by the Center for Translational
    Data Science at the University of Chicago. https://gen3.org
  example: 81944ba1-81d0-436e-8552-33d77a27834b
  homepage: https://nci-crdc.datacommons.io/
  mappings:
    miriam: dg.4dfc
  name: NCI Data Commons Framework Services
  pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
  preferred_prefix: dg.4dfc
  uri_format: https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1
dg.6vts:
  description: Full implementation of the DRS 1.1 standard with support for persistent
    identifiers. Open source DRS server that follows the Gen3 implementation. Gen3
    is a GA4GH compliant open source platform for developing framework services and
    data commons. Data commons accelerate and democratize the process of scientific
    discovery, especially over large or complex datasets. Gen3 is maintained by the
    Center for Translational Data Science at the University of Chicago. https://gen3.org
  example: 2afacf00-9a1d-4d80-8c32-69d3923d3913
  homepage: https://jcoin.datacommons.io
  mappings:
    miriam: dg.6vts
  name: JCOIN
  pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
  preferred_prefix: dg.6vts
  uri_format: https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1
dg.anv0:
  description: DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant
    open source platform for developing framework services and data commons. Data
    commons accelerate and democratize the process of scientific discovery, especially
    over large or complex datasets. Gen3 is maintained by the Center for Translational
    Data Science at the University of Chicago. https://gen3.org
  example: 00077f1c-c45a-47ba-8e6c-1bf6b6b43fce
  homepage: https://gen3.theanvil.io
  mappings:
    miriam: dg.anv0
  name: Anvil
  pattern: ^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$
  preferred_prefix: dg.anv0
  uri_format: https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1
dg.f82a1a:
  description: Full implementation of the DRS 1.1 standard with support for persistent
    identifiers. Open source DRS server that follows the Gen3 implementation. Gen3
    is a GA4GH compliant open source platform for developing framework services and
    data commons. Data commons accelerate and democratize the process of scientific
    discovery, especially over large or complex datasets. Gen3 is maintained by the
    Center for Translational Data Science at the University of Chicago. https://gen3.org
  example: 00026f50-858a-446b-8ed9-b0e3ecd7b20e
  homepage: https://kidsfirstdrc.org
  mappings:
    miriam: dg.f82a1a
  name: Kids First
  pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
  preferred_prefix: dg.f82a1a
  uri_format: https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1
dicom:
  description: DICOM Controlled Terminology
  example: '109082'
  homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html
  mappings:
    bioportal: DCM
    ols: dicom
  name: DICOM Controlled Terminology
  preferred_prefix: dicom
  version: 2021e_20211122
dictybase:
  description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics
  example: DDB0191090
  homepage: http://dictybase.org
  mappings:
    go: dictyBase
    ncbi: dictyBase
    prefixcommons: dictyBase
    uniprot: dictyBase
  name: dictyBase
  preferred_prefix: dictybase
  synonyms:
  - dictyBase
  uri_format: http://dictybase.org/gene/$1
dictybase.est:
  description: The dictyBase database provides data on the model organism Dictyostelium
    discoideum and related species. It contains the complete genome sequence, ESTs,
    gene models and functional annotations. This collection references expressed sequence
    tag (EST) information.
  example: DDB0016567
  homepage: http://dictybase.org/
  mappings:
    miriam: dictybase.est
    n2t: dictybase.est
    prefixcommons: DICTYBASE.EST
  name: dictyBase Expressed Sequence Tag
  part_of: dictybase
  pattern: ^DDB\d+$
  preferred_prefix: dictybase.est
  uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1
dictybase.gene:
  description: The dictyBase database provides data on the model organism Dictyostelium
    discoideum and related species. It contains the complete genome sequence, ESTs,
    gene models and functional annotations. This collection references gene information.
  example: DDB_G0267522
  homepage: http://dictybase.org/
  mappings:
    miriam: dictybase.gene
    n2t: dictybase.gene
    prefixcommons: DICTYBASE.GENE
  name: Dictybase Gene
  part_of: dictybase
  pattern: ^DDB_G\d+$
  preferred_prefix: dictybase.gene
  uri_format: http://dictybase.org/gene/$1
did:
  banana: did
  description: DIDs are an effort by the W3C Credentials Community Group and the wider
    Internet identity community to define identifiers that can be registered, updated,
    resolved, and revoked without any dependency on a central authority or intermediary.
  example: sov:WRfXPg8dantKVubE3HX8pw
  homepage: https://w3c-ccg.github.io/did-spec/
  mappings:
    miriam: did
    n2t: did
  name: Decentralized Identifier
  namespace_in_lui: true
  pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$
  preferred_prefix: did
  uri_format: https://uniresolver.io/#did:$1
dideo:
  banana: DIDEO
  contact:
    email: mbrochhausen@gmail.com
    github: mbrochhausen
    name: Mathias Brochhausen
    orcid: null
  description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
    Evidence Ontology
  example: 00000180
  homepage: https://github.com/DIDEO/DIDEO
  license: CC BY 4.0
  mappings:
    bioportal: DIDEO
    obofoundry: DIDEO
    ols: dideo
    ontobee: DIDEO
    prefixcommons: DIDEO
  name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
  preferred_prefix: DIDEO
  uri_format: http://purl.obolibrary.org/obo/DIDEO_$1
  version: '2021-06-11'
dinto:
  banana: DINTO
  contact:
    email: maria.herrero@kcl.ac.uk
    github: null
    name: Maria Herrero
    orcid: null
  deprecated: true
  description: A formal represention for drug-drug interactions knowledge.
  homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto
  license: CC BY 3.0
  mappings:
    bioportal: DINTO
    obofoundry: DINTO
    prefixcommons: DINTO
  name: The Drug-Drug Interactions Ontology
  preferred_prefix: DINTO
  uri_format: http://purl.obolibrary.org/obo/DINTO_$1
dip:
  description: The database of interacting protein (DIP) database stores experimentally
    determined interactions between proteins. It combines information from a variety
    of sources to create a single, consistent set of protein-protein interactions
  example: DIP-743N
  homepage: https://dip.doe-mbi.ucla.edu/
  mappings:
    miriam: dip
    n2t: dip
    prefixcommons: DIP
    uniprot: DIP
  name: Database of Interacting Proteins
  pattern: ^DIP(\:)?\-\d{1,}[ENXS]$
  preferred_prefix: dip
  uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1
disdriv:
  banana: DISDRIV
  contact:
    email: lynn.schriml@gmail.com
    github: lschriml
    name: Lynn Schriml
    orcid: null
  description: Ontology for drivers and triggers of human diseases, built to classify
    ExO ontology exposure stressors. An application ontology. Built in collaboration
    with EnvO, ExO, ECTO and ChEBI.
  example: '0000000'
  homepage: http://www.disease-ontology.org
  license: CC0 1.0
  mappings:
    obofoundry: DISDRIV
  name: Disease Drivers Ontology
  pattern: ^\d+$
  preferred_prefix: DISDRIV
  uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1
diseasesdb:
  description: 'The Diseases Database is a cross-referenced index of human disease,
    medications, symptoms, signs, abnormal investigation findings etc. This site provides
    a medical textbook-like index and search portal covering areas including: internal
    medical disorders, symptoms and signs, congenital and inherited disorders, infectious
    diseases and organisms, drugs and medications, common haematology and biochemistry
    investigation abnormalities.'
  example: '1784'
  homepage: http://www.diseasesdatabase.com/
  mappings:
    wikidata: P557
  name: Diseases Database
  preferred_prefix: diseasesdb
disprot:
  description: DisProt is a database of intrinsically disordered proteins and protein
    disordered regions, manually curated from literature.
  example: DP00003
  homepage: https://disprot.org/
  mappings:
    miriam: disprot
    n2t: disprot
    prefixcommons: DISPROT
    uniprot: DisProt
  name: DisProt
  pattern: ^DP\d{5}$
  preferred_prefix: disprot
  uri_format: https://disprot.org/$1
disprot.region:
  description: DisProt is a database of intrisically disordered proteins and protein
    disordered regions, manually curated from literature.
  example: DP00086r013
  homepage: https://www.disprot.org
  mappings:
    miriam: disprot.region
  name: DisProt region
  pattern: ^DP\d{5}r\d{3}$
  preferred_prefix: disprot.region
  uri_format: https://www.disprot.org/$1
dlxb:
  description: DOULIX lab-tested standard biological parts, in this case linear double
    stranded DNA sequences.
  example: 6VDC956
  homepage: https://doulix.com
  mappings:
    miriam: dlxb
  name: Linear double stranded DNA sequences
  part_of: dlx
  pattern: ^[A-Z0-9]{6,7}$
  preferred_prefix: dlxb
  uri_format: https://doulix.com/biomodules/$1
dlxc:
  description: DOULIX lab-tested standard biological parts, in this case, full length
    constructs.
  example: M77F7JM
  homepage: https://doulix.com
  mappings:
    miriam: dlxc
  name: Circular double stranded DNA sequences composed
  part_of: dlx
  pattern: ^[A-Z0-9]{6,7}$
  preferred_prefix: dlxc
  uri_format: https://doulix.com/constructs/$1
doi:
  description: The Digital Object Identifier System is for identifying content objects
    in the digital environment.
  example: 10.1038/nbt1156
  homepage: https://www.doi.org/
  mappings:
    biolink: doi
    cellosaurus: DOI
    go: DOI
    miriam: doi
    n2t: doi
    prefixcommons: DOI
    scholia: doi
  name: Digital Object Identifier
  pattern: ^(doi\:)?\d{2}\.\d{4}.*$
  preferred_prefix: doi
  providers:
  - code: 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/
    name: Scholia
    uri_format: https://scholia.toolforge.org/doi/$1
  uri_format: https://doi.org/$1
doid:
  banana: DOID
  contact:
    email: lynn.schriml@gmail.com
    github: lschriml
    name: Lynn Schriml
    orcid: null
  description: The Disease Ontology has been developed as a standardized ontology
    for human disease with the purpose of providing the biomedical community with
    consistent, reusable and sustainable descriptions of human disease terms, phenotype
    characteristics and related medical vocabulary disease concepts.
  example: 0110974
  homepage: http://www.disease-ontology.org
  license: CC0 1.0
  mappings:
    bioportal: DOID
    miriam: doid
    n2t: doid
    obofoundry: DOID
    ols: doid
    ontobee: DOID
    prefixcommons: DOID
    wikidata: P699
  name: Human Disease Ontology
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: DOID
  providers:
  - code: hdo
    description: Human Disease Ontology at Northwestern University
    homepage: http://disease-ontology.org/
    name: Human Disease Ontology at Northwestern University
    uri_format: http://disease-ontology.org/term/DOID:$1
  synonyms:
  - do
  uri_format: https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1
  version: '2021-11-17'
dommino:
  description: DOMMINO is a database of macromolecular interactions that includes
    the interactions between protein domains, interdomain linkers, N- and C-terminal
    regions and protein peptides.
  example: 2GC4
  homepage: http://korkinlab.org/dommino
  mappings:
    miriam: dommino
    n2t: dommino
    prefixcommons: DOMMINO
  name: Database of Macromolecular Interactions
  pattern: ^[0-9][A-Za-z0-9]{3}$
  preferred_prefix: dommino
  uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1
door:
  description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted
    operons of all the sequenced prokaryotic genomes. It includes operons for RNA
    genes.
  example: '1398574'
  homepage: http://csbl.bmb.uga.edu/DOOR/operon.php
  mappings:
    miriam: door
    n2t: door
    prefixcommons: DOOR
  name: Database for Prokaryotic Operons
  pattern: ^\d+$
  preferred_prefix: door
  uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1
doqcs.model:
  description: The Database of Quantitative Cellular Signaling is a repository of
    models of signaling pathways. It includes reaction schemes, concentrations, rate
    constants, as well as annotations on the models. The database provides a range
    of search, navigation, and comparison functions. This datatype provides access
    to specific models.
  example: '57'
  homepage: http://doqcs.ncbs.res.in/
  mappings:
    miriam: doqcs.model
    n2t: doqcs.model
    prefixcommons: DOQCS.MODEL
  name: 'Database of Quantitative Cellular Signaling: Model'
  part_of: doqcs
  pattern: ^\d+$
  preferred_prefix: doqcs.model
  uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1
doqcs.pathway:
  description: The Database of Quantitative Cellular Signaling is a repository of
    models of signaling pathways. It includes reaction schemes, concentrations, rate
    constants, as well as annotations on the models. The database provides a range
    of search, navigation, and comparison functions. This datatype provides access
    to pathways.
  example: '131'
  homepage: http://doqcs.ncbs.res.in/
  mappings:
    miriam: doqcs.pathway
    n2t: doqcs.pathway
    prefixcommons: DOQCS.PATHWAY
  name: 'Database of Quantitative Cellular Signaling: Pathway'
  part_of: doqcs
  pattern: ^\d+$
  preferred_prefix: doqcs.pathway
  uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1
dpo:
  banana: FBcv
  comment: DPO is a subset of terms from FBcv
  contact:
    email: cp390@cam.ac.uk
    github: Clare72
    name: Clare Pilgrim
    orcid: null
  description: An ontology for the description of Drosophila melanogaster phenotypes.
  homepage: http://purl.obolibrary.org/obo/fbcv
  license: CC BY 3.0
  mappings:
    bioportal: DPO
    obofoundry: FBcv
    ols: dpo
    ontobee: DPO
  name: Drosophila Phenotype Ontology
  no_own_terms: true
  part_of: fbcv
  preferred_prefix: DPO
  uri_format: http://purl.obolibrary.org/obo/FBcv_$1
  version: '2021-10-15'
dpv:
  description: Description of Plant Viruses (DPV) provides information about viruses,
    viroids and satellites of plants, fungi and protozoa. It provides taxonomic information,
    including brief descriptions of each family and genus, and classified lists of
    virus sequences. The database also holds detailed information for all sequences
    of viruses, viroids and satellites of plants, fungi and protozoa that are complete
    or that contain at least one complete gene.
  example: '100'
  homepage: http://www.dpvweb.net/
  mappings:
    miriam: dpv
    n2t: dpv
    prefixcommons: DPV
  name: Description of Plant Viruses
  pattern: ^\d+$
  preferred_prefix: dpv
  uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1
dragondb.allele:
  comment: Deprecated because the website is dead
  deprecated: true
  description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
    This collection refers to allele information.
  example: cho
  homepage: http://www.antirrhinum.net/
  mappings:
    miriam: dragondb.allele
    n2t: dragondb.allele
    prefixcommons: DRAGONDB.ALLELE
  name: DragonDB Allele
  part_of: dragondb
  pattern: ^\w+$
  preferred_prefix: dragondb.allele
  uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele
dragondb.dna:
  comment: Deprecated because the website is dead
  deprecated: true
  description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
    This collection refers to DNA sequence information.
  example: 3hB06
  homepage: http://www.antirrhinum.net/
  mappings:
    miriam: dragondb.dna
    n2t: dragondb.dna
    prefixcommons: DRAGONDB.DNA
  name: DragonDB DNA
  part_of: dragondb
  pattern: ^\d\w+$
  preferred_prefix: dragondb.dna
  uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA
dragondb.locus:
  comment: Deprecated because the website is dead
  deprecated: true
  description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
    This collection refers to Locus information.
  example: DEF
  homepage: http://www.antirrhinum.net/
  mappings:
    miriam: dragondb.locus
    n2t: dragondb.locus
    prefixcommons: DRAGONDB.LOCUS
  name: DragonDB Locus
  part_of: dragondb
  pattern: ^\w+$
  preferred_prefix: dragondb.locus
  uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus
dragondb.protein:
  comment: Deprecated because the website is dead
  deprecated: true
  description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
    This collection refers to protein sequence information.
  example: AMDEFA
  homepage: http://www.antirrhinum.net/
  mappings:
    miriam: dragondb.protein
    n2t: dragondb.protein
    prefixcommons: DRAGONDB.PROTEIN
  name: DragonDB Protein
  part_of: dragondb
  pattern: ^\w+$
  preferred_prefix: dragondb.protein
  uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide
dron:
  banana: DRON
  contact:
    email: hoganwr@gmail.com
    github: hoganwr
    name: William Hogan
    orcid: null
  description: We built this ontology primarily to support comparative effectiveness
    researchers studying claims data. They need to be able to query U.S. National
    Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade),
    physiological effect (diuresis), and therapeutic intent (anti-hypertensive).
  example: '00023232'
  homepage: https://github.com/ufbmi/dron
  license: CC BY 3.0
  mappings:
    bioportal: DRON
    obofoundry: DRON
    ols: dron
    ontobee: DRON
    prefixcommons: DRON
  name: The Drug Ontology
  preferred_prefix: DRON
  uri_format: http://purl.obolibrary.org/obo/DRON_$1
  version: '2021-10-20'
drsc:
  description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of
    reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen
    results. It maintains a list of Drosophila gene names, identifiers, symbols and
    synonyms and provides  information for cell-based or in vivo RNAi reagents, other
    types of reagents, screen results, etc. corresponding for a given gene.
  example: DRSC05221
  homepage: http://flyrnai.org/
  mappings:
    miriam: drsc
    n2t: drsc
    prefixcommons: DRSC
  name: Drosophila RNAi Screening Center
  pattern: ^DRSC\d+$
  preferred_prefix: drsc
  uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1
drugbank:
  description: The DrugBank database is a bioinformatics and chemoinformatics resource
    that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
    data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
    This collection references drug information.
  example: DB14938
  homepage: http://www.drugbank.ca
  mappings:
    cellosaurus: DrugBank
    cheminf: '000406'
    miriam: drugbank
    n2t: drugbank
    prefixcommons: DrugBank
    uniprot: DrugBank
    wikidata: P715
  name: DrugBank
  pattern: ^DB\d{5}$
  preferred_prefix: drugbank
  synonyms:
  - DRUGBANK_ID
  - DrugBank
  uri_format: http://www.drugbank.ca/drugs/$1
drugbank.salt:
  description: DrugBank is a web-enabled database containing comprehensive molecular
    information about drugs, their mechanisms, their interactions and their targets.
  example: DBSALT001211
  homepage: http://www.drugbank.ca
  mappings:
    prefixcommons: DRUGBANK.TARGET
  name: DrugBank Salts
  part_of: drugbank
  pattern: ^DBSALT\d{6}$
  preferred_prefix: drugbank.salt
  synonyms:
  - drugbank.target
  uri_format: https://go.drugbank.com/salts/$1
drugbankv4.target:
  description: The DrugBank database is a bioinformatics and chemoinformatics resource
    that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
    data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
    This collection references target information from version 4 of the database.
  example: BE0000048
  homepage: http://www.drugbank.ca/targets
  mappings:
    miriam: drugbankv4.target
    n2t: drugbankv4.target
    prefixcommons: DRUGBANKV4.TARGET
  name: DrugBank Target v4
  part_of: drugbank
  pattern: ^BE\d{7}$
  preferred_prefix: drugbankv4.target
  uri_format: http://www.drugbank.ca/biodb/bio_entities/$1
drugcentral:
  description: DrugCentral  provides information on active ingredients chemical entities,
    pharmaceutical products, drug mode of action, indications, pharmacologic action.
  example: '307'
  homepage: http://drugcentral.org
  mappings:
    biolink: DrugCentral
    uniprot: DrugCentral
  name: Drug Central
  preferred_prefix: drugcentral
  synonyms:
  - Drug_Central
  uri_format: http://drugcentral.org/drugcard/$1
dsmz:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Leibniz Institute DSMZ is the most diverse biological resource
    center in the world and one of the largest collections of microorganisms and cell
    cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages,
    plant viruses, genomic bacterial DNA as well as human and animal cell lines).
  example: ACC-1
  homepage: https://www.dsmz.de
  mappings:
    cellosaurus: DSMZ
  name: Deutsche Sammlung von Mikroorganismen und Zellkulturen
  preferred_prefix: dsmz
  uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1
dto:
  description: 'DTO integrates and harmonizes knowledge of the most important druggable
    protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.'
  example: '90000018'
  homepage: https://github.com/DrugTargetOntology/DTO
  mappings:
    bioportal: DTO
  name: Drug Target Ontology
  preferred_prefix: dto
duo:
  banana: DUO
  contact:
    email: mcourtot@gmail.com
    github: mcourtot
    name: Melanie Courtot
    orcid: null
  description: DUO is an ontology which represent data use conditions.
  example: '0000046'
  homepage: https://github.com/EBISPOT/DUO
  license: CC BY 4.0
  mappings:
    bioportal: DUO
    obofoundry: DUO
    ols: duo
    ontobee: DUO
    prefixcommons: DUO
  name: Data Use Ontology
  preferred_prefix: DUO
  uri_format: http://purl.obolibrary.org/obo/DUO_$1
  version: '2021-02-23'
eaglei:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Discovery tool for biomedical research resources available at institutions
    throughout the U.S.
  example: 0000012b-5661-2f63-2f73-b43980000000
  homepage: https://hawaii.eagle-i.net
  mappings:
    cellosaurus: eagle-i
  name: eagle-i
  preferred_prefix: eaglei
  uri_format: http://hawaii.eagle-i.net/i/$1
ecacc:
  description: The European Collection of Authenticated Cell Cultures (ECACC) is one
    of four Culture Collections of Public Health England. We supply authenticated
    and quality controlled cell lines, nucleic acids and induced Pluripotent Stem
    Cells (iPSCs).
  example: '90062901'
  homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx
  mappings:
    cellosaurus: ECACC
  name: European Collection of Authenticated Cell Culture
  preferred_prefix: ecacc
  uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1
ecao:
  banana: ECAO
  contact:
    email: ettensohn@cmu.edu
    github: ettensohn
    name: Charles Ettensohn
    orcid: null
  description: None
  example: 0107180
  homepage: https://github.com/echinoderm-ontology/ecao_ontology
  license: CC BY 3.0
  mappings:
    bioportal: ECAO
    obofoundry: ECAO
    ols: ecao
    ontobee: ECAO
  name: The Echinoderm Anatomy and Development Ontology
  preferred_prefix: ECAO
  uri_format: http://purl.obolibrary.org/obo/ECAO_$1
  version: '2020-05-22'
eccode:
  description: The Enzyme Classification contains the recommendations of the Nomenclature
    Committee of the International Union of Biochemistry and Molecular Biology on
    the nomenclature and classification of enzyme-catalysed reactions.
  example: 1.1.1.1
  homepage: https://www.ebi.ac.uk/intenz/
  mappings:
    go: EC
    miriam: ec-code
    n2t: ec-code
    prefixcommons: EC
    wikidata: P591
  name: Enzyme Nomenclature
  pattern: ^\d{1,2}(\.\d{0,3}){0,3}$
  preferred_prefix: eccode
  providers:
  - code: CURATOR_REVIEW
    description: KEGG Ligand Database for Enzyme Nomenclature
    homepage: https://www.genome.jp/dbget-bin/www_bfind?enzyme
    name: KEGG Ligand Database for Enzyme Nomenclature
    uri_format: https://www.genome.jp/dbget-bin/www_bget?ec:$1
  - code: expenz
    description: ExploreEnz at Trinity College
    homepage: http://www.enzyme-database.org/
    name: ExploreEnz at Trinity College
    uri_format: http://www.enzyme-database.org/query.php?ec=$1
  - code: enzymeportal
    description: Enzyme Portal through EMBL-EBI
    homepage: https://www.ebi.ac.uk/enzymeportal
    name: Enzyme Portal through EMBL-EBI
    uri_format: https://www.ebi.ac.uk/enzymeportal/ec/$1
  - code: expasy
    description: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)
    homepage: https://enzyme.expasy.org/
    name: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)
    uri_format: https://enzyme.expasy.org/EC/$1
  synonyms:
  - EC
  - EC-CODE
  - ECCODE
  - EC_CODE
  - ec-code
  - intenz
  uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1
ecg:
  description: The Electrocardiography (ECG) Ontology is a Driving Biological Project
    of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms,
    their capture method(s) and their waveforms.
  example: 000000159
  homepage: https://bioportal.bioontology.org/ontologies/ECG
  mappings:
    bioportal: ECG
  name: Electrocardiogram Ontology
  pattern: ^\d+$
  preferred_prefix: ecg
  synonyms:
  - ECGOntology
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.
  example: EB0170
  homepage: http://www.york.ac.uk/
  mappings:
    go: EchoBASE
    miriam: echobase
    n2t: echobase
    prefixcommons: ECHOBASE
    uniprot: EchoBASE
  name: EchoBASE post-genomic database for Escherichia coli
  pattern: ^EB\d+$
  preferred_prefix: echobase
  uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1
ecmdb:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "The ECMDB is an expertly curated database containing extensive metabolomic\
    \ data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655).\
    \ This database includes significant quantities of \u201Coriginal\u201D data compiled\
    \ by members of the Wishart laboratory as well as additional material derived\
    \ from hundreds of textbooks, scientific journals, metabolic reconstructions and\
    \ other electronic databases. Each metabolite is linked to more than 100 data\
    \ fields describing the compound, its ontology, physical properties, reactions,\
    \ pathways, references, external links and associated proteins or enzymes."
  example: ECMDB00005
  homepage: https://ecmdb.ca
  name: E. coli Metabolite Database
  pattern: ^ECMDB\d+$
  preferred_prefix: ecmdb
  synonyms:
  - ECMDB
  uri_format: http://ecmdb.ca/compounds/$1
eco:
  banana: ECO
  contact:
    email: mgiglio@som.umaryland.edu
    github: mgiglio99
    name: Michelle Giglio
    orcid: null
  description: Evidence codes can be used to specify the type of supporting evidence
    for a piece of knowledge. This allows inference of a 'level of support' between
    an entity and an annotation made to an entity.
  example: 0007807
  homepage: https://github.com/evidenceontology/evidenceontology/
  license: CC0 1.0
  mappings:
    bioportal: ECO
    go: ECO
    miriam: eco
    n2t: eco
    obofoundry: ECO
    ols: eco
    ontobee: ECO
    prefixcommons: ECO
  name: Evidence ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: ECO
  uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1
  version: '2021-10-20'
ecocore:
  banana: ECOCORE
  contact:
    email: p.buttigieg@gmail.com
    github: pbuttigieg
    name: Pier Luigi Buttigieg
    orcid: null
  description: Ecocore is a community ontology for the concise and controlled description
    of ecological traits of organisms.
  example: '00000001'
  homepage: https://github.com/EcologicalSemantics/ecocore
  license: CC BY 3.0
  mappings:
    bioportal: ECOCORE
    obofoundry: ECOCORE
    ols: ecocore
    ontobee: ECOCORE
    prefixcommons: ECOCORE
  name: An ontology of core ecological entities
  pattern: ^\d+$
  preferred_prefix: ECOCORE
  uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1
  version: '2021-02-17'
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.
  example: AICARTRANSIMPCYCLO-CPLX
  homepage: http://ecocyc.org/
  mappings:
    go: EcoCyc
    ncbi: ECOCYC
  name: EcoCyc
  preferred_prefix: ecocyc
  uri_format: https://biocyc.org/gene?id=$1
ecogene:
  description: The EcoGene database contains updated information about the E. coli
    K-12 genome and proteome sequences, including extensive gene bibliographies. A
    major EcoGene focus has been the re-evaluation of translation start sites.
  example: EG10173
  homepage: http://ecogene.org/
  mappings:
    miriam: ecogene
    n2t: ecogene
    ncbi: EcoGene
    prefixcommons: EcoGene
  name: Database of Escherichia coli Sequence and Function
  pattern: ^EG\d+$
  preferred_prefix: ecogene
  uri_format: http://www.ecogene.org/gene/$1
ecoliwiki:
  description: EcoliWiki is a wiki-based resource to store information related to
    non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This
    collection references genes.
  example: aaeA
  homepage: http://ecoliwiki.net/colipedia/
  mappings:
    go: EcoliWiki
    miriam: ecoliwiki
    n2t: ecoliwiki
    prefixcommons: ECOLIWIKI
  name: EcoliWiki from EcoliHub
  pattern: ^[A-Za-z0-9-]+$
  preferred_prefix: ecoliwiki
  uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene
ecto:
  banana: ECTO
  contact:
    email: annethessen@gmail.com
    github: diatomsRcool
    name: Anne Thessen
    orcid: null
  description: ECTO describes exposures to experimental treatments of plants and model
    organisms (e.g. exposures to modification of diet, lighting levels, temperature);
    exposures of humans or any other organisms to stressors through a variety of routes,
    for purposes of public health, environmental monitoring etc, stimuli, natural
    and experimental, any kind of environmental condition or change in condition that
    can be experienced by an organism or population of organisms on earth. The scope
    is very general and can include for example plant treatment regimens, as well
    as human clinical exposures (although these may better be handled by a more specialized
    ontology).
  example: '0000001'
  homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
  license: CC0 1.0
  mappings:
    biolink: ECTO
    bioportal: ECTO
    obofoundry: ECTO
    ols: ecto
    ontobee: ECTO
  name: Environmental conditions, treatments and exposures ontology
  pattern: ^\d{7}$
  preferred_prefix: ECTO
  uri_format: http://purl.obolibrary.org/obo/ECTO_$1
  version: '2021-08-25'
ecyano.entity:
  description: "E-cyanobacterium.org is a web-based platform for public sharing, annotation,\
    \ analysis, and visualisation of dynamical models and wet-lab experiments related\
    \ to cyanobacteria. It allows models to be represented at different levels of\
    \ abstraction \u2014 as biochemical reaction networks or ordinary differential\
    \ equations.It provides concise mappings of mathematical models to a formalised\
    \ consortium-agreed biochemical description, with the aim of connecting the world\
    \ of biological knowledge with benefits of mathematical description of dynamic\
    \ processes. This collection references entities."
  example: '23'
  homepage: http://www.e-cyanobacterium.org/bcs/entity/
  mappings:
    miriam: ecyano.entity
    n2t: ecyano.entity
    prefixcommons: ECYANO.ENTITY
  name: E-cyanobacterium entity
  part_of: ecyano
  pattern: ^\d+$
  preferred_prefix: ecyano.entity
  uri_format: https://www.e-cyanobacterium.org/bcs/entity/$1
ecyano.experiment:
  description: E-cyanobacterium experiments is a repository of wet-lab experiments
    related to cyanobacteria. The emphasis is placed on annotation via mapping to
    local database of biological knowledge and mathematical models along with the
    complete experimental setup supporting the reproducibility of the experiments.
  example: '18'
  homepage: https://www.e-cyanobacterium.org/experiments-repository/
  mappings:
    miriam: ecyano.experiment
  name: E-cyanobacterium Experimental Data
  part_of: ecyano
  pattern: ^\d+$
  preferred_prefix: ecyano.experiment
  uri_format: https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1
ecyano.model:
  description: "E-cyanobacterium.org is a web-based platform for public sharing, annotation,\
    \ analysis, and visualisation of dynamical models and wet-lab experiments related\
    \ to cyanobacteria. It allows models to be represented at different levels of\
    \ abstraction \u2014 as biochemical reaction networks or ordinary differential\
    \ equations.It provides concise mappings of mathematical models to a formalised\
    \ consortium-agreed biochemical description, with the aim of connecting the world\
    \ of biological knowledge with benefits of mathematical description of dynamic\
    \ processes. This collection references models."
  example: '26'
  homepage: http://e-cyanobacterium.org/models/
  mappings:
    miriam: ecyano.model
    n2t: ecyano.model
    prefixcommons: ECYANO.MODEL
  name: E-cyanobacterium model
  pattern: ^\d+$
  preferred_prefix: ecyano.model
  uri_format: https://e-cyanobacterium.org/models/model/$1
ecyano.rule:
  description: "E-cyanobacterium.org is a web-based platform for public sharing, annotation,\
    \ analysis, and visualisation of dynamical models and wet-lab experiments related\
    \ to cyanobacteria. It allows models to be represented at different levels of\
    \ abstraction \u2014 as biochemical reaction networks or ordinary differential\
    \ equations.It provides concise mappings of mathematical models to a formalised\
    \ consortium-agreed biochemical description, with the aim of connecting the world\
    \ of biological knowledge with benefits of mathematical description of dynamic\
    \ processes. This collection references rules."
  example: '56'
  homepage: http://www.e-cyanobacterium.org/bcs/rule/
  mappings:
    miriam: ecyano.rule
    n2t: ecyano.rule
    prefixcommons: ECYANO.RULE
  name: E-cyanobacterium rule
  part_of: ecyano
  pattern: ^\d+$
  preferred_prefix: ecyano.rule
  uri_format: https://e-cyanobacterium.org/bcs/rule/$1
edam:
  description: 'EDAM is an ontology of general bioinformatics concepts, including
    topics, data types, formats, identifiers and operations. EDAM provides a controlled
    vocabulary for the description, in semantic terms, of things such as: web services
    (e.g. WSDL files), applications, tool collections and packages, work-benches and
    workflow software, databases and ontologies, XSD data schema and data objects,
    data syntax and file formats, web portals and pages, resource catalogues and documents
    (such as scientific publications).'
  example: data_1664
  homepage: http://edamontology.org
  mappings:
    bioportal: EDAM
    miriam: edam
    n2t: edam
    ols: edam
    ontobee: EDAM
    prefixcommons: EDAM
  name: Bioinformatics operations, data types, formats, identifiers and topics
  pattern: ^(data|topic|operation|format)\_\d{4}$
  preferred_prefix: edam
  uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1
  version: '2019-07-17'
efo:
  description: The Experimental Factor Ontology (EFO) provides a systematic description
    of many experimental variables available in EBI databases. It combines parts of
    several biological ontologies, such as anatomy, disease and chemical compounds.
    The scope of EFO is to support the annotation, analysis and visualization of data
    handled by the EBI Functional Genomics Team.
  example: '0005147'
  homepage: http://www.ebi.ac.uk/efo
  license: Apache 2.0 License
  mappings:
    biolink: EFO
    bioportal: EFO
    cellosaurus: EFO
    miriam: efo
    n2t: efo
    ols: efo
    ontobee: EFO
    prefixcommons: EFO
  name: Experimental Factor Ontology
  pattern: ^\d{7}$
  preferred_prefix: EFO
  providers:
  - code: ebi
    description: EFO through Functional Genomics Group (EBI)
    homepage: https://www.ebi.ac.uk/efo/
    name: EFO through Functional Genomics Group (EBI)
    uri_format: https://www.ebi.ac.uk/efo/EFO_$1
  uri_format: http://www.ebi.ac.uk/efo/EFO_$1
  version: 3.36.0
ega.dataset:
  description: The EGA is a service for permanent archiving and sharing of all types
    of personally identifiable genetic and phenotypic data resulting from biomedical
    research projects. The EGA contains exclusive data collected from individuals
    whose consent agreements authorize data release only for specific research use
    or to bona fide researchers. Strict protocols govern how information is managed,
    stored and distributed by the EGA project. This collection references 'Datasets'.
  example: EGAD00000000001
  homepage: https://ega-archive.org/
  mappings:
    fairsharing: FAIRsharing.mya1ff
    miriam: ega.dataset
    n2t: ega.dataset
    prefixcommons: EGA.DATASET
  name: European Genome-phenome Archive Dataset
  pattern: ^EGAD\d{11}$
  preferred_prefix: ega.dataset
  providers:
  - code: omicsdi
    description: EGA Dataset through OmicsDI
    homepage: https://www.omicsdi.org/
    name: EGA Dataset through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/ega/$1
  uri_format: https://www.ebi.ac.uk/ega/datasets/$1
ega.study:
  description: The EGA is a service for permanent archiving and sharing of all types
    of personally identifiable genetic and phenotypic data resulting from biomedical
    research projects. The EGA contains exclusive data collected from individuals
    whose consent agreements authorize data release only for specific research use
    or to bona fide researchers. Strict protocols govern how information is managed,
    stored and distributed by the EGA project. This collection references 'Studies'
    which are experimental investigations of a particular phenomenon, often drawn
    from different datasets.
  example: EGAS00000000001
  homepage: https://www.ebi.ac.uk/ega/studies
  mappings:
    miriam: ega.study
    n2t: ega.study
    prefixcommons: EGA.STUDY
  name: European Genome-phenome Archive Study
  pattern: ^EGAS\d{11}$
  preferred_prefix: ega.study
  providers:
  - code: omicsdi
    description: EGA Study through OmicsDI
    homepage: https://www.omicsdi.org/
    name: EGA Study through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/ega/$1
  uri_format: https://www.ebi.ac.uk/ega/studies/$1
eggnog:
  description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
    Groups) is a database of orthologous groups of genes. The orthologous groups are
    annotated with functional description lines (derived by identifying a common denominator
    for the genes based on their various annotations), with functional categories
    (i.e derived from the original COG/KOG categories).'
  example: veNOG12876
  homepage: http://eggnog.embl.de/version_3.0/
  mappings:
    miriam: eggnog
    n2t: eggnog
    prefixcommons: EGGNOG
    uniprot: eggNOG
  name: eggNOG
  pattern: ^\w+$
  preferred_prefix: eggnog
  uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1
ehda:
  banana: EHDA
  contact:
    email: J.Bard@ed.ac.uk
    github: null
    name: Jonathan Bard
    orcid: null
  deprecated: true
  homepage: http://genex.hgu.mrc.ac.uk/
  mappings:
    bioportal: EHDA
    obofoundry: EHDA
    prefixcommons: EHDA
  name: Human developmental anatomy, timed version
  preferred_prefix: EHDA
  uri_format: http://purl.obolibrary.org/obo/EHDA_$1
ehdaa:
  banana: EHDAA
  contact:
    email: J.Bard@ed.ac.uk
    github: null
    name: Jonathan Bard
    orcid: null
  deprecated: true
  mappings:
    bioportal: EHDAA
    obofoundry: EHDAA
    prefixcommons: EHDAA
  name: Human developmental anatomy, abstract version
  preferred_prefix: EHDAA
  uri_format: http://purl.obolibrary.org/obo/EHDAA_$1
ehdaa2:
  banana: EHDAA2
  contact:
    email: J.Bard@ed.ac.uk
    github: null
    name: Jonathan Bard
    orcid: null
  description: A structured controlled vocabulary of stage-specific anatomical structures
    of the developing human.
  example: '0000000'
  homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology
  license: CC BY 4.0
  mappings:
    bioportal: EHDAA2
    obofoundry: EHDAA2
    ols: ehdaa2
    ontobee: EHDAA2
    prefixcommons: EHDAA2
  name: Human developmental anatomy, abstract
  pattern: ^\d{7}$
  preferred_prefix: EHDAA2
  synonyms:
  - EHDAA2_RETIRED
  - HDAA2
  - RETIRED_EHDAA2
  uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1
  version: '2013-07-04'
elm:
  description: Linear motifs are short, evolutionarily plastic components of regulatory
    proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif
    resource (ELM) is a database of curated motif classes and instances.
  example: CLV_MEL_PAP_1
  homepage: http://elm.eu.org/
  mappings:
    miriam: elm
    n2t: elm
    prefixcommons: ELM
    uniprot: ELM
  name: Eukaryotic Linear Motif Resource
  pattern: ^[A-Za-z_0-9]+$
  preferred_prefix: elm
  uri_format: http://elm.eu.org/elms/elmPages/$1.html
emap:
  banana: EMAP
  contact:
    email: Terry.Hayamizu@jax.org
    github: tfhayamizu
    name: Terry Hayamizu
    orcid: null
  deprecated: true
  description: A structured controlled vocabulary of stage-specific anatomical structures
    of the mouse (Mus).
  homepage: http://emouseatlas.org
  mappings:
    bioportal: EMAP
    obofoundry: EMAP
    prefixcommons: EMAP
  name: Mouse gross anatomy and development, timed
  preferred_prefix: EMAP
  uri_format: http://purl.obolibrary.org/obo/EMAP_$1
emapa:
  banana: EMAPA
  contact:
    email: Terry.Hayamizu@jax.org
    github: tfhayamizu
    name: Terry Hayamizu
    orcid: null
  description: An ontology for mouse anatomy covering embryonic development and postnatal
    stages.
  example: '26753'
  homepage: http://www.informatics.jax.org/expression.shtml
  license: CC BY 4.0
  mappings:
    bioportal: EMAPA
    go: EMAPA
    obofoundry: EMAPA
    ols: emapa
    ontobee: EMAPA
    prefixcommons: EMAPA
  name: Mouse Developmental Anatomy Ontology
  pattern: ^\d+$
  preferred_prefix: EMAPA
  synonyms:
  - EMAPA_RETIRED
  uri_format: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1
  version: '2021-09-01'
emdb:
  description: The Electron Microscopy Data Bank (EMDB) is a public repository for
    electron microscopy density maps of macromolecular complexes and subcellular structures.
    It covers a variety of techniques, including single-particle analysis, electron
    tomography, and electron (2D) crystallography. The EMDB map distribution format
    follows the CCP4 definition, which is widely recognized by software packages used
    by the structural biology community.
  example: EMD-1001
  homepage: https://www.ebi.ac.uk/pdbe/emdb/
  mappings:
    fairsharing: FAIRsharing.651n9j
    miriam: emdb
    n2t: emdb
    prefixcommons: EMDB
  name: Electron Microscopy Data Bank
  pattern: ^EMD-\d{4}$
  preferred_prefix: emdb
  uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1
emolecules:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Catalog of purchasable reagents and building blocks
  example: '491187'
  homepage: https://reaxys.emolecules.com
  name: Reaxys eMolecules
  pattern: ^\d+$
  preferred_prefix: emolecules
  uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1
empiar:
  description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource
    for raw, 2D electron microscopy images. Here, you can browse, upload and download
    the raw images used to build a 3D structure
  example: '10595'
  homepage: https://www.ebi.ac.uk/pdbe/emdb
  mappings:
    fairsharing: biodbcore-001140
  name: Electron Microscopy Public Image Archive
  preferred_prefix: empiar
  uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1
ena.embl:
  description: The European Nucleotide Archive (ENA) captures and presents information
    relating to experimental workflows that are based around nucleotide sequencing.
    ENA is made up of a number of distinct databases that includes EMBL-Bank, the
    Sequence Read Archive (SRA) and the Trace Archive each with their own data formats
    and standards. This collection references Embl-Bank identifiers.
  example: BN000065
  homepage: https://www.ebi.ac.uk/ena/
  mappings:
    go: ENA
    miriam: ena.embl
    n2t: ena.embl
    prefixcommons: ENA.EMBL
  name: European Nucleotide Archive
  pattern: ^[A-Z]+[0-9]+(\.\d+)?$
  preferred_prefix: ena.embl
  providers:
  - code: CURATOR_REVIEW
    description: ENA through GenBank
    homepage: https://www.ncbi.nlm.nih.gov/Genbank/
    name: ENA through GenBank
    uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
  synonyms:
  - ena
  uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
encode:
  description: The ENCODE Consortium is integrating multiple technologies and approaches
    in a collective effort to discover and define the functional elements encoded
    in the human genome, including genes, transcripts, and transcriptional regulatory
    regions, together with their attendant chromatin states and DNA methylation patterns.
  example: ENCSR163RYW
  homepage: https://www.encodeproject.org
  mappings:
    cellosaurus: ENCODE
    miriam: encode
    n2t: encode
    prefixcommons: ENCODE
  name: 'ENCODE: Encyclopedia of DNA Elements'
  pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$
  preferred_prefix: encode
  uri_format: https://www.encodeproject.org/$1
enm:
  description: 'The eNanoMapper project (www.enanomapper.net) is creating a pan-European
    computational infrastructure for toxicological data management for ENMs, based
    on semantic web standards and ontologies. > This ontology is an application ontology
    targeting the full domain of nanomaterial safety assessment. It re-uses several
    other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. '
  example: '8000221'
  homepage: http://www.enanomapper.net/
  license: CC BY 3.0
  mappings:
    bioportal: ENM
    ols: enm
  name: eNanoMapper Ontology
  preferred_prefix: enm
  version: '7.2'
ensembl:
  description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute  to
    develop a software system which produces and maintains automatic annotation on
    selected eukaryotic genomes. This collections also references outgroup organisms.
  example: ENSG00000139618
  homepage: https://www.ensembl.org/
  mappings:
    go: ENSEMBL
    miriam: ensembl
    n2t: ensembl
    ncbi: ENSEMBL
    prefixcommons: ENSEMBL
    uniprot: Ensembl
    wikidata: P594
  name: Ensembl gene ID
  pattern: ^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$
  preferred_prefix: ensembl
  providers:
  - code: bgee
    description: Gene expression in various tissues
    homepage: https://bgee.org
    name: Bgee
    uri_format: https://bgee.org/?page=gene&gene_id=$1
  - code: gnomad
    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
    name: Genome Aggregation database
    uri_format: https://gnomad.broadinstitute.org/gene/$1
  - code: CURATOR_REVIEW
    description: Ensembl US West mirror
    homepage: http://uswest.ensembl.org/
    name: Ensembl US West mirror
    uri_format: http://uswest.ensembl.org/id/$1
  - code: CURATOR_REVIEW
    description: Ensembl US East mirror
    homepage: http://useast.ensembl.org/
    name: Ensembl US East mirror
    uri_format: http://useast.ensembl.org/id/$1
  - code: CURATOR_REVIEW
    description: Ensembl Asia mirror
    homepage: http://asia.ensembl.org/
    name: Ensembl Asia mirror
    uri_format: http://asia.ensembl.org/id/$1
  synonyms:
  - Ensembl
  uri_format: https://www.ensembl.org/id/$1
ensembl.bacteria:
  description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
    fungi, plants and invertebrate metazoa) designed to complement the availability
    of vertebrate genomes in Ensembl. This collection is concerned with bacterial
    genomes.
  example: MU9_3181
  homepage: https://bacteria.ensembl.org/
  mappings:
    miriam: ensembl.bacteria
    n2t: ensembl.bacteria
    prefixcommons: ENSEMBL.BACTERIA
    uniprot: EnsemblBacteria
  name: Ensembl Bacteria
  pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$
  preferred_prefix: ensembl.bacteria
  uri_format: https://bacteria.ensembl.org/id/$1
ensembl.fungi:
  description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
    fungi, plants and invertebrate metazoa) designed to complement the availability
    of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.
  example: CADAFLAT00006211
  homepage: https://fungi.ensembl.org/
  mappings:
    go: EnsemblFungi
    miriam: ensembl.fungi
    n2t: ensembl.fungi
    prefixcommons: ENSEMBL.FUNGI
    uniprot: EnsemblFungi
  name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
  pattern: ^[A-Z-a-z0-9]+$
  preferred_prefix: ensembl.fungi
  uri_format: https://fungi.ensembl.org/id/$1
ensembl.metazoa:
  description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
    fungi, plants and invertebrate metazoa) designed to complement the availability
    of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes.
  example: FBtr0084214
  homepage: https://metazoa.ensembl.org/
  mappings:
    go: EnsemblMetazoa
    miriam: ensembl.metazoa
    n2t: ensembl.metazoa
    prefixcommons: ENSEMBL.METAZOA
    uniprot: EnsemblMetazoa
  name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from
    non-vertebrate metazoa.
  pattern: ^\w+(\.)?\d+$
  preferred_prefix: ensembl.metazoa
  uri_format: https://metazoa.ensembl.org/id/$1
ensembl.plant:
  description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
    fungi, plants and invertebrate metazoa) designed to complement the availability
    of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.
  example: AT1G73965
  homepage: https://plants.ensembl.org/
  mappings:
    miriam: ensembl.plant
    n2t: ensembl.plant
    prefixcommons: ENSEMBL.PLANT
  name: Ensembl Plants
  pattern: ^\w+(\.\d+)?(\.\d+)?$
  preferred_prefix: ensembl.plant
  uri_format: https://plants.ensembl.org/id/$1
ensembl.protist:
  description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
    fungi, plants and invertebrate metazoa) designed to complement the availability
    of vertebrate genomes in Ensembl. This collection is concerned with protist genomes.
  example: PF3D7_1328700
  homepage: https://protists.ensembl.org
  mappings:
    miriam: ensembl.protist
    n2t: ensembl.protist
    prefixcommons: ENSEMBL.PROTIST
  name: Ensembl Protists
  pattern: ^\w+$
  preferred_prefix: ensembl.protist
  uri_format: https://protists.ensembl.org/id/$1
ensemblglossary:
  description: The Ensembl glossary lists the terms, data types and file types that
    are used in Ensembl and describes how they are used.
  example: 0000198
  homepage: http://ensembl.org/glossary
  mappings:
    ols: ensemblglossary
  name: Ensembl Glossary
  preferred_prefix: ensemblglossary
  version: '2021-07-14'
envipath:
  description: enviPath is a database and prediction system for the microbial biotransformation
    of organic environmental contaminants. The database provides the possibility to
    store and view experimentally observed biotransformation pathways. The pathway
    prediction system provides different relative reasoning models to predict likely
    biotransformation pathways and products.
  example: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea
  homepage: https://envipath.org/
  mappings:
    miriam: envipath
  name: enviPath
  pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$
  preferred_prefix: envipath
  uri_format: https://envipath.org/package/$1
envo:
  banana: ENVO
  contact:
    email: p.buttigieg@gmail.com
    github: pbuttigieg
    name: Pier Luigi Buttigieg
    orcid: null
  description: The Environment Ontology is a resource and research target for the
    semantically controlled description of environmental entities. The ontology's
    initial aim was the representation of the biomes, environmental features, and
    environmental materials pertinent to genomic and microbiome-related investigations.
  example: 09200010
  homepage: http://environmentontology.org/
  license: CC BY 3.0
  mappings:
    bioportal: ENVO
    miriam: envo
    n2t: envo
    obofoundry: ENVO
    ols: envo
    ontobee: ENVO
    prefixcommons: ENVO
  name: Environment Ontology
  namespace_in_lui: true
  pattern: ^\d{7,8}$
  preferred_prefix: ENVO
  uri_format: https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1
  version: '2021-05-14'
enzo:
  description: Enzo Life Sciences is an antibody vendor.
  example: ALX-210-175
  homepage: https://www.enzolifesciences.com
  name: Enzo Life Sciences
  preferred_prefix: enzo
  synonyms:
  - Enzo Life Sciences
  uri_format: https://www.enzolifesciences.com/$1
eol:
  description: "L'ontologie EOL d\xE9crit les conditions d'environnement des \xE9\
    levages d'animaux domestiques. Elle d\xE9crit plus particuli\xE8rement les modalit\xE9\
    s de l'alimentation, de l'environnement, de la structure des \xE9levages et des\
    \ syst\xE8mes d'\xE9levage"
  example: 0001927
  homepage: http://www.atol-ontology.com
  mappings:
    bioportal: EOL
    ols: eol
  name: Environment Ontology for Livestock
  preferred_prefix: eol
  version: '2018-09-13'
epcc:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Collection of European paediatric cardiac coding files
  homepage: https://www.aepc.org/european-paediatric-cardiac-coding
  name: European Paediatric Cardiac Codes
  preferred_prefix: epcc
  proprietary: true
  references:
  - https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE
epd:
  description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant
    collection of eukaryotic POL II promoters, for which the transcription start site
    has been determined experimentally. Access to promoter sequences is provided by
    pointers to positions in nucleotide sequence entries. The annotation part of an
    entry includes description of the initiation site mapping data, cross-references
    to other databases, and bibliographic references. EPD is structured in a way that
    facilitates dynamic extraction of biologically meaningful promoter subsets for
    comparative sequence analysis.
  example: TA_H3
  homepage: http://epd.vital-it.ch/
  mappings:
    miriam: epd
    n2t: epd
    ncbi: EPD
    prefixcommons: EPD
    uniprot: EPD
  name: Eukaryotic Promoter Database
  pattern: ^[A-Z-_0-9]+$
  preferred_prefix: epd
  uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1
epo:
  banana: EPO
  deprecated: true
  description: An ontology designed to support the semantic annotation of epidemiology
    resources
  homepage: https://code.google.com/p/epidemiology-ontology/
  mappings:
    bioportal: EPO
    obofoundry: EPO
    ontobee: EPO
    prefixcommons: EPO
  name: Epidemiology Ontology
  preferred_prefix: EPO
  uri_format: http://purl.obolibrary.org/obo/EPO_$1
epso:
  banana: EPSO
  contact:
    email: alpha.tom.kodamullil@scai.fraunhofer.de
    github: akodamullil
    name: Alpha Tom Kodamullil
    orcid: null
  description: A application driven Epilepsy Ontology sith official terms from the
    ILAE.
  example: '0000400'
  homepage: https://github.com/phwegner/Epilepsyontology
  license: CC BY 4.0
  mappings:
    bioportal: EPSO
    obofoundry: EPSO
  name: Epilepsy Ontology
  preferred_prefix: EPSO
  uri_format: https://bio.scai.fraunhofer.de/ontology/$1
erm:
  description: The European Registry of Materials is a simple registry with the sole
    purpose to mint material identifiers to be used by research projects throughout
    the life cycle of their project.
  example: ERM00000044
  homepage: https://nanocommons.github.io/identifiers/
  mappings:
    miriam: erm
    n2t: erm
  name: European Registry of Materials
  pattern: ^ERM[0-9]{8}$
  preferred_prefix: erm
  uri_format: https://nanocommons.github.io/identifiers/registry#$1
ero:
  banana: ERO
  contact:
    email: Marc_Ciriello@hms.harvard.edu
    github: null
    name: Marc Ciriello
    orcid: null
  description: An ontology of research resources such as instruments. protocols, reagents,
    animal models and biospecimens.
  example: '0001655'
  homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
  license: CC BY 2.0
  mappings:
    bioportal: ERO
    obofoundry: ERO
    ols: ero
    ontobee: ERO
    prefixcommons: ERO
  name: eagle-i resource ontology
  preferred_prefix: ERO
  uri_format: http://purl.obolibrary.org/obo/ERO_$1
  version: '2016-07-27'
erv:
  description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a
    typical mammalian genome contains tens to hundreds of thousands of ERV elements.
    Most ERVs are evolutionarily old and have accumulated multiple mutations, playing
    important roles in physiology and disease processes. The Human Endogenous Retrovirus
    Database (hERV) is compiled from the human genome nucleotide sequences obtained
    from Human Genome Projects, and screens those sequences for hERVs, whilst continuously
    improving classification and characterization of retroviral families. It provides
    access to individual reconstructed HERV elements, their sequence, structure and
    features.
  example: THE1B
  homepage: https://herv.img.cas.cz/
  mappings:
    miriam: erv
    n2t: erv
    prefixcommons: ERV
  name: Human Endogenous Retrovirus Database
  pattern: ^[A-Za-z0-9\-\_]+$
  preferred_prefix: erv
  uri_format: https://herv.img.cas.cz/s/$1
eu89h:
  description: The JRC Data Catalogue gives access to the multidisciplinary data produced
    and maintained by the Joint Research Centre, the European Commission's in-house
    science service providing independent scientific advice and support to policies
    of the European Union.
  example: jrc-eurl-ecvam-chemagora
  homepage: http://data.jrc.ec.europa.eu/
  mappings:
    miriam: eu89h
    n2t: eu89h
    prefixcommons: EU89H
  name: JRC Data Catalogue
  pattern: ^[a-z0-9\-_]+$
  preferred_prefix: eu89h
  uri_format: http://data.europa.eu/89h/$1
euclinicaltrials:
  description: "The EU Clinical Trials Register contains information on clinical trials\
    \ conducted in the European Union (EU), or the European Economic Area (EEA) which\
    \ started after 1 May 2004.\r\nIt also includes trials conducted outside these\
    \ areas if they form part of a paediatric investigation plan (PIP), or are sponsored\
    \ by a marketing authorisation holder, and involve the use of a medicine in the\
    \ paediatric population."
  example: 2008-005144-16
  homepage: https://www.clinicaltrialsregister.eu/
  mappings:
    miriam: euclinicaltrials
    n2t: euclinicaltrials
    prefixcommons: EUCLINICALTRIALS
  name: EU Clinical Trials
  pattern: ^\d{4}\-\d{6}\-\d{2}$
  preferred_prefix: euclinicaltrials
  uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1
eupath:
  banana: EUPATH
  contact:
    email: stoeckrt@pennmedicine.upenn.edu
    github: cstoeckert
    name: Chris Stoeckert
    orcid: null
  description: The VEuPathDB ontology is an application ontology developed to encode
    our understanding of what data is about in the public resources developed and
    maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB;
    https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB
    ontology prior to EuPathDB joining with VectorBase.The ontology was built based
    on the Ontology of Biomedical Investigations (OBI) with integration of other OBO
    ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the
    VEuPath ontology is primarily intended to be used for support of the VEuPathDB
    sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will
    be submitted to OBO Foundry ontologies for subsequent import and replacement of
    those terms when they are available.
  example: '0010316'
  homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
  license: CC BY 4.0
  mappings:
    bioportal: EUPATH
    obofoundry: EUPATH
    ols: eupath
    ontobee: EUPATH
    prefixcommons: EUPATH
  name: VEuPathDB ontology
  preferred_prefix: EUPATH
  uri_format: http://purl.obolibrary.org/obo/EUPATH_$1
  version: '2021-09-09'
eurofir:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: EuroFir (European Food Information Resource Network), the world-leading
    European Network of Excellence on Food Composition Databank systems, is a partnership
    between 48 universities, research institutes and small-to-medium sized enterprises
    (SMEs) from 25 European countries.
  homepage: https://www.eurofir.org
  name: European Food Information Resource Network
  preferred_prefix: eurofir
  proprietary: true
ev:
  banana: EV
  contact:
    email: evoc@sanbi.ac.za
    github: null
    name: eVOC mailing list
    orcid: null
  deprecated: true
  homepage: http://www.evocontology.org/
  mappings:
    obofoundry: EV
    prefixcommons: EV
  name: eVOC (Expressed Sequence Annotation for Humans)
  preferred_prefix: EV
  references:
  - https://twitter.com/Bgeedb/status/1350124337815281664
  uri_format: http://purl.obolibrary.org/obo/EV_$1
evm:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: eVOC mouse development stage
  preferred_prefix: evm
  references:
  - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229
exac.gene:
  description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
    seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
    sequencing projects, and to make summary data available for the wider scientific
    community. The data pertains to unrelated individuals sequenced as part of various
    disease-specific and population genetic studies and serves as a reference set
    of allele frequencies for severe disease studies. This collection references gene
    information.
  example: ENSG00000169174
  homepage: http://exac.broadinstitute.org/
  mappings:
    miriam: exac.gene
    n2t: exac.gene
    prefixcommons: EXAC.GENE
  name: ExAC Gene
  pattern: ^ENSG\d{11}$
  preferred_prefix: exac.gene
  uri_format: http://exac.broadinstitute.org/gene/$1
exac.transcript:
  description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
    seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
    sequencing projects, and to make summary data available for the wider scientific
    community. The data pertains to unrelated individuals sequenced as part of various
    disease-specific and population genetic studies and serves as a reference set
    of allele frequencies for severe disease studies. This collection references transcript
    information.
  example: ENST00000407236
  homepage: http://exac.broadinstitute.org/
  mappings:
    miriam: exac.transcript
    n2t: exac.transcript
    prefixcommons: EXAC.TRANSCRIPT
  name: ExAC Transcript
  pattern: ^ENST\d{11}$
  preferred_prefix: exac.transcript
  uri_format: http://exac.broadinstitute.org/transcript/$1
exac.variant:
  description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
    seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
    sequencing projects, and to make summary data available for the wider scientific
    community. The data pertains to unrelated individuals sequenced as part of various
    disease-specific and population genetic studies and serves as a reference set
    of allele frequencies for severe disease studies. This collection references variant
    information.
  example: 22-46615880-T-C
  homepage: http://exac.broadinstitute.org/
  mappings:
    miriam: exac.variant
    n2t: exac.variant
    prefixcommons: EXAC.VARIANT
  name: ExAC Variant
  pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$
  preferred_prefix: exac.variant
  uri_format: http://exac.broadinstitute.org/variant/$1
exo:
  banana: ExO
  contact:
    email: cjgrondin@ncsu.edu
    github: cjgrondin
    name: Cynthia Grondin
    orcid: null
  description: ExO is intended to bridge the gap between exposure science and diverse
    environmental health disciplines including toxicology, epidemiology, disease surveillance,
    and epigenetics.
  example: 0000078
  homepage: http://ctdbase.org/help/exposureHelp.jsp
  license: CC BY 4.0
  mappings:
    biolink: ExO
    bioportal: EXO
    obofoundry: ExO
    ols: exo
    ontobee: ExO
    prefixcommons: EXO
  name: Exposure ontology
  pattern: ^\d{7}$
  preferred_prefix: ExO
  synonyms:
  - ExO
  uri_format: http://purl.obolibrary.org/obo/EXO_$1
  version: '2020-03-10'
facebase:
  description: FaceBase is a collaborative NIDCR-funded consortium to generate data
    in support of advancing research into craniofacial development and malformation.
    It serves as a community resource by generating large datasets of a variety of
    types and making them available to the wider research community via this website.
    Practices emphasize a comprehensive and multidisciplinary approach to understanding
    the developmental processes that create the face. The data offered spotlights
    high-throughput genetic, molecular, biological, imaging and computational techniques.
    One of the missions of this consortium is to facilitate cooperation and collaboration
    between projects.
  example: FB00000917
  homepage: https://www.facebase.org
  mappings:
    miriam: facebase
    n2t: facebase
    prefixcommons: FACEBASE
  name: FaceBase Data Repository
  pattern: ^FB\d{8}$
  preferred_prefix: facebase
  uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1
fairsharing:
  description: The web-based FAIRSharing catalogues aim to centralize bioscience data
    policies, reporting standards and links to other related portals. This collection
    references bioinformatics data exchange standards, which includes 'Reporting Guidelines',
    Format Specifications and Terminologies.
  example: bsg-000052
  homepage: https://fairsharing.org/
  mappings:
    miriam: fairsharing
    n2t: fairsharing
    prefixcommons: FAIRSHARING
  name: FAIRsharing
  pattern: ^bsg-[dscp]?\d{6}$
  preferred_prefix: fairsharing
  uri_format: https://fairsharing.org/$1
faldo:
  description: It is a simple ontology to describe sequence feature positions and
    regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics
    resources
  example: ForwardStrandPosition
  homepage: http://biohackathon.org/resource/faldo
  mappings:
    bioportal: FALDO
    prefixcommons: faldo
  name: 'Feature Annotation Location Description Ontology '
  preferred_prefix: faldo
  uri_format: http://biohackathon.org/resource/faldo#$1
fao:
  banana: FAO
  contact:
    email: mah79@cam.ac.uk
    github: mah11
    name: Midori Harris
    orcid: null
  description: A structured controlled vocabulary for the anatomy of fungi.
  example: '0000001'
  homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
  license: CC0 1.0
  mappings:
    bioportal: FAO
    obofoundry: FAO
    ols: fao
    ontobee: FAO
    prefixcommons: FAO
  name: Fungal gross anatomy
  pattern: ^\d{7}$
  preferred_prefix: FAO
  uri_format: http://purl.obolibrary.org/obo/FAO_$1
  version: '2020-05-07'
fbbi:
  banana: FBbi
  contact:
    email: dorloff@ncmir.ucsd.edu
    github: null
    name: David Orloff
    orcid: null
  description: A structured controlled vocabulary of sample preparation, visualization
    and imaging methods used in biomedical research.
  example: 00000268
  homepage: http://cellimagelibrary.org/
  license: CC BY 4.0
  mappings:
    bioportal: FBbi
    obofoundry: FBbi
    ols: fbbi
    ontobee: FBBI
    prefixcommons: FBbi
  name: Biological Imaging Methods Ontology
  pattern: ^\d+$
  preferred_prefix: FBbi
  synonyms:
  - FBbi
  uri_format: http://purl.obolibrary.org/obo/FBbi_$1
  version: '2020-11-06'
fbbt:
  banana: FBbt
  contact:
    email: cp390@cam.ac.uk
    github: Clare72
    name: Clare Pilgrim
    orcid: null
  description: An ontology of Drosophila melanogaster anatomy.
  example: 00007294
  homepage: http://purl.obolibrary.org/obo/fbbt
  license: CC BY 3.0
  mappings:
    bioportal: FB-BT
    go: FBbt
    obofoundry: FBbt
    ols: fbbt
    ontobee: FBBT
    prefixcommons: FBbt
  name: Drosophila gross anatomy
  part_of: flybase
  preferred_prefix: FBbt
  synonyms:
  - FBbt
  - FBbt_root
  uri_format: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1
  version: '2021-10-14'
fbcv:
  banana: FBcv
  contact:
    email: cp390@cam.ac.uk
    github: Clare72
    name: Clare Pilgrim
    orcid: null
  description: A miscellaneous ontology of terms used for curation in FlyBase, including
    the DPO.
  example: 0000586
  homepage: http://purl.obolibrary.org/obo/fbcv
  license: CC BY 3.0
  mappings:
    bioportal: FB-CV
    obofoundry: FBcv
    ols: fbcv
    ontobee: FBCV
    prefixcommons: FBcv
  name: FlyBase Controlled Vocabulary
  part_of: flybase
  pattern: ^\d{7}$
  preferred_prefix: FBcv
  synonyms:
  - FBcv
  uri_format: http://purl.obolibrary.org/obo/FBcv_$1
  version: '2021-10-18'
fbdv:
  banana: FBdv
  contact:
    email: cp390@cam.ac.uk
    github: Clare72
    name: Clare Pilgrim
    orcid: null
  description: An ontology of Drosophila melanogaster developmental stages.
  example: '00000000'
  homepage: http://purl.obolibrary.org/obo/fbdv
  license: CC BY 3.0
  mappings:
    bioportal: FB-DV
    obofoundry: FBdv
    ols: fbdv
    ontobee: FBdv
    prefixcommons: FBdv
  name: Drosophila development
  pattern: ^\d{8}$
  preferred_prefix: FBdv
  synonyms:
  - FBdv
  uri_format: http://purl.obolibrary.org/obo/FBdv_$1
  version: '2021-10-13'
fbol:
  comment: Website down, checked on 2021-10-07
  deprecated: true
  description: DNA barcoding is the use of short standardised segments of the genome
    for identification of species in all the Kingdoms of Life. The goal of the Fungal
    Barcoding site is to promote the DNA barcoding of fungi and other fungus-like
    organisms.
  example: '2224'
  homepage: http://www.fungalbarcoding.org/
  mappings:
    miriam: fbol
    n2t: fbol
    ncbi: FBOL
    prefixcommons: FBOL
  name: International Fungal Working Group Fungal Barcoding.
  pattern: ^\d+$
  preferred_prefix: fbol
  uri_format: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T
fbrf:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: FlyBase internal citation identifiers
  example: 0187632
  homepage: https://flybase.org
  name: FlyBase Reference Report
  part_of: flybase
  preferred_prefix: fbrf
  uri_format: https://flybase.org/reports/FBrf$1
fbsp:
  banana: FBSP
  contact:
    email: cp390@cam.ac.uk
    github: Clare72
    name: Clare Pilgrim
    orcid: null
  deprecated: true
  description: The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli)
    and of other taxa referred to in FlyBase.
  homepage: http://www.flybase.org/
  mappings:
    bioportal: FB-SP
    obofoundry: FBSP
    prefixcommons: FBSP
  name: Fly taxonomy
  part_of: flybase
  preferred_prefix: FBSP
  uri_format: http://purl.obolibrary.org/obo/FBSP_$1
fbtc:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The cell line vocabulary inside FlyBase
  example: 0000190
  homepage: https://flybase.org
  name: Flybase Cell Line
  part_of: flybase
  preferred_prefix: fbtc
  uri_format: https://flybase.org/reports/FBtc$1
fideo:
  banana: FIDEO
  contact:
    email: georgeta.bordea@u-bordeaux.fr
    github: getbordea
    name: Georgeta Bordea
    orcid: null
  description: "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents\
    \ Food-Drug Interactions and underlying interaction mechanisms described in scientific\
    \ publications, drug and adverse effects databases, and drug interactions compendia.\
    \ The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO\
    \ ontologies as well as the Th\xE9riaque database. This ontology is maintained\
    \ at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions\
    \ should be filed at the issue tracker there."
  example: '00000021'
  homepage: https://gitub.u-bordeaux.fr/erias/fideo
  license: CC0 1.0
  mappings:
    bioportal: FIDEO
    obofoundry: FIDEO
    ols: fideo
    ontobee: FIDEO
  name: Food Interactions with Drugs Evidence Ontology
  preferred_prefix: FIDEO
  uri_format: http://purl.obolibrary.org/obo/FIDEO_$1
fishbase.species:
  description: 'Global biodiversity database on finfishes. It offers a wide range
    of information on all species currently known in the world: taxonomy, biology,
    trophic ecology, life history, and uses, as well as historical data reaching back
    to 250 years.'
  example: '6472'
  homepage: http://fishbase.org
  mappings:
    wikidata: P938
  name: FishBase
  preferred_prefix: fishbase.species
  synonyms:
  - fishbase
fix:
  banana: FIX
  contact:
    email: null
    github: null
    name: chEBI
    orcid: null
  description: An ontology of physico-chemical methods and properties.
  example: 0000390
  homepage: https://www.ebi.ac.uk/chebi/
  mappings:
    bioportal: FIX
    obofoundry: FIX
    ols: fix
    ontobee: FIX
    prefixcommons: FIX
  name: Physico-chemical methods and properties
  part_of: chebi
  pattern: ^\d{7}$
  preferred_prefix: FIX
  uri_format: http://purl.obolibrary.org/obo/FIX_$1
  version: '2020-04-13'
flopo:
  banana: FLOPO
  contact:
    email: robert.hoehndorf@kaust.edu.sa
    github: leechuck
    name: Robert Hoehndorf
    orcid: null
  description: Traits and phenotypes of flowering plants occurring in digitized Floras
  example: '0005250'
  homepage: https://github.com/flora-phenotype-ontology/flopoontology
  license: CC0 1.0
  mappings:
    bioportal: FLOPO
    obofoundry: FLOPO
    ols: flopo
    ontobee: FLOPO
    prefixcommons: FLOPO
  name: Flora Phenotype Ontology
  preferred_prefix: FLOPO
  uri_format: http://purl.obolibrary.org/obo/FLOPO_$1
  version: '2019-09-09'
flowrepository:
  description: FlowRepository is a database of flow cytometry experiments where you
    can query and download data collected and annotated according to the MIFlowCyt
    standard. It is primarily used as a data deposition place for experimental findings
    published in peer-reviewed journals in the flow cytometry field.
  example: FR-FCM-ZYGW
  homepage: https://flowrepository.org/
  mappings:
    miriam: flowrepository
    n2t: flowrepository
  name: FlowRepository
  pattern: ^FR\-FCM\-\w{4}$
  preferred_prefix: flowrepository
  uri_format: https://flowrepository.org/id/$1
flu:
  banana: FLU
  contact:
    email: burkesquires@gmail.com
    github: null
    name: Burke Squires
    orcid: null
  deprecated: true
  homepage: http://purl.obolibrary.org/obo/flu/
  mappings:
    bioportal: FLU
    obofoundry: FLU
    prefixcommons: FLU
  name: Influenza Ontology
  preferred_prefix: FLU
  uri_format: http://purl.obolibrary.org/obo/FLU_$1
flybase:
  description: FlyBase is the database of the Drosophila Genome Projects and of associated
    literature.
  example: FBgn0011293
  homepage: http://flybase.org/
  mappings:
    cellosaurus: FlyBase
    go: FB
    miriam: fb
    n2t: fb
    ncbi: FLYBASE
    prefixcommons: FlyBase
    uniprot: FlyBase
    wikidata: P3852
  name: FlyBase Gene ID
  pattern: ^FB\w{2}\d{7}$
  preferred_prefix: FlyBase
  providers:
  - code: bioentitylink
    description: FlyBase through BioEntity Link
    homepage: https://bioentity.link/
    name: FlyBase through BioEntity Link
    uri_format: https://bioentity.link/#/lexicon/public/$1
  - code: agr
    description: FlyBase through the Alliance of Genome Resources
    homepage: https://www.alliancegenome.org
    name: FlyBase through the Alliance of Genome Resources
    uri_format: https://www.alliancegenome.org/gene/FB:$1
  synonyms:
  - FB
  - FlyBase
  uri_format: https://flybase.org/reports/$1
fma:
  banana: FMA
  contact:
    email: mejino@u.washington.edu
    github: null
    name: Onard Mejino
    orcid: null
  description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics
    ontology. It is concerned with the representation of classes or types and relationships
    necessary for the symbolic representation of the phenotypic structure of the human
    body.  Specifically, the FMA is a domain ontology that represents a coherent body
    of explicit declarative knowledge about human anatomy.
  example: '63189'
  homepage: http://si.washington.edu/projects/fma
  license: CC BY 3.0
  mappings:
    bioportal: FMA
    go: FMA
    miriam: fma
    n2t: fma
    obofoundry: FMA
    ols: fma
    ontobee: FMA
    prefixcommons: FMA
  name: Foundational Model of Anatomy
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: FMA
  synonyms:
  - FMAID
  - FMA_RETIRED
  uri_format: https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1
  version: '2020-04-13'
foaf:
  description: 'FOAF is a project devoted to linking people and information using
    the Web. Regardless of whether information is in people''s heads, in physical
    or digital documents, or in the form of factual data, it can be linked. FOAF integrates
    three kinds of network: social networks of human collaboration, friendship and
    association; representational networks that describe a simplified view of a cartoon
    universe in factual terms, and information networks that use Web-based linking
    to share independently published descriptions of this inter-connected world.'
  example: familyName
  homepage: http://xmlns.com/foaf/spec/
  mappings:
    biolink: foaf
    bioportal: FOAF
    prefixcommons: foaf
  name: Friend of a Friend
  preferred_prefix: foaf
  uri_format: http://xmlns.com/foaf/0.1/$1
fobi:
  banana: FOBI
  contact:
    email: polcaes@gmail.com
    github: pcastellanoescuder
    name: Pol Castellano Escuder
    orcid: null
  description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake
    data and associate it with metabolomic data
  example: 030719
  homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
  license: CC BY 3.0
  mappings:
    bioportal: FOBI
    obofoundry: FOBI
    ols: fobi
    ontobee: FOBI
  name: Food-Biomarker Ontology
  preferred_prefix: FOBI
  uri_format: http://purl.obolibrary.org/obo/FOBI_$1
foodb.compound:
  description: "FooDB is resource on food and its constituent compounds. It includes\
    \ data on the compound\u2019s nomenclature, its description, information on its\
    \ structure, chemical class, its physico-chemical data, its food source(s), its\
    \ color, its aroma, its taste, its physiological effect, presumptive health effects\
    \ (from published studies), and concentrations in various foods. This collection\
    \ references compounds."
  example: FDB002100
  homepage: https://foodb.ca/
  mappings:
    biolink: foodb.compound
    miriam: foodb.compound
    n2t: foodb.compound
    prefixcommons: FOODB.COMPOUND
  name: FooDB Compound
  pattern: ^FDB\d+$
  preferred_prefix: foodb.compound
  synonyms:
  - foodb
  uri_format: http://foodb.ca/compounds/$1
foodon:
  banana: FOODON
  contact:
    email: damion_dooley@sfu.ca
    github: Public-Health-Bioinformatics
    name: Damion Dooley
    orcid: null
  description: FoodOn is a comprehensive and easily accessible global farm-to-fork
    ontology about food that accurately and consistently describes foods commonly
    known in cultures from around the world. It is a consortium-driven project built
    to interoperate with the The Open Biological and Biomedical Ontology Foundry library
    of ontologies.
  example: 03307879
  homepage: https://foodon.org/
  license: CC BY 3.0
  mappings:
    bioportal: FOODON
    miriam: foodon
    n2t: foodon
    obofoundry: FOODON
    ols: foodon
    ontobee: FOODON
    prefixcommons: FOODON
  name: The Food Ontology
  namespace_in_lui: true
  pattern: ^[0-9]{8}$
  preferred_prefix: FOODON
  uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1
  version: '2021-11-25'
fovt:
  banana: FOVT
  contact:
    email: rlwalls2008@gmail.com
    github: https://github.com/futres/fovt
    name: FuTRES Ontology of Vertebrate Traits
    orcid: null
  description: None
  example: 0000009
  homepage: https://github.com/futres/fovt
  license: CC0 1.0
  mappings:
    bioportal: FOVT
    obofoundry: FOVT
    ols: fovt
    ontobee: FOVT
  name: FuTRES Ontology of Vertebrate Traits
  preferred_prefix: FOVT
  uri_format: http://purl.obolibrary.org/obo/FOVT_$1
  version: '2021-11-10'
fplx:
  description: FamPlex is a collection of resources for grounding biological entities
    from text and describing their hierarchical relationships.
  example: GPIb_IX_V
  homepage: https://sorgerlab.github.io/famplex/
  mappings:
    bioportal: FPLX
    miriam: fplx
    n2t: fplx
    prefixcommons: FPLX
  name: FamPlex
  pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$
  preferred_prefix: fplx
  synonyms:
  - famplex
  uri_format: https://sorgerlab.github.io/famplex/$1
fsnp:
  description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates
    information obtained from databases about the functional effects of SNPs. These
    effects are predicted and indicated at the splicing, transcriptional, translational
    and post-translational level. In particular, users can retrieve SNPs that disrupt
    genomic regions known to be functional, including splice sites and transcriptional
    regulatory regions. Users can also identify non-synonymous SNPs that may have
    deleterious effects on protein structure or function, interfere with protein translation
    or impede post-translational modification.
  example: rs17852708
  homepage: http://compbio.cs.queensu.ca/F-SNP/
  mappings:
    miriam: fsnp
    n2t: fsnp
    prefixcommons: FSNP
  name: F-SNP
  pattern: ^rs\d+$
  preferred_prefix: fsnp
  uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&amp;id_type=snp_id&amp;id_val=$1
funcbase.fly:
  description: Computational gene function prediction can serve to focus experimental
    resources on high-priority experimental tasks. FuncBase is a web resource for
    viewing quantitative machine learning-based gene function annotations. Quantitative
    annotations of genes, including fungal and mammalian genes, with Gene Ontology
    terms are accompanied by a community feedback system. Evidence underlying function
    annotations is shown. FuncBase provides links to external resources, and may be
    accessed directly or via links from species-specific databases. This collection
    references Drosophila data.
  example: '10194'
  homepage: http://func.mshri.on.ca/fly
  mappings:
    miriam: funcbase.fly
    n2t: funcbase.fly
    prefixcommons: FUNCBASE.FLY
  name: FuncBase Fly
  pattern: ^\d+$
  preferred_prefix: funcbase.fly
  uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1
funcbase.human:
  description: Computational gene function prediction can serve to focus experimental
    resources on high-priority experimental tasks. FuncBase is a web resource for
    viewing quantitative machine learning-based gene function annotations. Quantitative
    annotations of genes, including fungal and mammalian genes, with Gene Ontology
    terms are accompanied by a community feedback system. Evidence underlying function
    annotations is shown. FuncBase provides links to external resources, and may be
    accessed directly or via links from species-specific databases. This collection
    references human data.
  example: '119514'
  homepage: http://func.mshri.on.ca/human/
  mappings:
    miriam: funcbase.human
    n2t: funcbase.human
    prefixcommons: FUNCBASE.HUMAN
  name: FuncBase Human
  pattern: ^\d+$
  preferred_prefix: funcbase.human
  uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1
funcbase.mouse:
  description: Computational gene function prediction can serve to focus experimental
    resources on high-priority experimental tasks. FuncBase is a web resource for
    viewing quantitative machine learning-based gene function annotations. Quantitative
    annotations of genes, including fungal and mammalian genes, with Gene Ontology
    terms are accompanied by a community feedback system. Evidence underlying function
    annotations is shown. FuncBase provides links to external resources, and may be
    accessed directly or via links from species-specific databases. This collection
    references mouse.
  example: '1351341'
  homepage: http://func.mshri.on.ca/mouse/
  mappings:
    miriam: funcbase.mouse
    n2t: funcbase.mouse
    prefixcommons: FUNCBASE.MOUSE
  name: FuncBase Mouse
  pattern: ^\d+$
  preferred_prefix: funcbase.mouse
  uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1
funcbase.yeast:
  description: Computational gene function prediction can serve to focus experimental
    resources on high-priority experimental tasks. FuncBase is a web resource for
    viewing quantitative machine learning-based gene function annotations. Quantitative
    annotations of genes, including fungal and mammalian genes, with Gene Ontology
    terms are accompanied by a community feedback system. Evidence underlying function
    annotations is shown. FuncBase provides links to external resources, and may be
    accessed directly or via links from species-specific databases. This collection
    references yeast.
  example: '2701'
  homepage: http://func.mshri.on.ca/yeast
  mappings:
    miriam: funcbase.yeast
    n2t: funcbase.yeast
    prefixcommons: FUNCBASE.YEAST
  name: FuncBase Yeast
  pattern: ^\d+$
  preferred_prefix: funcbase.yeast
  uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1
funderregistry:
  description: The Funder Registry is an open registry of persistent identifiers for
    grant-giving organizations around the world.
  example: '100000001'
  homepage: https://www.crossref.org/
  mappings:
    miriam: funderregistry
  name: FunderRegistry
  pattern: ^\d{9,9}$
  preferred_prefix: funderregistry
  uri_format: http://data.crossref.org/fundingdata/funder/10.13039/$1
fungidb:
  description: FungiDB is a genomic resource for fungal genomes. It contains contains
    genome sequence and annotation from several fungal classes, including the Ascomycota
    classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota
    orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage
    Mucormycotina.
  example: CNBG_0001
  homepage: https://fungidb.org/fungidb
  mappings:
    miriam: fungidb
    n2t: fungidb
    prefixcommons: FUNGIDB
  name: FungiDB
  pattern: ^[A-Za-z_0-9]+$
  preferred_prefix: fungidb
  uri_format: https://fungidb.org/fungidb/app/record/gene/$1
fyler:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'A hierarchical classification of congenital heart disease '
  example: '4447'
  homepage: https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906
  name: Fyler
  pattern: ^\d+$
  preferred_prefix: fyler
  references:
  - https://github.com/obophenotype/human-phenotype-ontology/issues/2568
  - https://github.com/obophenotype/human-phenotype-ontology/issues/2511
fypo:
  banana: FYPO
  contact:
    email: mah79@cam.ac.uk
    github: mah11
    name: Midori Harris
    orcid: null
  description: A formal ontology of phenotypes observed in fission yeast.
  example: '0001707'
  homepage: https://github.com/pombase/fypo
  license: CC BY 4.0
  mappings:
    biolink: FYPO
    bioportal: FYPO
    go: FYPO
    obofoundry: FYPO
    ols: fypo
    ontobee: FYPO
    prefixcommons: FYPO
  name: Fission Yeast Phenotype Ontology
  pattern: ^\d{7}$
  preferred_prefix: FYPO
  uri_format: http://purl.obolibrary.org/obo/FYPO_$1
  version: '2021-12-02'
ga4ghdos:
  description: Assists in resolving data across cloud resources.
  example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d
  homepage: http://github.com/ga4gh/data-object-service-schemas
  mappings:
    miriam: ga4ghdos
    n2t: ga4ghdos
    prefixcommons: GA4GHDOS
  name: Data Object Service
  pattern: ^[a-zA-Z0-9\-:#/\.]+$
  preferred_prefix: ga4ghdos
  uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1
gabi:
  description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database)
    constitutes a repository for a wide array of heterogeneous data from high-throughput
    experiments in several plant species. These data (i.e. genomics, transcriptomics,
    proteomics and metabolomics), originating from different model or crop species,
    can be accessed through a central gene 'Green Card'.
  example: '2679240'
  homepage: http://www.gabipd.org/
  mappings:
    miriam: gabi
    n2t: gabi
    ncbi: GABI
    prefixcommons: GABI
  name: Network of Different Plant Genomic Research Projects
  pattern: ^\w+$
  preferred_prefix: gabi
  uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject
galen:
  deprecated: true
  example: MagnitudeValueType
  homepage: https://www.opengalen.org
  mappings:
    bioportal: GALEN
  name: Galen Ontology
  preferred_prefix: galen
gard:
  description: Database of rare diseases and related terms, including symptoms, healthcare
    resources, and organizations supporting research of the disease.
  example: '6038'
  homepage: https://rarediseases.info.nih.gov/diseases
  mappings:
    wikidata: P4317
  name: Genetic and Rare Diseases Information Center
  preferred_prefix: gard
  synonyms:
  - GARD
  - Genetic and Rare Diseases Information Center
gateway:
  description: The Health Data Research Innovation Gateway (the 'Gateway') provides
    a common entry point to discover and enquire about access to UK health datasets
    for research and innovation. It provides detailed information about the datasets,
    which are held by members of the UK Health Data Research Alliance, such as a description,
    size of the population, and the legal basis for access.
  example: fd8d0743-344a-4758-bb97-f8ad84a37357
  homepage: https://www.hdruk.ac.uk
  mappings:
    miriam: gateway
  name: Health Data Research Innovation Gateway
  pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$
  preferred_prefix: gateway
  uri_format: https://web.www.healthdatagateway.org/dataset/$1
gaz:
  banana: GAZ
  contact:
    email: lschriml@som.umaryland.edu
    github: lschriml
    name: Lynn Schriml
    orcid: null
  description: A gazetteer constructed on ontological principles
  example: '00620027'
  homepage: http://environmentontology.github.io/gaz/
  license: CC0 1.0
  mappings:
    bioportal: GAZ
    obofoundry: GAZ
    ols: gaz
    ontobee: GAZ
    prefixcommons: GAZ
    wikidata: P6778
  name: Gazetteer
  pattern: ^\d{8}$
  preferred_prefix: GAZ
  uri_format: http://purl.obolibrary.org/obo/GAZ_$1
  version: '2018-06-26'
gbif:
  description: "Database of living organisms, taxonomic. \n The GBIF\u2014the Global\
    \ Biodiversity Information Facility\u2014is 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."
  example: '4238'
  homepage: https://www.gbif.org/species
  mappings:
    wikidata: P846
  name: Global Biodiversity Information Facility
  preferred_prefix: gbif
  uri_format: https://www.gbif.org/species/$1
gc:
  comment: 'see comment here: https://github.com/obophenotype/ncbitaxon/issues/47'
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Genetic code, mitochontrial genetic code, and other linked information
    to NCBI taxonomy entries.
  example: '11'
  homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html
  name: Genetic Code
  pattern: ^\d+$
  preferred_prefix: gc
  references:
  - https://github.com/obophenotype/ncbitaxon/issues/47
  synonyms:
  - gc_id
  uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1
gcst:
  description: The GWAS Catalog provides a consistent, searchable, visualisable and
    freely available database of published SNP-trait associations, which can be easily
    integrated with other resources, and is accessed by scientists, clinicians and
    other users worldwide.
  example: GCST000035
  homepage: https://www.ebi.ac.uk
  mappings:
    miriam: gcst
    n2t: gcst
  name: GWAS Catalog
  pattern: ^GCST\d{6}\d*$
  preferred_prefix: gcst
  uri_format: https://www.ebi.ac.uk/gwas/studies/$1
gdc:
  description: The GDC Data Portal is a robust data-driven platform that allows cancer
    researchers and bioinformaticians to search and download cancer data for analysis.
  example: ae8c77fe-e6c8-44d5-8265-4a38c637bbef
  homepage: https://gdc.cancer.gov
  mappings:
    miriam: gdc
    n2t: gdc
    prefixcommons: GDC
  name: Genomic Data Commons Data Portal
  pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
  preferred_prefix: gdc
  uri_format: https://portal.gdc.cancer.gov/cases/$1
gdsc:
  description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed
    to facilitate an increased understanding of the molecular features that influence
    drug response in cancer cells and which will enable the design of improved cancer
    therapies.
  example: '1242'
  homepage: https://www.cancerrxgene.org
  mappings:
    cellosaurus: GDSC
    miriam: gdsc
    n2t: gdsc
  name: Genomics of Drug Sensitivity in Cancer
  pattern: ^[0-9]+$
  preferred_prefix: gdsc
  uri_format: https://www.cancerrxgene.org/translation/Drug/$1
gecko:
  banana: GECKO
  contact:
    email: rbca.jackson@gmail.com
    github: beckyjackson
    name: Rebecca Jackson
    orcid: null
  description: An ontology to represent genomics cohort attributes.
  example: '0000044'
  homepage: https://github.com/IHCC-cohorts/GECKO
  license: CC BY 4.0
  mappings:
    bioportal: GECKO
    obofoundry: GECKO
    ols: gecko
    ontobee: GECKO
  name: Genomics Cohorts Knowledge Ontology
  preferred_prefix: GECKO
  uri_format: http://purl.obolibrary.org/obo/GECKO_$1
  version: '2021-01-18'
genatlas:
  description: GenAtlas is a database containing information on human genes, markers
    and phenotypes.
  example: HBB
  homepage: http://genatlas.medecine.univ-paris5.fr/
  mappings:
    miriam: genatlas
    n2t: genatlas
    prefixcommons: GENATLAS
    uniprot: GenAtlas
  name: Genatlas
  pattern: ^\w+$
  preferred_prefix: genatlas
  uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1
genbank:
  description: "GenBank \xAE is the NIH genetic sequence database, an annotated collection\
    \ of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."
  example: U49845
  homepage: https://www.ncbi.nlm.nih.gov/genbank/
  mappings:
    cheminf: '000304'
    fairsharing: FAIRsharing.9kahy4
    go: GenBank
    prefixcommons: GenBank
    uniprot: GenBank
  name: GenBank
  preferred_prefix: genbank
  uri_format: https://www.ncbi.nlm.nih.gov/nucleotide/$1
genecards:
  description: The GeneCards human gene database stores gene related transcriptomic,
    genetic, proteomic, functional and disease information. It uses standard nomenclature
    and approved gene symbols. GeneCards presents a complete summary for each human
    gene.
  example: ABL1
  homepage: http://www.genecards.org/
  mappings:
    miriam: genecards
    n2t: genecards
    prefixcommons: GENECARDS
    uniprot: GeneCards
  name: GeneCards
  pattern: ^[A-Za-z-0-9_]+(\@)?$
  preferred_prefix: genecards
  uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1
genedb:
  description: GeneDB is a genome database for prokaryotic and eukaryotic organisms
    and provides a portal through which data generated by the "Pathogen Genomics"
    group at the Wellcome Trust Sanger Institute and other collaborating sequencing
    centres can be accessed.
  example: LinJ.20.0070
  homepage: https://www.genedb.org/
  mappings:
    go: GeneDB
    miriam: genedb
    n2t: genedb
    ncbi: GeneDB
    prefixcommons: GENEDB
    uniprot: GeneDB
    wikidata: P3382
  name: GeneDB ID
  pattern: ^[\w\d\.-]*$
  preferred_prefix: genedb
  uri_format: https://www.genedb.org/gene/$1
genefarm:
  description: GeneFarm is a database whose purpose is to store traceable annotations
    for Arabidopsis nuclear genes and gene products.
  example: '4892'
  homepage: http://urgi.versailles.inra.fr/Genefarm/
  mappings:
    miriam: genefarm
    n2t: genefarm
    prefixcommons: GENEFARM
  name: GeneFarm
  pattern: ^\d+$
  preferred_prefix: genefarm
  uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1
genepio:
  banana: GENEPIO
  contact:
    email: damion_dooley@sfu.ca
    github: null
    name: Damion Dooley
    orcid: null
  description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary
    to identify, document and research foodborne pathogens and associated outbreaks.
  example: 0001885
  homepage: http://genepio.org/
  license: CC BY 3.0
  mappings:
    obofoundry: GENEPIO
    ols: genepio
    ontobee: GENEPIO
    prefixcommons: GENEPIO
  name: Genomic Epidemiology Ontology
  preferred_prefix: GENEPIO
  uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1
  version: '2021-05-24'
genetree:
  description: Genetree displays the maximum likelihood phylogenetic (protein) trees
    representing the evolutionary history of the genes. These are constructed using
    the canonical protein for every gene in Ensembl.
  example: ENSGT00550000074763
  homepage: http://www.ensembl.org/
  mappings:
    miriam: genetree
    n2t: genetree
    prefixcommons: GENETREE
    uniprot: GeneTree
  name: GeneTree
  pattern: ^ENSGT\d+$
  preferred_prefix: genetree
  uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1
genewiki:
  description: The Gene Wiki is project which seeks to provide detailed information
    on human genes. Initial 'stub' articles are created in an automated manner, with
    further information added by the community. Gene Wiki can be accessed in wikipedia
    using Gene identifiers from NCBI.
  example: '1017'
  homepage: http://en.wikipedia.org/wiki/Gene_Wiki
  mappings:
    miriam: genewiki
    n2t: genewiki
    prefixcommons: GENEWIKI
    uniprot: GeneWiki
  name: Gene Wiki
  pattern: ^\d+$
  preferred_prefix: genewiki
  uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1
geno:
  banana: GENO
  contact:
    email: mhb120@gmail.com
    github: mbrush
    name: Matthew Brush
    orcid: null
  description: "GENO is an OWL model of genotypes, their more fundamental sequence\
    \ components, and links to related biological and experimental entities.  At present\
    \ many parts of the model are exploratory and set to undergo refactoring.  In\
    \ addition, many classes and properties have GENO URIs but are place holders for\
    \ classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI,\
    \ etc).  Furthermore, ongoing work will implement a model of genotype-to-phenotype\
    \ associations. This will support description of asserted and inferred relationships\
    \ between a genotypes, phenotypes, and environments, and the evidence/provenance\
    \ behind these associations. \n\nDocumentation is under development as well, and\
    \ for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"
  example: '0000632'
  homepage: https://github.com/monarch-initiative/GENO-ontology/
  license: CC BY-SA 2.0
  mappings:
    bioportal: GENO
    obofoundry: GENO
    ols: geno
    ontobee: GENO
    prefixcommons: GENO
  name: Genotype Ontology
  pattern: ^\d{7}$
  preferred_prefix: GENO
  uri_format: http://purl.obolibrary.org/obo/GENO_$1
  version: '2020-03-08'
genpept:
  description: The GenPept database is a collection of sequences based on translations
    from annotated coding regions in GenBank.
  example: CAA71118.1
  homepage: https://www.ncbi.nlm.nih.gov/protein
  mappings:
    miriam: genpept
    n2t: genpept
    prefixcommons: GENPEPT
  name: GenPept
  pattern: ^\w{3}\d{5}(\.\d+)?$
  preferred_prefix: genpept
  uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept
genprop:
  description: Genome properties is an annotation system whereby functional attributes
    can be assigned to a genome, based on the presence of a defined set of protein
    signatures within that genome.
  example: GenProp0699
  homepage: https://www.ebi.ac.uk/interpro/genomeproperties/
  mappings:
    miriam: genprop
    n2t: genprop
    prefixcommons: GENPROP
  name: Genome Properties
  pattern: ^GenProp\d+$
  preferred_prefix: genprop
  uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1
geo:
  description: The Gene Expression Omnibus (GEO) is a gene expression repository providing
    a curated, online resource for gene expression data browsing, query and retrieval.
  example: GDS1234
  homepage: https://www.ncbi.nlm.nih.gov/geo/
  mappings:
    cellosaurus: GEO
    fairsharing: FAIRsharing.5hc8vt
    go: GEO
    miriam: geo
    n2t: geo
    ontobee: GEO
    prefixcommons: GEO
  name: NCBI Gene Expression Omnibus
  pattern: ^G(PL|SM|SE|DS)\d+$
  preferred_prefix: geo
  uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1
geogeo:
  banana: GEO
  contact:
    email: hoganwr@gmail.com
    github: null
    name: Bill Hogan
    orcid: null
  description: An ontology and inventory of geopolitical entities such as nations
    and their components (states, provinces, districts, counties) and the actual physical
    territories over which they have jurisdiction.  We thus distinguish and assign
    different identifiers to the US in "The US declared war on Germany" vs. the US
    in "The plane entered US airspace".
  example: '000000021'
  homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki
  license: CC BY 4.0
  mappings:
    bioportal: GEO
    miriam: geogeo
    obofoundry: GEO
    ols: geo
    prefixcommons: GEO
  name: Geographical Entity Ontology
  pattern: ^\d{9}$
  preferred_prefix: GEOGEO
  uri_format: http://purl.obolibrary.org/obo/GEO_$1
  version: '2016-03-26'
gexo:
  description: Gene Expression Ontology
  homepage: http://www.semantic-systems-biology.org/apo
  mappings:
    bioportal: GEXO
    ols: gexo
  name: Gene Expression Ontology
  no_own_terms: true
  preferred_prefix: gexo
  version: '2019-09-18'
ghr:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: MedlinePlus Genetics contains detailed information about the effects
    of genetic variation on human health, covering more than 1,300 genetic conditions
    and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA).
  example: saddan
  homepage: https://medlineplus.gov/genetics/condition
  name: Genetics Home Reference
  preferred_prefix: ghr
  uri_format: https://medlineplus.gov/genetics/condition/$1
giardiadb:
  description: GiardiaDB is one of the databases that can be accessed through the
    EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
    of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
    Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
    database built upon the same infrastructure, the EuPathDB portal offers an entry
    point to all these resources, and the opportunity to leverage orthology for searches
    across genera.
  example: GL50803_102438
  homepage: https://giardiadb.org/giardiadb/
  mappings:
    miriam: giardiadb
    n2t: giardiadb
    prefixcommons: GIARDIADB
  name: GiardiaDB
  pattern: ^\w+$
  preferred_prefix: giardiadb
  uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1
github:
  description: GitHub is an online host of Git source code repositories.
  example: identifiers-org/registry
  homepage: https://github.com/
  mappings:
    miriam: github
  name: github
  pattern: ^[a-zA-Z0-9-_]+/[a-zA-Z0-9-_]+$
  preferred_prefix: github
  uri_format: https://github.com/$1
glida.gpcr:
  description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic
    database that is primarily focused on the correlation of information between GPCRs
    and their ligands. It provides correlation data between GPCRs and their ligands,
    along with chemical information on the ligands. This collection references G-protein
    coupled receptors.
  example: ACM1_HUMAN
  homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
  mappings:
    miriam: glida.gpcr
    n2t: glida.gpcr
    prefixcommons: GLIDA.GPCR
  name: GLIDA GPCR
  pattern: ^[A-Z-_0-9]+$
  preferred_prefix: glida.gpcr
  uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1
glida.ligand:
  description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic
    database that is primarily focused on the correlation of information between GPCRs
    and their ligands. It provides correlation data between GPCRs and their ligands,
    along with chemical information on the ligands. This collection references ligands.
  example: L000001
  homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
  mappings:
    miriam: glida.ligand
    n2t: glida.ligand
    prefixcommons: GLIDA.LIGAND
  name: GLIDA Ligand
  pattern: ^L\d+$
  preferred_prefix: glida.ligand
  uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1
glycoepitope:
  description: GlycoEpitope is a database containing useful information about carbohydrate
    antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can
    be used to analyze their expression. This collection references Glycoepitopes.
  example: EP0311
  homepage: https://www.glycoepitope.jp/epitopes/
  mappings:
    miriam: glycoepitope
    n2t: glycoepitope
    prefixcommons: GLYCOEPITOPE
  name: GlycoEpitope
  pattern: ^EP\d{4}$
  preferred_prefix: glycoepitope
  uri_format: https://www.glycoepitope.jp/epitopes/$1
glycomedb:
  comment: this is exactly the same as glytoucan. Idk why there are two different
    ones
  description: GlycomeDB is the result of a systematic data integration effort, and
    provides an overview of all carbohydrate structures available in public databases,
    as well as cross-links.
  example: G77500AY
  has_canonical: glytoucan
  homepage: https://glytoucan.org/
  mappings:
    miriam: glycomedb
    n2t: glycomedb
    prefixcommons: GLYCOMEDB
  name: GlycomeDB
  pattern: ^\w+$
  preferred_prefix: glycomedb
  uri_format: https://glytoucan.org/Structures/Glycans/$1
glyconavi:
  description: GlycoNAVI is a website for carbohydrate research. It consists of the
    "GlycoNAVI Database" that provides information such as existence ratios and names
    of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI
    tools" such as editing of 2D structures of glycans, glycan structure viewers,
    and conversion tools.
  example: GN_G03681DA
  homepage: https://www.noguchi.or.jp/
  mappings:
    miriam: glyconavi
  name: GlycoNAVI
  pattern: ^GN_[A-Za-z0-9]+$
  preferred_prefix: glyconavi
  uri_format: https://glyconavi.org/hub/?id=$1
glycopost:
  description: GlycoPOST is a mass spectrometry data repository for glycomics and
    glycoproteomics. Users can release their "raw/processed" data via this site with
    a unique identifier number for the paper publication. Submission conditions are
    in accordance with the Minimum Information Required for a Glycomics Experiment
    (MIRAGE) guidelines.
  example: GPST000024
  homepage: https://glycopost.glycosmos.org
  mappings:
    miriam: glycopost
  name: GlycoPOST
  pattern: ^GPST[0-9]{6}$
  preferred_prefix: glycopost
  uri_format: https://glycopost.glycosmos.org/entry/$1
glygen:
  description: GlyGen is a data integration and dissemination project for carbohydrate
    and glycoconjugate related data. GlyGen retrieves information from multiple international
    data sources and integrates and harmonizes this data.
  example: G24361QY
  homepage: https://glygen.org/glycan/
  mappings:
    uniprot: GlyGen
  name: 'GlyGen: Computational and Informatics Resources for Glycoscience'
  preferred_prefix: glygen
  uri_format: https://glygen.org/glycan/$1
glytoucan:
  description: GlyTouCan is the single worldwide registry of glycan (carbohydrate
    sugar chain) data.
  example: G00054MO
  homepage: https://glytoucan.org
  mappings:
    miriam: glytoucan
    n2t: glytoucan
    prefixcommons: GLYTOUCAN
  name: GlyTouCan
  pattern: ^G[0-9]{5}[A-Z]{2}$
  preferred_prefix: glytoucan
  uri_format: https://glytoucan.org/Structures/Glycans/$1
gmd:
  description: Golm Metabolome Database (GMD) provides public access to custom mass
    spectral libraries, metabolite profiling experiments as well as additional information
    and tools. This collection references metabolite information, relating the biologically
    active substance to metabolic pathways or signalling phenomena.
  example: 68513255-fc44-4041-bc4b-4fd2fae7541d
  homepage: http://gmd.mpimp-golm.mpg.de/
  mappings:
    miriam: gmd
    n2t: gmd
    prefixcommons: GMD
  name: Golm Metabolome Database
  pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
  preferred_prefix: gmd
  uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx
gmd.analyte:
  description: Golm Metabolome Database (GMD) provides public access to custom mass
    spectral libraries, metabolite profiling experiments as well as additional information
    and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically
    converted, i.e. derivatised into less polar and volatile compounds, so called
    analytes.  This collection references analytes.
  example: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80
  homepage: http://gmd.mpimp-golm.mpg.de/
  mappings:
    miriam: gmd.analyte
    n2t: gmd.analyte
    prefixcommons: GMD.ANALYTE
  name: Golm Metabolome Database Analyte
  pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
  preferred_prefix: gmd.analyte
  uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1
gmd.gcms:
  description: Golm Metabolome Database (GMD) provides public access to custom mass
    spectral libraries, metabolite profiling experiments as well as additional information
    and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer,
    which records the mass spectrum and the retention time linked to an analyte. This
    collection references GC-MS spectra.
  example: 53d583d8-40c6-40e1-9296-23f821cd77a5
  homepage: http://gmd.mpimp-golm.mpg.de/
  mappings:
    miriam: gmd.gcms
    n2t: gmd.gcms
    prefixcommons: GMD.GCMS
  name: Golm Metabolome Database GC-MS spectra
  pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
  preferred_prefix: gmd.gcms
  uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1
gmd.profile:
  description: Golm Metabolome Database (GMD) provides public access to custom mass
    spectral libraries, metabolite profiling experiments as well as additional information
    and tools. GMD's metabolite profiles provide relative metabolite concentrations
    normalised according to fresh weight (or comparable quantitative data, such as
    volume, cell count, etc.) and internal standards (e.g. ribotol) of biological
    reference conditions and tissues.
  example: 10b38aaf-b977-4950-85b8-f4775f66658d
  homepage: http://gmd.mpimp-golm.mpg.de/
  mappings:
    miriam: gmd.profile
    n2t: gmd.profile
    prefixcommons: GMD.PROFILE
  name: Golm Metabolome Database Profile
  pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
  preferred_prefix: gmd.profile
  uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1
gmd.ref:
  description: Golm Metabolome Database (GMD) provides public access to custom mass
    spectral libraries, metabolite profiling experiments as well as additional information
    and tools. Since metabolites often cannot be obtained in their respective native
    biological state, for example organic acids may be only acquirable as salts, the
    concept of reference substance was introduced. This collection references reference
    substances.
  example: 8cf84adb-b4db-4807-ac98-0004247c35df
  homepage: http://gmd.mpimp-golm.mpg.de/
  mappings:
    miriam: gmd.ref
    n2t: gmd.ref
    prefixcommons: GMD.REF
  name: Golm Metabolome Database Reference Substance
  pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
  preferred_prefix: gmd.ref
  uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1
gmelin:
  description: The Gmelin database is a large database of organometallic and inorganic
    compounds updated quarterly. It is based on the German publication Gmelins Handbuch
    der anorganischen Chemie which was originally published by Leopold Gmelin in 1817;
    the last print edition, the 8th, appeared in the 1990s.
  example: '1466'
  homepage: https://link.springer.com/bookseries/562
  mappings:
    wikidata: P1578
  name: Gmelins Handbuch der anorganischen Chemie
  pattern: ^[1-9][0-9]{3,6}$
  preferred_prefix: gmelin
  references:
  - https://en.wikipedia.org/wiki/Gmelin_database
gno:
  banana: GNO
  contact:
    email: nje5@georgetown.edu
    github: edwardsnj
    name: Nathan Edwards
    orcid: null
  description: An ontology for glycans based on GlyTouCan, but organized by subsumption.
  example: '10004892'
  homepage: https://gnome.glyomics.org/
  license: CC BY 4.0
  mappings:
    bioportal: GNO
    obofoundry: GNO
    ols: gno
    ontobee: GNO
  name: Glycan Naming and Subsumption Ontology
  pattern: ^\d{8}$
  preferred_prefix: GNO
  uri_format: http://purl.obolibrary.org/obo/GNO_$1
  version: 1.9.0
gnpis:
  description: GnpIS is an integrative information system focused on plants and fungal
    pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers,
    single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g.
    genomic sequences, physical maps, genome annotation and expression data) for species
    of agronomical interest.
  example: AY109603
  homepage: https://urgi.versailles.inra.fr/gnpis/
  mappings:
    miriam: gnpis
    n2t: gnpis
    prefixcommons: GNPIS
  name: GnpIS
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: gnpis
  uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1
go:
  banana: GO
  contact:
    email: suzia@stanford.edu
    github: null
    name: Suzi Aleksander
    orcid: null
  description: The Gene Ontology project provides a controlled vocabulary to describe
    gene and gene product attributes in any organism.
  example: '0032571'
  homepage: http://geneontology.org/
  license: CC BY 4.0
  mappings:
    bioportal: GO
    go: GO
    miriam: go
    n2t: go
    ncbi: GO
    obofoundry: GO
    ols: go
    ontobee: GO
    prefixcommons: GO
    uniprot: GO
    wikidata: P686
  name: Gene Ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: GO
  providers:
  - code: quickgo
    description: QuickGO (Gene Ontology browser)
    homepage: https://www.ebi.ac.uk/QuickGO/
    name: QuickGO (Gene Ontology browser)
    uri_format: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1
  - code: CURATOR_REVIEW
    description: GO Browser
    homepage: http://www.informatics.jax.org/searches/GO_form.shtml
    name: GO Browser
    uri_format: http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1
  - code: CURATOR_REVIEW
    description: GO through PANTHER
    homepage: http://www.pantherdb.org/
    name: GO through PANTHER
    uri_format: http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1
  synonyms:
  - gobp
  - gobpid
  - gocc
  - goccid
  - gomf
  - gomfid
  uri_format: http://amigo.geneontology.org/amigo/term/GO:$1
  version: '2021-11-16'
go.model:
  description: "GO-Causal Activity Models (GO-CAMs) use a defined \u201Cgrammar\u201D\
    \ for linking multiple GO annotations into larger models of biological function\
    \ (such as \u201Cpathways\u201D) in a semantically structured manner. GO-CAMs\
    \ are created by expert biocurators from the GO Consortium, using the Noctua Curation\
    \ Platform."
  example: 5fce9b7300001250
  homepage: http://www.geneontology.org/gocam
  mappings:
    go: gomodel
  name: Gene Ontology Causal Assembly Model
  preferred_prefix: go.model
  uri_format: noctua.geneontology.org/editor/graph/gomodel:$1
go.ref:
  banana: GO_REF
  description: The GO reference collection is a set of abstracts that can be cited
    in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files
    (in the Reference column). It provides two types of reference; It can be used
    to provide details of why specific Evidence codes (see http://identifiers.org/eco/)
    are assigned, or to present abstract-style descriptions of "GO content" meetings
    at which substantial changes in the ontologies are discussed and made.
  example: '0000041'
  homepage: http://www.geneontology.org/cgi-bin/references.cgi
  mappings:
    go: GO_REF
    miriam: go_ref
    n2t: go.ref
    prefixcommons: GO_REF
  name: Gene Ontology Database references
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: go.ref
  uri_format: https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md
goa:
  description: The GOA (Gene Ontology Annotation) project provides high-quality Gene
    Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB)
    and International Protein Index (IPI). This involves electronic annotation and
    the integration of high-quality manual GO annotation from all GO Consortium model
    organism groups and specialist groups.
  example: P12345
  homepage: https://www.ebi.ac.uk/GOA/
  mappings:
    miriam: goa
    n2t: goa
    ncbi: GOA
    prefixcommons: GOA
  name: Gene Ontology Annotation Database Identifier
  pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
    0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$
  preferred_prefix: goa
  uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1
goeco:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A GO annotation is a statement about the function of a particular gene.
    Each annotation includes an evidence code to indicate how the annotation to a
    particular term is supported.
  example: IPI
  homepage: http://geneontology.org/docs/guide-go-evidence-codes/
  name: GO Evidence Code
  preferred_prefix: goeco
gold:
  description: 'The Genomes OnLine Database (GOLD) catalogues genome and metagenome
    sequencing projects from around the world, along with their associated metadata.
    Information in GOLD is organized into four levels: Study, Biosample/Organism,
    Sequencing Project and Analysis Project.'
  example: Gs0000008
  homepage: https://gold.jgi.doe.gov/
  mappings:
    miriam: gold
  name: Genomes Online Database
  pattern: ^[A-Z][a-z][0-9]+$
  preferred_prefix: gold
  uri_format: https://gold.jgi.doe.gov/resolver?id=$1
gold.genome:
  description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\
    \ been superseeded by \u2018gold\u2019 prefix at https://registry.identifiers.org/registry/gold,\
    \ and this namespace is kept here for support to already existing citations, new\
    \ ones would need to use the pointed \u2018gold\u2019 namespace.\n\nThe GOLD (Genomes\
    \ OnLine Database)is a resource for centralised monitoring of genome and metagenome\
    \ projects worldwide. It stores information on complete and ongoing projects,\
    \ along with their associated metadata. This collection references the sequencing\
    \ status of individual genomes."
  example: Gi07796
  homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
  mappings:
    miriam: gold.genome
    n2t: gold.genome
    prefixcommons: GOLD.GENOME
  name: GOLD genome
  pattern: ^(Gi|Gc)\d+$
  preferred_prefix: gold.genome
  uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1
gold.meta:
  description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\
    \ been superseeded by \u2018gold\u2019 prefix at https://registry.identifiers.org/registry/gold,\
    \ and this namespace is kept here for support to already existing citations, new\
    \ ones would need to use the pointed \u2018gold\u2019 namespace. \n\nThe GOLD\
    \ (Genomes OnLine Database)is a resource for centralized monitoring of genome\
    \ and metagenome projects worldwide. It stores information on complete and ongoing\
    \ projects, along with their associated metadata. This collection references metadata\
    \ associated with samples."
  example: Gm00047
  homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
  mappings:
    miriam: gold.meta
    n2t: gold.meta
    prefixcommons: GOLD.META
  name: GOLD metadata
  pattern: ^Gm\d+$
  preferred_prefix: gold.meta
  uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1
google.patent:
  description: Google Patents covers the entire collection of granted patents and
    published patent applications from the USPTO, EPO, and WIPO. US patent documents
    date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using
    patent number, inventor, classification, and filing date.
  example: US4145692
  homepage: https://www.google.com/patents/
  mappings:
    cellosaurus: Patent
    miriam: google.patent
    n2t: google.patent
    prefixcommons: GOOGLE.PATENT
  name: Google Patents
  pattern: ^[A-Z]{2}\d+([A-Z])?$
  preferred_prefix: google.patent
  synonyms:
  - patent
  uri_format: https://www.google.com/patents/$1
google.scholar:
  description: 'Google Scholar provides a simple way to broadly search for scholarly
    literature. You can search across many disciplines and sources: articles, theses,
    books, abstracts and court opinions, from academic publishers, professional societies,
    online repositories, universities and other web sites.'
  example: PjrpzUIAAAAJ
  homepage: https://scholar.google.com/
  mappings:
    biolink: GSID
  name: Google Scholar Researcher ID
  preferred_prefix: google.scholar
gorel:
  description: Documentation of GO that provides a description of some of the commonly
    used relationships and conventions in GO.
  example: '0002005'
  homepage: http://geneontology.org/docs/ontology-relations/
  mappings:
    biolink: GOREL
    go: GOREL
  name: GO Relations
  preferred_prefix: gorel
gpcrdb:
  description: The G protein-coupled receptor database (GPCRDB) collects, large amounts
    of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding
    constants, mutations and oligomers, and derived data such as multiple sequence
    alignments and homology models.
  example: RL3R1_HUMAN
  homepage: http://www.gpcrdb.org/
  mappings:
    miriam: gpcrdb
    n2t: gpcrdb
    prefixcommons: GPCRDB
    uniprot: GPCRDB
  name: G protein-coupled receptor database
  pattern: ^\w+$
  preferred_prefix: gpcrdb
  uri_format: https://gpcrdb.org/protein/$1
gpmdb:
  description: The Global Proteome Machine Database was constructed to utilize the
    information obtained by GPM servers to aid in the difficult process of validating
    peptide MS/MS spectra as well as protein coverage patterns.
  example: GPM32310002988
  homepage: http://gpmdb.thegpm.org/
  mappings:
    miriam: gpmdb
    n2t: gpmdb
    prefixcommons: GPMDB
  name: Global Proteome Machine Database
  pattern: ^GPM\d+$
  preferred_prefix: gpmdb
  providers:
  - code: omicsdi
    description: GPMDB through OmicsDI
    homepage: https://www.omicsdi.org/
    name: GPMDB through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/gpmdb/$1
  uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1
gramene.gene:
  description: Gramene is a comparative genome mapping database for grasses and crop
    plants. It combines a semi-automatically generated database of cereal genomic
    and expressed sequence tag sequences, genetic maps, map relations, quantitative
    trait loci (QTL), and publications, with a curated database of mutants (genes
    and alleles), molecular markers, and proteins. This datatype refers to genes in
    Gramene.
  example: GR:0080039
  homepage: http://www.gramene.org/
  mappings:
    go: GR_GENE
    miriam: gramene.gene
    n2t: gramene.gene
    prefixcommons: GRAMENE.GENE
  name: Gramene Gene
  pattern: ^GR\:\d+$
  preferred_prefix: gramene.gene
  synonyms:
  - GR_GENE
  uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1
gramene.growthstage:
  banana: gramene.growthstage:GRO\
  description: Gramene is a comparative genome mapping database for grasses and crop
    plants. It combines a semi-automatically generated database of cereal genomic
    and expressed sequence tag sequences, genetic maps, map relations, quantitative
    trait loci (QTL), and publications, with a curated database of mutants (genes
    and alleles), molecular markers, and proteins. This collection refers to growth
    stage ontology information in Gramene.
  example: '0007133'
  homepage: http://www.gramene.org/
  mappings:
    miriam: gramene.growthstage
    n2t: gramene.growthstage
    prefixcommons: GRAMENE.GROWTHSTAGE
  name: Gramene Growth Stage Ontology
  pattern: ^\d{7}$
  preferred_prefix: gramene.growthstage
  uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1
gramene.protein:
  description: Gramene is a comparative genome mapping database for grasses and crop
    plants. It combines a semi-automatically generated database of cereal genomic
    and expressed sequence tag sequences, genetic maps, map relations, quantitative
    trait loci (QTL), and publications, with a curated database of mutants (genes
    and alleles), molecular markers, and proteins. This datatype refers to proteins
    in Gramene.
  example: '78073'
  homepage: http://www.gramene.org/
  mappings:
    go: GR_PROTEIN
    miriam: gramene.protein
    n2t: gramene.protein
    prefixcommons: GRAMENE.PROTEIN
  name: Gramene protein
  pattern: ^\d+$
  preferred_prefix: gramene.protein
  synonyms:
  - GR_PROTEIN
  uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1
gramene.qtl:
  description: Gramene is a comparative genome mapping database for grasses and crop
    plants. It combines a semi-automatically generated database of cereal genomic
    and expressed sequence tag sequences, genetic maps, map relations, quantitative
    trait loci (QTL), and publications, with a curated database of mutants (genes
    and alleles), molecular markers, and proteins. This datatype refers to quantitative
    trait loci identified in Gramene.
  example: CQG5
  homepage: http://www.gramene.org/
  mappings:
    go: GR_QTL
    miriam: gramene.qtl
    n2t: gramene.qtl
    prefixcommons: GRAMENE.QTL
  name: Gramene QTL
  pattern: ^\w+$
  preferred_prefix: gramene.qtl
  synonyms:
  - GR_QTL
  uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1
gramene.taxonomy:
  description: Gramene is a comparative genome mapping database for grasses and crop
    plants. It combines a semi-automatically generated database of cereal genomic
    and expressed sequence tag sequences, genetic maps, map relations, quantitative
    trait loci (QTL), and publications, with a curated database of mutants (genes
    and alleles), molecular markers, and proteins. This datatype refers to taxonomic
    information in Gramene.
  example: GR_tax:013681
  homepage: http://www.gramene.org/
  mappings:
    miriam: gramene.taxonomy
    n2t: gramene.taxonomy
    prefixcommons: GRAMENE.TAXONOMY
  name: Gramene Taxonomy
  pattern: ^GR\_tax\:\d+$
  preferred_prefix: gramene.taxonomy
  uri_format: http://www.gramene.org/db/ontology/search?id=$1
grassbase:
  contributor:
    email: null
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: GrassBase provides an interactive guide to nomenclature for the whole
    grass family. It provides lists of over 60,000 names for any given genus, geographical
    region or genus within a geographical region, helps find the accepted name, synonyms
    and distribution for any given name, and gives a desription for each species.
  example: imp10873
  homepage: https://www.kew.org/data/grasses-syn/index.htm
  name: GrassBase
  pattern: ^(imp|gen)\d{5}$
  preferred_prefix: grassbase
  uri_format: https://www.kew.org/data/grasses-db/www/$1
greengenes:
  description: A 16S rRNA gene database which provides chimera screening, standard
    alignment, and taxonomic classification using multiple published taxonomies.
  example: '100000'
  homepage: http://greengenes.lbl.gov/
  mappings:
    miriam: greengenes
    n2t: greengenes
    ncbi: Greengenes
    prefixcommons: GREENGENES
  name: 16S rRNA gene database
  pattern: ^\d+$
  preferred_prefix: greengenes
  uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1
grid:
  description: International coverage of the world's leading research organisations,
    indexing 92% of funding allocated globally.
  example: grid.225360.0
  homepage: https://www.grid.ac/
  mappings:
    miriam: grid
    n2t: grid
    prefixcommons: GRID
  name: Global Research Identifier Database
  pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$
  preferred_prefix: grid
  uri_format: https://www.grid.ac/institutes/$1
grin.taxonomy:
  description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants
    provides information on scientific and common names, classification, distribution,
    references, and economic impact.
  example: '19333'
  homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en
  mappings:
    go: GRIN
    miriam: grin.taxonomy
    n2t: grin.taxonomy
    ncbi: GRIN
    prefixcommons: GRIN.TAXONOMY
  name: Germplasm Resources Information Network
  pattern: ^\d+$
  preferred_prefix: grin.taxonomy
  uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1
gro:
  deprecated: true
  mappings:
    bioportal: GRO
  name: Gene Regulation Ontology
  preferred_prefix: gro
grsdb:
  description: GRSDB is a database of G-quadruplexes and contains information on composition
    and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped
    in the eukaryotic pre-mRNA sequences, including those that are alternatively processed
    (alternatively spliced or alternatively polyadenylated). The data stored in the
    GRSDB is based on computational analysis of NCBI Entrez Gene entries and their
    corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.
  example: '10142'
  homepage: http://bioinformatics.ramapo.edu/GRSDB2/
  mappings:
    miriam: grsdb
    n2t: grsdb
    prefixcommons: GRSDB
  name: G-Rich Sequences Database
  pattern: ^\d+$
  preferred_prefix: grsdb
  uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1
gsfa:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995)
    sets forth the conditions under which permitted food additives may be used in
    all foods, whether or not they have previously been standardized by Codex. The
    Preamble of the GSFA contains additional information for interpreting the data.
    Users are encouraged to consult the Preamble when using this database.
  example: '174'
  homepage: http://www.fao.org/gsfaonline
  name: General Standard for Food Additives (GSFA) Online Database
  preferred_prefix: gsfa
  synonyms:
  - FAO/WHO_standards
  uri_format: http://www.fao.org/gsfaonline/additives/details.html?id=$1
gsso:
  banana: GSSO
  contact:
    email: kronkcj@mail.uc.edu
    github: Superraptor
    name: Clair Kronk
    orcid: null
  description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary
    ontology connecting terms from biology, medicine, psychology, sociology, and gender
    studies, aiming to bridge gaps between linguistic variations inside and outside
    of the health care environment. A large focus of the ontology is its consideration
    of LGBTQIA+ terminology.
  example: 002368
  homepage: https://gsso.research.cchmc.org/
  license: Apache 2.0 License
  mappings:
    bioportal: GSSO
    miriam: gsso
    obofoundry: GSSO
    ols: gsso
    ontobee: GSSO
  name: Gender, Sex, and Sexual Orientation Ontology
  namespace_in_lui: true
  pattern: ^\d{6}$
  preferred_prefix: GSSO
  uri_format: http://purl.obolibrary.org/obo/GSSO_$1
  version: 2.0.5
gtex:
  description: The Genotype-Tissue Expression (GTEx) project aims to provide to the
    scientific community a resource with which to study human gene expression and
    regulation and its relationship to genetic variation.
  example: BRIP1
  homepage: https://www.gtexportal.org
  mappings:
    biolink: GTEx
    miriam: gtex
    n2t: gtex
    prefixcommons: GTEX
  name: Genotype-Tissue Expression
  pattern: ^\w.+$
  preferred_prefix: gtex
  uri_format: https://www.gtexportal.org/home/gene/$1
gtr:
  comment: Identifiers appearing in MONDO don't match any of the resources apparent
    endpoints
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "The Genetic Testing Registry (GTR\xAE) provides a central location\
    \ for voluntary submission of genetic test information by providers. The scope\
    \ includes the test's purpose, methodology, validity, evidence of the test's usefulness,\
    \ and laboratory contacts and credentials. The overarching goal of the GTR is\
    \ to advance the public health and research into the genetic basis of health and\
    \ disease"
  example: AN0097748
  homepage: https://www.ncbi.nlm.nih.gov/gtr/
  name: Genetic Testing Registry
  preferred_prefix: gtr
gudmap:
  description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is
    a consortium of laboratories working to provide the scientific and medical community
    with tools to facilitate research on the GenitoUrinary (GU) tract.
  example: Q-2958
  homepage: http://www.gudmap.org/
  mappings:
    miriam: gudmap
    n2t: gudmap
    prefixcommons: GUDMAP
  name: Genitourinary Development Molecular Anatomy Project
  pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
  preferred_prefix: gudmap
  uri_format: https://gudmap.org/id/$1
gwascentral.marker:
  description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
    information) is a database of summary level findings from genetic association
    studies, both large and small. It gathers datasets from public domain projects,
    and accepts direct data submission. It is based upon Marker information encompassing
    SNP and variant information from public databases, to which allele and genotype
    frequency data, and genetic association findings are additionally added. A Study
    (most generic level) contains one or more Experiments, one or more Sample Panels
    of test subjects, and one or more Phenotypes. This collection references a GWAS
    Central Marker.
  example: HGVM15354
  homepage: https://www.gwascentral.org/markers
  mappings:
    miriam: gwascentral.marker
    n2t: gwascentral.marker
    prefixcommons: GWASCENTRAL.MARKER
  name: GWAS Central Marker
  pattern: ^HGVM\d+$
  preferred_prefix: gwascentral.marker
  uri_format: https://www.gwascentral.org/marker/$1
gwascentral.phenotype:
  description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
    information) is a database of summary level findings from genetic association
    studies, both large and small. It gathers datasets from public domain projects,
    and accepts direct data submission. It is based upon Marker information encompassing
    SNP and variant information from public databases, to which allele and genotype
    frequency data, and genetic association findings are additionally added. A Study
    (most generic level) contains one or more Experiments, one or more Sample Panels
    of test subjects, and one or more Phenotypes. This collection references a GWAS
    Central Phenotype.
  example: HGVPM623
  homepage: https://www.gwascentral.org/phenotypes
  mappings:
    miriam: gwascentral.phenotype
    n2t: gwascentral.phenotype
    prefixcommons: GWASCENTRAL.PHENOTYPE
  name: GWAS Central Phenotype
  pattern: ^HGVPM\d+$
  preferred_prefix: gwascentral.phenotype
  uri_format: https://www.gwascentral.org/phenotype/$1
gwascentral.study:
  description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
    information) is a database of summary level findings from genetic association
    studies, both large and small. It gathers datasets from public domain projects,
    and accepts direct data submission. It is based upon Marker information encompassing
    SNP and variant information from public databases, to which allele and genotype
    frequency data, and genetic association findings are additionally added. A Study
    (most generic level) contains one or more Experiments, one or more Sample Panels
    of test subjects, and one or more Phenotypes. This collection references a GWAS
    Central Study.
  example: HGVST1828
  homepage: https://www.gwascentral.org/studies
  mappings:
    miriam: gwascentral.study
    n2t: gwascentral.study
    prefixcommons: GWASCENTRAL.STUDY
  name: GWAS Central Study
  pattern: ^HGVST\d+$
  preferred_prefix: gwascentral.study
  uri_format: https://www.gwascentral.org/study/$1
gxa.expt:
  description: The Gene Expression Atlas (GXA) is a semantically enriched database
    of meta-analysis based summary statistics over a curated subset of ArrayExpress
    Archive, servicing queries for condition-specific gene expression patterns as
    well as broader exploratory searches for biologically interesting genes/samples.
    This collection references experiments.
  example: E-MTAB-2037
  homepage: https://www.ebi.ac.uk/gxa/
  mappings:
    miriam: gxa.expt
    n2t: gxa.expt
    prefixcommons: GXA.EXPT
  name: GXA Expt
  pattern: ^[AEP]-\w{4}-\d+$
  preferred_prefix: gxa.expt
  providers:
  - code: omicsdi
    description: GXA Expt through OmicsDI
    homepage: https://www.omicsdi.org/
    name: GXA Expt through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/atlas-experiments/$1
  uri_format: https://www.ebi.ac.uk/gxa/experiments/$1
gxa.gene:
  description: The Gene Expression Atlas (GXA) is a semantically enriched database
    of meta-analysis based summary statistics over a curated subset of ArrayExpress
    Archive, servicing queries for condition-specific gene expression patterns as
    well as broader exploratory searches for biologically interesting genes/samples.
    This collection references genes.
  example: AT4G01080
  homepage: https://www.ebi.ac.uk/gxa/
  mappings:
    miriam: gxa.gene
    n2t: gxa.gene
    prefixcommons: GXA.GENE
  name: GXA Gene
  pattern: ^\w+$
  preferred_prefix: gxa.gene
  uri_format: https://www.ebi.ac.uk/gxa/genes/$1
habronattus:
  banana: HABRONATTUS
  contact:
    email: peteremidford@yahoo.com
    github: null
    name: Peter Midford
    orcid: null
  deprecated: true
  homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html
  mappings:
    obofoundry: HABRONATTUS
    prefixcommons: HABRONATTUS
  name: Habronattus courtship
  preferred_prefix: HABRONATTUS
  uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1
hamap:
  description: HAMAP is a system that identifies and semi-automatically annotates
    proteins that are part of well-conserved and orthologous microbial families or
    subfamilies. These are used to build rules which are used to propagate annotations
    to member bacterial, archaeal and plastid-encoded protein entries.
  example: MF_01400
  homepage: https://hamap.expasy.org/
  mappings:
    go: HAMAP
    miriam: hamap
    n2t: hamap
    prefixcommons: HAMAP
    uniprot: HAMAP
  name: High-quality Automated and Manual Annotation of microbial Proteomes
  pattern: ^MF_\d+$
  preferred_prefix: hamap
  uri_format: https://hamap.expasy.org/unirule/$1
hancestro:
  banana: HANCESTRO
  contact:
    email: danielle.welter@uni.lu
    github: null
    name: Danielle Welter
    orcid: null
  description: Human ancestry ontology for the NHGRI GWAS Catalog
  example: 0290
  homepage: https://github.com/EBISPOT/ancestro
  license: CC BY 4.0
  mappings:
    biolink: HANCESTRO
    bioportal: HANCESTRO
    obofoundry: HANCESTRO
    ols: hancestro
    ontobee: HANCESTRO
  name: Human Ancestry Ontology
  preferred_prefix: HANCESTRO
  uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1
  version: '2.5'
hao:
  banana: HAO
  contact:
    email: diapriid@gmail.com
    github: mjy
    name: Matt Yoder
    orcid: null
  description: A structured controlled vocabulary of the anatomy of the Hymenoptera
    (bees, wasps, and ants)
  example: 0000187
  homepage: http://hymao.org
  license: CC0 1.0
  mappings:
    bioportal: HAO
    obofoundry: HAO
    ols: hao
    ontobee: HAO
    prefixcommons: HAO
  name: Hymenoptera Anatomy Ontology
  pattern: ^\d{7}$
  preferred_prefix: HAO
  uri_format: http://purl.obolibrary.org/obo/HAO_$1
  version: '2021-03-05'
hcao:
  description: Application ontology for human cell types, anatomy and development
    stages for the Human Cell Atlas.
  homepage: https://www.humancellatlas.org
  mappings:
    ols: hcao
  name: Human Cell Atlas Ontology
  no_own_terms: true
  preferred_prefix: hcao
  version: '2021-11-16'
hcpcs:
  description: HCPCS is a collection of standardized codes that represent medical
    procedures, supplies, products and services. The codes are used to facilitate
    the processing of health insurance claims by Medicare and other insurers.
  example: G8944
  homepage: https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo
  mappings:
    biolink: HCPCS
    bioportal: HCPCS
  name: Healthcare Common Procedure Coding System
  preferred_prefix: hcpcs
hcvdb:
  description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr),
    a collection of computer-annotated sequences based on reference genomes.mainly
    dedicated to HCV protein sequences, 3D structures and functional analyses.
  example: M58335
  homepage: http://euhcvdb.ibcp.fr
  mappings:
    miriam: hcvdb
    n2t: hcvdb
    prefixcommons: HCVDB
  name: Hepatitis C Virus Database
  pattern: ^M\d{5}$
  preferred_prefix: hcvdb
  uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1
hdr:
  description: The Homeodomain Resource is a curated collection of sequence, structure,
    interaction, genomic and functional information on the homeodomain family. It
    contains sets of curated homeodomain sequences from fully sequenced genomes, including
    experimentally derived homeodomain structures, homeodomain protein-protein interactions,
    homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic
    disorders.
  example: '63'
  homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/
  mappings:
    miriam: hdr
    n2t: hdr
    prefixcommons: HDR
  name: Homeodomain Research
  pattern: ^\d+$
  preferred_prefix: hdr
  uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&amp;view=proteins&amp;id=$1
hgmd:
  description: The Human Gene Mutation Database (HGMD) collates data on germ-line
    mutations in nuclear genes associated with human inherited disease. It includes
    information on single base-pair substitutions in coding, regulatory and splicing-relevant
    regions; micro-deletions and micro-insertions; indels; triplet repeat expansions
    as well as gross deletions; insertions; duplications; and complex rearrangements.
    Each mutation entry is unique, and includes cDNA reference sequences for most
    genes, splice junction sequences, disease-associated and functional polymorphisms,
    as well as links to data present in publicly available online locus-specific mutation
    databases.
  example: CALM1
  homepage: http://www.hgmd.cf.ac.uk/ac/index.php
  mappings:
    miriam: hgmd
    n2t: hgmd
    prefixcommons: HGMD
  name: Human Gene Mutation Database
  pattern: ^[A-Z_0-9]+$
  preferred_prefix: hgmd
  uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1
hgnc:
  description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
    name and symbol (short-form abbreviation) for each known human gene.  All approved
    symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers
    refer to records in the HGNC symbol database.
  example: '16793'
  homepage: http://www.genenames.org
  mappings:
    bioportal: HGNC
    cellosaurus: HGNC
    go: HGNC
    miriam: hgnc
    n2t: hgnc
    ncbi: HGNC
    prefixcommons: HGNC
    uniprot: HGNC
    wikidata: P354
  name: HUGO Gene Nomenclature Committee
  pattern: ^((HGNC|hgnc):)?\d{1,5}$
  preferred_prefix: hgnc
  uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
hgnc.genefamily:
  deprecated: true
  description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
    name and symbol (short-form abbreviation) for each known human gene. All approved
    symbols are stored in the HGNC database, and each symbol is unique. In addition,
    HGNC also provides symbols for both structural and functional gene families. This
    collection refers to records using the HGNC family symbol.
  example: '2029'
  has_canonical: hgnc.genegroup
  homepage: http://www.genenames.org
  mappings:
    miriam: hgnc.family
    n2t: hgnc.genefamily
    prefixcommons: HGNC.GENEFAMILY
  name: HGNC Family
  pattern: ^[A-Z0-9-]+(#[A-Z0-9-]+)?$
  preferred_prefix: hgnc.genefamily
  synonyms:
  - GFAM
  - HGNC_GROUP
  - hgnc.family
  uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1
hgnc.genegroup:
  description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
    name and symbol (short-form abbreviation) for each known human gene. All approved
    symbols are stored in the HGNC database, and each symbol is unique. In addition,
    HGNC also provides a unique numerical ID to identify gene families, providing
    a display of curated hierarchical relationships between families.
  example: '141'
  homepage: https://www.genenames.org
  mappings:
    miriam: hgnc.genegroup
  name: HGNC Gene Group
  pattern: ^\d+$
  preferred_prefix: hgnc.genegroup
  uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1
hgnc.symbol:
  description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
    name and symbol (short-form abbreviation) for each known human gene. All approved
    symbols are stored in the HGNC database, and each symbol is unique. This collection
    refers to records using the HGNC symbol.
  example: DAPK1
  homepage: https://www.genenames.org/
  mappings:
    miriam: hgnc.symbol
    n2t: hgnc.symbol
    prefixcommons: HGNC.SYMBOL
  name: HGNC Symbol
  pattern: ^[A-Za-z-0-9_]+(\@)?$
  preferred_prefix: hgnc.symbol
  providers:
  - code: depmap
    description: DepMap summary of the given gene
    homepage: https://depmap.org
    name: DepMap Gene Summary
    uri_format: https://depmap.org/portal/gene/$1
  - code: pathwaycommons
    description: Interactions between a given gene and other molecular entities
    homepage: https://www.pathwaycommons.org/
    name: Pathway Commons Gene Interations
    uri_format: https://apps.pathwaycommons.org/interactions?source=$1
  - code: oncomx
    description: Mutation profiles for a gene
    homepage: https://oncomx.org
    name: OncoMX
    uri_format: https://oncomx.org/searchview/?gene=$1
  uri_format: https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1
hinv.locus:
  description: H-Invitational Database (H-InvDB) is an integrated database of human
    genes and transcripts. It provides curated annotations of human genes and transcripts
    including gene structures, alternative splicing isoforms, non-coding functional
    RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
    pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
    repeats), relation with diseases, gene expression profiling, molecular evolutionary
    features, protein-protein interactions (PPIs) and gene families/groups. This datatype
    provides access to the 'Locus' view.
  example: HIX0004394
  homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
  mappings:
    miriam: hinv.locus
    n2t: hinv.locus
    prefixcommons: HINV.LOCUS
  name: H-InvDb Locus
  pattern: ^HIX\d{7}(\.\d+)?$
  preferred_prefix: hinv.locus
  uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1
hinv.protein:
  description: H-Invitational Database (H-InvDB) is an integrated database of human
    genes and transcripts. It provides curated annotations of human genes and transcripts
    including gene structures, alternative splicing isoforms, non-coding functional
    RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
    pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
    repeats), relation with diseases, gene expression profiling, molecular evolutionary
    features, protein-protein interactions (PPIs) and gene families/groups. This datatype
    provides access to the 'Protein' view.
  example: HIP000030660
  homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
  mappings:
    miriam: hinv.protein
    n2t: hinv.protein
    prefixcommons: HINV.PROTEIN
  name: H-InvDb Protein
  pattern: ^HIP\d{9}(\.\d+)?$
  preferred_prefix: hinv.protein
  uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1
hinv.transcript:
  description: H-Invitational Database (H-InvDB) is an integrated database of human
    genes and transcripts. It provides curated annotations of human genes and transcripts
    including gene structures, alternative splicing isoforms, non-coding functional
    RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
    pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
    repeats), relation with diseases, gene expression profiling, molecular evolutionary
    features, protein-protein interactions (PPIs) and gene families/groups. This datatype
    provides access to the 'Transcript' view.
  example: HIT000195363
  homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
  mappings:
    miriam: hinv.transcript
    n2t: hinv.transcript
    prefixcommons: HINV.TRANSCRIPT
  name: H-InvDb Transcript
  pattern: ^HIT\d{9}(\.\d+)?$
  preferred_prefix: hinv.transcript
  uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1
hmdb:
  description: The Human Metabolome Database (HMDB) is a database containing detailed
    information about small molecule metabolites found in the human body.It contains
    or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
  example: HMDB00001
  homepage: http://www.hmdb.ca/
  mappings:
    cheminf: 000408
    miriam: hmdb
    n2t: hmdb
    prefixcommons: HMDB
    wikidata: P2057
  name: Human Metabolome Database
  pattern: ^HMDB\d+$
  preferred_prefix: hmdb
  synonyms:
  - HMDB
  uri_format: http://www.hmdb.ca/metabolites/$1
hms.lincs.compound:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database contains all publicly available HMS LINCS datasets and information
    for each dataset about experimental reagents (small molecule perturbagens, cells,
    antibodies, and proteins) and experimental and data analysis protocols.
  example: 10001-101
  homepage: https://lincs.hms.harvard.edu/db/sm/
  name: HMS LINCS Compound
  preferred_prefix: hms.lincs.compound
  synonyms:
  - HMS-LINCS
  - hmsl_id
  uri_format: https://lincs.hms.harvard.edu/db/sm/$1
hog:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Documentation of HOGS (Homologous Organs Groups). Contains links to
    HOGs download, HOGs onthology, HOGs creation, composition, etc.
  example: '0000255'
  homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships
  name: Homologous Organ Groups
  preferred_prefix: hog
hogenom:
  description: HOGENOM is a database of homologous genes from fully sequenced organisms
    (bacteria, archeae and eukarya). This collection references phylogenetic trees
    which can be retrieved using either UniProt accession numbers, or HOGENOM tree
    family identifier.
  example: HBG284870
  homepage: http://pbil.univ-lyon1.fr/databases/hogenom/
  mappings:
    miriam: hogenom
    n2t: hogenom
    prefixcommons: HOGENOM
    uniprot: HOGENOM
  name: Database of Complete Genome Homologous Genes Families
  pattern: ^\w+$
  preferred_prefix: hogenom
  uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1
hom:
  banana: HOM
  contact:
    email: bgee@sib.swiss
    github: fbastian
    name: Frederic Bastian
    orcid: null
  description: This ontology represents concepts related to homology, as well as other
    concepts used to describe similarity and non-homology.
  example: 0000049
  homepage: https://github.com/BgeeDB/homology-ontology
  license: CC0 1.0
  mappings:
    bioportal: HOM
    obofoundry: HOM
    ols: hom
    ontobee: HOM
    prefixcommons: HOM
  name: Homology Ontology
  preferred_prefix: HOM
  uri_format: http://purl.obolibrary.org/obo/HOM_$1
  version: '2015-01-07'
homd.seq:
  description: The Human Oral Microbiome Database (HOMD) provides a site-specific
    comprehensive database for the more than 600 prokaryote species that are present
    in the human oral cavity. It contains genomic information based on a curated 16S
    rRNA gene-based provisional naming scheme, and taxonomic information. This datatype
    contains genomic sequence information.
  example: SEQF1003
  homepage: http://www.homd.org/index.php
  mappings:
    miriam: homd.seq
    n2t: homd.seq
    prefixcommons: HOMD.SEQ
  name: HOMD Sequence Metainformation
  pattern: ^SEQF\d+$
  preferred_prefix: homd.seq
  uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1
homd.taxon:
  description: The Human Oral Microbiome Database (HOMD) provides a site-specific
    comprehensive database for the more than 600 prokaryote species that are present
    in the human oral cavity. It contains genomic information based on a curated 16S
    rRNA gene-based provisional naming scheme, and taxonomic information. This datatype
    contains taxonomic information.
  example: '811'
  homepage: http://www.homd.org/index.php
  mappings:
    miriam: homd.taxon
    n2t: homd.taxon
    prefixcommons: HOMD.TAXON
  name: HOMD Taxonomy
  pattern: ^\d+$
  preferred_prefix: homd.taxon
  uri_format: www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1
homologene:
  description: HomoloGene is a system for automated detection of homologs among the
    annotated genes of several completely sequenced eukaryotic genomes.
  example: '1000'
  homepage: https://www.ncbi.nlm.nih.gov/homologene/
  mappings:
    miriam: homologene
    n2t: homologene
    prefixcommons: HOMOLOGENE
    wikidata: P593
  name: HomoloGene ID
  pattern: ^\d+$
  preferred_prefix: homologene
  providers:
  - code: CURATOR_REVIEW
    description: Bio2RDF
    homepage: http://homologene.bio2rdf.org/fct
    name: Bio2RDF
    uri_format: http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1
  uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1
hovergen:
  description: HOVERGEN is a database of homologous vertebrate genes that allows one
    to select sets of homologous genes among vertebrate species, and to visualize
    multiple alignments and phylogenetic trees.
  example: HBG004341
  homepage: https://pbil.univ-lyon1.fr/databases/hovergen.php
  mappings:
    miriam: hovergen
    n2t: hovergen
    prefixcommons: HOVERGEN
  name: Homologous Vertebrate Genes Database
  pattern: ^HBG\d+$
  preferred_prefix: hovergen
  uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN
hp:
  banana: HP
  contact:
    email: dr.sebastian.koehler@gmail.com
    github: drseb
    name: Sebastian Koehler
    orcid: null
  description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary
    of phenotypic abnormalities encountered in human disease. Each term in the HPO
    describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently
    being developed using the medical literature, Orphanet, DECIPHER, and OMIM.
  example: '0011140'
  homepage: http://www.human-phenotype-ontology.org/
  license: hpo
  mappings:
    bioportal: HP
    miriam: hp
    n2t: hp
    obofoundry: HP
    ols: hp
    ontobee: HP
    prefixcommons: HP
    wikidata: P3841
  name: Human Phenotype Ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: HP
  uri_format: https://hpo.jax.org/app/browse/term/HP:$1
  version: '2021-10-10'
hpa:
  description: The Human Protein Atlas (HPA) is a publicly available database with
    high-resolution images showing the spatial distribution of proteins in different
    normal and cancer human cell lines. Primary access to this collection is through
    Ensembl Gene identifiers.
  example: ENSG00000026508
  homepage: http://www.proteinatlas.org/
  mappings:
    go: HPA
    miriam: hpa
    n2t: hpa
    prefixcommons: HPA
    uniprot: HPA
  name: Human Protein Atlas tissue profile information
  pattern: ^ENSG\d{11}$
  preferred_prefix: hpa
  uri_format: http://www.proteinatlas.org/$1
hpath:
  description: An ontology of histopathological morphologies used by pathologists
    to classify/categorise animal lesions observed histologically during regulatory
    toxicology studies. The ontology was developed using real data from over 6000
    regulatory toxicology studies donated by 13 companies spanning nine species.
  example: '2000191'
  homepage: https://github.com/Novartis/hpath
  mappings:
    ols: hpath
  name: Histopathology Ontology
  preferred_prefix: hpath
  version: '2019-07-05'
hpm.peptide:
  description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
    result from the draft map of the human proteome project. The project was based
    on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
    mass spectrometry. The HPM contains direct evidence of translation of a number
    of protein products derived from human genes, based on peptide identifications
    of multiple organs/tissues and cell types from individuals with clinically defined
    healthy tissues. The HPM portal provides data on individual proteins, as well
    as on individual peptide spectra. This collection references individual peptides
    through spectra.
  example: '9606117'
  homepage: http://www.humanproteomemap.org/index.php
  mappings:
    miriam: hpm.peptide
    n2t: hpm.peptide
    prefixcommons: HPM.PEPTIDE
  name: Human Proteome Map Peptide
  pattern: ^\d+$
  preferred_prefix: hpm.peptide
  uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1
hpm.protein:
  description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
    result from the draft map of the human proteome project. The project was based
    on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
    mass spectrometry. The HPM contains direct evidence of translation of a number
    of protein products derived from human genes, based on peptide identifications
    of multiple organs/tissues and cell types from individuals with clinically defined
    healthy tissues. The HPM portal provides data on individual proteins, as well
    as on individual peptide spectra. This collection references proteins.
  example: '1968'
  homepage: http://www.humanproteomemap.org/index.php
  mappings:
    miriam: hpm.protein
    n2t: hpm.protein
    prefixcommons: HPM.PROTEIN
  name: Human Proteome Map Protein
  pattern: ^\d+$
  preferred_prefix: hpm.protein
  uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1
hprd:
  description: The Human Protein Reference Database (HPRD) represents a centralized
    platform to visually depict and integrate information pertaining to domain architecture,
    post-translational modifications, interaction networks and disease association
    for each protein in the human proteome.
  example: '00001'
  homepage: http://www.hprd.org/
  mappings:
    miriam: hprd
    n2t: hprd
    prefixcommons: HPRD
  name: Human Protein Reference Database
  pattern: ^\d+$
  preferred_prefix: hprd
  uri_format: http://www.hprd.org/protein/$1
hpscreg:
  description: hPSCreg is a freely accessible global registry for human pluripotent
    stem cell lines (hPSC-lines).
  example: BCRTi001-A
  homepage: https://hpscreg.eu/
  mappings:
    cellosaurus: hPSCreg
    miriam: hpscreg
    n2t: hpscreg
  name: Human Pluripotent Stem Cell Registry
  pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$
  preferred_prefix: hpscreg
  uri_format: https://hpscreg.eu/cell-line/$1
hsapdv:
  banana: HsapDv
  contact:
    email: frederic.bastian@unil.ch
    github: fbastian
    name: "Fr\xE9d\xE9ric Bastian"
    orcid: null
  description: Life cycle stages for Human
  example: 0000194
  homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
  license: CC BY 3.0
  mappings:
    biolink: HsapDv
    bioportal: HSAPDV
    obofoundry: HsapDv
    ols: hsapdv
    ontobee: HSAPDV
    prefixcommons: HSAPDV
  name: Human Developmental Stages
  pattern: ^\d{7}$
  preferred_prefix: HsapDv
  synonyms:
  - HsapDv
  uri_format: http://purl.obolibrary.org/obo/HSAPDV_$1
  version: '2020-03-10'
hsdb:
  description: The Hazardous Substances Data Bank (HSDB) is a toxicology database
    that focuses on the toxicology of potentially hazardous chemicals. It provides
    information on human exposure, industrial hygiene, emergency handling procedures,
    environmental fate, regulatory requirements, nanomaterials, and related areas.
  example: '5621'
  homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb
  mappings:
    wikidata: P2062
  name: Hazardous Substances Data Bank
  preferred_prefix: hsdb
  uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1
hso:
  banana: HSO
  contact:
    email: fernanda.dorea@sva.se
    github: nandadorea
    name: Fernanda Dorea
    orcid: null
  description: The health Surveillance Ontology (HSO) focuses on "surveillance system
    level data", that is, data outputs from surveillance activities, such as number
    of samples collected, cases observed, etc. It aims to support One-Health surveillance,
    covering animal health, public health and food safety surveillance.
  example: '0000062'
  homepage: https://w3id.org/hso
  license: CC BY 3.0
  mappings:
    bioportal: HSO
    obofoundry: HSO
    ols: hso
    ontobee: HSO
  name: Health Surveillance Ontology
  preferred_prefix: HSO
  uri_format: http://purl.obolibrary.org/obo/HSO_$1
  version: '2020-11-28'
hssp:
  description: HSSP (homology-derived structures of proteins) is a derived database
    merging structural (2-D and 3-D) and sequence information (1-D). For each protein
    of known 3D structure from the Protein Data Bank, the database has a file with
    all sequence homologues, properly aligned to the PDB protein.
  example: 102l
  homepage: http://swift.cmbi.kun.nl/swift/hssp/
  mappings:
    miriam: hssp
    n2t: hssp
    ncbi: HSSP
    prefixcommons: HSSP
  name: Database of homology-derived secondary structure of proteins
  pattern: ^\w{4}$
  preferred_prefix: hssp
  providers:
  - code: CURATOR_REVIEW
    description: HSSP at CMBI
    homepage: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/
    name: HSSP at CMBI
    uri_format: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2
  uri_format: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2
htn:
  banana: HTN
  contact:
    email: aellenhicks@gmail.com
    github: null
    name: Amanda Hicks
    orcid: null
  description: An ontology for representing clinical data about hypertension, intended
    to support classification of patients according to various diagnostic guidelines
  example: '00000014'
  homepage: https://github.com/aellenhicks/htn_owl
  license: CC BY 4.0
  mappings:
    bioportal: HTN
    obofoundry: HTN
    ols: htn
    ontobee: HTN
  name: Hypertension Ontology
  preferred_prefix: HTN
  uri_format: http://purl.obolibrary.org/obo/HTN_$1
  version: '2019-06-10'
huge:
  description: The Human Unidentified Gene-Encoded (HUGE) protein database contains  results
    from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa
    cDNA sequencing project.
  example: KIAA0001
  homepage: http://www.kazusa.or.jp/huge/
  mappings:
    miriam: huge
    n2t: huge
    prefixcommons: HUGE
    uniprot: HUGE
  name: Human Unidentified Gene-Encoded
  pattern: ^KIAA\d{4}$
  preferred_prefix: huge
  uri_format: https://www.kazusa.or.jp/huge/gfpage/$1
iao:
  banana: IAO
  contact:
    email: jiezheng@pennmedicine.upenn.edu
    github: zhengj2007
    name: Jie Zheng
    orcid: null
  description: An ontology of information entities, originally driven by work by the
    Ontology of Biomedical Investigation (OBI) digital entity and realizable information
    entity branch.
  example: '0000030'
  homepage: https://github.com/information-artifact-ontology/IAO/
  license: CC BY 4.0
  mappings:
    bioportal: IAO
    go: IAO
    miriam: iao
    n2t: iao
    obofoundry: IAO
    ols: iao
    ontobee: IAO
    prefixcommons: IAO
  name: Information Artifact Ontology
  pattern: ^\d{7}$
  preferred_prefix: IAO
  uri_format: http://purl.obolibrary.org/obo/IAO_$1
  version: '2020-12-09'
icd10:
  description: The International Classification of Diseases is the international standard
    diagnostic classification for all general epidemiological and many health management
    purposes.
  example: C34
  homepage: https://icd.who.int/browse10
  mappings:
    biolink: ICD10
    bioportal: ICD10
    miriam: icd
    n2t: icd
    prefixcommons: ICD
    wikidata: P4229
  name: International Classification of Diseases
  pattern: ^[A-Z]\d+(\.[-\d+])?$
  preferred_prefix: icd10
  synonyms:
  - ICD
  - ICD-10
  - ICD10
  - ICD10CM
  uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1
icd11:
  description: Diagnostic tool for epidemiology, health management and clinical purposes,
    maintained by the World Health Organization (WHO). It provides a system of diagnostic
    codes for classifying diseases, including nuanced classifications of a wide variety
    of signs, symptoms, abnormal findings, complaints, social circumstances, and external
    causes of injury or disease.
  example: RA01.0
  homepage: https://icd.who.int/
  mappings:
    wikidata: P7807
  name: International Classification of Diseases 11th Revision
  preferred_prefix: icd11
  synonyms:
  - ICD-11
icd9:
  description: ICD-9-CM is the official system of assigning codes to diagnoses and
    procedures associated with hospital utilization in the United States.
  example: '277.9'
  homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm
  mappings:
    biolink: ICD9
    bioportal: ICD9CM
    wikidata: P493
  name: International Classification of Diseases 9th Revision
  preferred_prefix: icd9
  synonyms:
  - IC9CM
  - ICD9
  - ICD9CM
  - ICD9CM_2005
  - ICD9CM_2006
  - ICD9_2005
  - ICDCM_2005
  - MTHICD9_2006
icdc:
  description: The Integrated Canine Data Commons is one of several repositories within
    the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure
    that provides secure access to a large, comprehensive, and expanding collection
    of cancer research data. The ICDC was established to further research on human
    cancers by enabling comparative analysis with canine cancer.
  example: ICDC000101
  homepage: https://caninecommons.cancer.gov/#/
  mappings:
    miriam: icdc
  name: Integrated Canine Data Commons
  pattern: ^ICDC[0-9][0-9][0-9][0-9][0-9][0-9]$
  preferred_prefix: icdc
  uri_format: https://caninecommons.cancer.gov/#/study/$1
icdo:
  description: An ontologied version of ICD
  example: M9861/3
  homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/
  mappings:
    bioportal: ICDO
    ontobee: ICDO
    wikidata: P563
  name: The International Classification of Diseases for Oncology
  preferred_prefix: icdo
  synonyms:
  - ICD-O
  - ICDO
iceberg.element:
  description: ICEberg (Integrative and conjugative elements) is a database of integrative
    and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
    elements that can integrate into and excise from a host chromosome, and can carry
    likely virulence determinants, antibiotic-resistant factors and/or genes coding
    for other beneficial traits. It contains details of ICEs found in representatives
    bacterial species, and which are organised as families. This collection references
    ICE elements.
  example: '100'
  homepage: http://db-mml.sjtu.edu.cn/ICEberg/
  mappings:
    miriam: iceberg.element
    n2t: iceberg.element
    prefixcommons: ICEBERG.ELEMENT
  name: ICEberg element
  pattern: ^\d+$
  preferred_prefix: iceberg.element
  uri_format: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1
iceberg.family:
  description: ICEberg (Integrative and conjugative elements) is a database of integrative
    and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
    elements that can integrate into and excise from a host chromosome, and can carry
    likely virulence determinants, antibiotic-resistant factors and/or genes coding
    for other beneficial traits. It contains details of ICEs found in representatives
    bacterial species, and which are organised as families. This collection references
    ICE families.
  example: '1'
  homepage: http://db-mml.sjtu.edu.cn/ICEberg/
  mappings:
    miriam: iceberg.family
    n2t: iceberg.family
    prefixcommons: ICEBERG.FAMILY
  name: ICEberg family
  pattern: ^\d+$
  preferred_prefix: iceberg.family
  uri_format: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1
iceo:
  banana: ICEO
  contact:
    email: liumeng94@sjtu.edu.cn
    github: null
    name: Meng LIU
    orcid: null
  description: A biological ontology to standardize and integrate Integrative and
    Conjugative Element (ICE) information and to support computer-assisted reasoning.
  example: '0000712_1'
  homepage: https://github.com/ontoice/ICEO
  license: CC BY 4.0
  mappings:
    bioportal: ICEO
    obofoundry: ICEO
    ols: iceo
    ontobee: ICEO
  name: Integrative and Conjugative Element Ontology
  preferred_prefix: ICEO
  uri_format: http://purl.obolibrary.org/obo/ICEO_$1
  version: '2.1'
ico:
  banana: ICO
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqun Oliver He
    orcid: null
  description: The Informed Consent Ontology (ICO) is an ontology for the informed
    consent and informed consent process in the medical field.
  example: ICODEV_0000066
  homepage: https://github.com/ICO-ontology/ICO
  license: CC BY 3.0
  mappings:
    bioportal: ICO
    obofoundry: ICO
    ols: ico
    ontobee: ICO
    prefixcommons: ICO
  name: Informed Consent Ontology
  preferred_prefix: ICO
  uri_format: http://purl.obolibrary.org/obo/ICO_$1
  version: 1.0.187
ideal:
  description: IDEAL provides a collection of knowledge on experimentally verified
    intrinsically disordered proteins. It contains manual annotations by curators
    on intrinsically disordered regions, interaction regions to other molecules, post-translational
    modification sites, references and structural domain assignments.
  example: IID00001
  homepage: https://www.ideal-db.org
  mappings:
    miriam: ideal
    n2t: ideal
    prefixcommons: IDEAL
    uniprot: IDEAL
  name: Intrinsically Disordered proteins with Extensive Annotations and Literature
  pattern: ^IID\d+$
  preferred_prefix: ideal
  uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1
identifiers.namespace:
  description: Identifiers.org is an established resolving system that enables the
    referencing of data for the scientific community, with a current focus on the
    Life Sciences domain.
  example: pubmed
  homepage: https://www.ebi.ac.uk
  mappings:
    miriam: identifiers.namespace
  name: Identifiers.org namespace
  pattern: ^[a-z_\.]+$
  preferred_prefix: identifiers.namespace
  uri_format: https://registry.identifiers.org/registry/$1
ido:
  banana: IDO
  contact:
    email: Lindsay.Cowell@utsouthwestern.edu
    github: lgcowell
    name: Lindsay Cowell
    orcid: null
  description: Infectious Disease Ontology holds entities relevant to both biomedical
    and clinical aspects of most infectious diseases.
  example: '0000504'
  homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
  license: CC BY 3.0
  mappings:
    bioportal: IDO
    miriam: ido
    n2t: ido
    obofoundry: IDO
    ols: ido
    ontobee: IDO
    prefixcommons: IDO
  name: Infectious Disease Ontology
  pattern: ^[0-9]+$
  preferred_prefix: IDO
  uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1
  version: '2017-11-03'
idocovid19:
  description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension
    of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology
    (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal
    Ontology as its starting point, and covers epidemiology, classification, pathogenesis,
    and treatment of terms used to represent infection by the SARS-CoV-2 virus strain,
    and the associated COVID-19 disease.
  example: 0001191
  homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
  license: CC BY 3.0
  mappings:
    bioportal: IDO-COVID-19
    ols: idocovid19
  name: The COVID-19 Infectious Disease Ontology
  preferred_prefix: idocovid19
  version: '2020-07-21'
idoden:
  description: An ontology for dengue fever.
  example: '0003463'
  homepage: https://bioportal.bioontology.org/ontologies/IDODEN
  mappings:
    bioportal: IDODEN
  name: Dengue Fever Ontology
  preferred_prefix: idoden
  references:
  - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479
idomal:
  banana: IDOMAL
  contact:
    email: topalis@imbb.forth.gr
    github: null
    name: Pantelis Topalis
    orcid: null
  description: An application ontology to cover all aspects of malaria as well as
    the intervention attempts to control it.
  example: '0002350'
  homepage: https://www.vectorbase.org/ontology-browser
  license: CC0 1.0
  mappings:
    bioportal: IDOMAL
    obofoundry: IDOMAL
    ols: idomal
    ontobee: IDOMAL
    prefixcommons: IDOMAL
  name: Malaria Ontology
  pattern: ^\d{7}$
  preferred_prefix: IDOMAL
  uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1
  version: '2015-03-16'
idoo:
  description: Identifiers.org Ontology
  example: DataCollection
  homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology
  mappings:
    miriam: idoo
    n2t: idoo
  name: Identifiers.org Ontology
  pattern: ^[0-9a-zA-Z]+$
  preferred_prefix: idoo
  uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1
idot:
  description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful
    terms for describing datasets.
  example: identifierPattern
  homepage: http://biomodels.net/vocab/idot.rdf
  mappings:
    miriam: idot
    n2t: idot
    prefixcommons: IDOT
  name: Identifiers.org Terms
  pattern: ^[A-Za-z]+$
  preferred_prefix: idot
  uri_format: https://biomodels.net/vocab/idot.rdf#$1
idr:
  description: "Image Data Resource (IDR) is an online, public data repository that\
    \ seeks to store, integrate and serve image datasets from published scientific\
    \ studies. We have collected and are continuing to receive existing and newly\
    \ created \u201Creference image\" datasets that are valuable resources for a broad\
    \ community of users, either because they will be frequently accessed and cited\
    \ or because they can serve as a basis for re-analysis and the development of\
    \ new computational tools."
  example: '0001'
  homepage: https://idr.openmicroscopy.org
  mappings:
    fairsharing: FAIRsharing.6wf1zw
    miriam: idr
  name: Image Data Resource
  pattern: ^[0-9]{4}$
  preferred_prefix: idr
  uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1
iedb:
  description: The Immune Epitope Database (IEDB) is a freely available resource funded
    by NIAID. It catalogs experimental data on antibody and T cell epitopes studied
    in humans, non-human primates, and other animal species in the context of infectious
    disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools
    to assist in the prediction and analysis of epitopes.
  example: '1038233'
  homepage: https://www.lji.org/
  mappings:
    miriam: iedb
  name: Immune Epitope Database
  pattern: ^[0-9]+$
  preferred_prefix: iedb
  uri_format: https://www.iedb.org/reference/$1
iev:
  banana: IEV
  deprecated: true
  homepage: http://www.inoh.org
  mappings:
    obofoundry: IEV
    prefixcommons: IEV
  name: Event (INOH pathway ontology)
  preferred_prefix: IEV
  uri_format: http://purl.obolibrary.org/obo/IEV_$1
igsn:
  description: IGSN is a globally unique and persistent identifier for material samples
    and specimens.  IGSNs are obtained from IGSN e.V. Agents.
  example: AU124
  homepage: http://www.geosamples.org/
  mappings:
    miriam: igsn
    n2t: igsn
  name: International Geo Sample Number
  pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$
  preferred_prefix: igsn
  uri_format: http://igsn.org/$1
ihw:
  description: The International Histocompatibility Working Group provides a comprehensive
    inventory of HLA reference genes to support worldwide research in immunogenetics.
    We also offer selected cell lines and DNA from our substantial DNA Bank of more
    than 1,000 cell lines from selected families, as well as individuals with diverse
    ethnicity and immunologic characteristics.
  example: IHW09326
  homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html
  mappings:
    cellosaurus: IHW
  name: International Histocompatibility Workshop cell lines
  pattern: ^IHW\d+$
  preferred_prefix: ihw
imdrf:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The International Medical Device Regulators Forum (IMDRF) is a forum
    of voluntary medical device regulators from around the world who have come together
    to build on the strong foundational work of the Global Harmonization Task Force
    on Medical Devices (GHTF), and to accelerate international medical device regulatory
    harmonization and convergence.
  homepage: http://www.imdrf.org/
  name: International Medical Device Regulators Forum
  no_own_terms: true
  preferred_prefix: imdrf
  references:
  - https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes
imex:
  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.
  example: IM-19210-3
  homepage: https://www.imexconsortium.org/
  mappings:
    miriam: imex
    n2t: imex
    prefixcommons: IMEX
  name: International Molecular Exchange
  pattern: ^IM-\d+(-?)(\d+?)$
  preferred_prefix: imex
  providers:
  - code: CURATOR_REVIEW
    description: IMEx Consortium though Intact
    homepage: https://www.ebi.ac.uk/intact/
    name: IMEx Consortium though Intact
    uri_format: https://imexcentral.org/icentral/imex/rec/$1
  uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1
img.gene:
  description: The integrated microbial genomes (IMG) system is a data management,
    analysis and annotation platform for all publicly available genomes. IMG contains
    both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
    with all other publicly available genomes from all three domains of life, together
    with a large number of plasmids and viruses. This datatype refers to gene information.
  example: '638309541'
  homepage: http://img.jgi.doe.gov/
  mappings:
    miriam: img.gene
    n2t: img.gene
    prefixcommons: IMG.GENE
  name: Integrated Microbial Genomes Gene
  pattern: ^\d+$
  preferred_prefix: img.gene
  uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1
img.taxon:
  description: The integrated microbial genomes (IMG) system is a data management,
    analysis and annotation platform for all publicly available genomes. IMG contains
    both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
    with all other publicly available genomes from all three domains of life, together
    with a large number of plasmids and viruses. This datatype refers to taxon information.
  example: '648028003'
  homepage: http://img.jgi.doe.gov/
  mappings:
    miriam: img.taxon
    n2t: img.taxon
    prefixcommons: IMG.TAXON
  name: Integrated Microbial Genomes Taxon
  pattern: ^\d+$
  preferred_prefix: img.taxon
  uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1
imgt.hla:
  description: IMGT, the international ImMunoGeneTics project, is a collection of
    high-quality integrated databases specialising in Immunoglobulins, T cell receptors
    and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA
    is a database for sequences of the human MHC, referred to as HLA. It includes
    all the official sequences for the WHO Nomenclature Committee For Factors of the
    HLA System. This collection references allele information through the WHO nomenclature.
  example: A*01:01:01:01
  homepage: https://www.ebi.ac.uk/imgt/hla/allele.html
  mappings:
    cellosaurus: IPD-IMGT/HLA
    go: IMGT_HLA
    miriam: imgt.hla
    n2t: imgt.hla
    ncbi: IMGT/HLA
    prefixcommons: IMGT.HLA
  name: IMGT/HLA human major histocompatibility complex sequence database
  pattern: ^[A-Z0-9*:]+$
  preferred_prefix: imgt.hla
  synonyms:
  - IPD-IMGT/HLA
  uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1
imgt.ligm:
  description: IMGT, the international ImMunoGeneTics project, is a collection of
    high-quality integrated databases specialising in Immunoglobulins, T cell receptors
    and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM
    is a comprehensive database of fully annotated sequences of Immunoglobulins and
    T cell receptors from human and other vertebrates.
  example: M94112
  homepage: http://www.imgt.org/
  mappings:
    go: IMGT_LIGM
    miriam: imgt.ligm
    n2t: imgt.ligm
    ncbi: IMGT/LIGM
    prefixcommons: IMGT.LIGM
  name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors
  pattern: ^M\d+$
  preferred_prefix: imgt.ligm
  providers:
  - code: CURATOR_REVIEW
    description: IMGT LIGM through DKFZ (SRS)
    homepage: http://genius.embnet.dkfz-heidelberg.de/
    name: IMGT LIGM through DKFZ (SRS)
    uri_format: http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1']
  uri_format: http://www.imgt.org/ligmdb/view?id=$1
imr:
  banana: IMR
  contact:
    email: curator@inoh.org
    github: null
    name: INOH curators
    orcid: null
  deprecated: true
  homepage: http://www.inoh.org
  mappings:
    obofoundry: IMR
    prefixcommons: IMR
  name: Molecule role (INOH Protein name/family name ontology)
  preferred_prefix: IMR
  uri_format: http://purl.obolibrary.org/obo/IMR_$1
inchi:
  description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary
    identifier for chemical substances that can be used in printed and electronic
    data sources. It is derived solely from a structural representation of that substance,
    such that a single compound always yields the same identifier.
  example: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3
  homepage: http://www.chemspider.com/
  mappings:
    miriam: inchi
    n2t: inchi
    prefixcommons: INCHI
    wikidata: P234
  name: InChI
  pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$
  preferred_prefix: inchi
  providers:
  - code: CURATOR_REVIEW
    description: InChI through NIST
    homepage: http://webbook.nist.gov/chemistry
    name: InChI through NIST
    uri_format: http://webbook.nist.gov/cgi/cbook.cgi?$1
  - code: ebi
    description: InChI through ChEBI
    homepage: https://www.ebi.ac.uk/chebi/
    name: InChI through ChEBI
    uri_format: https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1
  - code: um
    description: InChI through RDF Open Molecules
    homepage: http://rdf.openmolecules.net/
    name: InChI through RDF Open Molecules
    uri_format: http://rdf.openmolecules.net/?$1
  uri_format: http://www.chemspider.com/$1
inchikey:
  description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383)
    is an identifier for chemical substances, and is derived solely from a structural
    representation of that substance. Since these can be quite unwieldly, particularly
    for web use, the InChIKey was developed. These are of a fixed length (25 character)
    and were created as a condensed, more web friendly, digital representation of
    the InChI.
  example: RYYVLZVUVIJVGH-UHFFFAOYSA-N
  homepage: http://www.chemspider.com/
  mappings:
    miriam: inchikey
    n2t: inchikey
    prefixcommons: INCHIKEY
    scholia: inchikey
    wikidata: P235
  name: InChIKey
  pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])$
  preferred_prefix: inchikey
  providers:
  - code: 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/
    name: Scholia
    uri_format: https://scholia.toolforge.org/inchikey/$1
  uri_format: http://www.chemspider.com/inchikey=$1
inn:
  comment: can not find a place to resolve to
  description: Documentation of GO that provides a description of some of the commonly
    used relationships and conventions in GO.
  example: fluticasone
  homepage: https://www.who.int/teams/health-product-and-policy-standards/inn
  mappings:
    wikidata: P2275
  name: International Nonproprietary Names
  preferred_prefix: inn
  synonyms:
  - INN_ID
  uri_format: https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1
ino:
  banana: INO
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqun Oliver He
    orcid: null
  description: he Interaction Network Ontology (INO) is an ontology in the domain
    of interactions and interaction networks. INO represents general and species-neutral
    types of interactions and interaction networks, and their related elements and
    relations. INO is a community-driven ontology, aligns with BFO, and is developed
    by following the OBO Foundry principles.
  example: '0000003'
  homepage: https://github.com/INO-ontology/ino
  license: CC BY 3.0
  mappings:
    biolink: INO
    bioportal: INO
    obofoundry: INO
    ols: ino
    ontobee: INO
  name: Interaction Network Ontology
  preferred_prefix: INO
  uri_format: http://purl.obolibrary.org/obo/INO_$1
  version: 1.0.112
insdc:
  description: The International Nucleotide Sequence Database Collaboration (INSDC)
    consists of a joint effort to collect and disseminate databases containing DNA
    and RNA sequences.
  example: X58356
  homepage: https://www.ncbi.nlm.nih.gov/Genbank/
  mappings:
    miriam: insdc
    n2t: insdc
    prefixcommons: INSDC
  name: Nucleotide Sequence Database
  pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
  preferred_prefix: insdc
  providers:
  - code: CURATOR_REVIEW
    description: INSDC through DDBJ
    homepage: http://www.ddbj.nig.ac.jp/
    name: INSDC through DDBJ
    uri_format: http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1
  - code: ebi
    description: INSDC through European Nucleotide Archive (ENA)
    homepage: https://www.ebi.ac.uk/ena/
    name: INSDC through European Nucleotide Archive (ENA)
    uri_format: https://www.ebi.ac.uk/ena/data/view/$1
  - code: ncbi
    description: INSDC through Nucleotide database at NCBI
    homepage: https://www.ncbi.nlm.nih.gov/nuccore/
    name: INSDC through Nucleotide database at NCBI
    uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
  uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
insdc.cds:
  description: The coding sequence or protein identifiers as maintained in INSDC.
  example: AAA35559
  has_canonical: ncbiprotein
  homepage: http://getentry.ddbj.nig.ac.jp
  mappings:
    miriam: insdc.cds
    n2t: insdc.cds
    prefixcommons: INSDC.CDS
  name: INSDC CDS
  pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
  preferred_prefix: insdc.cds
  providers:
  - code: CURATOR_REVIEW
    description: INSDC CDS through ENA
    homepage: https://www.ebi.ac.uk/ena
    name: INSDC CDS through ENA
    uri_format: https://www.ebi.ac.uk/ena/data/view/$1
  - code: CURATOR_REVIEW
    description: INSDC CDS through NCBI
    homepage: https://www.ncbi.nlm.nih.gov/protein/
    name: INSDC CDS through NCBI
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
  uri_format: http://getentry.ddbj.nig.ac.jp/getentry/dad/$1
insdc.gca:
  description: The genome assembly database contains detailed information about genome
    assemblies for eukaryota, bacteria and archaea. The scope of the genome collections
    database does not extend to viruses, viroids and bacteriophage.
  example: GCA_000155495.1
  homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database
  mappings:
    miriam: insdc.gca
    n2t: insdc.gca
    prefixcommons: INSDC.GCA
  name: Genome assembly database
  pattern: ^GC[AF]_[0-9]{9}\.[0-9]+$
  preferred_prefix: insdc.gca
  providers:
  - code: ncbi
    description: Genome assembly database NCBI
    homepage: https://www.ncbi.nlm.nih.gov/assembly/
    name: Genome assembly database NCBI
    uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1
  uri_format: https://www.ebi.ac.uk/ena/data/view/$1
insdc.run:
  comment: 'https://www.insdc.org/ is the authoritative source for INSDC. However,
    confusingly, they don''t mention runs in this table. I think we should ask them
    to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html
    Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | --'
  contributor:
    email: cjmungall@lbl.gov
    github: null
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: An experimental run, served thrugh the ENA
  example: ERR436051
  has_canonical: ena.embl
  homepage: https://www.insdc.org/
  name: International Nucleotide Sequence Database Collaboration (INSDC) Run
  pattern: ^(E|D|S)RR[0-9]{6,}$
  preferred_prefix: insdc.run
  reviewer:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
insdc.sra:
  description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the
    next generation of sequencing platforms Data submitted to SRA. It is organized
    using a metadata model consisting of six objects: study, sample, experiment, run,
    analysis and submission. The SRA study contains high-level information including
    goals of the study and literature references, and may be linked to the INSDC BioProject
    database.'
  example: SRX000007
  homepage: https://www.ncbi.nlm.nih.gov/sra
  mappings:
    fairsharing: FAIRsharing.g7t2hv
    miriam: insdc.sra
    n2t: insdc.sra
    prefixcommons: INSDC.SRA
  name: Sequence Read Archive
  pattern: ^[SED]R[APRSXZ]\d+$
  preferred_prefix: insdc.sra
  providers:
  - code: ebi
    description: European Nucleotide Archive (ENA)
    homepage: https://www.ebi.ac.uk/ena
    name: European Nucleotide Archive (ENA)
    uri_format: https://www.ebi.ac.uk/ena/data/view/$1
  - code: ddbj
    description: DDBJ Sequence Read Archive (DRA)
    homepage: http://trace.ddbj.nig.ac.jp/dra/
    name: DDBJ Sequence Read Archive (DRA)
    uri_format: http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$1
  uri_format: https://www.ncbi.nlm.nih.gov/sra/$1
intact:
  description: IntAct provides a freely available, open source database system and
    analysis tools for protein interaction data.
  example: EBI-2307691
  homepage: https://www.ebi.ac.uk/intact/
  mappings:
    go: IntAct
    miriam: intact
    n2t: intact
    prefixcommons: INTACT
    uniprot: IntAct
  name: IntAct protein interaction database
  pattern: ^EBI\-[0-9]+$
  preferred_prefix: intact
  uri_format: https://www.ebi.ac.uk/intact/interaction/$1
intact.molecule:
  description: IntAct provides a freely available, open source database system and
    analysis tools for protein interaction data. This collection references interactor
    molecules.
  example: EBI-366083
  homepage: https://www.ebi.ac.uk/intact/
  mappings:
    miriam: intact.molecule
    n2t: intact.molecule
    prefixcommons: INTACT.MOLECULE
  name: IntAct Molecule
  pattern: ^EBI\-[0-9]+$
  preferred_prefix: intact.molecule
  uri_format: https://www.ebi.ac.uk/intact/molecule/$1
interlex:
  description: 'InterLex is a dynamic lexicon, initially built on the foundation of
    NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed
    to help improve the way that biomedical scientists communicate about their data,
    so that information systems can find data more easily and provide more powerful
    means of integrating data across distributed resources and datasets. InterLex
    allows for the association of data fields and data values to common data elements
    and terminologies enabling the crowdsourcing of data-terminology mappings within
    and across communities. InterLex provides a stable layer on top of the many other
    existing terminologies, lexicons, ontologies, and common data element collections
    and provides a set of inter-lexical and inter-data-lexical mappings. '
  example: 0101963
  homepage: https://www.fdilab.org
  mappings:
    miriam: ilx
  name: InterLex
  pattern: ^[0-9]+$
  preferred_prefix: interlex
  references:
  - https://github.com/AllenInstitute/nomenclature
  synonyms:
  - ILX
  uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1
interpro:
  contact:
    email: interhelp@ebi.ac.uk
    github: null
    name: InterPro Help
    orcid: null
  description: InterPro is a database of protein families, domains and functional
    sites in which identifiable features found in known proteins can be applied to
    unknown protein sequences.
  example: IPR016380
  homepage: http://www.ebi.ac.uk/interpro/index.html
  mappings:
    biolink: interpro
    go: InterPro
    miriam: interpro
    n2t: interpro
    ncbi: InterPro
    obofoundry: IPR
    prefixcommons: IPR
    uniprot: InterPro
    wikidata: P2926
  name: InterPro
  pattern: ^IPR\d{6}$
  preferred_prefix: interpro
  providers:
  - code: CURATOR_REVIEW
    description: Bio2RDF
    homepage: http://interpro.bio2rdf.org/fct/
    name: Bio2RDF
    uri_format: http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$1
  synonyms:
  - IP
  - IPR
  - InterPro
  uri_format: https://www.ebi.ac.uk/interpro/entry/$1
ird.segment:
  description: Influenza Research Database (IRD) contains information related to influenza
    virus, including genomic sequence, strain, protein, epitope  and bibliographic
    information. The Segment Details page contains descriptive information and annotation
    data about a particular genomic segment and its encoded product(s).
  example: CY077097
  homepage: http://www.fludb.org/
  mappings:
    miriam: ird.segment
    n2t: ird.segment
    prefixcommons: IRD.SEGMENT
  name: IRD Segment Sequence
  pattern: ^\w+(\_)?\d+(\.\d+)?$
  preferred_prefix: ird.segment
  uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1
irefweb:
  description: 'iRefWeb is an interface to a relational database containing the latest
    build of the interaction Reference Index (iRefIndex) which integrates protein
    interaction data from ten different interaction databases: BioGRID, BIND, CORUM,
    DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates
    interactions with the PubMed record from which they are derived.'
  example: '617102'
  homepage: http://wodaklab.org/iRefWeb/
  mappings:
    miriam: irefweb
    n2t: irefweb
    prefixcommons: IREFWEB
  name: iRefWeb
  pattern: ^\d+$
  preferred_prefix: irefweb
  uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1
iro:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: 0000008
  name: Insect Resistance Ontology
  preferred_prefix: iro
  uri_format: https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1
isbn:
  description: The International Standard Book Number (ISBN) is for identifying printed
    books.
  example: '9781584885658'
  homepage: http://isbndb.com/
  mappings:
    biolink: isbn
    go: ISBN
    miriam: isbn
    n2t: isbn
    prefixcommons: ISBN-13
  name: International Standard Book Number
  pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[
    -]?(\d|X)$
  preferred_prefix: isbn
  providers:
  - code: CURATOR_REVIEW
    description: ISBN database at WorldCat
    homepage: http://www.worldcat.org/
    name: ISBN database at WorldCat
    uri_format: http://www.worldcat.org/isbn/$1
  synonyms:
  - ISBN-10
  - ISBN-13
  uri_format: http://isbndb.com/search-all.html?kw=$1
isfinder:
  description: ISfinder is a database of bacterial insertion sequences (IS). It assigns
    IS nomenclature and acts as a repository for ISs. Each IS is annotated with information
    such as the open reading frame DNA sequence, the sequence of the ends of the element
    and target sites, its origin and distribution together with a bibliography, where
    available.
  example: ISA1083-2
  homepage: http://www-is.biotoul.fr/i
  mappings:
    miriam: isfinder
    n2t: isfinder
    ncbi: ISFinder
    prefixcommons: ISFINDER
  name: Insertion sequence elements database
  pattern: ^IS\w+(\-\d)?$
  preferred_prefix: isfinder
  uri_format: https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1
isni:
  description: "ISNI is the ISO certified global standard number for identifying the\
    \ millions of contributors to creative works and those active in their distribution,\
    \ including researchers, inventors, writers, artists, visual creators, performers,\
    \ producers, publishers, aggregators, and more. It is part of a family of international\
    \ standard identifiers that includes identifiers of works, recordings, products\
    \ and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC,\
    \ and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is\
    \ to assign to the public name(s) of a researcher, inventor, writer, artist, performer,\
    \ publisher, etc. a persistent unique identifying number in order to resolve the\
    \ problem of name ambiguity in search and discovery; and diffuse each assigned\
    \ ISNI across all repertoires in the global supply chain so that every published\
    \ work can be unambiguously attributed to its creator wherever that work is described."
  example: 000000012281955X
  homepage: http://www.isni.org
  mappings:
    biolink: isni
    miriam: isni
    n2t: isni
  name: International Standard Name Identifier
  pattern: ^[0-9]{15}[0-9X]{1}$
  preferred_prefix: isni
  uri_format: http://www.isni.org/isni/$1
issn:
  description: The International Standard Serial Number (ISSN) is a unique eight-digit
    number used to identify a print or electronic periodical publication, rather than
    individual articles or books.
  example: 0745-4570
  homepage: https://portal.issn.org
  mappings:
    biolink: issn
    go: ISSN
    miriam: issn
    n2t: issn
    prefixcommons: ISSN
  name: International Standard Serial Number
  pattern: ^\d{4}-\d{3}[\dX]$
  preferred_prefix: issn
  providers:
  - code: CURATOR_REVIEW
    description: ISSN at Library of Congress
    homepage: http://catalog.loc.gov/webvoy.htm
    name: ISSN at Library of Congress
    uri_format: https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg=$1&searchType=1&recCount=25
  uri_format: https://portal.issn.org/resource/ISSN/$1
itis:
  description: Information system with taxonomic data on plants, animals, fungi, and
    microbes of North America and the world.
  example: '589462'
  homepage: https://www.itis.gov/
  mappings:
    wikidata: P815
  name: Integrated Taxonomic Information System
  pattern: ^\d+$
  preferred_prefix: itis
  uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1
ito:
  description: The Intelligence Task Ontology (ITO) provides a comprehensive map of
    machine intelligence tasks, as well as broader human intelligence or hybrid human/machine
    intelligence tasks.
  example: ITO_01625
  homepage: https://bioportal.bioontology.org/
  mappings:
    bioportal: ITO
    miriam: ito
  name: Intelligence Task Ontology
  pattern: ^.+$
  preferred_prefix: ito
  uri_format: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F$1
iuphar.family:
  description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
    properties of identified mammalian sodium, calcium and potassium channels, as
    well as the related cyclic nucleotide-modulated ion channels and the recently
    described transient receptor potential channels. It includes information on nomenclature
    systems, and on inter and intra-species molecular structure variation. This collection
    references families of receptors or subunits.
  example: '78'
  homepage: http://www.guidetopharmacology.org/
  mappings:
    miriam: iuphar.family
    n2t: iuphar.family
    prefixcommons: IUPHAR.FAMILY
  name: IUPHAR family
  pattern: ^\d+$
  preferred_prefix: iuphar.family
  synonyms:
  - IUPHARfam
  uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1
iuphar.ligand:
  description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
    properties of identified mammalian sodium, calcium and potassium channels, as
    well as the related cyclic nucleotide-modulated ion channels and the recently
    described transient receptor potential channels. It includes information on nomenclature
    systems, and on inter and intra-species molecular structure variation. This collection
    references ligands.
  example: '1755'
  homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all
  mappings:
    biolink: GTOPDB
    miriam: iuphar.ligand
    n2t: iuphar.ligand
    prefixcommons: IUPHAR.LIGAND
    wikidata: P595
  name: Guide to Pharmacology Ligand ID
  pattern: ^\d+$
  preferred_prefix: iuphar.ligand
  synonyms:
  - IUPHAR_LIGAND
  - IUPHAR_LIGAND_ID
  uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1
iuphar.receptor:
  description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
    properties of identified mammalian sodium, calcium and potassium channels, as
    well as the related cyclic nucleotide-modulated ion channels and transient receptor
    potential channels. It includes information on nomenclature systems, and on inter
    and intra-species molecular structure variation. This collection references individual
    receptors or subunits.
  example: '101'
  homepage: http://www.guidetopharmacology.org/targets.jsp
  mappings:
    go: IUPHAR_RECEPTOR
    miriam: iuphar.receptor
    n2t: iuphar.receptor
    prefixcommons: IUPHAR.RECEPTOR
    wikidata: P5458
  name: Guide to Pharmacology Target ID
  pattern: ^\d+$
  preferred_prefix: iuphar.receptor
  synonyms:
  - IUPHAR_GPCR
  - IUPHARobj
  uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1
jax:
  description: Information about the C57BL/6J. Includes genetic background and disease
    data.
  example: '004435'
  homepage: https://www.jax.org/strain
  mappings:
    prefixcommons: JAX
  name: Jackson Laboratories Strain
  preferred_prefix: jax
  uri_format: https://www.jax.org/strain/$1
jaxmice:
  description: JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory.
  example: '005012'
  homepage: http://jaxmice.jax.org/
  mappings:
    miriam: jaxmice
    n2t: jaxmice
    prefixcommons: JAXMICE
  name: JAX Mice
  pattern: ^\d+$
  preferred_prefix: jaxmice
  uri_format: http://jaxmice.jax.org/strain/$1.html
jcggdb:
  description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase)
    is a database that aims to integrate all glycan-related data held in various repositories
    in Japan. This includes databases for large-quantity synthesis of glycogenes and
    glycans, analysis and detection of glycan structure and glycoprotein, glycan-related
    differentiation markers, glycan functions, glycan-related diseases and transgenic
    and knockout animals, etc.
  example: JCGG-STR008690
  homepage: http://jcggdb.jp/index_en.html
  mappings:
    miriam: jcggdb
    n2t: jcggdb
    prefixcommons: JCGGDB
  name: Japan Consortium for Glycobiology and Glycotechnology Database
  pattern: ^JCGG-STR\d{6}$
  preferred_prefix: jcggdb
  uri_format: http://jcggdb.jp/idb/jcggdb/$1
jcm:
  description: The Japan Collection of Microorganisms (JCM) collects, catalogues,
    and distributes cultured microbial strains, restricted to those classified in
    Risk Group 1 or 2.
  example: '17254'
  homepage: http://www.jcm.riken.go.jp/
  mappings:
    miriam: jcm
    n2t: jcm
    ncbi: JCM
    prefixcommons: JCM
  name: Japan Collection of Microorganisms
  pattern: ^\d+$
  preferred_prefix: jcm
  uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1
jcsd:
  description: The Japan Chemical Substance Dictionary is an organic compound dictionary
    database prepared by the Japan Science and Technology Agency (JST).
  example: J55.713G
  homepage: http://jglobal.jst.go.jp/en/
  mappings:
    miriam: jcsd
    n2t: jcsd
    prefixcommons: JCSD
  name: Japan Chemical Substance Dictionary
  pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$
  preferred_prefix: jcsd
  uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1
jstor:
  description: JSTOR (Journal Storage) is a digital library containing digital versions
    of historical academic journals, as well as books, pamphlets and current issues
    of journals. Some public domain content is free to access, while other articles
    require registration.
  example: '3075966'
  homepage: http://www.jstor.org/
  mappings:
    go: JSTOR
    miriam: jstor
    n2t: jstor
    prefixcommons: JSTOR
  name: Digital archive of scholarly articles
  pattern: ^\d+$
  preferred_prefix: jstor
  uri_format: http://www.jstor.org/stable/$1
jws:
  description: JWS Online is a repository of curated biochemical pathway models, and
    additionally provides the ability to run simulations of these models in a web
    browser.
  example: achcar11
  homepage: http://jjj.biochem.sun.ac.za/models/
  mappings:
    miriam: jws
    n2t: jws
    prefixcommons: JWS
  name: JWS Online
  pattern: ^\w+$
  preferred_prefix: jws
  providers:
  - code: CURATOR_REVIEW
    description: JWS Online Model Repository at Manchester
    homepage: http://jjj.mib.ac.uk/index.html
    name: JWS Online Model Repository at Manchester
    uri_format: http://jjj.mib.ac.uk/models/$1
  - code: CURATOR_REVIEW
    description: JWS Online Model Repository at Amsterdam
    homepage: http://jjj.bio.vu.nl/models/
    name: JWS Online Model Repository at Amsterdam
    uri_format: http://jjj.bio.vu.nl/models/$1/
  uri_format: https://jjj.bio.vu.nl/models/$1
kaggle:
  description: Kaggle is a platform for sharing data, performing reproducible analyses,
    interactive data analysis tutorials, and machine learning competitions.
  example: nasa/kepler-exoplanet-search-results
  homepage: https://kaggle.com
  mappings:
    miriam: kaggle
    n2t: kaggle
  name: Kaggle
  pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$
  preferred_prefix: kaggle
  uri_format: https://www.kaggle.com/$1
kegg:
  comment: KEGG prefix has been split into several others
  deprecated: true
  description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource
    for understanding high-level functions and utilities of the biological system,
    such as the cell, the organism and the ecosystem, from molecular-level information,
    especially large-scale molecular datasets generated by genome sequencing and other
    high-throughput experimental technologies.
  example: hsa00190
  homepage: http://www.kegg.jp/
  mappings:
    cheminf: 000409
    go: KEGG
    miriam: kegg
    n2t: kegg
    prefixcommons: KEGG
    uniprot: KEGG
  name: Kyoto Encyclopedia of Genes and Genomes
  pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$
  preferred_prefix: kegg
  synonyms:
  - KEGG
  uri_format: http://www.kegg.jp/entry/$1
kegg.compound:
  description: KEGG compound contains our knowledge on the universe of chemical substances
    that are relevant to life.
  example: C12345
  homepage: https://www.genome.jp/kegg/ligand.html
  mappings:
    miriam: kegg.compound
    n2t: kegg.compound
    prefixcommons: KEGG.COMPOUND
    wikidata: P665
  name: KEGG Compound
  part_of: kegg
  pattern: ^C\d+$
  preferred_prefix: kegg.compound
  synonyms:
  - KEGG COMPOUND
  - KEGG.COMPOUND
  uri_format: https://www.kegg.jp/entry/$1
kegg.disease:
  description: The KEGG DISEASE database is a collection of disease entries capturing
    knowledge on genetic and environmental perturbations. Each disease entry contains
    a list of known genetic factors (disease genes), environmental factors, diagnostic
    markers, and therapeutic drugs. Diseases are viewed as perturbed states of the
    molecular system, and drugs as perturbants to the molecular system.
  example: H00076
  homepage: http://www.genome.jp/kegg/disease/
  mappings:
    miriam: kegg.disease
    n2t: kegg.disease
    prefixcommons: KEGG.DISEASE
  name: KEGG Disease
  part_of: kegg
  pattern: ^H\d+$
  preferred_prefix: kegg.disease
  uri_format: http://www.kegg.jp/entry/$1
kegg.drug:
  description: KEGG DRUG contains chemical structures of drugs and additional information
    such as therapeutic categories and target molecules.
  example: D00123
  homepage: https://www.genome.jp/kegg/drug/
  mappings:
    miriam: kegg.drug
    n2t: kegg.drug
    prefixcommons: KEGG.DRUG
    wikidata: P665
  name: KEGG Drug
  part_of: kegg
  pattern: ^D\d+$
  preferred_prefix: kegg.drug
  synonyms:
  - KEGG DRUG
  - KEGG.DRUG
  uri_format: https://www.kegg.jp/entry/$1
kegg.environ:
  description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential
    oils, and other health-promoting substances, which are mostly natural products
    of plants. It will contain environmental substances and other health-damagine
    substances as well. Each KEGG ENVIRON entry is identified by the E number and
    is associated with the chemical component, efficacy information, and source species
    information whenever applicable.
  example: ev:E00032
  homepage: http://www.genome.jp/kegg/drug/environ.html
  mappings:
    miriam: kegg.environ
    n2t: kegg.environ
    prefixcommons: KEGG.ENVIRON
  name: KEGG Environ
  part_of: kegg
  pattern: ^(ev\:)?E\d+$
  preferred_prefix: kegg.environ
  uri_format: http://www.kegg.jp/entry/$1
kegg.enzyme:
  description: KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number
    system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME
    is based on the ExplorEnz database at Trinity College Dublin, and is maintained
    in the KEGG relational database with additional annotation of reaction hierarchy
    and sequence data links.
  homepage: http://www.genome.jp/dbget-bin/www_bfind?enzyme
  mappings:
    biolink: KEGG.ENZYME
    go: KEGG_ENZYME
  name: KEGG Enzyme
  part_of: kegg
  preferred_prefix: kegg.enzyme
  provides: eccode
  uri_format: http://www.genome.jp/dbget-bin/www_bget?ec:$1
kegg.genes:
  description: KEGG GENES is a collection of gene catalogs for all complete genomes
    and some partial genomes, generated from publicly available resources.
  example: bsu:BSU01340
  homepage: http://www.genome.jp/kegg/genes.html
  mappings:
    biolink: KEGG.GENE
    miriam: kegg.genes
    n2t: kegg.genes
    prefixcommons: KEGG.GENES
    wikidata: P665
  name: KEGG Genes
  part_of: kegg
  pattern: ^\w+:[\w\d\.-]*$
  preferred_prefix: kegg.genes
  uri_format: http://www.kegg.jp/entry/$1
kegg.genome:
  description: KEGG Genome is a collection of organisms whose genomes have been completely
    sequenced.
  example: T06648
  homepage: http://www.genome.jp/kegg/catalog/org_list.html
  mappings:
    miriam: kegg.genome
    n2t: kegg.genome
    prefixcommons: KEGG.GENOME
    wikidata: P665
  name: KEGG Genome
  part_of: kegg
  pattern: ^(T0\d+|\w{3,5})$
  preferred_prefix: kegg.genome
  synonyms:
  - kegg_genome
  - kegg_genomes
  uri_format: http://www.kegg.jp/entry/$1
kegg.glycan:
  description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of
    experimentally determined glycan structures. It contains all unique structures
    taken from CarbBank, structures entered from recent publications, and structures
    present in KEGG pathways.
  example: G00123
  homepage: https://www.genome.jp/kegg/glycan/
  mappings:
    miriam: kegg.glycan
    n2t: kegg.glycan
    prefixcommons: KEGG.GLYCAN
  name: KEGG Glycan
  part_of: kegg
  pattern: ^G\d+$
  preferred_prefix: kegg.glycan
  uri_format: https://www.kegg.jp/entry/$1
kegg.ligand:
  comment: This database has been discontinued by KEGG. It now lives inside the compound
    database
  deprecated: true
  homepage: http://www.genome.ad.jp/kegg/docs/upd_ligand.html
  mappings:
    go: KEGG_LIGAND
  name: KEGG LIGAND
  part_of: kegg
  preferred_prefix: kegg.ligand
  uri_format: http://www.genome.jp/dbget-bin/www_bget?cpd:$1
kegg.metagenome:
  description: The KEGG Metagenome Database collection information on environmental
    samples (ecosystems) of genome sequences for multiple species.
  example: T30002
  homepage: http://www.genome.jp/kegg/catalog/org_list3.html
  mappings:
    miriam: kegg.metagenome
    n2t: kegg.metagenome
    prefixcommons: KEGG.METAGENOME
  name: KEGG Metagenome
  part_of: kegg
  pattern: ^T3\d+$
  preferred_prefix: kegg.metagenome
  uri_format: http://www.kegg.jp/entry/$1
kegg.module:
  description: KEGG Modules are manually defined functional units used in the annotation
    and biological interpretation of sequenced genomes. Each module corresponds to
    a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway,
    structural, functional or signature modules.
  example: M00002
  homepage: http://www.kegg.jp/kegg/module.html
  mappings:
    miriam: kegg.module
    n2t: kegg.module
    prefixcommons: KEGG.MODULE
  name: KEGG Module
  part_of: kegg
  pattern: ^([a-z]{3,5}_)?M\d{5}$
  preferred_prefix: kegg.module
  uri_format: http://www.kegg.jp/entry/$1
kegg.orthology:
  description: KEGG Orthology (KO) consists of manually defined, generalised ortholog
    groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all
    organisms.
  example: K00001
  homepage: http://www.genome.jp/kegg/ko.html
  mappings:
    miriam: kegg.orthology
    n2t: kegg.orthology
    prefixcommons: KEGG.ORTHOLOGY
  name: KEGG Orthology
  part_of: kegg
  pattern: ^K\d+$
  preferred_prefix: kegg.orthology
  uri_format: http://www.kegg.jp/entry/$1
kegg.pathway:
  description: KEGG PATHWAY is a collection of manually drawn pathway maps representing
    our knowledge on the molecular interaction and reaction networks.
  example: rsk00410
  homepage: https://www.genome.jp/kegg/pathway.html
  mappings:
    biolink: KEGG.PATHWAY
    go: KEGG_PATHWAY
    miriam: kegg.pathway
    n2t: kegg.pathway
    prefixcommons: KEGG-path
    wikidata: P665
  name: KEGG Pathways Database
  part_of: kegg
  pattern: ^\w{2,4}\d{5}$
  preferred_prefix: kegg.pathway
  synonyms:
  - KEGG-path
  - KEGG_PATHWAY
  uri_format: https://www.kegg.jp/entry/$1
kegg.reaction:
  description: KEGG reaction contains our knowledge on the universe of reactions that
    are relevant to life.
  example: R00100
  homepage: https://www.genome.jp/kegg/reaction/
  mappings:
    go: KEGG_REACTION
    miriam: kegg.reaction
    n2t: kegg.reaction
    prefixcommons: KEGG.REACTION
    wikidata: P665
  name: KEGG ID
  part_of: kegg
  pattern: ^R\d+$
  preferred_prefix: kegg.reaction
  synonyms:
  - KEGG_REACTION
  uri_format: https://www.kegg.jp/entry/$1
knapsack:
  description: 'KNApSAcK provides information on metabolites and the

    taxonomic class with which they are associated.'
  example: C00000001
  homepage: http://www.knapsackfamily.com/KNApSAcK/
  mappings:
    miriam: knapsack
    n2t: knapsack
    prefixcommons: KNAPSACK
    wikidata: P2064
  name: KNApSAcK ID
  pattern: ^C\d{8}$
  preferred_prefix: knapsack
  uri_format: http://www.knapsackfamily.com/knapsack_core/information.php?word=$1
kupo:
  comment: Website is down, now it redirects to something else that is not related
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: 0001009
  homepage: http://www.kupkb.org/
  name: Kidney and Urinary Pathway Ontology
  preferred_prefix: kupo
  references:
  - https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7
labo:
  banana: LABO
  contact:
    email: paul.fabry@usherbrooke.ca
    github: null
    name: Paul Fabry
    orcid: null
  description: LABO is an ontology of informational entities formalizing clinical
    laboratory tests prescriptions and reporting documents.
  example: '0000124'
  homepage: https://github.com/OpenLHS/LABO
  license: CC BY 4.0
  mappings:
    bioportal: LABO
    obofoundry: LABO
    ols: labo
    ontobee: LABO
  name: clinical LABoratory Ontology
  preferred_prefix: LABO
  uri_format: http://purl.obolibrary.org/obo/LABO_$1
  version: '2021-06-08'
lbo:
  description: A vocabulary for cattle, chicken, horse, pig, and sheep breeds.
  example: 0000487
  homepage: http://bioportal.bioontology.org/ontologies/LBO
  mappings:
    bioportal: LBO
    ols: lbo
  name: Livestock Breed Ontology
  preferred_prefix: lbo
  version: '2019-03-26'
lei:
  description: Established by the Financial Stability Board in June 2014, the Global
    Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation
    and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen
    by the LEI Regulatory Oversight Committee, representing public authorities from
    around the globe that have come together to jointly drive forward transparency
    within the global financial markets. GLEIF is a supra-national not-for-profit
    organization headquartered in Basel, Switzerland.
  example: HWUPKR0MPOU8FGXBT394
  homepage: https://www.gleif.org/
  mappings:
    miriam: lei
    n2t: lei
  name: Global LEI Index
  pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$
  preferred_prefix: lei
  uri_format: https://www.gleif.org/lei/$1
lgai.cede:
  description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset
    with molecular instance level annotations (i.e. atom-bond level position annotations
    within an image) for molecular structure images. This dataset was designed to
    encourage research on detection-based pipelines for Optical Chemical Structure
    Recognition (OCSR).
  example: LGCEDe-S-000002244
  homepage: https://www.lgresearch.ai
  mappings:
    miriam: lgai.cede
  name: LG Chemical Entity Detection Dataset (LGCEDe)
  pattern: ^LGCEDe-S-\d{9}$
  preferred_prefix: lgai.cede
  uri_format: https://s3.us-east-2.amazonaws.com/lg.cede/$1
lgic:
  comment: Website is gone
  deprecated: true
  description: The Ligand-Gated Ion Channel database provides nucleic and proteic
    sequences of the subunits of ligand-gated ion channels. These transmembrane proteins
    can exist under different conformations, at least one of which forms a pore through
    the membrane connecting two neighbouring compartments. The database can be used
    to generate multiple sequence alignments from selected subunits, and gives the
    atomic coordinates of subunits, or portion of subunits, where available.
  example: 5HT3Arano
  homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
  mappings:
    miriam: lgic
    n2t: lgic
    prefixcommons: LGIC
  name: Ligand-Gated Ion Channel database
  pattern: ^\w+$
  preferred_prefix: lgic
  uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php
licebase:
  description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major
    pathogens of salmon,  significantly impacting upon the global salmon farming industry.
    Lice control is primarily accomplished through chemotherapeutants, though emerging
    resistance necessitates the development of new treatment methods (biological agents,
    prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing
    genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome
    browser, and access to related high-thoughput genomics data. LiceBase also mines
    and stores data from related genome sequencing and functional genomics projects.
  example: EMLSAT00000003403
  homepage: https://licebase.org
  mappings:
    miriam: licebase
    n2t: licebase
    prefixcommons: LICEBASE
  name: LiceBase
  pattern: ^[A-Za-z0-9\-\/]+$
  preferred_prefix: licebase
  uri_format: https://licebase.org/?q=$1
ligandbook:
  description: Ligandbook is a public repository for force field parameters with a
    special emphasis on small molecules and known ligands of proteins. It acts as
    a warehouse for parameter files that are supplied by the community.
  example: '785'
  homepage: https://ligandbook.org/
  mappings:
    miriam: ligandbook
    n2t: ligandbook
  name: LigandBook
  pattern: ^[0-9]+$
  preferred_prefix: ligandbook
  uri_format: https://ligandbook.org/package/$1
ligandbox:
  description: LigandBox is a database of 3D compound structures.  Compound information
    is collected from the catalogues of various commercial suppliers, with approved
    drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical
    compound in the database has several 3D conformers with hydrogen atoms and atomic
    charges, which are ready to be docked into receptors using docking programs. Various
    physical properties, such as aqueous solubility (LogS) and carcinogenicity have
    also been calculated to characterize the ADME-Tox properties of the compounds.
  example: D00001
  homepage: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en
  mappings:
    miriam: ligandbox
    n2t: ligandbox
    prefixcommons: LIGANDBOX
  name: LigandBox
  pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$
  preferred_prefix: ligandbox
  uri_format: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1
ligandexpo:
  description: Ligand Expo is a data resource for finding information about small
    molecules bound to proteins and nucleic acids.
  example: ABC
  homepage: http://ligand-depot.rutgers.edu/index.html
  mappings:
    miriam: ligandexpo
    n2t: ligandexpo
    prefixcommons: LIGANDEXPO
  name: Ligand Expo
  pattern: ^(\w){3}$
  preferred_prefix: ligandexpo
  providers:
  - code: CURATOR_REVIEW
    description: Ligand Expo at Rutgers
    homepage: http://ligand-expo.rcsb.org/
    name: Ligand Expo at Rutgers
    uri_format: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid
  uri_format: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid
lincs.cell:
  description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims
    to  create a network-based understanding of biology by cataloging changes in gene
    expression and other cellular processes that occur when cells are exposed to a
    variety of perturbing agents. The LINCS cell model system can have the following
    cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated
    cells, and embryonic stem cells. The metadata contains information provided by
    each LINCS Data and Signature Generation Center (DSGC) and the association with
    a tissue or organ from which the cells were derived, in many cases are also associated
    to a disease.'
  example: LCL-2085
  homepage: http://lincsportal.ccs.miami.edu/cells/
  mappings:
    miriam: lincs.cell
    n2t: lincs.cell
    prefixcommons: LINCS.CELL
  name: LINCS Cell
  pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$
  preferred_prefix: lincs.cell
  uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1
lincs.data:
  description: The Library of Network-Based Cellular Signatures (LINCS) Program aims
    to create a network-based understanding of biology by cataloguing changes in gene
    expression and other cellular processes that occur when cells are exposed to perturbing
    agents. The data is organized and available as datasets, each including experimental
    data, metadata and a description of the dataset and assay. The dataset group comprises
    datasets for the same experiment but with different data level results (data processed
    to a different level).
  example: LDS-1110
  homepage: http://lincsportal.ccs.miami.edu/datasets/
  mappings:
    miriam: lincs.data
    n2t: lincs.data
    prefixcommons: LINCS.DATA
  name: LINCS Data
  pattern: ^[EL]D[SG]-\d+$
  preferred_prefix: lincs.data
  providers:
  - code: omicsdi
    description: Lincs through OmicsDI
    homepage: https://www.omicsdi.org/
    name: Lincs through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/lincs/$1
  uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1
lincs.protein:
  description: The HMS LINCS Database currently contains information on experimental
    reagents (small molecule perturbagens, cells, and proteins). It aims to collect
    and disseminate information relating to the fundamental principles of cellular
    response in humans to perturbation. This collection references proteins.
  example: '200282'
  homepage: http://lincs.hms.harvard.edu/db/proteins/
  mappings:
    miriam: lincs.protein
    n2t: lincs.protein
    prefixcommons: LINCS.PROTEIN
  name: LINCS Protein
  pattern: ^\d+$
  preferred_prefix: lincs.protein
  uri_format: https://lincs.hms.harvard.edu/db/proteins/$1
lincs.smallmolecule:
  description: The Library of Network-Based Cellular Signatures (LINCS) Program aims
    to create a network-based understanding of biology by cataloging changes in gene
    expression and other cellular processes that occur when cells are exposed to a
    variety of perturbing agents. The LINCS small molecule collection is used as perturbagens
    in LINCS experiments. The small molecule metadata includes substance-specific
    batch information provided by each LINCS Data and Signature Generation Center
    (DSGC).
  example: LSM-6306
  homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/
  mappings:
    miriam: lincs.smallmolecule
    n2t: lincs.smallmolecule
    prefixcommons: LINCS.SMALLMOLECULE
  name: LINCS Small Molecule
  pattern: ^LSM-\d+$
  preferred_prefix: lincs.smallmolecule
  synonyms:
  - lincs
  uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1
linguist:
  description: Registry of programming languages for the Linguist program for detecting
    and highlighting programming languages.
  example: Python
  homepage: https://github.com/
  mappings:
    miriam: linguist
  name: Linguist
  pattern: ^[a-zA-Z0-9 +#'*]+$
  preferred_prefix: linguist
  uri_format: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1
lipidbank:
  description: LipidBank is an open, publicly free database of natural lipids including
    fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
  example: BBA0001
  homepage: http://lipidbank.jp/index.html
  mappings:
    miriam: lipidbank
    n2t: lipidbank
    prefixcommons: LIPIDBANK
  name: LipidBank
  pattern: ^\w+\d+$
  preferred_prefix: lipidbank
  uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1
lipidmaps:
  description: The LIPID MAPS Lipid Classification System is comprised of eight lipid
    categories, each with its own subclassification hierarchy. All lipids in the LIPID
    MAPS Structure Database (LMSD) have been classified using this system and have
    been assigned LIPID MAPS ID's which reflects their position in the classification
    hierarchy.
  example: LMPR0102010012
  homepage: http://www.lipidmaps.org
  mappings:
    cheminf: '000564'
    miriam: lipidmaps
    n2t: lipidmaps
    prefixcommons: LIPIDMAPS
    scholia: lipidmaps
    wikidata: P2063
  name: LIPID MAPS
  pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$
  preferred_prefix: lipidmaps
  providers:
  - code: 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/
    name: Scholia
    uri_format: https://scholia.toolforge.org/lipidmaps/$1
  synonyms:
  - LIPID MAPS
  - LIPID_MAPS_class
  - LIPID_MAPS_instance
  uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1
lipro:
  banana: LIPRO
  contact:
    email: bakerc@unb.ca
    github: null
    name: Christipher Baker
    orcid: null
  deprecated: true
  description: An ontology representation of the LIPIDMAPS nomenclature classification.
  mappings:
    bioportal: LIPRO
    obofoundry: LIPRO
    prefixcommons: LIPRO
  name: Lipid Ontology
  preferred_prefix: LIPRO
  uri_format: http://purl.obolibrary.org/obo/LIPRO_$1
lncipedia:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A comprehensive compendium of human long non-coding RNAs
  example: SNHG3
  homepage: https://lncipedia.org
  name: LNCipedia
  preferred_prefix: lncipedia
loggerhead:
  banana: LOGGERHEAD
  contact:
    email: peteremidford@yahoo.com
    github: null
    name: Peter Midford
    orcid: null
  deprecated: true
  homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html
  mappings:
    obofoundry: LOGGERHEAD
    prefixcommons: LOGGERHEAD
  name: Loggerhead nesting
  preferred_prefix: LOGGERHEAD
  uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1
loinc:
  description: The international standard for identifying health measurements, observations,
    and documents.
  example: LL379-9
  homepage: https://loinc.org/
  mappings:
    biolink: LOINC
    bioportal: LOINC
  name: Logical Observation Identifiers Names and Codes
  preferred_prefix: loinc
  uri_format: https://loinc.org/$1
lotus:
  comment: IDs are actually leading to the structural part of LOTUS only, which might
    change in the future. Will adapt the regexp in case.
  contact:
    email: adriano.rutz@ik.me
    github: adafede
    name: Adriano Rutz
    orcid: 0000-0003-0443-9902
  contributor:
    email: null
    github: null
    name: Adriano Rutz
    orcid: 0000-0003-0443-9902
  description: "LOTUS, actually, represents the most exhaustive resource of documented\
    \ structure-organism pairs. Within the frame of current computational approaches\
    \ in Natural Produts\u2019s research and related fields, these documented structure-organism\
    \ pairs should allow a more complete understanding of organisms and their chemistry."
  example: LTS0004651
  homepage: https://lotus.naturalproducts.net
  name: LOTUS Initiative for Open Natural Products Research
  pattern: ^LTS\d{7}$
  preferred_prefix: lotus
  reviewer:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://lotus.naturalproducts.net/compound/lotus_id/$1
lrg:
  description: A Locus Reference Genomic (LRG) is a manually curated record that contains
    stable genomic, transcript and protein reference sequences for reporting clinically
    relevant sequence variants. All LRGs are generated and maintained by the NCBI
    and EMBL-EBI.
  example: LRG_1
  homepage: http://www.lrg-sequence.org/
  mappings:
    miriam: lrg
    n2t: lrg
    prefixcommons: LRG
  name: Locus Reference Genomic
  pattern: ^LRG_\d+$
  preferred_prefix: lrg
  providers:
  - code: CURATOR_REVIEW
    description: Locus Reference Genomic through Ensembl
    homepage: http://www.ensembl.org/
    name: Locus Reference Genomic through Ensembl
    uri_format: http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1
  - code: CURATOR_REVIEW
    description: Locus Reference Genomic through Ensembl mirror (asia)
    homepage: http://asia.ensembl.org/
    name: Locus Reference Genomic through Ensembl mirror (asia)
    uri_format: http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1
  - code: CURATOR_REVIEW
    description: Locus Reference Genomic through Ensembl mirror (US west)
    homepage: http://uswest.ensembl.org/
    name: Locus Reference Genomic through Ensembl mirror (US west)
    uri_format: http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1
  - code: CURATOR_REVIEW
    description: Locus Reference Genomic through Ensembl mirror (US east)
    homepage: http://useast.ensembl.org/
    name: Locus Reference Genomic through Ensembl mirror (US east)
    uri_format: http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1
  uri_format: ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml
lspci:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Internal identifiers form the LSP for ChEBML compound classes (e.g.,
    combining various salts and ions)
  example: '1'
  homepage: https://labsyspharm.github.io/lspci/
  name: Laboratory of Systems Pharmacology Compound ID
  pattern: ^\d+$
  preferred_prefix: lspci
  uri_format: https://labsyspharm.github.io/lspci/$1
ma:
  banana: MA
  contact:
    email: Terry.Hayamizu@jax.org
    github: tfhayamizu
    name: Terry Hayamizu
    orcid: null
  description: A structured controlled vocabulary of the adult anatomy of the mouse
    (Mus)
  example: '0002502'
  homepage: https://github.com/obophenotype/mouse-anatomy-ontology
  license: CC BY 4.0
  mappings:
    bioportal: MA
    go: MA
    miriam: ma
    n2t: ma
    obofoundry: MA
    ols: ma
    ontobee: MA
    prefixcommons: MA
  name: Mouse adult gross anatomy
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: MA
  uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1
  version: '2017-02-07'
macie:
  description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database
    of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction
    describing the chemical compounds involved, as well as the species name in which
    the reaction occurs. The individual reaction stages for each overall reaction
    are listed with mechanisms, alternative mechanisms, and amino acids involved.
  example: M0001
  homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html
  mappings:
    miriam: macie
    n2t: macie
    prefixcommons: MACIE
  name: Mechanism, Annotation and Classification in Enzymes
  pattern: ^M\d{4}$
  preferred_prefix: macie
  uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1
maizegdb.locus:
  description: MaizeGDB is the maize research community's central repository for genetics
    and genomics information.
  example: '25011'
  homepage: http://www.maizegdb.org/
  mappings:
    go: MaizeGDB_Locus
    miriam: maizegdb.locus
    n2t: maizegdb.locus
    prefixcommons: MAIZEGDB.LOCUS
  name: MaizeGDB Locus
  pattern: ^\d+$
  preferred_prefix: maizegdb.locus
  uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1
mamo:
  banana: MAMO
  contact:
    email: n.lenovere@gmail.com
    github: null
    name: Nicolas Le Novere
    orcid: null
  description: The Mathematical Modelling Ontology (MAMO) is a classification of the
    types of mathematical models used mostly in the life sciences, their variables,
    relationships and other relevant features.
  example: '0000026'
  homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/
  license: Artistic License 2.0
  mappings:
    bioportal: MAMO
    miriam: mamo
    n2t: mamo
    obofoundry: MAMO
    ols: mamo
    ontobee: MAMO
    prefixcommons: MAMO
  name: Mathematical modeling ontology
  pattern: ^\d{7}$
  preferred_prefix: MAMO
  uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1
  version: '2020-08-24'
mao:
  banana: MAO
  contact:
    email: julie@igbmc.u-strasbg.fr
    github: null
    name: Julie Thompson
    orcid: null
  deprecated: true
  homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html
  mappings:
    obofoundry: MAO
    prefixcommons: MAO
  name: Multiple alignment
  preferred_prefix: MAO
  uri_format: http://purl.obolibrary.org/obo/MAO_$1
massbank:
  description: MassBank is a federated database of reference spectra from different
    instruments, including high-resolution mass spectra of small metabolites (<3000
    Da).
  example: PB000166
  homepage: http://www.massbank.jp
  mappings:
    miriam: massbank
    n2t: massbank
    prefixcommons: MASSBANK
    wikidata: P6689
  name: MassBank
  pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$
  preferred_prefix: massbank
  providers:
  - code: CURATOR_REVIEW
    description: MassBank in Europe
    homepage: https://massbank.eu/
    name: MassBank in Europe
    uri_format: https://massbank.eu/MassBank/RecordDisplay?id=$1
  uri_format: http://www.massbank.jp/RecordDisplay?id=$1
massive:
  description: MassIVE is a community resource developed by the NIH-funded Center
    for Computational Mass Spectrometry to promote the global, free exchange of mass
    spectrometry data.
  example: MSV000082131
  homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
  mappings:
    fairsharing: FAIRsharing.LYsiMd
    miriam: massive
    n2t: massive
    prefixcommons: MASSIVE
    uniprot: MassIVE
  name: MassIVE
  pattern: ^MSV\d+$
  preferred_prefix: massive
  providers:
  - code: omicsdi
    description: MassIVE through OmicsDI
    homepage: https://www.omicsdi.org/
    name: MassIVE through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/massive/$1
  uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1
mat:
  banana: MAT
  contact:
    email: j.bard@ed.ac.uk
    github: null
    name: Jonathan Bard
    orcid: null
  deprecated: true
  mappings:
    bioportal: MAT
    obofoundry: MAT
    prefixcommons: MAT
  name: Minimal Anatomical Terminology
  preferred_prefix: MAT
  uri_format: http://purl.obolibrary.org/obo/MAT_$1
matrixdb:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: MatrixDB is a freely available database focused on interactions established
    by extracellular matrix proteins, proteoglycans and polysaccharides
  example: MULT_4_VAR1_bovine
  homepage: http://matrixdb.univ-lyon1.fr/
  name: MatrixDB
  preferred_prefix: matrixdb
  uri_format: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1
matrixdb.association:
  description: MatrixDB stores experimentally determined interactions involving at
    least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan
    interactions, as well as interactions with lipids and cations.
  example: P00747__P07355
  homepage: http://matrixdb.univ-lyon1.fr/
  mappings:
    miriam: matrixdb.association
    n2t: matrixdb.association
    prefixcommons: MATRIXDB.ASSOCIATION
  name: MatrixDB Association
  pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z,
    0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$
  preferred_prefix: matrixdb.association
  uri_format: http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association
maxo:
  banana: MAXO
  contact:
    email: Leigh.Carmody@jax.org
    github: LCCarmody
    name: Leigh Carmody
    orcid: null
  description: An ontology to represent medically relevant actions, procedures, therapies,
    interventions, and recommendations.
  example: 0000008
  homepage: https://github.com/monarch-initiative/MAxO
  license: CC BY 3.0
  mappings:
    biolink: MAXO
    bioportal: MAXO
    obofoundry: MAXO
    ols: maxo
    ontobee: MAXO
  name: Medical Action Ontology
  preferred_prefix: MAXO
  uri_format: http://purl.obolibrary.org/obo/MAXO_$1
  version: '2021-08-19'
mcc:
  deprecated: true
  mappings:
    bioportal: MCCL
  name: Cell Line Ontology [derivative]
  preferred_prefix: mcc
mco:
  banana: MCO
  contact:
    email: citlalli.mejiaalmonte@gmail.com
    github: null
    name: "Citlalli Mej\xEDa-Almonte"
    orcid: null
  description: Microbial Conditions Ontology is an ontology...
  example: 0000858
  homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
  license: CC BY 3.0
  mappings:
    bioportal: MCO
    obofoundry: MCO
    ols: mco
    ontobee: MCO
  name: Microbial Conditions Ontology
  pattern: ^\d+$
  preferred_prefix: MCO
  uri_format: http://purl.obolibrary.org/obo/MCO_$1
  version: '2019-05-15'
mdm:
  description: The MDM (Medical Data Models) Portal is a meta-data registry for creating,
    analysing, sharing and reusing medical forms. Electronic forms are central in
    numerous processes involving data, including the collection of data through electronic
    health records (EHRs), Electronic Data Capture (EDC), and as case report forms
    (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous
    export formats, facilitating the sharing and reuse of medical data models and
    exchange between information systems.
  example: '4776'
  homepage: https://medical-data-models.org/
  mappings:
    bioportal: MDM
    miriam: mdm
    n2t: mdm
    prefixcommons: MDM
  name: Medical Data Models
  pattern: ^\d+$
  preferred_prefix: mdm
  uri_format: https://medical-data-models.org/forms/$1
meddra:
  description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed
    by the International Council for Harmonisation of Technical Requirements for Registration
    of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology
    to facilitate sharing of regulatory information internationally for medical products
    used by humans. It is used within regulatory processes, safety monitoring, as
    well as for marketing activities. Products covered by the scope of MedDRA include
    pharmaceuticals, biologics, vaccines and drug-device combination products. The
    MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level
    Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into
    Lowest Level Terms (LLT).
  example: '10015919'
  homepage: http://bioportal.bioontology.org/ontologies/MEDDRA
  mappings:
    bioportal: MEDDRA
    miriam: meddra
    n2t: meddra
    prefixcommons: MEDDRA
    wikidata: P3201
  name: Medical Dictionary for Regulatory Activities Terminology
  pattern: ^\d+$
  preferred_prefix: meddra
  synonyms:
  - MEDRA
  - MeDRA
  - MedDRA
  - Medical Dictionary for Regulatory Activities
  uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1
medgen:
  description: MedGen is a portal for information about conditions and phenotypes
    related to Medical Genetics. Terms from multiple sources are aggregated into concepts,
    each of which is assigned a unique identifier and a preferred name and symbol.
    The core content of the record may include names, identifiers used by other databases,
    mode of inheritance, clinical features, and map location of the loci affecting
    the disorder.
  example: '760050'
  homepage: https://www.ncbi.nlm.nih.gov/medgen/
  mappings:
    biolink: medgen
    miriam: medgen
    n2t: medgen
    ncbi: MedGen
    prefixcommons: MedGen
  name: Human Medical Genetics
  pattern: ^[CN]*\d{4,7}$
  preferred_prefix: medgen
  uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1
medlineplus:
  description: MedlinePlus is the National Institutes of Health's Web site for patients
    and their families and friends. Produced by the National Library of Medicine,
    it provides information about diseases, conditions, and wellness issues using
    non-technical terms and language.
  example: 002804
  homepage: http://www.nlm.nih.gov/medlineplus/
  mappings:
    bioportal: MEDLINEPLUS
    miriam: medlineplus
    n2t: medlineplus
    prefixcommons: MEDLINEPLUS
  name: MedlinePlus Health Topics
  pattern: ^\d+$
  preferred_prefix: medlineplus
  uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm
merops:
  description: The MEROPS database is an information resource for peptidases (also
    termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
    them.
  example: S01.001
  homepage: http://merops.sanger.ac.uk/index.htm
  mappings:
    go: MEROPS
    miriam: merops
    n2t: merops
    prefixcommons: MEROPS
    uniprot: MEROPS
  name: MEROPS peptidase database
  pattern: ^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$
  preferred_prefix: merops
  uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$1
merops.family:
  description: The MEROPS database is an information resource for peptidases (also
    termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
    them. These are hierarchically classified and assigned to a Family on the basis
    of statistically significant similarities in amino acid sequence. Families thought
    to be homologous are grouped together in a Clan. This collection references peptidase
    families.
  example: S1
  homepage: http://merops.sanger.ac.uk/index.htm
  mappings:
    miriam: merops.family
    n2t: merops.family
    prefixcommons: MEROPS.FAMILY
  name: MEROPS Family
  pattern: ^[SCTAGMNU]\d+$
  preferred_prefix: merops.family
  uri_format: http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1
merops.inhibitor:
  description: The MEROPS database is an information resource for peptidases (also
    termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
    them. This collections references inhibitors.
  example: I31.952
  homepage: http://merops.sanger.ac.uk/index.htm
  mappings:
    miriam: merops.inhibitor
    n2t: merops.inhibitor
    prefixcommons: MEROPS.INHIBITOR
  name: MEROPS Inhibitor
  pattern: ^I\d{2}\.\d{3}$
  preferred_prefix: merops.inhibitor
  uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1
mesh:
  description: MeSH (Medical Subject Headings) is the National Library of Medicine's
    controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
    in a hierarchical structure that permits searching at various levels of specificity.
    This thesaurus is used by NLM for indexing articles from biomedical journals,
    cataloguing of books, documents, etc.
  example: C063233
  homepage: http://id.nlm.nih.gov/mesh/
  mappings:
    biolink: MESH
    bioportal: MESH
    cellosaurus: MeSH
    go: MeSH
    miriam: mesh
    n2t: mesh
    prefixcommons: MESH
    scholia: mesh
    wikidata: P486
  name: Medical Subject Headings
  pattern: ^(C|D)\d{6,9}$
  preferred_prefix: mesh
  synonyms:
  - MESH
  - MESHA
  - MESHC
  - MESHCS
  - MESHD
  - MESHPP
  - MESH_DESCRIPTOR_UI
  - MESH_SUPPLEMENTAL_RECORD_UI
  - MSH
  uri_format: https://meshb.nlm.nih.gov/record/ui?ui=$1
mesh.2012:
  description: MeSH (Medical Subject Headings) is the National Library of Medicine's
    controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
    in a hierarchical structure that permits searching at various levels of specificity.
    This thesaurus is used by NLM for indexing articles from biomedical journals,
    cataloging of books, documents, etc. This collection references MeSH terms published
    in 2012.
  example: '17186'
  homepage: http://www.nlm.nih.gov/mesh/
  mappings:
    miriam: mesh.2012
    n2t: mesh.2012
    prefixcommons: MESH.2012
  name: MeSH 2012
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: mesh.2012
  uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded
mesh.2013:
  description: MeSH (Medical Subject Headings) is the National Library of Medicine's
    controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
    in a hierarchical structure that permits searching at various levels of specificity.
    This thesaurus is used by NLM for indexing articles from biomedical journals,
    cataloging of books, documents, etc. This collection references MeSH terms published
    in 2013.
  example: '17165'
  homepage: http://www.nlm.nih.gov/mesh/
  mappings:
    miriam: mesh.2013
    n2t: mesh.2013
    prefixcommons: MESH.2013
  name: MeSH 2013
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: mesh.2013
  uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded
metabolights:
  description: MetaboLights is a database for Metabolomics experiments and derived
    information. The database is cross-species, cross-technique and covers metabolite
    structures and their reference spectra as well as their biological roles, locations
    and concentrations, and experimental data from metabolic experiments. This collection
    references individual metabolomics studies.
  example: MTBLS1
  homepage: https://www.ebi.ac.uk/metabolights/
  mappings:
    cellosaurus: MetaboLights
    miriam: metabolights
    n2t: metabolights
    prefixcommons: METABOLIGHTS
    wikidata: P3890
  name: MetaboLights Compound ID
  pattern: ^MTBLS\d+$
  preferred_prefix: metabolights
  providers:
  - code: omicsdi
    description: MataboLights through OmicsDI
    homepage: https://www.omicsdi.org/
    name: MataboLights through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/metabolights_dataset/$1
  uri_format: https://www.ebi.ac.uk/metabolights/$1
metacyc.compound:
  description: MetaCyc is a curated database of experimentally elucidated metabolic
    pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different
    organisms. MetaCyc contains pathways involved in both primary and secondary metabolism,
    as well as associated metabolites, reactions, enzymes, and genes. The goal of
    MetaCyc is to catalog the universe of metabolism by storing a representative sample
    of each experimentally elucidated pathway.
  example: CPD-10330
  homepage: https://metacyc.org
  mappings:
    biolink: MetaCyc
    go: MetaCyc
    miriam: metacyc.compound
    n2t: metacyc.compound
    prefixcommons: METACYC.COMPOUND
  name: Metabolic Encyclopedia of metabolic and other pathways
  pattern: ^[A-Za-z0-9+_.%-:]+$
  preferred_prefix: metacyc.compound
  synonyms:
  - MetaCyc
  uri_format: https://metacyc.org/compound?orgid=META&id=$1
metacyc.reaction:
  description: MetaCyc is a curated database of experimentally elucidated metabolic
    pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different
    organisms. MetaCyc contains pathways involved in both primary and secondary metabolism,
    as well as associated metabolites, reactions, enzymes, and genes. The goal of
    MetaCyc is to catalog the universe of metabolism by storing a representative sample
    of each experimentally elucidated pathway.
  example: RXN-14904
  homepage: https://metacyc.org
  mappings:
    biolink: metacyc.reaction
    miriam: metacyc.reaction
    n2t: metacyc.reaction
    prefixcommons: METACYC.REACTION
  name: MetaCyc Reaction
  pattern: ^[A-Za-z0-9+_.%-:]+$
  preferred_prefix: metacyc.reaction
  uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1
metanetx.chemical:
  description: MetaNetX/MNXref integrates various information from genome-scale metabolic
    network reconstructions such as information on reactions, metabolites and compartments.
    This information undergoes a reconciliation process to minimise for discrepancies
    between different data sources, and makes the data accessible under a common namespace.
    This collection references chemical or metabolic components.
  example: MNXM1723
  homepage: https://www.metanetx.org/
  mappings:
    miriam: metanetx.chemical
    n2t: metanetx.chemical
    prefixcommons: METANETX.CHEMICAL
  name: MetaNetX chemical
  pattern: ^(MNXM\d+|BIOMASS|WATER)$
  preferred_prefix: metanetx.chemical
  uri_format: https://www.metanetx.org/chem_info/$1
metanetx.compartment:
  description: MetaNetX/MNXref integrates various information from genome-scale metabolic
    network reconstructions such as information on reactions, metabolites and compartments.
    This information undergoes a reconciliation process to minimise for discrepancies
    between different data sources, and makes the data accessible under a common namespace.
    This collection references cellular compartments.
  example: MNXC15
  homepage: https://www.metanetx.org/
  mappings:
    miriam: metanetx.compartment
    n2t: metanetx.compartment
    prefixcommons: METANETX.COMPARTMENT
  name: MetaNetX compartment
  pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$
  preferred_prefix: metanetx.compartment
  uri_format: https://www.metanetx.org/comp_info/$1
metanetx.reaction:
  description: MetaNetX/MNXref integrates various information from genome-scale metabolic
    network reconstructions such as information on reactions, metabolites and compartments.
    This information undergoes a reconciliation process to minimise for discrepancies
    between different data sources, and makes the data accessible under a common namespace.
    This collection references reactions.
  example: MNXR101574
  homepage: https://www.metanetx.org/
  mappings:
    biolink: METANETX.REACTION
    miriam: metanetx.reaction
    n2t: metanetx.reaction
    prefixcommons: METANETX.REACTION
  name: MetaNetX reaction
  pattern: ^(MNXR\d+|EMPTY)$
  preferred_prefix: metanetx.reaction
  uri_format: https://www.metanetx.org/equa_info/$1
metlin:
  description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a
    repository of metabolite information as well as tandem mass spectrometry data,
    providing public access to its comprehensive MS and MS/MS metabolite data. An
    annotated list of known metabolites and their mass, chemical formula, and structure
    are available, with each metabolite linked to external resources for further reference
    and inquiry.
  example: '1455'
  homepage: http://masspec.scripps.edu/
  mappings:
    miriam: metlin
    n2t: metlin
    prefixcommons: METLIN
  name: Metabolite and Tandem Mass Spectrometry Database
  pattern: ^\d{4}$
  preferred_prefix: metlin
  uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1
mex:
  description: A public place to process, interpret and share GC/MS metabolomics datasets.
  example: '36'
  homepage: https://www.metabolome-express.org/
  mappings:
    miriam: mex
    n2t: mex
    prefixcommons: MEX
  name: Metabolome Express
  pattern: ^\d+$
  preferred_prefix: mex
  providers:
  - code: omicsdi
    description: Metabolome Express through OmicsDI
    homepage: https://www.omicsdi.org/
    name: Metabolome Express through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/metabolome_express/MEX$1
  uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1
mf:
  banana: MF
  contact:
    email: janna.hastings@gmail.com
    github: jannahastings
    name: Janna Hastings
    orcid: null
  description: The Mental Functioning Ontology is an overarching ontology for all
    aspects of mental functioning.
  example: 0000091
  homepage: https://github.com/jannahastings/mental-functioning-ontology
  license: CC BY 3.0
  mappings:
    bioportal: MF
    obofoundry: MF
    ols: mf
    ontobee: MF
    prefixcommons: MF
  name: Mental Functioning Ontology
  preferred_prefix: MF
  uri_format: http://purl.obolibrary.org/obo/MF_$1
  version: '2021-11-17'
mfmo:
  banana: MFMO
  contact:
    email: druzinsk@uic.edu
    github: RDruzinsky
    name: Robert Druzinsky
    orcid: null
  description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the
    muscles of the head and neck that participate in feeding, swallowing, and other
    oral-pharyngeal behaviors.
  example: 0000208
  homepage: https://github.com/rdruzinsky/feedontology
  license: CC BY 3.0
  mappings:
    bioportal: MFMO
    obofoundry: MFMO
    ols: mfmo
    ontobee: MFMO
    prefixcommons: MFMO
  name: Mammalian Feeding Muscle Ontology
  preferred_prefix: MFMO
  uri_format: http://purl.obolibrary.org/obo/MFMO_$1
  version: '2013-11-16'
mfo:
  banana: MFO
  contact:
    email: Thorsten.Henrich@embl-heidelberg.de
    github: null
    name: Thorsten Henrich
    orcid: null
  deprecated: true
  description: A structured controlled vocabulary of the anatomy and development of
    the Japanese medaka fish, <i>Oryzias latipes</i>.
  mappings:
    bioportal: MFO
    obofoundry: MFO
    prefixcommons: MFO
  name: Medaka fish anatomy and development
  preferred_prefix: MFO
  uri_format: http://purl.obolibrary.org/obo/MFO_$1
mfoem:
  banana: MFOEM
  contact:
    email: janna.hastings@gmail.com
    github: jannahastings
    name: Janna Hastings
    orcid: null
  description: An ontology of affective phenomena such as emotions, moods, appraisals
    and subjective feelings.
  example: '000204'
  homepage: https://github.com/jannahastings/emotion-ontology
  license: CC BY 3.0
  mappings:
    bioportal: MFOEM
    obofoundry: MFOEM
    ols: mfoem
    ontobee: MFOEM
    prefixcommons: MFOEM
  name: Emotion Ontology
  preferred_prefix: MFOEM
  uri_format: http://purl.obolibrary.org/obo/MFOEM_$1
  version: '2021-11-17'
mfomd:
  banana: MFOMD
  contact:
    email: janna.hastings@gmail.com
    github: null
    name: Janna Hastings
    orcid: null
  description: The Mental Disease Ontology is developed to facilitate representation
    for all aspects of mental disease. It is an extension of the Ontology for General
    Medical Science (OGMS) and Mental Functioning Ontology (MF).
  example: '0000046'
  homepage: https://github.com/jannahastings/mental-functioning-ontology
  license: CC BY 3.0
  mappings:
    bioportal: MFOMD
    obofoundry: MFOMD
    ols: mfomd
    ontobee: MFOMD
    prefixcommons: MFOMD
  name: Mental Disease Ontology
  preferred_prefix: MFOMD
  uri_format: http://purl.obolibrary.org/obo/MFOMD_$1
  version: '2020-04-26'
mge:
  banana: mge
  description: ACLAME is a database dedicated to the collection and classification
    of mobile genetic elements (MGEs) from various sources, comprising all known phage
    genomes, plasmids and transposons.
  example: '2'
  homepage: http://aclame.ulb.ac.be/
  mappings:
    miriam: mge
    n2t: mge
  name: Aclame
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: mge
  uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1
mgi:
  banana: MGI
  description: The Mouse Genome Database (MGD) project includes data on gene characterization,
    nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes,
    allelic variants and mutants, and strain data.
  example: '6017782'
  homepage: http://www.informatics.jax.org/
  mappings:
    cellosaurus: MGI
    go: MGI
    miriam: mgi
    n2t: mgi
    ncbi: MGI
    prefixcommons: MGI
    uniprot: MGI
    wikidata: P671
  name: Mouse Genome Informatics
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: MGI
  providers:
  - code: bioentitylink
    description: MGD through BioEntity Link
    homepage: https://bioentity.link/
    name: MGD through BioEntity Link
    uri_format: https://bioentity.link/#/lexicon/public/MGI:$1
  - code: agr
    description: MGI through the Alliance of Genome Resources
    homepage: https://www.alliancegenome.org
    name: MGI through the Alliance of Genome Resources
    uri_format: https://www.alliancegenome.org/gene/MGI:$1
  synonyms:
  - MGD
  - MGI
  uri_format: http://www.informatics.jax.org/accession/MGI:$1
mgnify.analysis:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Analyses of microbiome data within MGnify
  example: MGYA00002270
  homepage: https://www.ebi.ac.uk/metagenomics/
  name: MGnify Analysis
  pattern: ^MGYA\d+$
  preferred_prefix: mgnify.analysis
  uri_format: https://www.ebi.ac.uk/metagenomics/analyses/$1
mgnify.proj:
  description: MGnify is a resource for the analysis and archiving of microbiome data
    to help determine the taxonomic diversity and functional & metabolic potential
    of environmental samples. Users can submit their own data for analysis or freely
    browse all of the analysed public datasets held within the repository. In addition,
    users can request analysis of any appropriate dataset within the European Nucleotide
    Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on
    request, prior to analysis.
  example: ERP004492
  homepage: https://www.ebi.ac.uk/metagenomics
  mappings:
    miriam: mgnify.proj
    n2t: mgnify.proj
  name: MGnify Project
  pattern: ^[A-Z]+[0-9]+$
  preferred_prefix: mgnify.proj
  uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1
mgnify.samp:
  description: The EBI Metagenomics service is an automated pipeline for the analysis
    and archiving of metagenomic data that aims to provide insights into the phylogenetic
    diversity as well as the functional and metabolic potential of a sample. Metagenomics
    is the study of all genomes present in any given environment without the need
    for prior individual identification or amplification. This collection references
    samples.
  example: SRS086444
  homepage: https://www.ebi.ac.uk/metagenomics
  mappings:
    miriam: mgnify.samp
    n2t: mgnify.samp
  name: MGnify Sample
  pattern: ^[A-Z]+[0-9]+$
  preferred_prefix: mgnify.samp
  uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1
mi:
  banana: MI
  contact:
    email: pporras@ebi.ac.uk
    github: null
    name: "Pablo Porras Mill\xE1n"
    orcid: null
  description: The Molecular Interactions (MI) ontology forms a structured controlled
    vocabulary for the annotation of experiments concerned with protein-protein interactions.
    MI is developed by the HUPO Proteomics Standards Initiative.
  example: 0058
  homepage: https://github.com/HUPO-PSI/psi-mi-CV
  license: CC BY 4.0
  mappings:
    biolink: MI
    bioportal: MI
    go: PSI-MI
    miriam: mi
    n2t: psimi
    obofoundry: MI
    ols: mi
    ontobee: MI
    prefixcommons: MI
  name: Molecular Interactions Controlled Vocabulary
  namespace_in_lui: true
  pattern: ^\d{4}$
  preferred_prefix: MI
  synonyms:
  - PSI-MI
  uri_format: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1
  version: '2020-04-13'
miaa:
  comment: same as MAT
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Minimal Information About Anatomy ontology
  preferred_prefix: miaa
  references:
  - https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf
miapa:
  banana: MIAPA
  contact:
    email: hilmar.lapp@duke.edu
    github: hlapp
    name: Hilmar Lapp
    orcid: null
  description: 'The MIAPA ontology is intended to be an application ontology for the
    purpose of semantic annotation of phylogenetic data according to the requirements
    and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA)
    metadata reporting standard. The ontology leverages (imports) primarily from the
    CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and
    SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds
    some assertions of its own, as well as some classes and individuals that may eventually
    get pushed down into one of the respective source ontologies.


    This ontology is maintained at http://github.com/miapa/miapa, and requests for
    changes or additions should be filed at the issue tracker there. The discussion
    list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be
    found at the project''s main page at http://evoio.org/wiki/MIAPA.'
  example: '0000010'
  homepage: http://www.evoio.org/wiki/MIAPA
  license: CC0 1.0
  mappings:
    bioportal: MIAPA
    obofoundry: MIAPA
    ols: miapa
    ontobee: MIAPA
    prefixcommons: MIAPA
  name: MIAPA Ontology
  preferred_prefix: MIAPA
  uri_format: http://purl.obolibrary.org/obo/MIAPA_$1
  version: '2017-05-09'
micro:
  banana: MICRO
  contact:
    email: carrine.blank@umontana.edu
    github: carrineblank
    name: Carrine Blank
    orcid: null
  description: An ontology of prokaryotic phenotypic and metabolic characters
  example: 0002999
  homepage: https://github.com/carrineblank/MicrO
  license: CC BY 2.0
  mappings:
    obofoundry: MICRO
    ols: micro
    ontobee: MicrO
    prefixcommons: MICRO
  name: Ontology of Prokaryotic Phenotypic and Metabolic Characters
  preferred_prefix: MICRO
  uri_format: http://purl.obolibrary.org/obo/MICRO_$1
  version: 1.5.1
microscope:
  description: MicroScope is an integrative resource that supports systematic and
    efficient revision of microbial genome annotation, data management and comparative
    analysis.
  example: '5601141'
  homepage: http://www.genoscope.cns.fr/agc/microscope
  mappings:
    miriam: microscope
    n2t: microscope
    prefixcommons: MICROSCOPE
  name: MicroScope
  pattern: ^\d+$
  preferred_prefix: microscope
  uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1
microsporidia:
  description: MicrosporidiaDB is one of the databases that can be accessed through
    the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic
    pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium,
    Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported
    by a taxon-specific database built upon the same infrastructure, the EuPathDB
    portal offers an entry point to all these resources, and the opportunity to leverage
    orthology for searches across genera.
  example: ECU03_0820i
  homepage: http://microsporidiadb.org/micro/
  mappings:
    miriam: microsporidia
    n2t: microsporidia
    prefixcommons: MICROSPORIDIA
  name: MicrosporidiaDB
  pattern: ^\w+$
  preferred_prefix: microsporidia
  uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
mim:
  description: Online Mendelian Inheritance in Man is a catalog of human genes and
    genetic disorders.
  example: '603903'
  homepage: https://omim.org/
  mappings:
    bioportal: MIM
    go: OMIM
    miriam: mim
    n2t: mim
    ncbi: MIM
    prefixcommons: OMIM
    uniprot: MIM
    wikidata: P492
  name: OMIM ID
  pattern: ^\d+$
  preferred_prefix: mim
  providers:
  - code: CURATOR_REVIEW
    description: OMIM mirror at John Hopkins
    homepage: http://mirror.omim.org/
    name: OMIM mirror at John Hopkins
    uri_format: http://mirror.omim.org/entry/$1
  synonyms:
  - OMIM
  uri_format: https://omim.org/entry/$1
mim.ps:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar
    phenotypes across the genome.
  example: PS214100
  homepage: https://www.omim.org/phenotypicSeriesTitles/all
  name: OMIM Phenotypic Series
  preferred_prefix: mim.ps
  synonyms:
  - OMIMPS
  - PS
  uri_format: https://omim.org/phenotypicSeries/$1
mimodb:
  description: MimoDB is a database collecting peptides that have been selected from
    random peptide libraries based on their ability to bind small compounds, nucleic
    acids, proteins, cells, tissues and organs. It also stores other information such
    as the corresponding target, template, library, and structures. As of March 2016,
    this database was renamed Biopanning Data Bank.
  example: '1'
  homepage: http://immunet.cn/bdb/
  mappings:
    miriam: mimodb
    n2t: mimodb
    prefixcommons: MIMODB
  name: MimoDB
  pattern: ^\d+$
  preferred_prefix: mimodb
  uri_format: http://immunet.cn/bdb/index.php/mimoset/$1
minid:
  description: Minid are identifiers used to provide robust reference to intermediate
    data generated during the course of a research investigation.
  example: b97957
  homepage: https://fair-research.org
  mappings:
    miriam: minid
    n2t: minid
    prefixcommons: MINID
  name: Minimal Viable Identifier
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: minid
  uri_format: https://hdl.handle.net/hdl:20.500.12582/$1
minid.test:
  description: 'Minid are identifiers used to provide robust reference to intermediate
    data generated during the course of a research investigation. This is a prefix
    for referencing identifiers in the minid test namespace. '
  example: 3SBPLMKKVEVR
  homepage: https://fair-research.org
  mappings:
    miriam: minid.test
  name: MINID Test
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: minid.test
  uri_format: https://hdl.handle.net/hdl:20.500.12633/$1
mint:
  description: The Molecular INTeraction database (MINT) stores, in a structured format,
    information about molecular interactions by extracting experimental details from
    work published in peer-reviewed journals.
  example: MINT-10000
  homepage: http://mint.bio.uniroma2.it/mint/
  mappings:
    miriam: mint
    n2t: mint
    prefixcommons: MINT
    uniprot: MINT
  name: Molecular Interaction Database
  pattern: ^MINT\-\d{1,7}$
  preferred_prefix: mint
  providers:
  - code: ebi
    description: MINT subset through IntAct
    homepage: https://www.ebi.ac.uk/intact/
    name: MINT subset through IntAct
    uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:$1
  uri_format: http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$1
mipmod:
  description: MIPModDb is a database of comparative protein structure models of MIP
    (Major Intrinsic Protein) family of proteins, identified from complete genome
    sequence. It provides key information of MIPs based on their sequence and structures.
  example: HOSAPI0399
  homepage: http://bioinfo.iitk.ac.in/MIPModDB
  mappings:
    miriam: mipmod
    n2t: mipmod
    prefixcommons: MIPMOD
  name: MIPModDB
  pattern: ^\w+$
  preferred_prefix: mipmod
  uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1
mir:
  banana: MIR
  description: "The Identifiers.org registry contains registered namespace and provider\
    \ prefixes with associated access URIs for a large number of high quality data\
    \ collections. These prefixes are used in web resolution of compact identifiers\
    \ of the form \u201CPREFIX:ACCESSION\u201D or \"PROVIDER/PREFIX:ACCESSION\u201D\
    \ commonly used to specify bioinformatics and other data resources."
  example: '00100037'
  homepage: https://registry.identifiers.org/registry
  mappings:
    miriam: mir
    n2t: mir
    prefixcommons: MIR
  name: Identifiers.org Registry
  namespace_in_lui: true
  pattern: ^\d{8}$
  preferred_prefix: mir
  uri_format: https://registry.identifiers.org/registry?query="MIR:$1"
mirbase:
  description: The miRBase Sequence Database is a searchable database of published
    miRNA sequences and annotation. The data were previously provided by the miRNA
    Registry. Each entry in the miRBase Sequence database represents a predicted hairpin
    portion of a miRNA transcript (termed mir in the database), with information on
    the location and sequence of the mature miRNA sequence (termed miR).
  example: MI0026471
  homepage: http://www.mirbase.org/
  mappings:
    biolink: mirbase
    miriam: mirbase
    n2t: mirbase
    ncbi: miRBase
    prefixcommons: MIRBASE
    wikidata: P2870
  name: miRBase pre-miRNA ID
  pattern: ^MI\d{7}$
  preferred_prefix: mirbase
  uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1
mirbase.family:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The miRBase database is a searchable database of published miRNA sequences
    and annotation. 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). Both hairpin
    and mature sequences are available for searching and browsing, and entries can
    also be retrieved by name, keyword, references and annotation. All sequence and
    annotation data are also available for download.
  example: MIPF0000002
  homepage: http://www.mirbase.org/
  name: miRBase Families
  preferred_prefix: mirbase.family
  synonyms:
  - MIRBASE_FAMILY
  uri_format: http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1
mirbase.mature:
  description: The miRBase Sequence Database is a searchable database of published
    miRNA sequences and annotation. This collection refers specifically to the mature
    miRNA sequence.
  example: MIMAT0046872
  homepage: http://www.mirbase.org/
  mappings:
    miriam: mirbase.mature
    n2t: mirbase.mature
    prefixcommons: MIRBASE.MATURE
    wikidata: P2871
  name: miRBase mature miRNA ID
  pattern: ^MIMAT\d{7}$
  preferred_prefix: mirbase.mature
  synonyms:
  - MIRBASEM
  uri_format: http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1
mirex:
  description: "mirEX is a comprehensive platform for comparative analysis of primary\
    \ microRNA expression data, storing RT\u2013qPCR-based gene expression profile\
    \ over seven development stages of Arabidopsis. It also provides RNA structural\
    \ models, publicly available deep sequencing results and experimental procedure\
    \ details. This collection provides profile information for a single microRNA\
    \ over all development stages."
  example: 165a
  homepage: http://comgen.pl/mirex/?page=home
  mappings:
    miriam: mirex
    n2t: mirex
    prefixcommons: MIREX
  name: mirEX
  pattern: ^\d+(\w+)?$
  preferred_prefix: mirex
  uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes
miriam.collection:
  deprecated: true
  description: MIRIAM Registry is an online resource created to catalogue collections
    (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources
    (physical locations) providing access to those data collections. The Registry
    provides unique and perennial URIs for each entity of those data collections.
  example: MIR:00000008
  homepage: https://www.ebi.ac.uk/miriam/
  mappings:
    miriam: miriam.collection
    n2t: miriam.collection
    prefixcommons: MIRIAM.COLLECTION
  name: MIRIAM Registry collection
  pattern: ^MIR:000\d{5}$
  preferred_prefix: miriam.collection
  uri_format: https://www.ebi.ac.uk/miriam/main/$1
miriam.resource:
  comment: yo dawg i heard you like registries...
  description: MIRIAM Registry is an online resource created to catalogue data types
    (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding
    resources (or physical locations), whether these are controlled vocabularies or
    databases.
  example: MIR:00100005
  homepage: https://www.ebi.ac.uk/miriam/
  mappings:
    miriam: miriam.resource
    n2t: miriam.resource
    prefixcommons: MIRIAM.RESOURCE
  name: MIRIAM Registry resource
  pattern: ^MIR:001\d{5}$
  preferred_prefix: miriam.resource
  uri_format: https://www.ebi.ac.uk/miriam/main/resources/$1
mirnao:
  banana: MIRNAO
  contact:
    email: topalis@imbb.forth.gr
    github: null
    name: Pantelis Topalis
    orcid: null
  deprecated: true
  description: An application ontology for use with miRNA databases.
  homepage: http://code.google.com/p/mirna-ontology/
  license: CC0 1.0
  mappings:
    bioportal: MIRNAO
    obofoundry: MIRNAO
    ontobee: miRNAO
    prefixcommons: MIRNAO
  name: microRNA Ontology
  preferred_prefix: MIRNAO
  uri_format: http://purl.obolibrary.org/obo/MIRNAO_$1
mirnest:
  description: miRNEST is a database of animal, plant and virus microRNAs, containing  miRNA
    predictions conducted on Expressed Sequence Tags of animal and  plant species.
  example: MNEST029358
  homepage: http://rhesus.amu.edu.pl/mirnest/copy/
  mappings:
    miriam: mirnest
    n2t: mirnest
    prefixcommons: MIRNEST
  name: miRNEST
  pattern: ^MNEST\d+$
  preferred_prefix: mirnest
  uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1
miro:
  banana: MIRO
  contact:
    email: louis@imbb.forth.gr
    github: null
    name: C. Louis
    orcid: null
  description: Application ontology for entities related to insecticide resistance
    in mosquitos
  example: '40000617'
  homepage: http://anobase.vectorbase.org
  mappings:
    bioportal: MIRO
    obofoundry: MIRO
    ols: miro
    ontobee: MIRO
    prefixcommons: MIRO
  name: Mosquito insecticide resistance
  pattern: ^\d{8}$
  preferred_prefix: MIRO
  uri_format: http://purl.obolibrary.org/obo/MIRO_$1
  version: '2014-05-14'
mirtarbase:
  description: miRTarBase is a database of miRNA-target interactions (MTIs), collected
    manually from relevant literature, following Natural Language Processing of the
    text to identify research articles related to functional studies of miRNAs. Generally,
    the collected MTIs are validated experimentally by reporter assay, western blot,
    microarray and next-generation sequencing experiments.
  example: MIRT000002
  homepage: http://mirtarbase.mbc.nctu.edu.tw/
  mappings:
    miriam: mirtarbase
    n2t: mirtarbase
    prefixcommons: MIRTARBASE
  name: miRTarBase
  pattern: ^MIRT\d{6}$
  preferred_prefix: mirtarbase
  uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1
mirte:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: This website provides access to our 2003 and 2005 miRNA-Target predictions
    for Drosophila miRNAs
  example: miR-1
  homepage: http://www.russelllab.org/miRNAs/
  name: miRNA Target Prediction at EMBL
  preferred_prefix: mirte
mlc:
  description: MLCommons Association artifacts, including benchmark results, datasets,
    and saved models.
  example: 0.7-123
  homepage: https://mlcommons.org/en/
  mappings:
    miriam: mlc
  name: MLCommons Association
  pattern: ^[0-9a-zA-Z\.\-\_]+$
  preferred_prefix: mlc
  uri_format: https://www.mlcommons.org/mlc-id/$1
mmdb:
  description: The Molecular Modeling Database (MMDB) is a database of experimentally
    determined structures obtained from the Protein Data Bank (PDB). Since structures
    are known for a large fraction of all protein families, structure homologs may
    facilitate inference of biological function, or the identification of binding
    or catalytic sites.
  example: '50885'
  homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure
  mappings:
    miriam: mmdb
    n2t: mmdb
    prefixcommons: MMDB
  name: Molecular Modeling Database
  pattern: ^\d{1,5}$
  preferred_prefix: mmdb
  uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1
mmmp.biomaps:
  description: A collection of molecular interaction maps and pathways involved in
    cancer development and progression with a focus on melanoma.
  example: '37'
  homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp
  mappings:
    miriam: mmmp:biomaps
    n2t: biomaps
    prefixcommons: MMMP:BIOMAPS
  name: Melanoma Molecular Map Project Biomaps
  pattern: ^\d+$
  preferred_prefix: mmmp.biomaps
  synonyms:
  - mmmp:biomaps
  uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1
mmo:
  banana: MMO
  contact:
    email: jrsmith@mcw.edu
    github: null
    name: Jennifer Smith
    orcid: null
  description: 'A representation of the variety of methods used to make clinical and
    phenotype measurements. '
  example: '0000574'
  homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000
  license: CC0 1.0
  mappings:
    bioportal: MMO
    obofoundry: MMO
    ols: mmo
    ontobee: MMO
    prefixcommons: MMO
  name: Measurement method ontology
  pattern: ^\d{7}$
  preferred_prefix: MMO
  uri_format: http://purl.obolibrary.org/obo/MMO_$1
  version: '2019-03-27'
mmp.cat:
  description: MarCat is a gene (protein) catalogue of uncultivable and cultivable
    marine genes and proteins derived from metagenomics samples.
  example: MMP743597.11
  homepage: https://mmp.sfb.uit.no/databases/marcat/
  mappings:
    miriam: mmp.cat
    n2t: mmp.cat
    prefixcommons: MMP.CAT
  name: MarCat
  pattern: ^MMP\d+.\d+$
  preferred_prefix: mmp.cat
  uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1
mmp.db:
  description: MarDB includes all sequenced marine microbial genomes regardless of
    level of completeness.
  example: MMP02954345.1
  homepage: https://mmp.sfb.uit.no/databases/mardb/
  mappings:
    miriam: mmp.db
    n2t: mmp.db
    prefixcommons: MMP.DB
  name: MarDB
  pattern: ^MMP\d+.\d+$
  preferred_prefix: mmp.db
  uri_format: https://mmp.sfb.uit.no/databases/mardb/#/records/$1
mmp.fun:
  description: MarFun is manually curated database for marine fungi which is a part
    of the MAR databases.
  example: MMP3888430
  homepage: https://mmp.sfb.uit.no/databases/marfun
  mappings:
    miriam: mmp.fun
  name: MarFun
  pattern: ^MMP\d+.\d+$
  preferred_prefix: mmp.fun
  uri_format: https://mmp.sfb.uit.no/databases/marfun/#/records/$1
mmp.ref:
  description: MarRef is a manually curated marine microbial reference genome database
    that contains completely sequenced genomes.
  example: MMP3312982.2
  homepage: https://mmp.sfb.uit.no/databases/marref/
  mappings:
    miriam: mmp.ref
    n2t: mmp.ref
    prefixcommons: MMP.REF
  name: MarRef
  pattern: ^MMP\d+.\d+$
  preferred_prefix: mmp.ref
  uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1
mmrrc:
  description: The MMRRC database is a repository of available mouse stocks and embryonic
    stem cell line collections.
  example: '70'
  homepage: https://www.mmrrc.org
  mappings:
    cellosaurus: MMRRC
    miriam: mmrrc
    n2t: mmrrc
    prefixcommons: MMRRC
  name: Mutant Mouse Resource and Research Centers
  pattern: ^\d+$
  preferred_prefix: mmrrc
  uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1
mmsl:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Lexicon is a foundational database with comprehensive drug product
    and disease nomenclature information. It includes drug names, drug product information,
    disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names
    and common abbreviations. A comprehensive list of standard or customized disease
    names and ICD-9 codes is also included.
  example: '3355'
  homepage: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html
  name: Multum MediSource Lexicon
  preferred_prefix: mmsl
  synonyms:
  - MMSL_CODE
mmusdv:
  banana: MmusDv
  contact:
    email: frederic.bastian@unil.ch
    github: fbastian
    name: "Fr\xE9d\xE9ric Bastian"
    orcid: null
  description: Life cycle stages for Mus Musculus
  example: '0000066'
  homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv
  license: CC BY 3.0
  mappings:
    bioportal: MMUSDV
    obofoundry: MmusDv
    ols: mmusdv
    ontobee: MMUSDV
    prefixcommons: MMUSDV
  name: Mouse Developmental Stages
  pattern: ^\d{7}$
  preferred_prefix: MmusDv
  synonyms:
  - MmusDv
  uri_format: http://purl.obolibrary.org/obo/MMUSDV_$1
  version: '2020-03-10'
mo:
  banana: MO
  contact:
    email: stoeckrt@pcbi.upenn.edu
    github: null
    name: Chris Stoeckert
    orcid: null
  deprecated: true
  description: The MGED Ontology (MO) provides terms for annotating all aspects of
    a microarray experiment from the design of the experiment and array layout, through
    to the preparation of the biological sample and the protocols used to hybridize
    the RNA and analyze the data.
  example: ArrayGroup
  homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php
  mappings:
    bioportal: MO
    miriam: mo
    n2t: mo
    obofoundry: MO
    prefixcommons: MO
  name: Microarray experimental conditions
  pattern: ^\w+$
  preferred_prefix: MO
  providers:
  - code: ebi
    description: MGED Ontology at SourceForge
    homepage: https://mged.sourceforge.net/ontologies/MGEDontology.php
    name: MGED Ontology at SourceForge
    uri_format: https://mged.sourceforge.net/ontologies/MGEDontology.php#$1
  uri_format: http://purl.obolibrary.org/obo/MO_$1
mobidb:
  description: MobiDB is a database of protein disorder and mobility annotations.
  example: P10636
  homepage: http://mobidb.bio.unipd.it
  mappings:
    miriam: mobidb
    n2t: mobidb
    prefixcommons: MOBIDB
    uniprot: MobiDB
  name: MobiDB
  pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$
  preferred_prefix: mobidb
  uri_format: https://mobidb.org/$1
mod:
  banana: MOD
  contact:
    email: pierre-alain.binz@chuv.ch
    github: null
    name: Pierre-Alain Binz
    orcid: null
  description: The Proteomics Standards Initiative modification ontology (PSI-MOD)  aims
    to define a concensus nomenclature and ontology reconciling, in a hierarchical
    representation, the complementary descriptions of residue modifications.
  example: '01467'
  homepage: http://www.psidev.info/MOD
  license: CC BY 4.0
  mappings:
    bioportal: PSIMOD
    go: PSI-MOD
    miriam: mod
    n2t: mod
    obofoundry: MOD
    ols: mod
    ontobee: MOD
    prefixcommons: MOD
  name: Protein modification
  namespace_in_lui: true
  pattern: ^\d{5}$
  preferred_prefix: MOD
  uri_format: https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1
  version: '2020-04-14'
modeldb:
  description: ModelDB is a curated, searchable database of published models in the
    computational neuroscience domain. It accommodates models expressed in textual
    form, including procedural or declarative languages (e.g. C++, XML dialects) and
    source code written for any simulation environment.
  example: '45539'
  homepage: http://senselab.med.yale.edu/ModelDB/
  mappings:
    miriam: modeldb
    n2t: modeldb
    prefixcommons: MODELDB
  name: ModelDB
  pattern: ^\d+$
  preferred_prefix: modeldb
  uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1
molbase:
  description: Molbase provides compound data information for researchers as well
    as listing suppliers and price information. It can be searched by keyword or CAS
    indetifier.
  example: 128796-39-4
  homepage: http://www.molbase.com/
  mappings:
    miriam: molbase
    n2t: molbase
    prefixcommons: MOLBASE
  name: Molbase
  pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$
  preferred_prefix: molbase
  uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1
molbase.sheffield:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  description: An online database of inorganic compounds, MolBase was constructed
    by Dr Mark Winter of the University of Sheffield with input from undergraduate
    students.
  example: '1868'
  homepage: https://winter.group.shef.ac.uk/molbase/
  name: MolBase
  pattern: ^\d+$
  preferred_prefix: molbase.sheffield
molmedb:
  description: 'MolMeDB is an open chemistry database about interactions of molecules
    with membranes. We collect information on how chemicals interact with individual
    membranes either from experiment or from simulations. '
  example: MM00040
  homepage: http://www.upol.cz/en/
  mappings:
    miriam: molmedb
  name: MolMeDB
  pattern: ^[m,M]{2}[0-9]{5}[0-9]*$
  preferred_prefix: molmedb
  uri_format: https://molmedb.upol.cz/mol/$1
mondo:
  banana: MONDO
  contact:
    email: nicole@tislab.org
    github: nicolevasilevsky
    name: Nicole Vasilevsky
    orcid: null
  description: A semi-automatically constructed ontology that merges in multiple disease
    resources to yield a coherent merged ontology.
  example: '0000001'
  homepage: https://monarch-initiative.github.io/mondo
  license: CC BY 4.0
  mappings:
    bioportal: MONDO
    obofoundry: MONDO
    ols: mondo
    ontobee: MONDO
    prefixcommons: MONDO
    wikidata: P5270
  name: Monarch Disease Ontology
  pattern: ^\d{7}$
  preferred_prefix: MONDO
  uri_format: http://purl.obolibrary.org/obo/MONDO_$1
  version: '2021-12-01'
mop:
  banana: MOP
  contact:
    email: batchelorc@rsc.org
    github: batchelorc
    name: Colin Batchelor
    orcid: null
  description: MOP is the molecular process ontology. It contains the molecular processes
    that underlie the name reaction ontology RXNO, for example cyclization, methylation
    and demethylation.
  example: 0000079
  homepage: https://github.com/rsc-ontologies/rxno
  license: CC BY 4.0
  mappings:
    bioportal: MOP
    obofoundry: MOP
    ols: mop
    ontobee: MOP
    prefixcommons: MOP
  name: Molecular Process Ontology
  pattern: ^\d{7}$
  preferred_prefix: MOP
  uri_format: http://purl.obolibrary.org/obo/MOP_$1
  version: '2014-09-03'
morpheus:
  description: 'The Morpheus model repository is an open-access data resource to store,
    search and retrieve unpublished and published computational models of spatio-temporal
    and multicellular biological systems, encoded in the MorpheusML language and readily
    executable with the Morpheus software.

    '
  example: M0001
  homepage: https://morpheus.gitlab.io/
  mappings:
    miriam: morpheus
  name: Morpheus model repository
  pattern: ^M[0-9]{4,}$
  preferred_prefix: morpheus
  uri_format: https://morpheus.gitlab.io/models/$1
mp:
  banana: MP
  contact:
    email: pheno@jax.org
    github: null
    name: JAX phenotype list
    orcid: null
  description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic
    information related to the mouse and other mammalian species. This ontology has
    been applied to mouse phenotype descriptions in various databases allowing comparisons
    of data from diverse mammalian sources. It can facilitate in the identification
    of appropriate experimental disease models, and aid in the discovery of candidate
    disease genes and molecular signaling pathways.
  example: '0005452'
  homepage: http://www.informatics.jax.org/searches/MP_form.shtml
  license: CC BY 4.0
  mappings:
    bioportal: MP
    miriam: mp
    n2t: mp
    obofoundry: MP
    ols: mp
    ontobee: MP
    prefixcommons: MP
  name: Mammalian Phenotype Ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: MP
  uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1
  version: '2019-11-11'
mpath:
  banana: MPATH
  contact:
    email: pns12@hermes.cam.ac.uk
    github: null
    name: Paul Schofield
    orcid: null
  description: A structured controlled vocabulary of mutant and transgenic mouse pathology
    phenotypes
  example: '728'
  homepage: http://www.pathbase.net
  license: CC BY 3.0
  mappings:
    bioportal: MPATH
    obofoundry: MPATH
    ols: mpath
    ontobee: MPATH
    prefixcommons: MPATH
  name: Mouse pathology ontology
  pattern: ^\d+$
  preferred_prefix: MPATH
  synonyms:
  - MPATH
  uri_format: http://purl.obolibrary.org/obo/MPATH_$1
  version: '2020-05-19'
mpid:
  description: The microbial protein interaction database (MPIDB) provides physical
    microbial interaction data. The interactions are manually curated from the literature
    or imported from other databases, and are linked to supporting experimental evidence,
    as well as evidences based on interaction conservation, protein complex membership,
    and 3D domain contacts.
  example: '172'
  homepage: http://www.jcvi.org/mpidb/about.php
  mappings:
    miriam: mpid
    n2t: mpid
    prefixcommons: MPID
  name: Microbial Protein Interaction Database
  pattern: ^\d+$
  preferred_prefix: mpid
  providers:
  - code: ebi
    description: Microbial Protein Interaction Database subset through IntAct
    homepage: https://www.ebi.ac.uk/intact/
    name: Microbial Protein Interaction Database subset through IntAct
    uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1
  uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1
mpio:
  banana: MPIO
  contact:
    email: mbrochhausen@uams.edu
    github: mbrochhausen
    name: Mathias Brochhausen
    orcid: null
  description: An ontology of minimum information regarding potential drug-drug interaction
    information.
  example: '0000004'
  homepage: https://github.com/MPIO-Developers/MPIO
  license: CC BY 4.0
  mappings:
    bioportal: MPIO
    obofoundry: MPIO
    ols: mpio
    ontobee: MPIO
    prefixcommons: MPIO
  name: Minimum PDDI Information Ontology
  preferred_prefix: MPIO
  uri_format: http://purl.obolibrary.org/obo/MPIO_$1
  version: '2019-01-30'
mro:
  banana: MRO
  contact:
    email: bpeters@lji.org
    github: bpeters42
    name: Bjoern Peters
    orcid: null
  description: The MHC Restriction Ontology is an application ontology capturing how
    Major Histocompatibility Complex (MHC) restriction is defined in experiments,
    spanning exact protein complexes, individual protein chains, serotypes, haplotypes
    and mutant molecules, as well as evidence for MHC restrictions.
  example: '0000634'
  homepage: https://github.com/IEDB/MRO
  license: CC BY 3.0
  mappings:
    bioportal: MRO
    obofoundry: MRO
    ols: mro
    ontobee: MRO
    prefixcommons: MRO
  name: MHC Restriction Ontology
  preferred_prefix: MRO
  uri_format: http://purl.obolibrary.org/obo/MRO_$1
  version: '2021-11-29'
ms:
  banana: MS
  contact:
    email: gerhard.mayer@rub.de
    github: null
    name: Gerhard Mayer
    orcid: null
  description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the
    PSI MS-related data standards. The CV contains a logical hierarchical structure
    to ensure ease of maintenance and the development of software that makes use of
    complex semantics. The CV contains terms required for a complete description of
    an MS analysis pipeline used in proteomics, including sample labeling, digestion
    enzymes, instrumentation parts and parameters, software used for identification
    and quantification of peptides/proteins and the parameters and scores used to
    determine their significance.
  example: '1000560'
  homepage: http://www.psidev.info/groups/controlled-vocabularies
  license: CC BY 3.0
  mappings:
    bioportal: MS
    miriam: ms
    n2t: ms
    obofoundry: MS
    ols: ms
    ontobee: MS
    prefixcommons: MS
  name: Mass spectrometry ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: MS
  uri_format: https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1
  version: '2019-11-21'
msigdb:
  description: The Molecular Signatures Database (MSigDB) is a collection of annotated
    gene sets for use with GSEA software. From this web site, you can
  example: NADELLA_PRKAR1A_TARGETS_DN
  homepage: https://www.gsea-msigdb.org
  mappings:
    biolink: MSigDB
  name: Molecular Signatures Database
  preferred_prefix: msigdb
  synonyms:
  - msig
msio:
  description: an application ontology for supporting description and annotation of
    mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics
    studies.
  example: '0000111'
  homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO
  mappings:
    ols: msio
  name: Metabolomics Standards Initiative Ontology
  preferred_prefix: msio
  version: 1.0.1
multicellds:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: MultiCellDS is data standard for multicellular simulation, experimental,
    and clinical data. A digital cell line is a hierarchical organization of quantitative
    phenotype data for a single biological cell line, including the microenvironmental
    context of the measurements and essential metadata.
  example: MCDS_S_0000000001
  homepage: http://multicellds.org/MultiCellDB.php
  name: MultiCellDS
  preferred_prefix: multicellds
  uri_format: http://multicellds.org/MultiCellDB/$1
multicellds.cell_line:
  description: MultiCellDS is data standard for multicellular simulation, experimental,
    and clinical data. A digital cell line is a hierarchical organization of quantitative
    phenotype data for a single biological cell line, including the microenvironmental
    context of the measurements and essential metadata.
  example: MCDS_L_0000000001
  homepage: http://multicellds.org/MultiCellDB.php
  mappings:
    miriam: multicellds.cell_line
    n2t: multicellds.cell_line
    prefixcommons: MULTICELLDS.CELL_LINE
  name: MultiCellDS Digital Cell Line
  part_of: multicellds
  pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$
  preferred_prefix: multicellds.cell_line
  uri_format: http://multicellds.org/MultiCellDB/$1
multicellds.collection:
  description: MultiCellDS is data standard for multicellular simulation, experimental,
    and clinical data. A collection groups one or more individual uniquely identified
    cell lines, snapshots, or collections. Primary uses are times series (collections
    of snapshots), patient cohorts (collections of cell lines), and studies (collections
    of time series collections).
  example: MCDS_C_0000000001
  homepage: http://multicellds.org/MultiCellDB.php
  mappings:
    miriam: multicellds.collection
    n2t: multicellds.collection
    prefixcommons: MULTICELLDS.COLLECTION
  name: MultiCellDS collection
  part_of: multicellds
  pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$
  preferred_prefix: multicellds.collection
  uri_format: http://multicellds.org/MultiCellDB/$1
multicellds.snapshot:
  description: MultiCellDS is data standard for multicellular simulation, experimental,
    and clinical data. A digital snapshot is a single-time output of the microenvironment
    (including basement membranes and the vascular network), any cells contained within,
    and essential metadata. Cells may include phenotypic data.
  example: MCDS_S_0000000001
  homepage: http://multicellds.org/MultiCellDB.php
  mappings:
    miriam: multicellds.snapshot
    n2t: multicellds.snapshot
    prefixcommons: MULTICELLDS.SNAPSHOT
  name: MultiCellDS Digital snapshot
  part_of: multicellds
  pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$
  preferred_prefix: multicellds.snapshot
  uri_format: http://multicellds.org/MultiCellDB/$1
mw.project:
  description: Metabolomics Workbench stores metabolomics data for small and large
    studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository
    and Coordinating Center (DRCC).
  example: PR000001
  homepage: http://www.metabolomicsworkbench.org/
  mappings:
    miriam: mw.project
    n2t: mw.project
    prefixcommons: MW.PROJECT
  name: Metabolomics Workbench Project
  pattern: ^PR[0-9]{6}$
  preferred_prefix: mw.project
  uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1
mw.study:
  description: Metabolomics Workbench stores metabolomics data for small and large
    studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository
    and Coordinating Center (DRCC).
  example: ST000900
  homepage: http://www.metabolomicsworkbench.org/
  mappings:
    miriam: mw.study
    n2t: mw.study
    prefixcommons: MW.STUDY
  name: Metabolomics Workbench Study
  pattern: ^ST[0-9]{6}$
  preferred_prefix: mw.study
  providers:
  - code: omicsdi
    description: Metabolomics Workbench Study through OmicsDI
    homepage: https://www.omicsdi.org/
    name: Metabolomics Workbench Study through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/metabolomics_workbench/$1
  uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1
myco.lepra:
  description: Mycobrowser is a resource that provides both in silico generated and
    manually reviewed information within databases dedicated to the complete genomes
    of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
    Mycobacterium smegmatis. This collection references Mycobacteria leprae information.
  example: ML0224
  homepage: http://mycobrowser.epfl.ch/leprosy.html
  mappings:
    miriam: myco.lepra
    n2t: myco.lepra
    prefixcommons: MYCO.LEPRA
  name: MycoBrowser leprae
  pattern: ^ML\w+$
  preferred_prefix: myco.lepra
  uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1
myco.marinum:
  description: Mycobrowser is a resource that provides both in silico generated and
    manually reviewed information within databases dedicated to the complete genomes
    of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
    Mycobacterium smegmatis. This collection references Mycobacteria marinum information.
  example: MMAR_2462
  homepage: http://mycobrowser.epfl.ch/marinolist.html
  mappings:
    miriam: myco.marinum
    n2t: myco.marinum
    prefixcommons: MYCO.MARINUM
  name: MycoBrowser marinum
  pattern: ^MMAR\_\d+$
  preferred_prefix: myco.marinum
  uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1
myco.smeg:
  description: Mycobrowser is a resource that provides both in silico generated and
    manually reviewed information within databases dedicated to the complete genomes
    of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
    Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.
  example: MSMEG_3769
  homepage: http://mycobrowser.epfl.ch/smegmalist.html
  mappings:
    miriam: myco.smeg
    n2t: myco.smeg
    prefixcommons: MYCO.SMEG
  name: MycoBrowser smegmatis
  pattern: ^MSMEG\w+$
  preferred_prefix: myco.smeg
  uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1
myco.tuber:
  description: Mycobrowser is a resource that provides both in silico generated and
    manually reviewed information within databases dedicated to the complete genomes
    of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
    Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis
    information.
  example: Rv1908c
  homepage: http://tuberculist.epfl.ch/
  mappings:
    miriam: myco.tuber
    n2t: myco.tuber
    prefixcommons: MYCO.TUBER
  name: MycoBrowser tuberculosis
  pattern: ^Rv\d{4}(A|B|c)?$
  preferred_prefix: myco.tuber
  uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1
mycobank:
  description: MycoBank is an online database, documenting new mycological names and
    combinations, eventually combined with descriptions and illustrations.
  example: '349124'
  homepage: http://www.mycobank.org/
  mappings:
    miriam: mycobank
    n2t: mycobank
    ncbi: MycoBank
    prefixcommons: MYCOBANK
  name: Fungal Nomenclature and Species Bank
  pattern: ^\d+$
  preferred_prefix: mycobank
  uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1
mzspec:
  banana: mzspec
  description: The Universal Spectrum Identifier (USI) is a compound identifier that
    provides an abstract path to refer to a single spectrum generated by a mass spectrometer,
    and potentially the ion that is thought to have produced it.
  example: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2
  homepage: http://proteomecentral.proteomexchange.org/
  mappings:
    miriam: mzspec
    n2t: mzspec
    prefixcommons: MZSPEC
  name: Universal Spectrum Identifier
  namespace_in_lui: true
  pattern: ^.+$
  preferred_prefix: mzspec
  providers:
  - code: CURATOR_REVIEW
    description: Universal Spectrum Identifier through Peptide Atlas
    homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum
    name: Universal Spectrum Identifier through Peptide Atlas
    uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1
  uri_format: http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1
namerxn:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The nomenclature used for named reactions in text mining software from
    NextMove. While it's proprietary, there are a few publications listing parts.
    487/1,855 have mappings to the Reaction Ontology (RXNO).
  example: 4.2.78
  homepage: https://www.nextmovesoftware.com/namerxn.html
  name: NameRXN
  preferred_prefix: namerxn
  proprietary: true
  references:
  - https://www.nextmovesoftware.com/products/HazELNutPoster.pdf
  - https://twitter.com/cthoyt/status/1443929184745758723
  - https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.6b00153
  - https://www.nature.com/articles/s42256-020-00284-w
napdi:
  description: The Natural Product-Drug Interaction Research Data Repository, a publicly
    accessible database where researchers can access scientific results, raw data,
    and recommended approaches to optimally assess the clinical significance of pharmacokinetic
    natural product-drug interactions (PK-NPDIs).
  example: '28'
  homepage: https://repo.napdi.org/
  mappings:
    miriam: napdi
    n2t: napdi
    prefixcommons: NAPDI
  name: Natural Product-Drug Interaction Research Data Repository
  pattern: ^[0-9]+$
  preferred_prefix: napdi
  uri_format: https://repo.napdi.org/study/$1
napp:
  description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based
    on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic
    regions from a reference genome are compared with other genomes to identify RNA
    rich clusters.
  example: '351'
  homepage: http://napp.u-psud.fr/
  mappings:
    miriam: napp
    n2t: napp
    prefixcommons: NAPP
  name: Nucleic Acids Phylogenetic Profiling
  pattern: ^\d+$
  preferred_prefix: napp
  uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1
narcis:
  description: NARCIS provides access to scientific information, including (open access)
    publications from the repositories of all the Dutch universities, KNAW, NWO and
    a number of research institutes, which is not referenced in other citation databases.
  example: oai:cwi.nl:4725
  homepage: http://www.narcis.nl
  mappings:
    miriam: narcis
    n2t: narcis
    prefixcommons: NARCIS
  name: National Academic Research and Collaborations Information System
  pattern: ^oai\:cwi\.nl\:\d+$
  preferred_prefix: narcis
  uri_format: http://www.narcis.nl/publication/RecordID/$1
nasc:
  description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information
    resources to the International Arabidopsis Genome Programme and the wider research
    community.
  example: N1899
  homepage: http://arabidopsis.info/
  mappings:
    miriam: nasc
    n2t: nasc
    prefixcommons: NASC
  name: NASC code
  pattern: ^(\w+)?\d+$
  preferred_prefix: nasc
  uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1
nbn:
  description: The National Bibliography Number (NBN), is a URN-based publication
    identifier system employed by a variety of national libraries such as those of
    Germany, the Netherlands and Switzerland.  They are used to identify documents
    archived in national libraries, in their native format or language, and are typically
    used for documents which do not have a publisher-assigned identifier.
  example: urn:nbn:fi:tkk-004781
  homepage: http://nbn-resolving.org/resolve_urn.htm
  mappings:
    miriam: nbn
    n2t: nbn
    prefixcommons: NBN
  name: National Bibliography Number
  pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$
  preferred_prefix: nbn
  uri_format: http://nbn-resolving.org/resolver?identifier=$1&verb=redirect
nbo:
  banana: NBO
  contact:
    email: g.gkoutos@bham.ac.uk
    github: gkoutos
    name: George Gkoutos
    orcid: null
  description: An ontology of human and animal behaviours and behavioural phenotypes
  example: '0000564'
  homepage: https://github.com/obo-behavior/behavior-ontology/
  license: CC BY 3.0
  mappings:
    bioportal: NBO
    obofoundry: NBO
    ols: nbo
    ontobee: NBO
    prefixcommons: NBO
  name: Neuro Behavior Ontology
  pattern: ^\d{7}$
  preferred_prefix: NBO
  uri_format: http://purl.obolibrary.org/obo/NBO_$1
  version: '2021-02-15'
nbrc:
  description: NITE Biological Research Center (NBRC) provides a collection of microbial
    resources, performing taxonomic characterization of individual microorganisms
    such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages
    and DNA resources for academic research and industrial applications. A catalogue
    is maintained which states strain nomenclature, synonyms, and culture and sequence
    information.
  example: '00001234'
  homepage: http://www.nbrc.nite.go.jp/e/index.html
  mappings:
    miriam: nbrc
    n2t: nbrc
    ncbi: NBRC
    prefixcommons: NBRC
  name: NITE Biological Resource Center
  pattern: ^\d+$
  preferred_prefix: nbrc
  uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1
ncats.drug:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The National Center for Advancing Translational Sciences (NCATS) has
    developed Inxight: Drugs as a comprehensive portal for drug development information.
    NCATS Inxight: Drugs  contains information on ingredients in medicinal products,
    including:'
  example: '44259'
  homepage: https://drugs.ncats.io/
  name: NCATS Drugs
  preferred_prefix: ncats.drug
  uri_format: https://drugs.ncats.io/drug/$1
ncbigene:
  description: Entrez Gene is the NCBI's database for gene-specific information, focusing
    on completely sequenced genomes, those with an active research community to contribute
    gene-specific information, or those that are scheduled for intense sequence analysis.
  example: '100010'
  homepage: https://www.ncbi.nlm.nih.gov/gene
  mappings:
    biolink: NCBIGene
    go: NCBIGene
    miriam: ncbigene
    n2t: ncbigene
    ncbi: GeneID
    prefixcommons: NCBIGene
    scholia: ncbi-gene
    wikidata: P351
  name: Entrez Gene ID
  pattern: ^\d+$
  preferred_prefix: NCBIGene
  providers:
  - code: marrvel
    description: Helps browse potential orthologs in model organisms for a given gene
    homepage: http://marrvel.org
    name: Model organism Aggregated Resources for Rare Variant ExpLoration
    uri_format: http://marrvel.org/model/gene/$1
  - code: CURATOR_REVIEW
    description: Bio2RDF
    homepage: http://ncbigene.bio2rdf.org/fct
    name: Bio2RDF
    uri_format: http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$1
  synonyms:
  - EGID
  - NCBIGene
  - entrez
  - entrez gene/locuslink
  uri_format: https://www.ncbi.nlm.nih.gov/gene/$1
ncbiprotein:
  description: The Protein database is a collection of sequences from several sources,
    including translations from annotated coding regions in GenBank, RefSeq and TPA,
    as well as records from SwissProt, PIR, PRF, and PDB.
  example: CAA71118.1
  homepage: https://www.ncbi.nlm.nih.gov/protein
  mappings:
    go: NCBI_NP
    miriam: ncbiprotein
    n2t: ncbiprotein
    prefixcommons: NCBIProtein
  name: NCBI Protein
  pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$
  preferred_prefix: NCBIProtein
  uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
ncbitaxon:
  contact:
    email: frederic.bastian@unil.ch
    github: fbastian
    name: Frederic Bastian
    orcid: null
  description: The taxonomy contains the relationships between all living forms for
    which nucleic acid or protein sequence have been determined.
  example: '2170610'
  homepage: https://github.com/obophenotype/ncbitaxon
  license: CC0 1.0
  mappings:
    bioportal: NCBITAXON
    cellosaurus: NCBI_TaxID
    go: taxon
    miriam: taxonomy
    n2t: taxonomy
    ncbi: taxon
    obofoundry: NCBITaxon
    ols: ncbitaxon
    ontobee: NCBITaxon
    prefixcommons: NCBITaxon
    scholia: ncbi-taxon
    wikidata: P685
  name: NCBI organismal classification
  pattern: ^\d+$
  preferred_prefix: NCBITaxon
  providers:
  - code: CURATOR_REVIEW
    description: Taxonomy through UniProt PURL
    homepage: https://www.uniprot.org/taxonomy/
    name: Taxonomy through UniProt PURL
    uri_format: https://purl.uniprot.org/taxonomy/$1
  - code: ebi
    description: European Nucleotide Archive (ENA)
    homepage: https://www.ebi.ac.uk/ena/
    name: European Nucleotide Archive (ENA)
    uri_format: https://www.ebi.ac.uk/ena/data/view/Taxon:$1
  - code: CURATOR_REVIEW
    description: Bio2RDF
    homepage: https://bio2rdf.org/
    name: Bio2RDF
    uri_format: https://bio2rdf.org/taxonomy:$1
  synonyms:
  - NCBITaxon
  - NCBI_Taxon_ID
  - NCBI_taxid
  - TAX
  - TaxonomyID
  - taxid
  - taxon
  - taxonomy
  uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1
  version: '2021-06-10'
ncim:
  description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database
    that covers most terminologies used by NCI for clinical care, translational and
    basic research, and public information and administrative activities. It integrates
    terms and definitions from different terminologies, including NCI Thesaurus, however
    the representation is not identical.
  example: C0026339
  homepage: http://ncim.nci.nih.gov/
  mappings:
    miriam: ncim
    n2t: ncim
    prefixcommons: NCIM
  name: NCI Metathesaurus
  pattern: ^C\d+$
  preferred_prefix: ncim
  uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1
ncit:
  contact:
    email: haendel@ohsu.edu
    github: mellybelly
    name: Melissa Haendel
    orcid: null
  description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary
    for clinical care, translational and basic research, and public information and
    administrative activities, providing a stable and unique identification code.
  example: C138986
  homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
  license: CC BY 4.0
  mappings:
    bioportal: NCIT
    cellosaurus: NCIt
    miriam: ncit
    n2t: ncit
    obofoundry: NCIT
    ols: ncit
    ontobee: NCIT
    prefixcommons: NCIT
    wikidata: P1748
  name: NCI Thesaurus
  pattern: ^C\d+$
  preferred_prefix: NCIT
  synonyms:
  - NCI
  - NCI2004_11_17
  - NCIT
  - NCIT_Thesaurus
  - NCITm
  - NCITt
  - NCI_Thesaurus
  - NCIt
  - ncithesaurus
  uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1
  version: 21.07d
ncro:
  banana: NCRO
  contact:
    email: huang@southalabama.edu
    github: Huang-OMIT
    name: Jingshan Huang
    orcid: null
  description: An ontology for non-coding RNA, both of biological origin, and engineered.
  example: 0002927
  homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology
  license: CC BY 4.0
  mappings:
    bioportal: NCRO
    obofoundry: NCRO
    ols: ncro
    ontobee: NCRO
    prefixcommons: NCRO
  name: Non-Coding RNA Ontology
  preferred_prefix: NCRO
  uri_format: http://purl.obolibrary.org/obo/NCRO_$1
  version: '2015-12-10'
ndc:
  description: The National Drug Code (NDC) is a unique, three-segment number used
    by the Food and Drug Administration (FDA) to identify drug products for commercial
    use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates
    the listed NDC numbers daily.
  example: 0002-1975-61
  homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/
  mappings:
    miriam: ndc
    n2t: ndc
    prefixcommons: NDC
  name: National Drug Code
  pattern: ^\d+\-\d+\-\d+$
  preferred_prefix: ndc
  providers:
  - code: CURATOR_REVIEW
    description: Bio2RDF
    homepage: http://ndc.bio2rdf.org/fct
    name: Bio2RDF
    uri_format: http://ndc.bio2rdf.org/describe/?url=http://bio2rdf.org/ndc:$1
  uri_format: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1
nddf:
  description: FDB MedKnowledge encompasses medications approved by the U.S. Food
    and Drug Administration, and information on commonly-used over-the-counter and
    alternative therapy agents such as herbals, nutraceuticals and dietary supplements.
  example: 002678
  homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF
  mappings:
    biolink: NDDF
    bioportal: NDDF
  name: National Drug Data File
  preferred_prefix: nddf
ndex:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Network Data Exchange (NDEx) is an open-source framework where
    scientists and organizations can store, share, manipulate, and publish biological
    network knowledge.
  example: aa78a43f-9c4d-11eb-9e72-0ac135e8bacf
  homepage: https://www.ndexbio.org
  name: Network Data Exchange
  preferred_prefix: ndex
  uri_format: https://www.ndexbio.org/viewer/networks/$1
ndfrt:
  description: 'NDF-RT combines the NDF hierarchical drug classification with a multi-category
    reference model. The categories are: Cellular or Molecular Interactions [MoA];
    Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases,
    Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form];
    Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories
    [TC]; and VA Drug Interactions [VA Drug Interaction].'
  example: N0000001662
  homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT
  mappings:
    bioportal: NDFRT
    ontobee: NDF-RT
    wikidata: P2115
  name: National Drug File - Reference Terminology
  preferred_prefix: ndfrt
  synonyms:
  - NUI
  - ndf-rt
nemo:
  description: This namespace is about Neuroscience Multi-Omic data, specially focused
    on that data generated from the BRAIN Initiative and related brain research projects.
  example: smp-m3w9hbe
  homepage: https://www.nemoarchive.org
  mappings:
    bioportal: NEMO
    miriam: nemo
  name: Neural ElectroMagnetic Ontology
  pattern: ^[a-z]{3}-[a-km-z0-9]{7}$
  preferred_prefix: nemo
  uri_format: https://assets.nemoarchive.org/$1
neurolex:
  description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience.  It
    is supported by the Neuroscience Information Framework project and incorporates
    information from the NIF standardised ontology (NIFSTD), and its predecessor,
    the Biomedical Informatics Research Network Lexicon (BIRNLex).
  example: Birnlex_721
  homepage: http://www.neurolex.org/wiki/Main_Page
  mappings:
    miriam: neurolex
    n2t: neurolex
    prefixcommons: NEUROLEX
  name: NeuroLex
  pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$
  preferred_prefix: neurolex
  uri_format: http://www.neurolex.org/wiki/$1
neuromorpho:
  description: NeuroMorpho.Org is a centrally curated inventory of  digitally reconstructed
    neurons.
  example: Rosa2
  homepage: http://neuromorpho.org/index.jsp
  mappings:
    miriam: neuromorpho
    n2t: neuromorpho
    prefixcommons: NEUROMORPHO
  name: NeuroMorpho
  pattern: ^\w+$
  preferred_prefix: neuromorpho
  uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1
neuronames:
  description: BrainInfo is designed to help you identify structures in the brain.
    If you provide the name of a structure, BrainInfo will show it and tell you about
    it.
  example: '268'
  homepage: http://braininfo.rprc.washington.edu/
  mappings:
    wikidata: P4394
  name: NeuroNames
  preferred_prefix: neuronames
  references:
  - https://en.wikipedia.org/wiki/NeuroNames
  synonyms:
  - neuroname
  uri_format: https://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1
neurondb:
  description: 'NeuronDB provides a dynamically searchable database of three types
    of neuronal properties: voltage gated conductances, neurotransmitter receptors,
    and neurotransmitter substances. It contains tools that provide for integration
    of these properties in a given type of neuron and compartment, and for comparison
    of properties across different types of neurons and compartments.'
  example: '265'
  homepage: http://senselab.med.yale.edu/NeuronDB/
  mappings:
    miriam: neurondb
    n2t: neurondb
    prefixcommons: NEURONDB
  name: NeuronDB
  pattern: ^\d+$
  preferred_prefix: neurondb
  uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1
neurovault.collection:
  description: Neurovault is an online repository for statistical maps, parcellations
    and atlases of the brain. This collection references sets (collections) of images.
  example: '3304'
  homepage: http://neurovault.org
  mappings:
    miriam: neurovault.collection
    n2t: neurovault.collection
    prefixcommons: NEUROVAULT.COLLECTION
  name: NeuroVault Collection
  pattern: ^[1-9][0-9]*$
  preferred_prefix: neurovault.collection
  uri_format: https://neurovault.org/collections/$1
neurovault.image:
  description: Neurovault is an online repository for statistical maps, parcellations
    and atlases of the brain. This collection references individual images.
  example: '58788'
  homepage: http://neurovault.org
  mappings:
    miriam: neurovault.image
    n2t: neurovault.image
    prefixcommons: NEUROVAULT.IMAGE
  name: NeuroVault Image
  pattern: ^[1-9][0-9]*$
  preferred_prefix: neurovault.image
  uri_format: https://neurovault.org/images/$1
nextdb:
  description: NextDb is a database that provides information on the expression pattern
    map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done
    through EST analysis and systematic whole mount in situ hybridization. Information
    available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237
    cDNA clones.
  example: 6b1
  homepage: http://nematode.lab.nig.ac.jp/
  mappings:
    miriam: nextdb
    n2t: nextdb
    ncbi: NextDB
    prefixcommons: NEXTDB
  name: Nematode Expression Pattern DataBase
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: nextdb
  uri_format: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1
nextprot:
  description: "neXtProt is a resource on human proteins, and includes information\
    \ such as proteins\u2019 function, subcellular location, expression, interactions\
    \ and role in diseases."
  example: NX_O00165
  homepage: https://www.nextprot.org/
  mappings:
    miriam: nextprot
    n2t: nextprot
    prefixcommons: NEXTPROT
    uniprot: neXtProt
  name: nextProt
  pattern: ^NX_\w+$
  preferred_prefix: nextprot
  synonyms:
  - NXP
  uri_format: https://www.nextprot.org/db/entry/$1
nextprot.family:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "NeXtProt is a comprehensive human-centric discovery platform, offering\
    \ its users a seamless integration of and navigation through protein-related data.\
    \ \n(Developed by the SIB Swiss Institute of Bioinformatics)"
  example: '01406'
  homepage: https://www.nextprot.org/
  name: neXtProt family
  pattern: ^\d+$
  preferred_prefix: nextprot.family
  synonyms:
  - NXPFA
  uri_format: https://www.nextprot.org/term/FA-$1
ngl:
  description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression,
    and metabolic profiles, interfaces with existing databases for expanded research,
    will offer tools to conduct data analysis, and is in the process of creating a
    place online where scientists, researchers, teachers and students can connect
    with their peers, share their results, and communicate with NASA.
  example: GLDS-141
  homepage: https://genelab-data.ndc.nasa.gov/genelab/
  mappings:
    miriam: ngl
    n2t: ngl
    prefixcommons: NGL
  name: NASA GeneLab
  pattern: ^GLDS-\d+$
  preferred_prefix: ngl
  uri_format: https://genelab-data.ndc.nasa.gov/genelab/accession/$1
niaest:
  description: A catalog of mouse genes expressed in early embryos, embryonic and
    adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute
    on Aging) assembled.This collection represents the name and sequence from individual
    cDNA clones.
  example: J0705A10
  homepage: http://lgsun.grc.nia.nih.gov/cDNA/
  mappings:
    miriam: niaest
    n2t: niaest
    ncbi: niaEST
    prefixcommons: NIAEST
  name: NIA Mouse cDNA Project
  pattern: ^\w\d{4}\w\d{2}(\-[35])?$
  preferred_prefix: niaest
  uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1
nif_cell:
  banana: NIF_CELL
  contact:
    email: smtifahim@gmail.com
    github: null
    name: Fahim Imam
    orcid: null
  deprecated: true
  description: Neuronal cell types
  homepage: http://neuinfo.org/
  mappings:
    bioportal: NIFCELL
    obofoundry: NIF_CELL
    prefixcommons: NIF_CELL
  name: NIF Cell
  preferred_prefix: NIF_CELL
  uri_format: http://purl.obolibrary.org/obo/NIF_CELL_$1
nif_dysfunction:
  banana: NIF_DYSFUNCTION
  contact:
    email: smtifahim@gmail.com
    github: null
    name: Fahim Imam
    orcid: null
  deprecated: true
  homepage: http://neuinfo.org/
  mappings:
    obofoundry: NIF_DYSFUNCTION
    prefixcommons: NIF_DYSFUNCTION
  name: NIF Dysfunction
  preferred_prefix: NIF_DYSFUNCTION
  uri_format: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1
nif_grossanatomy:
  banana: NIF_GROSSANATOMY
  contact:
    email: smtifahim@gmail.com
    github: null
    name: Fahim Imam
    orcid: null
  deprecated: true
  homepage: http://neuinfo.org/
  mappings:
    obofoundry: NIF_GROSSANATOMY
    prefixcommons: NIF_GROSSANATOMY
  name: NIF Gross Anatomy
  preferred_prefix: NIF_GROSSANATOMY
  uri_format: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1
nist:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The NIST Chemistry WebBook provides users with easy access to chemical
    and physical property data for chemical species through the internet. The data
    provided in the site are from collections maintained by the NIST Standard Reference
    Data Program and outside contributors. Data in the WebBook system are organized
    by chemical species.
  homepage: https://webbook.nist.gov/chemistry/
  name: NIST Chemistry WebBook
  no_own_terms: true
  preferred_prefix: nist
  synonyms:
  - NIST
  - NIST Chemistry WebBook
nlm:
  description: Bibliographic data for all the journals, books, audiovisuals, computer
    software, electronic resources and other materials that are in the library's holdings.
  example: '101775319'
  homepage: https://www.ncbi.nlm.nih.gov/nlmcatalog
  mappings:
    biolink: NLMID
  name: National Library of Medicine (NLM) Catalog
  preferred_prefix: nlm
  uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1
nlxanat:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The InterLex project - a core component of SciCrunch and supported
    by projects such as the Neuroscience Information Framework project (NIF), the
    NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury
    - is a dynamic lexicon of biomedical terms.
  example: 090201
  homepage: https://scicrunch.org/scicrunch/interlex/dashboard
  name: NeuroLex Anatomy
  part_of: neurolex
  preferred_prefix: nlxanat
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1
nlxdys:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The InterLex project - a core component of SciCrunch and supported
    by projects such as the Neuroscience Information Framework project (NIF), the
    NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury
    - is a dynamic lexicon of biomedical terms.
  example: '20090303'
  homepage: https://scicrunch.org/scicrunch/interlex/dashboard
  name: NeuroLex Dysfunction
  part_of: neurolex
  preferred_prefix: nlxdys
  uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1
nmdc:
  contact:
    email: donny@polyneme.xyz
    github: null
    name: Donny Winston
    orcid: 0000-0002-8424-0604
  contributor:
    email: donny@polyneme.xyz
    github: null
    name: Donny Winston
    orcid: 0000-0002-8424-0604
  description: An initiative to empower the research community to harness microbiome
    data exploration and discovery through a collaborative integrative data science
    ecosystem.
  example: y3ax-8bq3-60
  homepage: https://microbiomedata.org/
  mappings:
    miriam: nmdc
  name: National Microbiome Data Collaborative
  pattern: ^[\w\-.]{3,}$
  preferred_prefix: nmdc
  reviewer:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://drs.microbiomedata.org/objects/$1
nmr:
  banana: NMR
  contact:
    email: schober@imbi.uni-freiburg.de
    github: null
    name: Schober Daniel
    orcid: null
  deprecated: true
  description: nmrCV is a controlled vocabulary to deliver standardized descriptors
    for the open mark-up language for NMR raw and spectrum data, sanctioned by the
    metabolomics standards initiative msi.
  example: '1000003'
  homepage: http://msi-ontology.sourceforge.net/
  mappings:
    bioportal: NMR
    miriam: nmr
    n2t: nmr
    obofoundry: NMR
    ols: nmrcv
    prefixcommons: NMR
  name: NMR-instrument specific component of metabolomics investigations
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: NMR
  synonyms:
  - nmrcv
  uri_format: https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1
  version: 1.1.0
nmrshiftdb2:
  description: NMR database for organic structures and their nuclear magnetic resonance
    (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as
    well as for searching spectra, structures and other properties.
  example: '234'
  homepage: https://nmrshiftdb.nmr.uni-koeln.de
  mappings:
    miriam: nmrshiftdb2
  name: NMR Shift Database
  pattern: ^[0-9]+$
  preferred_prefix: nmrshiftdb2
  uri_format: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1
nomen:
  banana: NOMEN
  contact:
    email: diapriid@gmail.com
    github: mjy
    name: Matt Yoder
    orcid: null
  description: NOMEN is a nomenclatural ontology for biological names (not concepts).  It
    encodes the goverened rules of nomenclature.
  example: 0000295
  homepage: https://github.com/SpeciesFileGroup/nomen
  license: CC0 1.0
  mappings:
    bioportal: NOMEN
    obofoundry: NOMEN
    ols: nomen
    ontobee: NOMEN
  name: NOMEN - A nomenclatural ontology for biological names
  preferred_prefix: NOMEN
  uri_format: http://purl.obolibrary.org/obo/NOMEN_$1
  version: '2019-04-17'
noncodev3:
  description: NONCODE is a database of expression and functional lncRNA (long noncoding
    RNA) data obtained from microarray studies. LncRNAs have been shown to play key
    roles in various biological processes such as imprinting control, circuitry controlling
    pluripotency and differentiation, immune responses and chromosome dynamics. The
    collection references NONCODE version 3. This was replaced in 2013 by version
    4.
  example: '377550'
  homepage: http://www.noncode.org/
  mappings:
    miriam: noncodev3
    n2t: noncodev3
    prefixcommons: NONCODEV3
  name: NONCODE v3
  pattern: ^\d+$
  preferred_prefix: noncodev3
  uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1
noncodev4.gene:
  description: NONCODE is a database of expression and functional lncRNA (long noncoding
    RNA) data obtained from microarray studies. LncRNAs have been shown to play key
    roles in various biological processes such as imprinting control, circuitry controlling
    pluripotency and differentiation, immune responses and chromosome dynamics. The
    collection references NONCODE version 4 and relates to gene regions.
  example: NONHSAG00001
  homepage: http://www.bioinfo.org/NONCODEv4/
  mappings:
    miriam: noncodev4.gene
    n2t: noncodev4.gene
    prefixcommons: NONCODEV4.GENE
  name: NONCODE v4 Gene
  pattern: ^NONHSAG\d{5}$
  preferred_prefix: noncodev4.gene
  uri_format: http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1
noncodev4.rna:
  description: NONCODE is a database of expression and functional lncRNA (long noncoding
    RNA) data obtained from microarray studies. LncRNAs have been shown to play key
    roles in various biological processes such as imprinting control, circuitry controlling
    pluripotency and differentiation, immune responses and chromosome dynamics. The
    collection references NONCODE version 4 and relates to individual transcripts.
  example: NONHSAT000001
  homepage: http://www.bioinfo.org/NONCODEv4/
  mappings:
    miriam: noncodev4.rna
    n2t: noncodev4.rna
    prefixcommons: NONCODEV4.RNA
  name: NONCODE v4 Transcript
  pattern: ^NONHSAT\d{6}$
  preferred_prefix: noncodev4.rna
  uri_format: http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1
norine:
  description: Norine is a database dedicated to nonribosomal peptides (NRPs). In
    bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis,
    an alternative ribosome-independent pathway called NRP synthesis allows peptide
    production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic
    amino acids whose primary structure is not always linear, often being more complex
    and containing cycles and branchings.
  example: NOR00681
  homepage: http://bioinfo.lifl.fr/norine/
  mappings:
    miriam: norine
    n2t: norine
    prefixcommons: NORINE
  name: Nonribosomal Peptides Database
  pattern: ^NOR\d+$
  preferred_prefix: norine
  uri_format: http://bioinfo.lifl.fr/norine/result.jsp?ID=$1
novus:
  description: A vendor of antibodies and other biologics
  example: nb100-56351
  homepage: https://www.novusbio.com
  name: Novus Biologicals
  preferred_prefix: novus
  uri_format: https://www.novusbio.com/products/$1
npass:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'Database for integrating species source of natural products & connecting
    natural products to biological targets via  experimental-derived quantitative
    activity data.

    '
  example: NPC139585
  homepage: http://bidd.group/NPASS/
  name: Natural Product Activity and Species Source Database
  pattern: ^NPC\d+$
  preferred_prefix: npass
nuclearbd:
  description: NucleaRDB is an information system that stores heterogenous data on
    Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding
    constants and mutations for NHRs.
  example: prgr_human
  homepage: http://www.receptors.org/nucleardb/
  mappings:
    miriam: nuclearbd
    n2t: nuclearbd
    prefixcommons: NUCLEARBD
  name: NucleaRDB
  pattern: ^\w+\_\w+$
  preferred_prefix: nuclearbd
  uri_format: http://www.receptors.org/nucleardb/proteins/$1
nucleotide:
  description: The Nucleotide database is a collection of sequences from several sources,
    including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data
    provide the foundation for biomedical research and discovery.
  example: '880798137'
  has_canonical: insdc
  homepage: https://www.ncbi.nlm.nih.gov/
  mappings:
    miriam: nucleotide
  name: Nucleotide
  pattern: ^[a-zA-Z0-9_\.]+$
  preferred_prefix: nucleotide
  uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1
oa:
  description: The W3C Web Annotation Working Group is chartered to develop a set
    of specifications for an interoperable, sharable, distributed Web Annotation architecture.
  example: sourceDateStart
  homepage: http://www.w3.org/ns/oa
  mappings:
    bioportal: OA
    prefixcommons: oa
  name: Web Annotation Ontology
  preferred_prefix: oa
  uri_format: http://www.w3.org/ns/oa#$1
oae:
  banana: OAE
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqunh He
    orcid: null
  description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the
    domain of adverse events. OAE aims to standardize adverse event annotation, integrate
    various adverse event data, and support computer-assisted reasoning.  OAE is a
    community-based ontology. Its development follows the OBO Foundry principles.
    Vaccine adverse events have been used as an initial testing use case. OAE also
    studies adverse events associated with the administration of drug and nutritional
    products, the operation of surgeries, and the usage of medical devices, etc.
  example: 0002959
  homepage: https://github.com/OAE-ontology/OAE/
  license: CC BY 3.0
  mappings:
    bioportal: OAE
    obofoundry: OAE
    ols: oae
    ontobee: OAE
    prefixcommons: OAE
  name: Ontology of Adverse Events
  preferred_prefix: OAE
  uri_format: http://purl.obolibrary.org/obo/OAE_$1
  version: 1.2.44
oarcs:
  banana: OARCS
  contact:
    email: mjyoder@illinois.edu
    github: mjy
    name: Matt Yoder
    orcid: null
  description: OArCS is an ontology describing the Arthropod ciruclatory system.
  example: 0000029
  homepage: https://github.com/aszool/oarcs
  license: CC BY 3.0
  mappings:
    bioportal: OARCS
    obofoundry: OARCS
    ols: oarcs
    ontobee: OARCS
    prefixcommons: OARCS
  name: Ontology of Arthropod Circulatory Systems
  preferred_prefix: OARCS
  uri_format: http://purl.obolibrary.org/obo/OARCS_$1
  version: '2019-04-18'
oba:
  banana: OBA
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: null
  description: A collection of biological attributes (traits) covering all kingdoms
    of life.
  example: '0000001'
  homepage: https://github.com/obophenotype/bio-attribute-ontology
  license: CC0 1.0
  mappings:
    bioportal: OBA
    obofoundry: OBA
    ols: oba
    ontobee: OBA
    prefixcommons: OBA
  name: Ontology of Biological Attributes
  pattern: ^\d{7}$
  preferred_prefix: OBA
  uri_format: http://purl.obolibrary.org/obo/OBA_$1
  version: '2019-05-22'
obcs:
  banana: OBCS
  contact:
    email: jiezheng@pennmedicine.upenn.edu
    github: null
    name: Jie Zheng
    orcid: null
  description: 'OBCS stands for the Ontology of Biological and Clinical Statistics.
    OBCS is an ontology in the domain of biological and clinical statistics. It is
    aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations
    (OBI). OBCS imports all possible biostatistics terms in OBI and includes many
    additional biostatistics terms, some of which were proposed and discussed in the
    OBI face-to-face workshop in Ann Arbor in 2012.  '
  example: '0000121'
  homepage: https://github.com/obcs/obcs
  license: CC BY 3.0
  mappings:
    bioportal: OBCS
    obofoundry: OBCS
    ols: obcs
    ontobee: OBCS
    prefixcommons: OBCS
  name: Ontology of Biological and Clinical Statistics
  preferred_prefix: OBCS
  uri_format: http://purl.obolibrary.org/obo/OBCS_$1
  version: '101'
obi:
  banana: OBI
  contact:
    email: bpeters@lji.org
    github: null
    name: Bjoern Peters
    orcid: null
  description: The Ontology for Biomedical Investigations (OBI) project is developing
    an integrated ontology for the description of biological and clinical investigations.
    The ontology will represent the design of an investigation, the protocols and
    instrumentation used, the material used, the data generated and the type analysis
    performed on it. Currently OBI is being built under the Basic Formal Ontology
    (BFO).
  example: 0400109
  homepage: http://obi-ontology.org
  license: CC BY 4.0
  mappings:
    bioportal: OBI
    go: OBI
    miriam: obi
    n2t: obi
    obofoundry: OBI
    ols: obi
    ontobee: OBI
    prefixcommons: OBI
  name: Ontology for Biomedical Investigations
  pattern: ^\d{7}$
  preferred_prefix: OBI
  uri_format: http://purl.obolibrary.org/obo/OBI_$1
  version: '2021-08-18'
obib:
  banana: OBIB
  contact:
    email: jiezheng@pennmedicine.upenn.edu
    github: null
    name: Jie Zheng
    orcid: null
  description: The Ontology for Biobanking (OBIB) is an ontology for the annotation
    and modeling of the activities, contents, and administration of a biobank. Biobanks
    are facilities that store specimens, such as bodily fluids and tissues, typically
    along with specimen annotation and clinical data. OBIB is based on a subset of
    the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology
    (BFO) as its upper ontology, and is developed following OBO Foundry principles.
    The first version of OBIB resulted from the merging of two existing biobank-related
    ontologies, OMIABIS and biobank ontology.
  example: 0000389
  homepage: https://github.com/biobanking/biobanking
  license: CC BY 4.0
  mappings:
    bioportal: OBIB
    obofoundry: OBIB
    ols: obib
    ontobee: OBIB
    prefixcommons: OBIB
  name: Ontology for Biobanking
  preferred_prefix: OBIB
  uri_format: http://purl.obolibrary.org/obo/OBIB_$1
  version: '2021-11-12'
obo:
  description: Community development of interoperable ontologies for the biological
    sciences
  homepage: http://www.obofoundry.org/
  mappings:
    prefixcommons: OBO
  name: Internal OBO and PyOBO Relations
  preferred_prefix: obo
  uri_format: http://purl.obolibrary.org/obo/$1
oboinowl:
  description: This meta-ontology is self-describing. OBO metamodel properties are
    described using OBO metamodel properties
  example: hasDbXref
  homepage: https://github.com/geneontology/go-ontology/tree/master/contrib
  mappings:
    prefixcommons: OIO
  name: OBO in OWL
  preferred_prefix: oboInOwl
  synonyms:
  - oio
  uri_format: http://www.geneontology.org/formats/oboInOwl#$1
occ:
  description: The OpenCitations Corpus is open repository of scholarly citation data
    made available under a Creative Commons public domain dedication (CC0), which
    provides accurate bibliographic references harvested from the scholarly literature
    that others may freely build upon, enhance and reuse for any purpose, without
    restriction under copyright or database law.
  example: br/1
  homepage: https://w3id.org/oc/corpus
  mappings:
    miriam: occ
    n2t: occ
  name: OpenCitations Corpus
  pattern: ^[a-z][a-z]/[0-9]+$
  preferred_prefix: occ
  uri_format: https://w3id.org/oc/corpus/$1
oci:
  description: "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number,\
    \ where \u201Coci:\u201D is the identifier prefix, and is used to identify a citation\
    \ as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/\
    \ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations\
    \ Corpus are constructed by combining the OpenCitations Corpus local identifiers\
    \ for the citing and cited bibliographic resources, separating them with a dash.\
    \ For example, oci:2544384-7295288 is a valid OCI for the citation between two\
    \ papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created\
    \ for bibliographic resources described in an external bibliographic database,\
    \ if they are similarly identified there by identifiers having a unique numerical\
    \ part. For example, the OCI for the citation that exists between Wikidata resources\
    \ Q27931310 and Q22252312 is oci:01027931310\u201301022252312.\r\n\r\nOCIs can\
    \ also be created for bibliographic resources described in external bibliographic\
    \ database such as Crossref or DataCite where they are identified by alphanumeric\
    \ Digital Object Identifiers (DOIs), rather than purely numerical strings."
  example: 1-18
  homepage: http://opencitations.net
  mappings:
    miriam: oci
    n2t: oci
    prefixcommons: OCI
  name: Open Citation Identifier
  pattern: ^[0-9]+-[0-9]+$
  preferred_prefix: oci
  uri_format: https://w3id.org/oc/oci/$1
ocid:
  banana: ocid
  description: '''ocid'' stands for "Ontology Concept Identifiers" and are 12 digit
    long integers covering IDs in topical ontologies from anatomy up to toxicology.'
  example: '190000021540'
  homepage: https://ontochem.com/
  mappings:
    miriam: ocid
  name: Ontology Concept Identifiers
  namespace_in_lui: true
  pattern: ^[0-9]{12}$
  preferred_prefix: ocid
  uri_format: https://ocid.ontochem.com/prefname?ocid=$1
oclc:
  description: The global library cooperative OCLC maintains WorldCat. WorldCat is
    the world's largest network of library content and services. WorldCat libraries
    are dedicated to providing access to their resources on the Web, where most people
    start their search for information.
  example: '634515043'
  homepage: https://www.oclc.org/en/about.html
  mappings:
    miriam: oclc
    n2t: oclc
    prefixcommons: OCLC
  name: Online Computer Library Center (OCLC) WorldCat
  pattern: ^[0-9]+$
  preferred_prefix: oclc
  uri_format: https://www.worldcat.org/oclc/$1
odam:
  description: Experimental data table management software to make research data accessible
    and available for reuse with minimal effort on the part of the data provider.
    Designed to manage experimental data tables in an easy way for users, ODAM provides
    a model for structuring both data and metadata that facilitates data handling
    and analysis. It also encourages data dissemination according to FAIR principles
    by making the data interoperable and reusable by both humans and machines, allowing
    the dataset to be explored and then extracted in whole or in part as needed.
  example: frim1
  homepage: https://metabolome.cgfb.u-bordeaux.fr/
  mappings:
    miriam: odam
  name: Open Data for Access and Mining
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: odam
  uri_format: http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1
odc.sci:
  description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven
    repository to store, share, and publish spinal cord injury research data.
  example: '602'
  homepage: https://odc-sci.org
  mappings:
    miriam: odc.sci
  name: Open Data Commons for Spinal Cord Injury
  pattern: ^[0-9]*$
  preferred_prefix: odc.sci
  uri_format: https://odc-sci.org/data/$1
odc.tbi:
  description: The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven
    repository to store, share, and publish traumatic brain injury research data.
  example: '408'
  homepage: https://odc-tbi.org
  mappings:
    miriam: odc.tbi
  name: Open Data Commons for Traumatic Brain Injury
  pattern: ^[0-9]*$
  preferred_prefix: odc.tbi
  uri_format: https://odc-tbi.org/data/$1
odor:
  description: OdorDB stores information related to odorous compounds, specifically
    identifying those that have been shown to interact with olfactory receptors
  example: '74'
  homepage: http://senselab.med.yale.edu/OdorDB
  mappings:
    miriam: odor
    n2t: odor
    prefixcommons: ODOR
  name: Odor Molecules DataBase
  pattern: ^\d+$
  preferred_prefix: odor
  uri_format: http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5
ogg:
  banana: OGG
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqun Oliver He
    orcid: null
  description: 'OGG is a biological ontology in the area of genes and genomes. OGG
    uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document
    contains the genes and genomes of a list of selected organisms, including human,
    two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M,
    E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa
    strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish,
    fruit fly, yeast, etc.) may be found in other OGG subsets. '
  example: '3000887619'
  homepage: https://bitbucket.org/hegroup/ogg
  license: CC BY 3.0
  mappings:
    bioportal: OGG
    obofoundry: OGG
    ols: ogg
    ontobee: OGG
    prefixcommons: OGG
  name: The Ontology of Genes and Genomes
  preferred_prefix: OGG
  uri_format: http://purl.obolibrary.org/obo/OGG_$1
  version: 1.0.59
ogi:
  banana: OGI
  description: "OGI formalized the genomic element by defining an upper class 'genetic\
    \ interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous\
    \ physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.)\
    \ between and including two points (Nucleic Acid Base Residue) on a chromosome\
    \ or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated\
    \ paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) \u201CGenome, Gene, Interval and\
    \ Ontology\u201D Interdisciplinary Ontology Vol.2 - Proceedings of the Second\
    \ Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\n\
    Yu Lin, Hiroshi Tarui, Peter Simons (2009) \u201CFrom Ontology for Genetic Interval(OGI)\
    \ to Sequence Assembly \u2013 Ontology apply to next generation sequencing\u201D\
    \ Proceeding of the Semantic Web Applications and Tools for Life Science Workshop,\
    \ Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin,\
    \ Peter Simons (2010) \u201CDNA sequence from below: A Nominalist Approach\u201D\
    \ Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary\
    \ Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\
    \n\n"
  example: 0000019
  homepage: https://code.google.com/p/ontology-for-genetic-interval/
  mappings:
    bioportal: OGI
    obofoundry: OGI
    ols: ogi
    ontobee: OGI
    prefixcommons: OGI
  name: Ontology for genetic interval
  preferred_prefix: OGI
  uri_format: http://purl.obolibrary.org/obo/OGI_$1
  version: '2.0'
ogms:
  banana: OGMS
  contact:
    email: baeverma@jcvi.org
    github: null
    name: Brian Aevermann
    orcid: null
  description: 'The Ontology for General Medical Science (OGMS) is an ontology of
    entities involved in a clinical encounter. OGMS includes very general terms that
    are used across medical disciplines, including: ''disease'', ''disorder'', ''disease
    course'', ''diagnosis'', ''patient'', and ''healthcare provider''. OGMS uses the
    Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted
    to humans, but many terms can be applied to a variety of organisms. OGMS provides
    a formal theory of disease that can be further elaborated by specific disease
    ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology
    relations and is available in OWL and OBO formats.


    OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis
    and On Carcinomas and Other Pathological Entities. The ontology attempts to address
    some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX)
    and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly
    called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal
    Ontology.'
  example: '0000031'
  homepage: https://github.com/OGMS/ogms
  license: CC BY 4.0
  mappings:
    bioportal: OGMS
    obofoundry: OGMS
    ols: ogms
    ontobee: OGMS
    prefixcommons: OGMS
  name: Ontology for General Medical Science
  preferred_prefix: OGMS
  synonyms:
  - ogms/OMRE
  uri_format: http://purl.obolibrary.org/obo/OGMS_$1
  version: '2021-08-19'
ogsf:
  banana: OGSF
  contact:
    email: linikujp@gmail.com
    github: linikujp
    name: Asiyah Yu Lin
    orcid: null
  description: An application ontology to represent genetic susceptibility to a specific
    disease, adverse event, or a pathological process.
  example: '0000025'
  homepage: https://github.com/linikujp/OGSF
  license: CC BY 3.0
  mappings:
    bioportal: OGSF
    obofoundry: OGSF
    ols: ogsf
    ontobee: OGSF
    prefixcommons: OGSF
  name: Ontology of Genetic Susceptibility Factor
  preferred_prefix: OGSF
  uri_format: http://purl.obolibrary.org/obo/OGSF_$1
  version: '2.0'
ohd:
  banana: OHD
  contact:
    email: alanruttenberg@gmail.com
    github: alanruttenberg
    name: Alan Ruttenberg
    orcid: null
  description: The Oral Health and Disease Ontology was created, initially, to represent
    the content of dental practice health records.
  example: '0000006'
  homepage: https://purl.obolibrary.org/obo/ohd/home
  license: CC BY 4.0
  mappings:
    bioportal: OHD
    obofoundry: OHD
    ols: ohd
    ontobee: OHD
    prefixcommons: OHD
  name: The Oral Health and Disease Ontology
  preferred_prefix: OHD
  uri_format: http://purl.obolibrary.org/obo/OHD_$1
  version: '2016-06-27'
ohmi:
  banana: OHMI
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqun Oliver He
    orcid: null
  description: OHMI is a biomedical ontology that represents the entities and relations
    in the domain of host-microbiome interactions.
  example: '0000460'
  homepage: https://github.com/ohmi-ontology/ohmi
  license: CC BY 4.0
  mappings:
    bioportal: OHMI
    obofoundry: OHMI
    ols: ohmi
    ontobee: OHMI
    prefixcommons: OHMI
  name: Ontology of Host-Microbiome Interactions
  preferred_prefix: OHMI
  uri_format: http://purl.obolibrary.org/obo/OHMI_$1
  version: '2019-09-17'
ohpi:
  banana: OHPI
  contact:
    email: edong@umich.edu
    github: null
    name: Edison Ong
    orcid: null
  description: OHPI is a biomedical ontology in the area of host-pathogen interactions.
    OHPI is developed by following the OBO Foundry Principles (e.g., openness and
    collaboration).
  example: '9001411'
  homepage: https://github.com/OHPI/ohpi
  license: CC BY 4.0
  mappings:
    bioportal: OHPI
    obofoundry: OHPI
    ols: ohpi
    ontobee: OHPI
  name: Ontology of Host Pathogen Interactions
  preferred_prefix: OHPI
  uri_format: http://purl.obolibrary.org/obo/OHPI_$1
  version: '2019-10-02'
oid:
  description: OIDs provide a persistent identification of objects based on a hierarchical
    structure of Registration Authorities (RA), where each parent has an object identifier
    and allocates object identifiers to child nodes.
  example: 2.16.840
  homepage: http://www.oid-info.com/introduction.htm
  mappings:
    miriam: oid
    n2t: oid
  name: OID Repository
  pattern: ^[\d.]+$
  preferred_prefix: oid
  uri_format: http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display
olatdv:
  banana: OlatDv
  contact:
    email: frederic.bastian@unil.ch
    github: fbastian
    name: "Fr\xE9d\xE9ric Bastian"
    orcid: null
  description: Life cycle stages for Medaka
  example: '0000210'
  homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv
  license: CC BY 3.0
  mappings:
    bioportal: OLATDV
    obofoundry: OlatDv
    ols: olatdv
    ontobee: OLATDV
    prefixcommons: OLATDV
  name: Medaka Developmental Stages
  pattern: ^\d{7}$
  preferred_prefix: OlatDv
  uri_format: http://purl.obolibrary.org/obo/OLATDV_$1
  version: '2020-03-10'
om:
  description: 'The OM ontology provides classes, instances, and properties that represent
    the different concepts used for defining and using measures and units. It includes,
    for instance, common units such as the SI units meter and kilogram, but also units
    from other systems of units such as the mile or nautical mile. For many application
    areas it includes more specific units and quantities, such as the unit of the
    Hubble constant: km/s/Mpc, or the quantity vaselife.  OM defines the complete
    set of concepts in the domain as distinguished in the textual standards. As a
    result the ontology can answer a wider range of competency questions than the
    existing approaches do. The following application areas are supported by OM:  Geometry;
    Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics;
    Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics;
    Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics;
    Information technology; Typography; Shipping; Food engineering; Post-harvest;
    technology; Dynamics of texture and taste; Packaging'
  example: Dimension
  homepage: https://github.com/HajoRijgersberg/OM
  license: CC BY 4.0
  mappings:
    bioportal: OM
    ols: om
  name: Ontology of units of Measure
  preferred_prefix: om
  version: 2.0.34
oma.grp:
  description: OMA (Orthologous MAtrix) is a database that identifies orthologs among
    publicly available, complete genome sequences. It identifies orthologous relationships
    which can be accessed either group-wise, where all group members are orthologous
    to all other group members, or on a sequence-centric basis, where for a given
    protein all its orthologs in all other species are displayed. This collection
    references groupings of orthologs.
  example: LCSCCPN
  homepage: https://omabrowser.org/cgi-bin/gateway.pl
  mappings:
    miriam: oma.grp
    n2t: oma.grp
    prefixcommons: OMA.GRP
  name: OMA Group
  pattern: ^[A-Z]+$
  preferred_prefix: oma.grp
  uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1
oma.hog:
  banana: HOG
  description: 'Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix)
    database. Hierarchical orthologous groups are sets of genes that have started
    diverging from a single common ancestor gene at a certain taxonomic level of reference. '
  example: 0459895
  homepage: https://omabrowser.org
  mappings:
    miriam: oma.hog
  name: OMA HOGs
  pattern: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$
  preferred_prefix: oma.hog
  uri_format: https://omabrowser.org/oma/hog/HOG:$1
oma.protein:
  description: OMA (Orthologous MAtrix) is a database that identifies orthologs among
    publicly available, complete genome sequences. It identifies orthologous relationships
    which can be accessed either group-wise, where all group members are orthologous
    to all other group members, or on a sequence-centric basis, where for a given
    protein all its orthologs in all other species are displayed. This collection
    references individual protein records.
  example: HUMAN16963
  homepage: https://omabrowser.org/cgi-bin/gateway.pl
  mappings:
    miriam: oma.protein
    n2t: oma.protein
    prefixcommons: OMA.PROTEIN
  name: OMA Protein
  pattern: ^[A-Z0-9]{5}\d+$
  preferred_prefix: oma.protein
  uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1
omia:
  comment: website is down as of 2021-10-04
  deprecated: true
  description: Online Mendelian Inheritance in Animals is a a database of genes, inherited
    disorders and traits in animal species (other than human and mouse).
  example: '1000'
  homepage: http://omia.angis.org.au/
  mappings:
    miriam: omia
    n2t: omia
    prefixcommons: OMIA
  name: Online Mendelian Inheritance in Animals
  pattern: ^\d+$
  preferred_prefix: omia
  uri_format: http://omia.angis.org.au/$1/
omiabis:
  banana: OMIABIS
  contact:
    email: mbrochhausen@gmail.com
    github: null
    name: Mathias Brochhausen
    orcid: null
  deprecated: true
  description: An ontological version of MIABIS (Minimum Information About BIobank
    data Sharing)
  example: 0001079
  homepage: https://github.com/OMIABIS/omiabis-dev
  license: CC BY 3.0
  mappings:
    bioportal: OMIABIS
    obofoundry: OMIABIS
    ols: omiabis
    ontobee: OMIABIS
    prefixcommons: OMIABIS
  name: Ontologized MIABIS
  preferred_prefix: OMIABIS
  uri_format: http://purl.obolibrary.org/obo/OMIABIS_$1
  version: '2014-05-28'
omit:
  banana: OMIT
  contact:
    email: huang@southalabama.edu
    github: null
    name: Huang, Jingshan
    orcid: null
  description: The purpose of the OMIT ontology is to establish data exchange standards
    and common data elements in the microRNA (miR) domain. Biologists (cell biologists
    in particular) and bioinformaticians can make use of OMIT to leverage emerging
    semantic technologies in knowledge acquisition and discovery for more effective
    identification of important roles performed by miRs in humans' various diseases
    and biological processes (usually through miRs' respective target genes).
  example: 0000069
  homepage: http://omit.cis.usouthal.edu/
  license: CC BY 3.0
  mappings:
    bioportal: OMIT
    miriam: omit
    n2t: omit
    obofoundry: OMIT
    ols: omit
    ontobee: OMIT
    prefixcommons: OMIT
    wikidata: Q55118529
  name: Ontology for MicroRNA Target
  pattern: ^\d{7}$
  preferred_prefix: OMIT
  synonyms:
  - OMIT
  uri_format: https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1
  version: '2019-06-07'
omo:
  banana: OMO
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: null
  description: An ontology specifies terms that are used to annotate ontology terms
    for all OBO ontologies. The ontology was developed as part of Information Artifact
    Ontology (IAO).
  homepage: https://github.com/information-artifact-ontology/ontology-metadata
  license: CC0 1.0
  mappings:
    bioportal: OMO
    obofoundry: OMO
    ols: omo
    ontobee: OMO
  name: OBO Metadata Ontology
  no_own_terms: true
  preferred_prefix: OMO
  uri_format: http://purl.obolibrary.org/obo/OMO_$1
  version: '2020-06-08'
omop:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The OMOP Common Data Model allows for the systematic analysis of disparate
    observational databases. The concept behind this approach is to transform data
    contained within those databases into a common format (data model) as well as
    a common representation (terminologies, vocabularies, coding schemes), and then
    perform systematic analyses using a library of standard analytic routines that
    have been written based on the common format.
  homepage: https://www.ohdsi.org/data-standardization/the-common-data-model/
  name: Observational Medical Outcomes Partnership
  no_own_terms: true
  preferred_prefix: omop
  references:
  - https://github.com/callahantiff/OMOP2OBO
omp:
  banana: OMP
  contact:
    email: jimhu@tamu.edu
    github: null
    name: James C. Hu
    orcid: null
  description: An ontology of phenotypes covering microbes
  example: '0005067'
  homepage: http://microbialphenotypes.org
  license: CC BY 3.0
  mappings:
    bioportal: OMP
    obofoundry: OMP
    ols: omp
    ontobee: OMP
    prefixcommons: OMP
  name: Ontology of Microbial Phenotypes
  pattern: ^\d{7}$
  preferred_prefix: OMP
  uri_format: http://purl.obolibrary.org/obo/OMP_$1
  version: '2021-09-13'
omrse:
  banana: OMRSE
  contact:
    email: hoganwr@gmail.com
    github: hoganwr
    name: Bill Hogan
    orcid: null
  description: This ontology covers the domain of social entities that are related
    to health care, such as demographic information and the roles of various individuals
    and organizations.
  example: '00000022'
  homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview
  license: CC BY 4.0
  mappings:
    bioportal: OMRSE
    obofoundry: OMRSE
    ols: omrse
    ontobee: OMRSE
    prefixcommons: OMRSE
  name: Ontology of Medically Related Social Entities
  preferred_prefix: OMRSE
  uri_format: http://purl.obolibrary.org/obo/OMRSE_$1
  version: '2021-08-30'
oncotree:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: OncoTree is a dynamic and flexible community-driven cancer classification
    platform encompassing rare and common cancers that provides clinically relevant
    and appropriately granular cancer classification for clinical decision support
    systems and oncology research.
  example: BLL
  homepage: http://oncotree.mskcc.org
  name: OncoTree
  preferred_prefix: oncotree
  uri_format: http://oncotree.mskcc.org/api/tumorTypes/search/code/$1
one:
  banana: ONE
  contact:
    email: chen.yang@ugent.be
    github: cyang0128
    name: Chen Yang
    orcid: null
  description: An ontology to standardize research output of nutritional epidemiologic
    studies.
  example: '0001021'
  homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies
  license: CC BY 4.0
  mappings:
    bioportal: ONE
    obofoundry: ONE
    ols: one
    ontobee: ONE
  name: Ontology for Nutritional Epidemiology
  preferred_prefix: ONE
  uri_format: http://purl.obolibrary.org/obo/ONE_$1
ons:
  banana: ONS
  contact:
    email: francesco.vitali@ibba.cnr.it
    github: FrancescoVit
    name: Francesco Vitali
    orcid: null
  description: The Ontology for Nutritional Studies (ONS) has been developed as part
    of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define
    a common language and building ontologies for nutritional studies.
  example: '0000060'
  homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
  license: CC BY 4.0
  mappings:
    bioportal: ONS
    obofoundry: ONS
    ols: ons
    ontobee: ONS
  name: Ontology for Nutritional Studies
  preferred_prefix: ONS
  uri_format: http://purl.obolibrary.org/obo/ONS_$1
  version: June 2021 release
ontoavida:
  banana: ONTOAVIDA
  contact:
    email: fortuna@ebd.csic.es
    github: miguelfortuna
    name: Miguel A. Fortuna
    orcid: null
  description: OntoAvida develops an integrated vocabulary for the description of
    the most widely-used computational approach for studying evolution using digital
    organisms (i.e., self-replicating computer programs that evolve within a user-defined
    computational environment).
  homepage: https://gitlab.com/fortunalab/ontoavida
  license: CC BY 4.0
  mappings:
    obofoundry: ONTOAVIDA
  name: 'OntoAvida: ontology for Avida digital evolution platform'
  preferred_prefix: ONTOAVIDA
  uri_format: http://purl.obolibrary.org/obo/ONTOAVIDA_$1
ontoneo:
  banana: ONTONEO
  contact:
    email: fernanda.farinelli@gmail.com
    github: null
    name: Fernanda Farinelli
    orcid: null
  description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary
    to provide a representation of the data from electronic health records (EHRs)
    involved in the care of the pregnant woman, and of her baby.
  example: 00000098
  homepage: http://ontoneo.com
  license: CC BY 3.0
  mappings:
    bioportal: ONTONEO
    obofoundry: ONTONEO
    ols: ontoneo
    ontobee: ONTONEO
    prefixcommons: ONTONEO
  name: Obstetric and Neonatal Ontology
  preferred_prefix: ONTONEO
  uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1
  version: v1.6
oostt:
  banana: OOSTT
  contact:
    email: mbrochhausen@gmail.com
    github: null
    name: Mathias Brochhausen
    orcid: null
  description: An ontology built for representating the organizational components
    of trauma centers and trauma systems.
  example: 00000099
  homepage: https://github.com/OOSTT/OOSTT
  license: CC BY 4.0
  mappings:
    bioportal: OOSTT
    obofoundry: OOSTT
    ols: oostt
    ontobee: OOSTT
    prefixcommons: OOSTT
  name: Ontology of Organizational Structures of Trauma centers and Trauma systems
  preferred_prefix: OOSTT
  uri_format: http://purl.obolibrary.org/obo/OOSTT_$1
  version: '2021-01-11'
opb:
  description: The OPB is a reference ontology of classical physics as applied to
    the dynamics of biological systems. It is designed to encompass the multiple structural
    scales (multiscale atoms to organisms) and multiple physical domains (multidomain
    fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered
    in the study and analysis of biological organisms.
  example: '00573'
  homepage: http://bioportal.bioontology.org/ontologies/OPB
  mappings:
    bioportal: OPB
    miriam: opb
    n2t: opb
    prefixcommons: OPB
  name: Ontology of Physics for Biology
  pattern: ^\d+$
  preferred_prefix: opb
  uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1
opl:
  banana: OPL
  contact:
    email: preets79@gmail.com
    github: null
    name: Priti Parikh
    orcid: null
  description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage
    details of various parasites, including Trypanosoma sp., Leishmania major, and
    Plasmodium sp., etc. In addition to life cycle stages, the ontology also models
    necessary contextual details, such as host information, vector information, and
    anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows
    the rules set by the OBO Foundry consortium.
  example: 0000319
  homepage: https://github.com/OPL-ontology/OPL
  license: CC BY 4.0
  mappings:
    bioportal: OPL
    obofoundry: OPL
    ols: opl
    ontobee: OPL
    prefixcommons: OPL
  name: Ontology for Parasite LifeCycle
  preferred_prefix: OPL
  uri_format: http://purl.obolibrary.org/obo/OPL_$1
  version: '2021-01-28'
opm:
  description: The Orientations of Proteins in Membranes (OPM) database provides spatial
    positions of membrane-bound peptides and proteins of known three-dimensional structure
    in the lipid bilayer, together with their structural classification, topology
    and intracellular localization.
  example: 1h68
  homepage: http://opm.phar.umich.edu/
  mappings:
    miriam: opm
    n2t: opm
    prefixcommons: OPM
  name: Orientations of Proteins in Membranes Database
  pattern: ^[0-9][A-Za-z0-9]{3}$
  preferred_prefix: opm
  uri_format: http://opm.phar.umich.edu/protein.php?pdbid=$1
opmi:
  banana: OPMI
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqun Oliver He
    orcid: null
  description: OPMI is a biomedical ontology in the area of precision medicine and
    its related investigations. It is community-driven and developed by following
    the OBO Foundry ontology development principles.
  example: '0000101'
  homepage: https://github.com/OPMI/opmi
  license: CC BY 4.0
  mappings:
    bioportal: OPMI
    obofoundry: OPMI
    ols: opmi
    ontobee: OPMI
  name: Ontology of Precision Medicine and Investigation
  preferred_prefix: OPMI
  uri_format: http://purl.obolibrary.org/obo/OPMI_$1
  version: 1.0.130
orcid:
  description: ORCID (Open Researcher and Contributor ID) is an open, non-profit,
    community-based effort to create and maintain a registry of unique identifiers
    for individual researchers. ORCID records hold non-sensitive information such
    as name, email, organization name, and research activities.
  example: 0000-0002-5355-2576
  homepage: https://orcid.org
  mappings:
    biolink: ORCID
    miriam: orcid
    n2t: orcid
    prefixcommons: ORCID
    scholia: orcid
    wikidata: P496
  name: Open Researcher and Contributor ID
  pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$
  preferred_prefix: orcid
  synonyms:
  - ORCID
  - ORCiD
  uri_format: https://orcid.org/$1
ordb:
  description: The Olfactory Receptor Database (ORDB) is a repository of genomics
    and proteomics information of olfactory receptors (ORs). It includes a broad range
    of chemosensory genes and proteins, that includes in addition to ORs the taste
    papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory
    receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal
    pheromone receptors (FPRs).
  example: '8497'
  homepage: http://senselab.med.yale.edu/OrDB/
  mappings:
    miriam: ordb
    n2t: ordb
    prefixcommons: ORDB
  name: Olfactory Receptor Database
  pattern: ^\d+$
  preferred_prefix: ordb
  uri_format: http://senselab.med.yale.edu/ORDB/Data/$1
oridb.sacch:
  description: OriDB is a database of collated genome-wide mapping studies of confirmed
    and predicted replication origin sites in Saccharomyces cerevisiae and the fission
    yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.
  example: '1'
  homepage: http://cerevisiae.oridb.org/index.php
  mappings:
    miriam: oridb.sacch
    n2t: oridb.sacch
    prefixcommons: ORIDB.SACCH
  name: OriDB Saccharomyces
  pattern: ^\d+$
  preferred_prefix: oridb.sacch
  uri_format: http://cerevisiae.oridb.org/details.php?id=$1
oridb.schizo:
  description: OriDB is a database of collated genome-wide mapping studies of confirmed
    and predicted replication origin sites in Saccharomyces cerevisiae and the fission
    yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces
    pombe.
  example: '1'
  homepage: http://pombe.oridb.org/index.php
  mappings:
    miriam: oridb.schizo
    n2t: oridb.schizo
    prefixcommons: ORIDB.SCHIZO
  name: OriDB Schizosaccharomyces
  pattern: ^\d+$
  preferred_prefix: oridb.schizo
  uri_format: http://pombe.oridb.org/details.php?id=$1
ornaseq:
  banana: ORNASEQ
  contact:
    email: safisher@upenn.edu
    github: null
    name: Stephen Fisher
    orcid: null
  description: An application ontology designed to annotate next-generation sequencing
    experiments performed on RNA.
  example: '0000010'
  homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml
  license: CC BY 4.0
  mappings:
    bioportal: ORNASEQ
    obofoundry: ORNASEQ
    ols: ornaseq
    ontobee: ORNASEQ
  name: Ontology of RNA Sequencing
  preferred_prefix: ORNASEQ
  uri_format: http://purl.obolibrary.org/obo/ORNASEQ_$1
  version: '2019-07-08'
orphanet:
  description: "Orphanet is a reference portal for information on rare diseases and\
    \ orphan drugs. It\u2019s aim is to help improve the diagnosis, care and treatment\
    \ of patients with rare diseases."
  example: '85163'
  homepage: http://www.orpha.net/consor/
  mappings:
    miriam: orphanet
    n2t: orphanet
    prefixcommons: Orphanet
    uniprot: Orphanet
    wikidata: P1550
  name: Orphanet
  pattern: ^\d+$
  preferred_prefix: orphanet
  providers:
  - code: CURATOR_REVIEW
    description: Bio2RDF
    homepage: http://orphanet.bio2rdf.org/fct
    name: Bio2RDF
    uri_format: http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$1
  uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1
orphanet.ordo:
  description: "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary\
    \ for rare diseases, capturing relationships between diseases, genes and other\
    \ relevant features which will form a useful resource for the computational analysis\
    \ of rare diseases.\r\nIt integrates a nosology (classification of rare diseases),\
    \ relationships (gene-disease relations, epiemological data) and connections with\
    \ other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC,\
    \ ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."
  example: Orphanet_C023
  homepage: https://www.ebi.ac.uk/ols/ontologies/ordo
  license: CC BY 4.0
  mappings:
    biolink: ORPHA
    bioportal: ORDO
    cellosaurus: ORDO
    miriam: orphanet.ordo
    n2t: orphanet.ordo
    ols: ordo
    prefixcommons: ORPHANET.ORDO
  name: Orphanet Rare Disease Ontology
  pattern: ^Orphanet(_|:)C?\d+$
  preferred_prefix: orphanet.ordo
  synonyms:
  - ordo
  uri_format: http://www.orpha.net/ORDO/Orphanet_$1
  version: '3.2'
orth:
  description: 'The need of a common ontology for describing orthology information
    in biological research communities has led to the creation of the Orthology Ontology
    (ORTH). ORTH ontology is designed to describe sequence homology data available
    in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and
    etc.). By sequence homology data, we mostly mean gene region, gene and protein
    centric orthology, paralogy, and xenology information. Depending on the database,
    the homology information is structured in different ways. ORTH ontology accommodates
    these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster
    of homologous sequences and homologous-pairwise relations between sequences. In
    addition to the specific ORTH terms, this specification includes terms of the
    imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are
    pertinents to represent the information from various orthology databases in a
    homogeneous way.'
  example: HomologyRelation
  homepage: http://purl.org/net/orth
  mappings:
    bioportal: ORTH
    ols: orth
  name: Orthology Ontology
  preferred_prefix: orth
  version: 'This ontology is the second version of the orthology ontology first published
    in 2015 and available at http://purl.bioontology.org/ontology/ORTH .

    @authors T.M. de Farias, H. Chiba, J.T. Fernandez-Breis, E. Antezana, D. Kuznetsov,
    C. Dessimoz and F. Villiers.'
orthodb:
  description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding
    genes across vertebrates, arthropods, and fungi. Orthology refers to the last
    common ancestor of the species under consideration, and thus OrthoDB explicitly
    delineates orthologs at each radiation along the species phylogeny. The database
    of orthologs presents available protein descriptors, together with Gene Ontology
    and InterPro attributes, which serve to provide general descriptive annotations
    of the orthologous groups
  example: Q9P0K8
  homepage: http://cegg.unige.ch/orthodb4
  mappings:
    miriam: orthodb
    n2t: orthodb
    prefixcommons: ORTHODB
    uniprot: OrthoDB
  name: OrthoDB
  pattern: ^\w+$
  preferred_prefix: orthodb
  uri_format: http://cegg.unige.ch/orthodb/results?searchtext=$1
oryzabase.gene:
  description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
    plant by integrating biological data with molecular genomic information. It contains
    information about rice development and anatomy, rice mutants, and genetic resources,
    especially for wild varieties of rice. Developmental and anatomical descriptions
    include in situ gene expression data serving as stage and tissue markers. This
    collection references gene information.
  example: '117'
  homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
  mappings:
    miriam: oryzabase.gene
    n2t: oryzabase.gene
    prefixcommons: ORYZABASE.GENE
  name: Oryzabase Gene
  pattern: ^\d+$
  preferred_prefix: oryzabase.gene
  uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1
oryzabase.mutant:
  description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
    plant by integrating biological data with molecular genomic information. It contains
    information about rice development and anatomy, rice mutants, and genetic resources,
    especially for wild varieties of rice. Developmental and anatomical descriptions
    include in situ gene expression data serving as stage and tissue markers. This
    collection references mutant strain information.
  example: '21393'
  homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
  mappings:
    miriam: oryzabase.mutant
    n2t: oryzabase.mutant
    prefixcommons: ORYZABASE.MUTANT
  name: Oryzabase Mutant
  pattern: ^\d+$
  preferred_prefix: oryzabase.mutant
  uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1
oryzabase.reference:
  description: The Oryzabase is a comprehensive rice science database established
    in 2000 by rice researcher's committee in Japan.
  example: '42840'
  homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
  mappings:
    miriam: oryzabase.reference
    n2t: oryzabase.reference
  name: Oryzabase Reference
  pattern: ^\d+$
  preferred_prefix: oryzabase.reference
  uri_format: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1
oryzabase.stage:
  description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
    plant by integrating biological data with molecular genomic information. It contains
    information about rice development and anatomy, rice mutants, and genetic resources,
    especially for wild varieties of rice. Developmental and anatomical descriptions
    include in situ gene expression data serving as stage and tissue markers. This
    collection references development stage information.
  example: '34'
  homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
  mappings:
    miriam: oryzabase.stage
    n2t: oryzabase.stage
    prefixcommons: ORYZABASE.STAGE
  name: Oryzabase Stage
  pattern: ^\d+$
  preferred_prefix: oryzabase.stage
  uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1
oryzabase.strain:
  description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
    plant by integrating biological data with molecular genomic information. It contains
    information about rice development and anatomy, rice mutants, and genetic resources,
    especially for wild varieties of rice. Developmental and anatomical descriptions
    include in situ gene expression data serving as stage and tissue markers. This
    collection references wild strain information.
  example: '1'
  homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
  mappings:
    miriam: oryzabase.strain
    n2t: oryzabase.strain
    prefixcommons: ORYZABASE.STRAIN
  name: Oryzabase Strain
  pattern: ^\d+$
  preferred_prefix: oryzabase.strain
  uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1
otl:
  description: Oryza Tag Line is a database that was developed to collect information
    generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion
    lines resulting in potential gene disruptions. It collates morpho-physiological
    alterations observed during field evaluation, with each insertion line documented
    through a generic passport data including production records, seed stocks and
    FST information.
  example: AADB12
  homepage: http://oryzatagline.cirad.fr/
  mappings:
    miriam: otl
    n2t: otl
    prefixcommons: OTL
  name: Oryza Tag Line
  pattern: ^A[A-Z]+\d+$
  preferred_prefix: otl
  uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1
ovae:
  banana: OVAE
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqunh He
    orcid: null
  description: 'OVAE is a biomedical ontology in the area of vaccine adverse events.
    OVAE is an extension of the community-based Ontology of Adverse Events (OAE). '
  example: 0000609
  homepage: http://www.violinet.org/ovae/
  license: CC BY 3.0
  mappings:
    bioportal: OVAE
    obofoundry: OVAE
    ols: ovae
    ontobee: OVAE
    prefixcommons: OVAE
  name: Ontology of Vaccine Adverse Events
  preferred_prefix: OVAE
  uri_format: http://purl.obolibrary.org/obo/OVAE_$1
  version: 1.0.34
owl:
  description: 'Overview of the Web Ontology Language (OWL) which provides an introduction
    to OWL by informally describing the features of each of the sublanguages. '
  example: Ontology
  homepage: https://www.w3.org/TR/owl-features/
  mappings:
    prefixcommons: owl
  name: OWL Ontology
  preferred_prefix: owl
  uri_format: http://www.w3.org/2002/07/owl#$1
p3db.protein:
  description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides
    information on experimentally determined phosphorylation sites in the proteins
    of various plant species. This collection references plant proteins that contain
    phosphorylation sites.
  example: '70'
  homepage: http://www.p3db.org/
  mappings:
    miriam: p3db.protein
    n2t: p3db.protein
    prefixcommons: P3DB.PROTEIN
  name: P3DB Protein
  pattern: ^\d+$
  preferred_prefix: p3db.protein
  uri_format: http://www.p3db.org/protein.php?id=$1&amp;ref=0
p3db.site:
  description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides
    information on experimentally determined phosphorylation sites in the proteins
    of various plant species. This collection references phosphorylation sites in
    proteins.
  example: '65'
  homepage: http://www.p3db.org/
  mappings:
    miriam: p3db.site
    n2t: p3db.site
    prefixcommons: P3DB.SITE
  name: P3DB Site
  pattern: ^\d+$
  preferred_prefix: p3db.site
  uri_format: http://www.p3db.org/phosphosite.php?id=$1&ref=0
paleodb:
  description: The Paleobiology Database seeks to provide researchers and the public
    with information about the entire fossil record. It stores global, collection-based
    occurrence and taxonomic data for marine and terrestrial animals and plants of
    any geological age, as well as web-based software for statistical analysis of
    the data.
  example: '83088'
  homepage: http://paleodb.org/
  mappings:
    miriam: paleodb
    n2t: paleodb
    prefixcommons: PALEODB
  name: Paleobiology Database
  pattern: ^\d+$
  preferred_prefix: paleodb
  uri_format: http://fossilworks.org/?a=taxonInfo&taxon_no=$1
panorama:
  description: Panorama is a freely-available, open-source repository server application
    for targeted mass spectrometry assays that integrates into a Skyline mass spec
    workflow. It makes links to the Proteomics Exchange when possible.
  example: FxnI151FMs
  homepage: https://panoramaweb.org
  mappings:
    fairsharing: FAIRsharing.uBpQ1q
  name: Panorama Public
  preferred_prefix: panorama
  uri_format: https://panoramaweb.org/$1.url
panther.family:
  description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification
    System is a resource that classifies genes by their functions, using published
    scientific experimental evidence and evolutionary relationships to predict function
    even in the absence of direct experimental evidence. This collection references
    groups of genes that have been organised as families.
  example: PTHR12345
  homepage: http://www.pantherdb.org/
  mappings:
    biolink: PANTHER.FAMILY
    go: PANTHER
    miriam: panther.family
    n2t: panther.family
    prefixcommons: PANTHER.FAMILY
  name: Protein ANalysis THrough Evolutionary Relationships Classification System
  pattern: ^PTHR\d{5}(\:SF\d{1,3})?$
  preferred_prefix: panther.family
  uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1
panther.node:
  description: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships)\
    \ Classification System is a resource that classifies genes by their functions,\
    \ using published scientific experimental evidence and evolutionary relationships\
    \ to predict function even in the absence of direct experimental evidence. PANTHER\
    \ tree is a key element of the PANTHER System to represent \u2018all\u2019 of\
    \ the evolutionary events in the gene family. PANTHER nodes represent the evolutionary\
    \ events, either speciation or duplication, within the tree. PANTHER is maintaining\
    \ stable identifier for these nodes."
  example: PTN000000026
  homepage: http://pantree.org/
  mappings:
    miriam: panther.node
    n2t: panther.node
    prefixcommons: PANTHER.NODE
  name: PANTHER Node
  pattern: ^PTN\d{9}$
  preferred_prefix: panther.node
  uri_format: http://www.pantree.org/node/annotationNode.jsp?id=$1
panther.pathway:
  description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification
    System is a resource that classifies genes by their functions, using published
    scientific experimental evidence and evolutionary relationships to predict function
    even in the absence of direct experimental evidence. The PANTHER Pathway collection
    references pathway information, primarily for signaling pathways, each with subfamilies
    and protein sequences mapped to individual pathway components.
  example: P00024
  homepage: http://www.pantherdb.org/
  mappings:
    miriam: panther.pathway
    n2t: panther.pathway
    prefixcommons: PANTHER.PATHWAY
  name: PANTHER Pathway
  pattern: ^P\d{5}$
  preferred_prefix: panther.pathway
  uri_format: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1
panther.pthcmp:
  description: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships)\
    \ Classification System is a resource that classifies genes by their functions,\
    \ using published scientific experimental evidence and evolutionary relationships\
    \ to predict function even in the absence of direct experimental evidence. The\
    \ PANTHER Pathway Component collection references specific classes of molecules\
    \ that play the same mechanistic role within a pathway, across species. Pathway\r\
    \ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified\
    \ component is a protein, DNA, or transcribed RNA, it is associated with protein\
    \ sequences in the PANTHER protein family trees through manual curation."
  example: P00266
  homepage: http://www.pantherdb.org/
  mappings:
    miriam: panther.pthcmp
    n2t: panther.pthcmp
    prefixcommons: PANTHER.PTHCMP
  name: PANTHER Pathway Component
  pattern: ^(G|P|U|C|S)\d{5}$
  preferred_prefix: panther.pthcmp
  uri_format: http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1
pao:
  banana: PAO
  contact:
    email: jaiswalp@science.oregonstate.edu
    github: null
    name: Pankaj Jaiswal
    orcid: null
  deprecated: true
  homepage: http://www.plantontology.org
  mappings:
    obofoundry: PAO
    prefixcommons: PAO
  name: Plant Anatomy Ontology
  preferred_prefix: PAO
  uri_format: http://purl.obolibrary.org/obo/PAO_$1
pass2:
  deprecated: true
  description: The PASS2 database provides alignments of proteins related at the superfamily
    level and are characterized by low sequence identity.
  example: '46977'
  homepage: http://caps.ncbs.res.in/pass2
  mappings:
    miriam: pass2
    n2t: pass2
    prefixcommons: PASS2
  name: Protein Alignment organised as Structural Superfamily
  pattern: ^\d+$
  preferred_prefix: pass2
  uri_format: http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1
pathbank:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: PathBank is an interactive, visual database containing more than 100
    000 machine-readable pathways found in model organisms such as humans, mice, E.
    coli, yeast, and Arabidopsis thaliana.
  example: SMP0000219
  homepage: https://pathbank.org
  name: PathBank
  pattern: ^(SMP|PW)\d+$
  preferred_prefix: pathbank
  uri_format: https://pathbank.org/view/$1
pathwaycommons:
  description: Pathway Commons is a convenient point of access to biological pathway
    information collected from public pathway databases, which you can browse or search.
    It is a collection of publicly available pathways from multiple organisms that
    provides researchers with convenient access to a comprehensive collection of pathways
    from multiple sources represented in a common language.
  example: '485991'
  homepage: http://www.pathwaycommons.org/pc/
  mappings:
    miriam: pathwaycommons
    n2t: pathwaycommons
    prefixcommons: PATHWAYCOMMONS
    uniprot: PathwayCommons
  name: Pathway Commons
  pattern: ^\d+$
  preferred_prefix: pathwaycommons
  uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1
pato:
  banana: PATO
  contact:
    email: g.gkoutos@gmail.com
    github: gkoutos
    name: George Gkoutos
    orcid: null
  description: PATO is an ontology of phenotypic qualities, intended for use in a
    number of applications, primarily defining composite phenotypes and phenotype  annotation.
  example: 0001998
  homepage: https://github.com/pato-ontology/pato/
  license: CC BY 3.0
  mappings:
    bioportal: PATO
    go: PATO
    miriam: pato
    n2t: pato
    obofoundry: PATO
    ols: pato
    ontobee: PATO
    prefixcommons: PATO
  name: Phenotype And Trait Ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: PATO
  uri_format: https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1
  version: '2021-11-05'
pav:
  contributor:
    email: null
    github: null
    name: Nico Matentzoglu
    orcid: 0000-0002-7356-1779
  description: PAV is a lightweight ontology for tracking provenance, authorship,
    and versioning. It specializes the W3C provenance ontology PROV-O in order to
    describe authorship, curation and digital creation of online resources.
  example: authoredBy
  homepage: https://pav-ontology.github.io/pav/
  mappings:
    biolink: pav
    bioportal: PAV
    prefixcommons: pav
  name: Provenance, Authoring, and Versioning Vocabulary
  pattern: ^[a-z][a-zA-Z]+$
  preferred_prefix: pav
  reviewer:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://pav-ontology.github.io/pav/index.html#http://purl.org/pav/$1
paxdb.organism:
  description: PaxDb is a resource dedicated to integrating information on absolute
    protein abundance levels across different organisms. Publicly available experimental
    data are mapped onto a common namespace and, in the case of tandem mass spectrometry
    data, re-processed using a standardized spectral counting pipeline. Data sets
    are scored and ranked to assess consistency against externally provided protein-network
    information. PaxDb provides whole-organism data as well as tissue-resolved data,
    for numerous proteins. This collection references protein abundance information
    by species.
  example: '9606'
  homepage: http://pax-db.org/
  mappings:
    miriam: paxdb.organism
    n2t: paxdb.organism
    prefixcommons: PAXDB.ORGANISM
  name: PaxDb Organism
  pattern: ^\d+$
  preferred_prefix: paxdb.organism
  uri_format: http://pax-db.org/#!species/$1
paxdb.protein:
  description: PaxDb is a resource dedicated to integrating information on absolute
    protein abundance levels across different organisms. Publicly available experimental
    data are mapped onto a common namespace and, in the case of tandem mass spectrometry
    data, re-processed using a standardized spectral counting pipeline. Data sets
    are scored and ranked to assess consistency against externally provided protein-network
    information. PaxDb provides whole-organism data as well as tissue-resolved data,
    for numerous proteins. This collection references individual protein abundance
    levels.
  example: '977869'
  homepage: http://pax-db.org/
  mappings:
    miriam: paxdb.protein
    n2t: paxdb.protein
    prefixcommons: PAXDB.PROTEIN
  name: PaxDb Protein
  pattern: ^\d+$
  preferred_prefix: paxdb.protein
  uri_format: http://pax-db.org/#!protein/$1
pazar:
  description: The PAZAR database unites independently created and maintained data
    collections of transcription factor and regulatory sequence annotation. It provides
    information on the sequence and target of individual transcription factors.
  example: TF0001053
  homepage: http://www.pazar.info/
  mappings:
    miriam: pazar
    n2t: pazar
    prefixcommons: PAZAR
  name: Pazar Transcription Factor
  pattern: ^TF\w+$
  preferred_prefix: pazar
  uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1
pco:
  banana: PCO
  contact:
    email: rlwalls2008@gmail.com
    github: ramonawalls
    name: Ramona Walls
    orcid: null
  description: The Population and Community Ontology (PCO) describes material entities,
    qualities, and processes related to collections of interacting organisms such
    as populations and communities. It is taxon neutral, and can be used for any species,
    including humans. The classes in the PCO are useful for describing evolutionary
    processes, organismal interactions, and ecological experiments. Practical applications
    of the PCO include community health care, plant pathology, behavioral studies,
    sociology, and ecology.
  example: '0000021'
  homepage: https://github.com/PopulationAndCommunityOntology/pco
  license: CC0 1.0
  mappings:
    bioportal: PCO
    obofoundry: PCO
    ols: pco
    ontobee: PCO
    prefixcommons: PCO
  name: Population and Community Ontology
  pattern: ^\d{7}$
  preferred_prefix: PCO
  uri_format: http://purl.obolibrary.org/obo/PCO_$1
  version: '2021-05-03'
pd_st:
  banana: PD_ST
  contact:
    email: henrich@embl.de
    github: null
    name: Thorsten Heinrich
    orcid: null
  deprecated: true
  homepage: http://4dx.embl.de/platy
  mappings:
    obofoundry: PD_ST
    prefixcommons: PD_ST
  name: Platynereis stage ontology
  preferred_prefix: PD_ST
  uri_format: http://purl.obolibrary.org/obo/PD_ST_$1
pdb:
  description: The Protein Data Bank is the single worldwide archive of structural
    data of biological macromolecules.
  example: 2gc4
  homepage: https://www.pdb.org/
  mappings:
    fairsharing: FAIRsharing.2t35ja
    go: PDB
    miriam: pdb
    n2t: pdb
    ncbi: PDB
    prefixcommons: PDB
    uniprot: PDB
    wikidata: P638
  name: PDB structure ID
  pattern: ^[0-9][A-Za-z0-9]{3}$
  preferred_prefix: pdb
  providers:
  - code: CURATOR_REVIEW
    description: Proteopedia
    homepage: http://www.proteopedia.org/
    name: Proteopedia
    uri_format: http://proteopedia.org/wiki/index.php/$1
  - code: ebi
    description: Protein Databank through PDBsum
    homepage: https://www.ebi.ac.uk/pdbsum/
    name: Protein Databank through PDBsum
    uri_format: https://www.ebi.ac.uk/pdbsum/$1
  synonyms:
  - pdbe
  - wwpdb
  uri_format: https://www.rcsb.org/structure/$1
pdb-ccd:
  comment: might be same as pdb.ligand, not sure though
  description: The Chemical Component Dictionary is as an external reference file
    describing all residue and small molecule components found in Protein Data Bank
    entries. It contains detailed chemical descriptions for standard and modified
    amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical
    definition includes descriptions of chemical properties such as stereochemical
    assignments, aromatic bond assignments, idealized coordinates, chemical descriptors
    (SMILES & InChI), and systematic chemical names.
  example: AB0
  has_canonical: pdb.ligand
  homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/
  mappings:
    miriam: pdb-ccd
    n2t: pdb-ccd
    prefixcommons: PDB-CCD
  name: Chemical Component Dictionary
  pattern: ^\w{3}$
  preferred_prefix: pdb-ccd
  synonyms:
  - pdbechem
  uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
pdb.ligand:
  description: The Protein Data Bank is the single worldwide archive of structural
    data of biological macromolecules. This collection references ligands.
  example: TRQ
  homepage: http://www.pdb.org/
  mappings:
    miriam: pdb.ligand
    n2t: pdb.ligand
    prefixcommons: PDB.LIGAND
    wikidata: P3636
  name: Protein Data Bank Ligand
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: pdb.ligand
  providers:
  - code: CURATOR_REVIEW
    description: PDB Ligand at Protein Databank in Europe (PDBe)
    homepage: https://www.pdbe.org/
    name: PDB Ligand at Protein Databank in Europe (PDBe)
    uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
  synonyms:
  - PDB_CHEM_ID
  uri_format: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1
pdro:
  banana: PDRO
  contact:
    email: paul.fabry@usherbrooke.ca
    github: pfabry
    name: Paul Fabry
    orcid: null
  description: An ontology to describe entities related to prescription of drugs
  example: 0010039
  homepage: https://github.com/OpenLHS/PDRO
  license: CC BY 4.0
  mappings:
    bioportal: PDRO
    obofoundry: PDRO
    ols: pdro
    ontobee: PDRO
    prefixcommons: PDRO
  name: The Prescription of Drugs Ontology
  preferred_prefix: PDRO
  uri_format: http://purl.obolibrary.org/obo/PDRO_$1
  version: '2021-06-08'
pdumdv:
  banana: PdumDv
  contact:
    email: frederic.bastian@unil.ch
    github: fbastian
    name: "Fr\xE9d\xE9ric Bastian"
    orcid: null
  description: Life cycle stages for Platynereis dumerilii
  example: '0001410'
  homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv
  license: CC BY 3.0
  mappings:
    bioportal: PDUMDV
    obofoundry: PdumDv
    ols: pdumdv
    ontobee: PDUMDV
    prefixcommons: PDUMDV
  name: Platynereis Developmental Stages
  pattern: ^\d{7}$
  preferred_prefix: PdumDv
  synonyms:
  - PdumDv
  uri_format: http://purl.obolibrary.org/obo/PDUMDV_$1
  version: '2020-03-10'
peco:
  banana: EO
  contact:
    email: jaiswalp@science.oregonstate.edu
    github: null
    name: Pankaj Jaiswal
    orcid: null
  deprecated: true
  description: The Plant Environment Ontology is a set of standardized controlled
    vocabularies to describe various types of treatments given to an individual plant
    / a population or a cultured tissue and/or cell type sample to evaluate the response
    on its exposure. It also includes the study types, where the terms can be used
    to identify the growth study facility. Each growth facility such as field study,
    growth chamber, green house etc is a environment on its own it may also involve
    instances of biotic and abiotic environments as supplemental treatments used in
    these studies.
  example: '0007114'
  homepage: http://planteome.org/
  license: CC BY 4.0
  mappings:
    bioportal: PECO
    miriam: eo
    n2t: eo
    obofoundry: EO
    ols: peco
    ontobee: PECO
    prefixcommons: PECO
  name: Plant Environment Ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: PECO
  synonyms:
  - eo
  uri_format: http://archive.gramene.org/db/ontology/search?query=EO:$1
  version: '2020-08-21'
ped:
  description: The Protein Ensemble Database is an open access database for the deposition
    of structural ensembles, including intrinsically disordered proteins.
  example: PED00037
  homepage: https://proteinensemble.org/
  mappings:
    miriam: ped
  name: Protein Ensemble Database
  pattern: ^PED\d{5}$
  preferred_prefix: ped
  uri_format: https://proteinensemble.org/$1
ped.ensemble:
  description: The Protein Ensemble Database is an open access database for the deposition
    of structural ensembles, including intrinsically disordered proteins.
  example: PED00017e001
  homepage: https://proteinensemble.org/
  mappings:
    miriam: ped.ensemble
  name: Protein Ensemble Database ensemble
  part_of: ped
  pattern: ^PED\d{5}e\d{3}$
  preferred_prefix: ped.ensemble
  uri_format: https://proteinensemble.org/$1
peff:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: '0001011'
  homepage: https://www.psidev.info/peff
  name: PSI Extended File Format
  preferred_prefix: peff
peptideatlas:
  description: The PeptideAtlas Project provides a publicly accessible database of
    peptides identified in tandem mass spectrometry proteomics studies and software
    tools.
  example: PAp00000009
  homepage: http://www.peptideatlas.org/
  mappings:
    miriam: peptideatlas
    n2t: peptideatlas
    prefixcommons: PEPTIDEATLAS
    uniprot: PeptideAtlas
  name: PeptideAtlas
  pattern: ^PAp[0-9]{8}$
  preferred_prefix: peptideatlas
  uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1
peptideatlas.dataset:
  description: Experiment details about PeptideAtlas entries. Each PASS entry provides
    direct access to the data files submitted to PeptideAtlas.
  example: PASS01237
  homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary
  mappings:
    miriam: peptideatlas.dataset
    n2t: peptideatlas.dataset
  name: PeptideAtlas Dataset
  pattern: ^PASS\d{5}$
  preferred_prefix: peptideatlas.dataset
  uri_format: http://www.peptideatlas.org/PASS/$1
peroxibase:
  description: Peroxibase provides access to peroxidase sequences from all kingdoms
    of life, and provides a series of bioinformatics tools and facilities suitable
    for analysing these sequences.
  example: '5282'
  homepage: http://peroxibase.toulouse.inra.fr/
  mappings:
    miriam: peroxibase
    n2t: peroxibase
    prefixcommons: PEROXIBASE
    uniprot: PeroxiBase
  name: Peroxibase
  pattern: ^\d+$
  preferred_prefix: peroxibase
  uri_format: http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1
pesticides:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "The Alan Wood\u2019s Pesticides is a compendium of pesticides which\
    \ contain nomenclature data sheets for more than 1700 different active ingredients."
  example: derivatives%2Fthiocyclam%20hydrochloride
  homepage: http://www.alanwood.net/pesticides
  name: Alan Wood's Pesticides
  preferred_prefix: pesticides
  uri_format: http://www.alanwood.net/pesticides/$1.html
pfam:
  description: The Pfam database contains information about protein domains and families.
    For each entry a protein sequence alignment and a Hidden Markov Model is stored.
  example: PF11779
  homepage: https://pfam.xfam.org/
  mappings:
    go: Pfam
    miriam: pfam
    n2t: pfam
    ncbi: PFAM
    prefixcommons: PFAM
    uniprot: Pfam
    wikidata: P3519
  name: Pfam ID
  pattern: ^PF\d{5}$
  preferred_prefix: pfam
  synonyms:
  - PF
  uri_format: https://pfam.xfam.org/family/$1
pfam.clan:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Higher order grouping of Pfam families
  example: CL0192
  homepage: https://pfam.xfam.org
  name: Pfam Clans
  pattern: ^CL\d+$
  preferred_prefix: pfam.clan
  uri_format: https://pfam.xfam.org/clan/$1
pfr:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Database that provides a central location for scientists to browse
    uniquely observed proteoforms and to contribute their own datasets.
  example: '1001'
  homepage: http://repository.topdownproteomics.org/proteoforms
  name: Proteoform Atlas
  pattern: ^\d+$
  preferred_prefix: pfr
  synonyms:
  - TDR
  uri_format: http://repository.topdownproteomics.org/proteoforms/$1
pgdso:
  banana: PGDSO
  contact:
    email: po-discuss@plantontology.org
    github: null
    name: Plant Ontology Administrators
    orcid: null
  deprecated: true
  homepage: http://www.plantontology.org
  mappings:
    obofoundry: PGDSO
    prefixcommons: PGDSO
  name: Plant Growth and Development Stage
  preferred_prefix: PGDSO
  uri_format: http://purl.obolibrary.org/obo/PGDSO_$1
pgs:
  description: The Polygenic Score (PGS) Catalog is an open database of PGS and the
    relevant metadata required for accurate application and evaluation.
  example: PGS000018
  homepage: http://pgscatalog.org
  mappings:
    miriam: pgs
  name: Polygenic Score Catalog
  pattern: ^PGS[0-9]{6}$
  preferred_prefix: pgs
  uri_format: https://www.pgscatalog.org/pgs/$1
pgx:
  description: The Progenetix database provides an overview of mutation data in cancer,
    with a focus on copy number abnormalities (CNV / CNA), for all types of human
    malignancies. The resource contains genome profiles of more than 130'000 individual
    samples and represents about 700 cancer types, according to the NCIt "neoplasm"
    classification. Additionally to this genome profiles and associated metadata,
    the website present information about thousands of publications referring to cancer
    genome profiling experiments, and services for mapping cancer classifications
    and accessing supplementary data through its APIs.
  example: pgxbs-kftva5zv
  homepage: https://progenetix.org/
  mappings:
    miriam: pgx
    n2t: pgx
    prefixcommons: PGX
  name: Progenetix
  pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$
  preferred_prefix: pgx
  uri_format: https://progenetix.org/services/ids/$1
pharmacodb.cell:
  description: Web-application assembling the largest in vitro drug screens in a single
    database, and allowing users to easily query the union of studies released to
    date. Query by cell line.
  example: 22RV1_12_2019
  homepage: https://pharmacodb.ca/cell_lines
  mappings:
    cellosaurus: PharmacoDB
  name: PharmacoDB Cells
  preferred_prefix: pharmacodb.cell
  uri_format: https://pharmacodb.ca/cell_lines/$1
pharmacodb.dataset:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Web-application assembling the largest in vitro drug screens in a single
    database, and allowing users to easily query the union of studies released to
    date. Query by dataset.
  example: '1'
  homepage: https://pharmacodb.ca/datasets
  name: PharmacoDB Datasets
  preferred_prefix: pharmacodb.dataset
  uri_format: https://pharmacodb.ca/datasets/$1
pharmacodb.tissue:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Web-application assembling the largest in vitro drug screens in a single
    database, and allowing users to easily query the union of studies released to
    date. Query by tissue.
  example: '13'
  homepage: https://pharmacodb.ca/tissues
  name: PharmacoDB Tissues
  preferred_prefix: pharmacodb.tissue
  uri_format: https://pharmacodb.ca/tissues/$1
pharmgkb.disease:
  description: The PharmGKB database is a central repository for genetic, genomic,
    molecular and cellular phenotype data and clinical information about people who
    have participated in pharmacogenomics research studies. The data includes, but
    is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research
    in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
    domains.
  example: PA447218
  homepage: http://www.pharmgkb.org/
  mappings:
    miriam: pharmgkb.disease
    n2t: pharmgkb.disease
    prefixcommons: PHARMGKB.DISEASE
    wikidata: P7001
  name: PharmGKB Disease
  pattern: ^PA\d+$
  preferred_prefix: pharmgkb.disease
  uri_format: http://www.pharmgkb.org/disease/$1
pharmgkb.drug:
  description: The PharmGKB database is a central repository for genetic, genomic,
    molecular and cellular phenotype data and clinical information about people who
    have participated in pharmacogenomics research studies. The data includes, but
    is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research
    in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
    domains.
  example: PA448710
  homepage: http://www.pharmgkb.org/
  mappings:
    miriam: pharmgkb.drug
    n2t: pharmgkb.drug
    prefixcommons: PHARMGKB.DRUG
    wikidata: P7001
  name: PharmGKB Drug
  pattern: ^PA\d+$
  preferred_prefix: pharmgkb.drug
  uri_format: http://www.pharmgkb.org/drug/$1
pharmgkb.gene:
  description: The PharmGKB database is a central repository for genetic, genomic,
    molecular and cellular phenotype data and clinical information about people who
    have participated in pharmacogenomics research studies. The data includes, but
    is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research
    in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
    domains.
  example: PA131
  homepage: http://www.pharmgkb.org/
  mappings:
    bioportal: PHARMGKB
    go: PharmGKB
    miriam: pharmgkb.gene
    n2t: pharmgkb.gene
    prefixcommons: PHARMGKB.GENE
    wikidata: P7001
  name: Pharmacogenetics and Pharmacogenomics Knowledge Base
  pattern: ^PA\w+$
  preferred_prefix: pharmgkb.gene
  uri_format: http://www.pharmgkb.org/gene/$1
pharmgkb.pathways:
  description: "The PharmGKB database is a central repository for genetic, genomic,\
    \ molecular and cellular phenotype data and clinical information about people\
    \ who have participated in pharmacogenomics research studies. The data includes,\
    \ but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic\
    \ research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter\
    \ domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways\
    \ which focus on candidate genes and gene groups and associated genotype and phenotype\
    \ data of relevance for pharmacogenetic and pharmacogenomic studies."
  example: PA146123006
  homepage: http://www.pharmgkb.org/
  mappings:
    miriam: pharmgkb.pathways
    n2t: pharmgkb.pathways
    prefixcommons: PHARMGKB.PATHWAYS
    wikidata: P7001
  name: PharmGKB Pathways
  pattern: ^PA\d+$
  preferred_prefix: pharmgkb.pathways
  uri_format: http://www.pharmgkb.org/pathway/$1
phenolexplorer:
  description: Phenol-Explorer is an electronic database on polyphenol content in
    foods. Polyphenols form a wide group of natural antioxidants present in a large
    number of foods and beverages. They contribute to food characteristics such as
    taste, colour or shelf-life. They also participate in the prevention of several
    major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative
    diseases or osteoporosis.
  example: '75'
  homepage: http://www.phenol-explorer.eu/foods/
  mappings:
    miriam: phenolexplorer
    n2t: phenolexplorer
    prefixcommons: PHENOLEXPLORER
  name: Phenol-Explorer
  pattern: ^\d+$
  preferred_prefix: phenolexplorer
  uri_format: http://phenol-explorer.eu/foods/$1
phipo:
  banana: PHIPO
  contact:
    email: alayne.cuzick@rothamsted.ac.uk
    github: null
    name: Alayne Cuzick
    orcid: null
  description: Ontology of species-neutral phenotypes observed in pathogen-host interactions.
  example: '0000001'
  homepage: https://github.com/PHI-base/phipo
  license: CC BY 3.0
  mappings:
    bioportal: PHIPO
    obofoundry: PHIPO
    ols: phipo
    ontobee: PHIPO
  name: Pathogen Host Interaction Phenotype Ontology
  pattern: ^\d{7}$
  preferred_prefix: PHIPO
  uri_format: http://purl.obolibrary.org/obo/PHIPO_$1
  version: '2021-07-14'
phosphopoint.kinase:
  description: PhosphoPOINT is a database of the human kinase and phospho-protein
    interactome. It describes the interactions among kinases, their potential substrates
    and their interacting (phospho)-proteins. It also incorporates gene expression
    and uses gene ontology (GO) terms to annotate interactions. This collection references
    kinase information.
  example: AURKA
  homepage: http://kinase.bioinformatics.tw/
  mappings:
    miriam: phosphopoint.kinase
    n2t: phosphopoint.kinase
    prefixcommons: PHOSPHOPOINT.KINASE
  name: PhosphoPoint Kinase
  pattern: ^\w+$
  preferred_prefix: phosphopoint.kinase
  uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1
phosphopoint.protein:
  description: PhosphoPOINT is a database of the human kinase and phospho-protein
    interactome. It describes the interactions among kinases, their potential substrates
    and their interacting (phospho)-proteins. It also incorporates gene expression
    and uses gene ontology (GO) terms to annotate interactions. This collection references
    phosphoprotein information.
  example: AURKA
  homepage: http://kinase.bioinformatics.tw/
  mappings:
    miriam: phosphopoint.protein
    n2t: phosphopoint.protein
    prefixcommons: PHOSPHOPOINT.PROTEIN
  name: PhosphoPoint Phosphoprotein
  pattern: ^\w+$
  preferred_prefix: phosphopoint.protein
  uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0
phosphosite.protein:
  description: PhosphoSite is a mammalian protein database that provides information
    about in vivo phosphorylation sites. This datatype refers to protein-level information,
    providing a list of phosphorylation sites for each protein in the database.
  example: '12300'
  homepage: http://www.phosphosite.org/homeAction.do
  mappings:
    miriam: phosphosite.protein
    n2t: phosphosite.protein
    prefixcommons: PHOSPHOSITE.PROTEIN
  name: PhosphoSite Protein
  pattern: ^\d{5}$
  preferred_prefix: phosphosite.protein
  uri_format: http://www.phosphosite.org/proteinAction.do?id=$1
phosphosite.residue:
  description: PhosphoSite is a mammalian protein database that provides information
    about in vivo phosphorylation sites. This datatype refers to residue-level information,
    providing a information about a single modification position in a specific protein
    sequence.
  example: '2842'
  homepage: http://www.phosphosite.org/homeAction.do
  mappings:
    miriam: phosphosite.residue
    n2t: phosphosite.residue
    prefixcommons: PHOSPHOSITE.RESIDUE
  name: PhosphoSite Residue
  pattern: ^\d+$
  preferred_prefix: phosphosite.residue
  uri_format: http://www.phosphosite.org/siteAction.do?id=$1
phylomedb:
  description: PhylomeDB is a database of complete phylomes derived for different
    genomes within a specific taxonomic range. It provides alignments, phylogentic
    trees and tree-based orthology predictions for all encoded proteins.
  example: Phy000CLXM_RAT
  homepage: http://phylomedb.org/
  mappings:
    miriam: phylomedb
    n2t: phylomedb
    prefixcommons: PHYLOMEDB
    uniprot: PhylomeDB
  name: PhylomeDB
  pattern: ^\w+$
  preferred_prefix: phylomedb
  uri_format: http://phylomedb.org/?seqid=$1
phytozome.locus:
  description: Phytozome is a project to facilitate comparative genomic studies amongst
    green plants. Famlies of orthologous and paralogous genes that represent the modern
    descendents of ancestral gene sets are constructed at key phylogenetic nodes.
    These families allow easy access to clade specific orthology/paralogy relationships
    as well as clade specific genes and gene expansions. This collection references
    locus information.
  example: Glyma0021s00410
  homepage: http://www.phytozome.net/
  mappings:
    miriam: phytozome.locus
    n2t: phytozome.locus
    ncbi: Phytozome
    prefixcommons: PHYTOZOME.LOCUS
  name: Plant Genome Network
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: phytozome.locus
  synonyms:
  - JGI Phytozome
  uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1
pictar:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  example: hsa-let-7a
  homepage: https://pictar.mdc-berlin.de/
  name: PicTar
  preferred_prefix: pictar
  synonyms:
  - pictar-vert
pid.pathway:
  description: The Pathway Interaction Database is a highly-structured, curated collection
    of information about known human biomolecular interactions and key cellular processes
    assembled into signaling pathways. This datatype provides access to pathway information.
  example: eff796f3-6195-11e5-8ac5-06603eb7f303
  homepage: http://pid.nci.nih.gov/
  mappings:
    miriam: pid.pathway
    n2t: pid.pathway
    prefixcommons: PID.PATHWAY
  name: 'NCI Pathway Interaction Database: Pathway'
  pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
  preferred_prefix: pid.pathway
  synonyms:
  - pid
  uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1
pigqtldb:
  description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
    designed to house publicly all available QTL and single-nucleotide polymorphism/gene
    association data on livestock animal species. This collection references pig QTLs.
  example: '14'
  homepage: https://www.animalgenome.org/QTLdb
  mappings:
    miriam: pigqtldb
    n2t: pigqtldb
    prefixcommons: PIGQTLDB
  name: Animal Genome Pig QTL
  part_of: qtldb
  pattern: ^\d+$
  preferred_prefix: pigqtldb
  uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
pina:
  description: Protein Interaction Network Analysis (PINA) platform is an integrated
    platform for protein interaction network construction, filtering, analysis, visualization
    and management. It integrates protein-protein interaction data from six public
    curated databases and builds a complete, non-redundant protein interaction dataset
    for six model organisms.
  example: Q13485
  homepage: http://cbg.garvan.unsw.edu.au/pina/
  mappings:
    miriam: pina
    n2t: pina
    prefixcommons: PINA
  name: Protein Interaction Network Analysis
  pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
    0-9][A-Z, 0-9][0-9])$
  preferred_prefix: pina
  uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null
piroplasma:
  description: PiroplasmaDB is one of the databases that can be accessed through the
    EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
    of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
    Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
    database built upon the same infrastructure, the EuPathDB portal offers an entry
    point to all these resources, and the opportunity to leverage orthology for searches
    across genera.
  example: TA14985
  homepage: http://piroplasmadb.org/
  mappings:
    miriam: piroplasma
    n2t: piroplasma
    prefixcommons: PIROPLASMA
  name: PiroplasmaDB
  pattern: ^TA\d+$
  preferred_prefix: piroplasma
  uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
pirsf:
  description: The PIR SuperFamily concept is being used as a guiding principle to
    provide comprehensive and non-overlapping clustering of UniProtKB sequences into
    a hierarchical order to reflect their evolutionary relationships.
  example: PIRSF000100
  homepage: https://pir.georgetown.edu/
  mappings:
    go: PIRSF
    miriam: pirsf
    n2t: pirsf
    prefixcommons: PIRSF
    uniprot: PIRSF
  name: PIR Superfamily Classification System
  pattern: ^PIRSF\d{6}$
  preferred_prefix: pirsf
  uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1
pkdb:
  description: 'PK-DB an open database for pharmacokinetics information from clinical
    trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality
    pharmacokinetics data enriched with the required meta-information for computational
    modeling and data integration. '
  example: PKDB00198
  homepage: https://www.hu-berlin.de/?set_language=en&cl=en
  mappings:
    miriam: pkdb
  name: PK-DB
  pattern: ^PKDB[0-9]{5}$
  preferred_prefix: pkdb
  uri_format: https://pk-db.com/data/$1
plana:
  banana: PLANA
  contact:
    email: smr@stowers.org
    github: srobb1
    name: Sofia Robb
    orcid: null
  description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental
    stages and adult biotypes of Schmidtea mediterranea.
  example: '0000001'
  homepage: https://github.com/obophenotype/planaria-ontology
  license: CC BY 3.0
  mappings:
    bioportal: PLANA
    obofoundry: PLANA
    ols: plana
    ontobee: PLANA
    prefixcommons: PLANA
  name: planaria-ontology
  pattern: ^\d{7}$
  preferred_prefix: PLANA
  uri_format: http://purl.obolibrary.org/obo/PLANA_$1
  version: '2021-10-21'
planp:
  banana: PLANP
  contact:
    email: smr@stowers.org
    github: srobb1
    name: Sofia Robb
    orcid: null
  description: Planarian Phenotype Ontology is an ontology of phenotypes observed
    in the planarian Schmidtea mediterranea.
  example: '0000001'
  homepage: https://github.com/obophenotype/planarian-phenotype-ontology
  license: CC BY 3.0
  mappings:
    bioportal: PLANP
    obofoundry: PLANP
    ols: planp
    ontobee: PLANP
  name: Planarian Phenotype Ontology
  pattern: ^\d+$
  preferred_prefix: PLANP
  uri_format: http://purl.obolibrary.org/obo/PLANP_$1
  version: '2020-03-28'
planttfdb:
  description: The Plant TF database (PlantTFDB) systematically identifies transcription
    factors for plant species. It includes annotation for identified TFs, including
    information on expression, regulation, interaction, conserved elements, phenotype
    information. It also provides curated descriptions and cross-references to other
    life science databases, as well as identifying evolutionary relationship among
    identified factors.
  example: Ath_AT1G01030.1
  homepage: http://planttfdb.cbi.pku.edu.cn
  mappings:
    miriam: planttfdb
    n2t: planttfdb
    prefixcommons: PLANTTFDB
  name: Plant Transcription Factor Database
  pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$
  preferred_prefix: planttfdb
  uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1
plasmodb:
  description: AmoebaDB is one of the databases that can be accessed through the EuPathDB
    (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
    the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
    Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
    database built upon the same infrastructure, the EuPathDB portal offers an entry
    point to all these resources, and the opportunity to leverage orthology for searches
    across genera.
  example: PF11_0344
  homepage: http://plasmodb.org/plasmo/
  mappings:
    go: ApiDB_PlasmoDB
    miriam: plasmodb
    n2t: plasmodb
    ncbi: ApiDB_PlasmoDB
    prefixcommons: PLASMODB
  name: PlasmoDB Plasmodium Genome Resource
  pattern: ^\w+$
  preferred_prefix: plasmodb
  synonyms:
  - ApiDB_PlasmoDB
  uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
plo:
  banana: PLO
  contact:
    email: mb4@sanger.ac.uk
    github: null
    name: Matt Berriman
    orcid: null
  deprecated: true
  homepage: http://www.sanger.ac.uk/Users/mb4/PLO/
  mappings:
    obofoundry: PLO
    prefixcommons: PLO
  name: Plasmodium Life Cycle
  preferred_prefix: PLO
  uri_format: http://purl.obolibrary.org/obo/PLO_$1
pmap.cutdb:
  description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
    PMAP is comprised of five databases, linked together in one environment. CutDB
    is a database of individual proteolytic events (cleavage sites).
  example: '25782'
  homepage: http://cutdb.burnham.org
  mappings:
    miriam: pmap.cutdb
    n2t: pmap.cutdb
    prefixcommons: PMAP.CUTDB
  name: CutDB
  pattern: ^\d+$
  preferred_prefix: pmap.cutdb
  uri_format: http://cutdb.burnham.org/relation/show/$1
pmap.substratedb:
  description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
    PMAP is comprised of five databases, linked together in one environment. SubstrateDB
    contains molecular information on documented protease substrates.
  example: '1915'
  homepage: http://substrate.burnham.org/
  mappings:
    miriam: pmap.substratedb
    n2t: pmap.substratedb
    prefixcommons: PMAP.SUBSTRATEDB
  name: SubstrateDB
  pattern: ^\d+$
  preferred_prefix: pmap.substratedb
  uri_format: http://substrate.burnham.org/protein/annotation/$1/html
pmc:
  description: PMC International (PMCI) is a free full-text archive of biomedical
    and life sciences journal literature. PMCI is a collaborative effort between the
    U.S. National Institutes of Health and the National Library of Medicine, the publishers
    whose journal content makes up the PMC archive, and organizations in other countries
    that share NIH's and NLM's interest in archiving life sciences literature.
  example: PMC3084216
  homepage: http://europepmc.org/
  mappings:
    go: PMCID
    miriam: pmc
    n2t: pmc
    prefixcommons: PMCID
    wikidata: P932
  name: Pubmed Central
  pattern: ^PMC\d+$
  preferred_prefix: pmc
  providers:
  - code: ncbi
    description: PubMed Central
    homepage: https://www.ncbi.nlm.nih.gov/pmc/
    name: PubMed Central
    uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pubmed
  synonyms:
  - PMC
  - PMCID
  uri_format: http://europepmc.org/articles/$1
pmdb:
  description: The Protein Model DataBase (PMDB), is a database that collects manually
    built three dimensional protein models, obtained by different structure prediction
    techniques.
  example: PM0012345
  homepage: https://bioinformatics.cineca.it/PMDB/
  mappings:
    miriam: pmdb
    n2t: pmdb
    prefixcommons: PMDB
  name: Protein Model Database
  pattern: ^PM\d{7}$
  preferred_prefix: pmdb
  uri_format: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1
pmp:
  description: The number of known protein sequences exceeds those of experimentally
    solved protein structures. Homology (or comparative) modeling methods make use
    of experimental protein structures to build models for evolutionary related proteins.
    The Protein Model Portal (PMP) provides a single portal to access these models,
    which are accessed through their UniProt identifiers.
  example: Q0VCA6
  homepage: http://www.proteinmodelportal.org/
  mappings:
    miriam: pmp
    n2t: pmp
    prefixcommons: PMP
  name: Protein Model Portal
  pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
    0-9][A-Z, 0-9][0-9])$
  preferred_prefix: pmp
  provides: uniprot
  uri_format: http://www.proteinmodelportal.org/query/uniprot/$1
pmr:
  description: Resource for the community to store, retrieve, search, reference, and
    reuse CellML models.
  example: ebf69ca24298b28b2361e7d43eb52d6c
  homepage: https://www.auckland.ac.nz/en.html
  mappings:
    bioportal: PMR
    miriam: pmr
  name: Physical Medicine and Rehabilitation
  pattern: ^[a-z0-9]{32,32}$
  preferred_prefix: pmr
  uri_format: https://models.physiomeproject.org/exposure/$1
po:
  banana: PO
  contact:
    email: jaiswalp@science.oregonstate.edu
    github: jaiswalp
    name: Pankaj Jaiswal
    orcid: null
  description: The Plant Ontology is a structured vocabulary and database resource
    that links plant anatomy, morphology and growth and development to plant genomics
    data.
  example: 0009089
  homepage: http://browser.planteome.org/amigo
  license: CC BY 4.0
  mappings:
    bioportal: PO
    go: PO
    miriam: po
    n2t: po
    obofoundry: PO
    ols: po
    ontobee: PO
    prefixcommons: PO
  name: Plant Ontology
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: PO
  uri_format: http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1
  version: '2021-08-13'
pocketome:
  description: Pocketome is an encyclopedia of conformational ensembles of all druggable
    binding sites that can be identified experimentally from co-crystal structures
    in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule
    binding site in a protein which has been co-crystallized in complex with at least
    one drug-like small molecule, and is represented in at least two PDB entries.
  example: 1433C_TOBAC_1_252
  homepage: http://www.pocketome.org/sfSearch.cgi?act=browseall
  mappings:
    miriam: pocketome
    n2t: pocketome
    prefixcommons: POCKETOME
  name: Pocketome
  pattern: ^[A-Za-z_0-9]+$
  preferred_prefix: pocketome
  uri_format: http://www.pocketome.org/files/$1.html
polbase:
  description: Polbase is a database of DNA polymerases providing information on polymerase
    protein sequence, target DNA sequence, enzyme structure, sequence mutations and
    details on polymerase activity.
  example: 19-T4
  homepage: http://polbase.neb.com/
  mappings:
    miriam: polbase
    n2t: polbase
    prefixcommons: POLBASE
  name: PolBase
  pattern: ^[A-Za-z-0-9]+$
  preferred_prefix: polbase
  uri_format: https://polbase.neb.com/polymerases/$1#sequences
pombase:
  description: PomBase is a model organism database established to provide access
    to molecular data and biological information for the fission yeast Schizosaccharomyces
    pombe. It encompasses annotation of genomic sequence and features, comprehensive
    manual literature curation and genome-wide data sets.
  example: SPCC13B11.01
  homepage: http://www.pombase.org/
  mappings:
    go: PomBase
    miriam: pombase
    n2t: pombase
    ncbi: PomBase
    prefixcommons: PomBase
    uniprot: PomBase
    wikidata: P6245
  name: PomBase systematic ID
  pattern: ^S\w+(\.)?\w+(\.)?$
  preferred_prefix: pombase
  synonyms:
  - PomBase
  uri_format: http://www.pombase.org/spombe/result/$1
poro:
  banana: PORO
  contact:
    email: robert.thacker@stonybrook.edu
    github: null
    name: Bob Thacker
    orcid: null
  description: An ontology describing the anatomical structures and characteristics
    of Porifera (sponges)
  example: '0000550'
  homepage: https://github.com/obophenotype/porifera-ontology
  license: CC BY 3.0
  mappings:
    bioportal: PORO
    obofoundry: PORO
    ols: poro
    ontobee: PORO
    prefixcommons: PORO
  name: Porifera Ontology
  pattern: ^\d{7}$
  preferred_prefix: PORO
  uri_format: http://purl.obolibrary.org/obo/PORO_$1
  version: '2016-10-06'
ppdb:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'PPDB is a comprehensive source of data on pesticide chemical, physical
    and biological properties. '
  example: '1484'
  homepage: https://sitem.herts.ac.uk/aeru/ppdb/
  name: Pesticide Properties DataBase
  preferred_prefix: ppdb
  uri_format: https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm
ppo:
  banana: PPO
  contact:
    email: rlwalls2008@gmail.com
    github: ramonawalls
    name: Ramona Walls
    orcid: null
  description: An ontology for describing the phenology of individual plants and populations
    of plants, and for integrating plant phenological data across sources and scales.
  example: 0002058
  homepage: https://github.com/PlantPhenoOntology/PPO
  license: CC BY 3.0
  mappings:
    bioportal: PPO
    obofoundry: PPO
    ols: ppo
    ontobee: PPO
    prefixcommons: PPO
  name: Plant Phenology Ontology
  preferred_prefix: PPO
  uri_format: http://purl.obolibrary.org/obo/PPO_$1
  version: '2018-10-26'
ppr:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Preprints are articles which have not been peer-reviewed from various
    preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ
    Preprints and F1000.
  example: ppr103739
  homepage: https://europepmc.org
  name: Europe PMC Preprints
  preferred_prefix: ppr
  uri_format: https://europepmc.org/article/ppr/$1
pr:
  banana: PR
  contact:
    email: dan5@georgetown.edu
    github: nataled
    name: Darren Natale
    orcid: null
  description: The PRotein Ontology (PRO) has been designed to describe the relationships
    of proteins and protein evolutionary classes, to delineate the multiple protein
    forms of a gene locus (ontology for protein forms), and to interconnect existing
    ontologies.
  example: '000000024'
  homepage: http://proconsortium.org
  license: CC BY 4.0
  mappings:
    bioportal: PR
    go: PR
    miriam: pr
    n2t: pr
    obofoundry: PR
    ols: pr
    ontobee: PR
    prefixcommons: PR
    uniprot: PRO
    wikidata: P4926
  name: Protein Ontology
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: PR
  synonyms:
  - PR
  - PRO
  uri_format: https://proconsortium.org/app/entry/PR:$1
  version: '63.0'
pride:
  description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
    compliant, public data repository that provides protein and peptide identifications
    together with supporting evidence. This collection references experiments and
    assays.
  example: '1'
  homepage: https://github.com/PRIDE-Utilities/pride-ontology
  mappings:
    cellosaurus: PRIDE
    fairsharing: FAIRsharing.e1byny
    miriam: pride
    n2t: pride
    ols: pride
    prefixcommons: PRIDE
    uniprot: PRIDE
  name: PRIDE Controlled Vocabulary
  pattern: ^\d+$
  preferred_prefix: pride
  uri_format: https://www.ebi.ac.uk/pride/archive/assays/$1
pride.project:
  description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
    compliant, public data repository that provides protein and peptide identifications
    together with supporting evidence. This collection references projects.
  example: PXD000440
  homepage: https://www.ebi.ac.uk/pride/
  mappings:
    miriam: pride.project
    n2t: pride.project
    prefixcommons: PRIDE.PROJECT
  name: PRIDE Project
  pattern: ^P(X|R)D\d{6}$
  preferred_prefix: pride.project
  providers:
  - code: omicsdi
    description: PRIDE Project through OmicsDI
    homepage: https://www.omicsdi.org/
    name: PRIDE Project through OmicsDI
    uri_format: https://www.omicsdi.org/dataset/pride/$1
  uri_format: https://www.ebi.ac.uk/pride/archive/projects/$1
prints:
  description: PRINTS is a compendium of protein fingerprints. A fingerprint is a
    group of conserved motifs used to characterise a protein family; its diagnostic
    power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually
    the motifs do not overlap, but are separated along a sequence, though they may
    be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities
    more flexibly and powerfully than can single motifs, full diagnostic potency deriving
    from the mutual context provided by motif neighbours.
  example: PR00001
  homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/
  mappings:
    go: PRINTS
    miriam: prints
    n2t: prints
    prefixcommons: PRINTS
    uniprot: PRINTS
  name: PRINTS compendium of protein fingerprints
  pattern: ^PR\d{5}$
  preferred_prefix: prints
  uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false&regexpr=off
probonto:
  description: ProbOnto, is an ontology-based knowledge base of probability distributions,
    featuring uni- and multivariate distributions with their defining functions, characteristics,
    relationships and reparameterisation formulae.  It can be used for annotation
    of models, facilitating the encoding of distribution-based models, related functions
    and quantities.
  example: PROB_c0000005
  homepage: http://probonto.org
  mappings:
    miriam: probonto
    n2t: probonto
    ols: probonto
    prefixcommons: PROBONTO
  name: Probability Distribution Ontology
  pattern: ^PROB_c\d+$
  preferred_prefix: probonto
  uri_format: https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1
  version: 2.5.0
prodom:
  description: ProDom is a database of protein domain families generated from the
    global comparison of all available protein sequences.
  example: PD10000
  homepage: http://prodom.prabi.fr/prodom/current/html/home.php
  mappings:
    miriam: prodom
    n2t: prodom
    prefixcommons: PRODOM
  name: ProDom
  pattern: ^PD\d+$
  preferred_prefix: prodom
  uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1
proglyc:
  description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial
    and archaeal glycoproteins with at least one experimentally validated glycosite
    (glycosylated residue). Each entry in the database is fully cross-referenced and
    enriched with available published information about source organism, coding gene,
    protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl
    transferases (OSTs/GTs), supporting references, and applicable additional information.
  example: AC119
  homepage: http://www.proglycprot.org/
  mappings:
    miriam: proglyc
    n2t: proglyc
    prefixcommons: PROGLYC
  name: ProGlycProt
  pattern: ^[A-Z]C\d{1,3}$
  preferred_prefix: proglyc
  uri_format: http://www.proglycprot.org/detail.aspx?ProId=$1
propreo:
  banana: PROPREO
  contact:
    email: satya30@uga.edu
    github: null
    name: Satya S. Sahoo
    orcid: null
  deprecated: true
  homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/
  mappings:
    bioportal: PROPREO
    obofoundry: PROPREO
    prefixcommons: PROPREO
  name: Proteomics data and process provenance
  preferred_prefix: PROPREO
  uri_format: http://purl.obolibrary.org/obo/PROPREO_$1
prosite:
  description: PROSITE consists of documentation entries describing protein domains,
    families and functional sites as well as associated patterns and profiles to identify
    them.
  example: PS00001
  homepage: https://www.expasy.org/prosite/
  mappings:
    go: Prosite
    miriam: prosite
    n2t: prosite
    prefixcommons: PROSITE
    uniprot: PROSITE
    wikidata: P4355
  name: PROSITE documentation ID
  pattern: ^PS\d{5}$
  preferred_prefix: prosite
  uri_format: https://prosite.expasy.org/$1
protclustdb:
  description: ProtClustDB is a collection of related protein sequences (clusters)
    consisting of Reference Sequence proteins encoded by complete genomes. This database
    contains both curated and non-curated clusters.
  example: O80725
  homepage: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters
  mappings:
    miriam: protclustdb
    n2t: protclustdb
    prefixcommons: PROTCLUSTDB
  name: ProtClustDB
  pattern: ^\w+$
  preferred_prefix: protclustdb
  uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1
proteomicsdb.peptide:
  comment: The fact that this has .peptide as a subspace is a bit of a misnomer. Its
    original registration with MIRIAM uses a subview over the protein to point to
    peptides, but the identifiers in this semantic space seem to be about proteins.
  description: ProteomicsDB is an effort dedicated to expedite the identification
    of the human proteome and its use across the scientific community. This human
    proteome data is assembled primarily using information from liquid chromatography
    tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell
    lines and body fluids. Information is accessible for individual proteins, or on
    the basis of protein coverage on the encoding chromosome, and for peptide components
    of a protein. This collection provides access to the peptides identified for a
    given protein.
  example: '53504'
  homepage: https://www.proteomicsdb.org/#peptideSearch
  mappings:
    miriam: proteomicsdb.peptide
    n2t: proteomicsdb.peptide
    prefixcommons: PROTEOMICSDB.PEPTIDE
  name: ProteomicsDB Peptide
  pattern: ^\d+$
  preferred_prefix: proteomicsdb.peptide
  uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1
proteomicsdb.protein:
  description: ProteomicsDB is an effort dedicated to expedite the identification
    of the human proteome and its use across the scientific community. This human
    proteome data is assembled primarily using information  from liquid chromatography
    tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell
    lines and body fluids. Information is accessible for individual proteins, or on
    the basis of protein coverage on the encoding chromosome, and for peptide components
    of a protein. This collection provides access to individual proteins.
  example: '53504'
  homepage: https://www.proteomicsdb.org/#human
  mappings:
    miriam: proteomicsdb.protein
    n2t: proteomicsdb.protein
    prefixcommons: PROTEOMICSDB.PROTEIN
  name: ProteomicsDB Protein
  pattern: ^\d+$
  preferred_prefix: proteomicsdb.protein
  uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary
protonet.cluster:
  description: ProtoNet provides automatic hierarchical classification of protein
    sequences in the UniProt database, partitioning the protein space into clusters
    of similar proteins. This collection references cluster information.
  example: '4349895'
  homepage: http://www.protonet.cs.huji.ac.il/
  mappings:
    miriam: protonet.cluster
    n2t: protonet.cluster
    prefixcommons: PROTONET.CLUSTER
  name: ProtoNet Cluster
  pattern: ^\d+$
  preferred_prefix: protonet.cluster
  uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1
protonet.proteincard:
  description: ProtoNet provides automatic hierarchical classification of protein
    sequences in the UniProt database, partitioning the protein space into clusters
    of similar proteins. This collection references protein information.
  example: '16941567'
  homepage: http://www.protonet.cs.huji.ac.il/
  mappings:
    miriam: protonet.proteincard
    n2t: protonet.proteincard
    prefixcommons: PROTONET.PROTEINCARD
  name: ProtoNet ProteinCard
  pattern: ^\d+$
  preferred_prefix: protonet.proteincard
  uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1
prov:
  description: The namespace name http://www.w3.org/ns/prov# is intended for use with
    the PROV family of documents that support the interchange of provenance on the
    web.
  example: Activity
  homepage: https://www.w3.org/ns/prov
  mappings:
    biolink: prov
    ols: prov
    prefixcommons: prov
  name: PROV Namespace
  preferred_prefix: prov
  uri_format: https://www.w3.org/ns/prov#$1
  version: '2013-04-30'
pscdb:
  description: The PSCDB (Protein Structural Change DataBase) collects information
    on the relationship between protein structural change upon ligand binding. Each
    entry page provides detailed information about this structural motion.
  example: '051'
  homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html
  mappings:
    miriam: pscdb
    n2t: pscdb
    prefixcommons: PSCDB
  name: Protein Structural Change Database
  pattern: ^\d+$
  preferred_prefix: pscdb
  uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html
psdo:
  banana: PSDO
  contact:
    email: zachll@umich.edu
    github: zachll
    name: Zach Landis-Lewis
    orcid: null
  description: Performance Summary Display Ontology (PSDO) (pronounced "pseudo" or
    "sudo") is an application ontology about charts, tables, and graphs that are used
    to communicate performance information to employees and teams in organizations.
    PSDO's domain focus is on healthcare organizations that use performance summary
    displays in clinical dashboards and feedback interventions for healthcare professionals
    and teams. The displays commonly show information about the quality of care and
    health outcomes that has been derived from clinical data using performance measures
    (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal
    Ontology as its upper level ontology. This work is not peer-reviewed.
  example: '0000055'
  homepage: https://github.com/Display-Lab/psdo
  license: CC BY 3.0
  mappings:
    bioportal: PSDO
    obofoundry: PSDO
    ols: psdo
    ontobee: PSDO
  name: Performance Summary Display Ontology
  preferred_prefix: PSDO
  uri_format: http://purl.obolibrary.org/obo/PSDO_$1
  version: 1.0.0
pseudogene:
  description: This site contains a comprehensive database of identified pseudogenes,
    utilities used to find pseudogenes, various publication data sets and a pseudogene
    knowledgebase.
  example: PGOHUM00000289843
  homepage: http://www.pseudogene.org
  mappings:
    bioportal: pseudo
  name: PseudoGene
  preferred_prefix: pseudogene
  synonyms:
  - pseudogene.org
pseudomonas:
  description: The Pseudomonas Genome Database is a resource for peer-reviewed, continually
    updated annotation for all Pseudomonas species. It includes gene and protein sequence
    information, as well as regulation and predicted function and annotation.
  example: PSEEN0001
  homepage: http://www.pseudomonas.com/
  mappings:
    miriam: pseudomonas
    n2t: pseudomonas
    prefixcommons: PSEUDOMONAS
  name: Pseudomonas Genome Database
  pattern: ^P\w+$
  preferred_prefix: pseudomonas
  uri_format: http://www.pseudomonas.com/feature/show/?locus_tag=$1
psipar:
  description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled
    vocabulary for the annotation of experiments concerned with interactions, and
    interactor production methods. PAR is developed by the HUPO Proteomics Standards
    Initiative and contains the majority of the terms from the PSI-MI controlled vocabular,
    as well as additional terms.
  example: PAR:0116
  homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR
  mappings:
    miriam: psipar
    n2t: psipar
    prefixcommons: PSIPAR
  name: Protein Affinity Reagents
  pattern: ^PAR:\d+$
  preferred_prefix: psipar
  uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=$1
pso:
  banana: PSO
  contact:
    email: cooperl@science.oregonstate.edu
    github: null
    name: Laurel Cooper
    orcid: null
  description: The Plant Stress Ontology describes...
  example: '0000013'
  homepage: https://github.com/Planteome/plant-stress-ontology
  license: CC BY 3.0
  mappings:
    bioportal: PSO
    obofoundry: PSO
    ols: pso
    ontobee: PSO
  name: Plant Stress Ontology
  preferred_prefix: PSO
  uri_format: http://purl.obolibrary.org/obo/PSO_$1
  version: '2020-05-19'
pspub:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Documentation of the Phenoscape Curation Workflow
  homepage: https://wiki.phenoscape.org/wiki/Curation_workflow
  name: Phenoscape Publication
  preferred_prefix: pspub
pubchem.bioassay:
  description: PubChem provides information on the biological activities of small
    molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
    PubChem bioassay archives active compounds and bioassay results.
  example: '1018'
  homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay
  mappings:
    go: PubChem_BioAssay
    miriam: pubchem.bioassay
    n2t: pubchem.bioassay
    prefixcommons: PUBCHEM.BIOASSAY
  name: NCBI PubChem database of bioassay records
  pattern: ^\d+$
  preferred_prefix: pubchem.bioassay
  uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1
pubchem.compound:
  description: PubChem provides information on the biological activities of small
    molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
    PubChem Compound archives chemical structures and records.
  example: '100101'
  homepage: https://pubchem.ncbi.nlm.nih.gov/
  mappings:
    biolink: CID
    cellosaurus: PubChem
    cheminf: '000140'
    go: PubChem_Compound
    miriam: pubchem.compound
    n2t: pubchem.compound
    prefixcommons: CID
    scholia: pubchem
    wikidata: P662
  name: PubChem CID
  pattern: ^\d+$
  preferred_prefix: pubchem.compound
  providers:
  - code: 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/
    name: Scholia
    uri_format: https://scholia.toolforge.org/pubchem/$1
  synonyms:
  - CID
  - DSSTox_CID
  - PUBCHEM_CID
  - PubChem_Compound_CID
  - Pubchem
  - pubchem_id
  uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1
pubchem.substance:
  description: PubChem provides information on the biological activities of small
    molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
    PubChem Substance archives chemical substance records.
  example: '100101'
  homepage: https://pubchem.ncbi.nlm.nih.gov/
  mappings:
    cheminf: '000141'
    go: PubChem_Substance
    miriam: pubchem.substance
    n2t: pubchem.substance
    prefixcommons: PUBCHEM.SUBSTANCE
    wikidata: P2153
  name: PubChem Substance ID (SID)
  pattern: ^\d+$
  preferred_prefix: pubchem.substance
  synonyms:
  - DSSTox_Generic_SID
  uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1
publons.researcher:
  description: Database of researchers to track publications, citation metrics, peer
    reviews, and journal editing work.
  example: '1981638'
  homepage: https://publons.com/researcher
  mappings:
    biolink: ResearchID
  name: Publons Researcher ID
  preferred_prefix: publons.researcher
  uri_format: https://publons.com/researcher/$1
pubmed:
  description: PubMed is a service of the U.S. National Library of Medicine that includes
    citations from MEDLINE and other life science journals for biomedical articles
    back to the 1950s.
  example: '16333295'
  homepage: https://www.ncbi.nlm.nih.gov/PubMed/
  mappings:
    cellosaurus: PubMed
    cheminf: '000302'
    go: PMID
    miriam: pubmed
    n2t: pubmed
    prefixcommons: PMID
    scholia: pubmed
    wikidata: P698
  name: PubMed
  pattern: ^\d+$
  preferred_prefix: pubmed
  providers:
  - code: hubmed
    description: HubMed
    homepage: http://www.hubmed.org/
    name: HubMed
    uri_format: http://www.hubmed.org/display.cgi?uids=$1
  - code: epmc
    description: Europe PMC
    homepage: http://europepmc.org/
    name: Europe PMC
    uri_format: http://europepmc.org/abstract/MED/$1
  - code: CURATOR_REVIEW
    description: PubMed through Linkedlife data
    homepage: http://linkedlifedata.com/
    name: PubMed through Linkedlife data
    uri_format: http://linkedlifedata.com/resource/pubmed/id/$1
  - code: 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/
    name: Scholia
    uri_format: https://scholia.toolforge.org/pubmed/$1
  synonyms:
  - MEDLINE
  - PMID
  - pmid
  uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1
pw:
  banana: PW
  contact:
    email: gthayman@mcw.edu
    github: null
    name: G. Thomas Hayman
    orcid: null
  description: 'The Pathway Ontology captures information on biological networks,
    the relationships between netweorks and the alterations or malfunctioning of such
    networks within a hierarchical structure. The five main branches of the ontology
    are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor
    complex human conditions.'
  example: '0000423'
  homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
  license: CC BY 4.0
  mappings:
    bioportal: PW
    miriam: pw
    n2t: pw
    obofoundry: PW
    ols: pw
    ontobee: PW
    prefixcommons: PW
    wikidata: P7333
  name: Pathway ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: PW
  uri_format: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1
  version: '2019-10-23'
px:
  description: The ProteomeXchange provides a single point of submission of Mass Spectrometry
    (MS) proteomics data for the main existing proteomics repositories, and encourages
    the data exchange between them for optimal data dissemination.
  example: PXD000500
  homepage: http://www.proteomexchange.org/
  mappings:
    miriam: px
    n2t: px
    prefixcommons: PX
  name: ProteomeXchange
  pattern: ^(R)?PXD\d{6}$
  preferred_prefix: px
  uri_format: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1
pypi:
  description: The Python Package Index (PyPI) is a repository for Python packages.
  example: numpy
  homepage: https://www.python.org/psf/
  mappings:
    miriam: pypi
  name: PyPI
  pattern: ^[a-zA-Z_][a-zA-Z0-9\-_]+$
  preferred_prefix: pypi
  uri_format: https://pypi.org/project/$1
qtldb:
  description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
    designed to house publicly all available QTL and single-nucleotide polymorphism/gene
    association data on livestock animal species. This collection is species-independent.
  example: '4685'
  homepage: https://www.animalgenome.org/QTLdb
  mappings:
    miriam: qtldb
  name: Animal Genome QTL
  pattern: ^\d+$
  preferred_prefix: qtldb
  uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
qudt:
  description: Ontologies that aim to provide semantic specifications for units of
    measure, quantity kind, dimensions and data types.
  example: baseDimensionEnumeration
  homepage: https://qudt.org
  mappings:
    biolink: qud
    bioportal: QUDT
  name: Quantities, Units, Dimensions, and Types Ontology
  preferred_prefix: qudt
  uri_format: http://qudt.org/schema/qudt#$1
radiomics:
  description: The Radiomics Ontology aims to cover the radiomics feature domain with
    a strong focus on first order, shape, textural radiomics features. In addition,
    in the original version. it includes classes about segmentation algorithms and
    imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers
    Standardization Initiative), the ontology has been expanded (v 1.6) and it includes
    all the entities presented in the IBSI document. Therefore, a broad coverage of
    not only radiomics features, but also every entity (e.g. software properties,
    filter properties, features extraction parameters) involved into radiomics computation
    has been added. In the latest version (v2.0), the ontology URIs have been updated
    to reflect the codes avaialble in the IBSI latest manual. [bioportal]
  example: LK99
  homepage: http://www.radiomics.org/RO
  mappings:
    bioportal: RO
  name: Radiomics Ontology
  preferred_prefix: radiomics
rapdb.locus:
  description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza
    sativa) annotation database established in 2004 upon the completion of the Oryza
    sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice
    Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome
    annotation, gene expression, DNA markers, genetic diversity, etc.) for biological
    and agricultural research communities. This collection provides locus information
    in RAP-DB.
  example: Os01g0883800
  homepage: https://rapdb.dna.affrc.go.jp/
  mappings:
    miriam: rapdb.locus
  name: RAP-DB Locus
  pattern: ^Os\S+g\d{7}$
  preferred_prefix: rapdb.locus
  uri_format: https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1
rapdb.transcript:
  description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza
    sativa) annotation database established in 2004 upon the completion of the Oryza
    sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice
    Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome
    annotation, gene expression, DNA markers, genetic diversity, etc.) for biological
    and agricultural research communities. This collection provides transcript information
    in RAP-DB.
  example: Os01t0883800-02
  homepage: https://rapdb.dna.affrc.go.jp/
  mappings:
    miriam: rapdb.transcript
  name: RAP-DB Transcript
  pattern: ^Os\S+t\d{7}-\d{2}$
  preferred_prefix: rapdb.transcript
  uri_format: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1
rbk:
  description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects
    working to optimize approaches for the isolation, expansion, and differentiation
    of appropriate kidney cell types and their integration into complex structures
    that replicate human kidney function.
  example: Q-2958
  homepage: https://www.rebuildingakidney.org/
  mappings:
    miriam: rbk
    n2t: rbk
    prefixcommons: RBK
  name: Rebuilding a Kidney
  pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
  preferred_prefix: rbk
  uri_format: https://www.rebuildingakidney.org/id/$1
rbo:
  banana: RBO
  contact:
    email: daniel.c.berrios@nasa.gov
    github: DanBerrios
    name: Daniel C. Berrios
    orcid: null
  description: RBO is an ontology for the effects of radiation on biota in terrestrial
    and space environments.
  example: '00000105'
  homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO
  license: CC BY 3.0
  mappings:
    bioportal: RBO
    obofoundry: RBO
    ols: rbo
    ontobee: RBO
  name: Radiation Biology Ontology
  preferred_prefix: RBO
  uri_format: http://purl.obolibrary.org/obo/RBO_$1
  version: '2021-08-30'
rcb:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Collection of many cell lines derived from human and other various
    animals, preserved by the RIKEN BioResource Research Center.
  example: RCB0002
  homepage: https://cell.brc.riken.jp/en/rcb
  mappings:
    cellosaurus: RCB
  name: RIKEN Bioresource Center Cell Bank
  pattern: ^RCB\d+$
  preferred_prefix: rcb
  uri_format: https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1
rdf:
  description: This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace,
    defined in RDF 1.1 Concepts
  example: RDF
  homepage: http://www.w3.org/1999/02/22-rdf-syntax-ns
  mappings:
    prefixcommons: rdf
  name: Resource Description Framework
  preferred_prefix: rdf
  uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1
rdfs:
  description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema
    is an extension of the basic RDF vocabulary.
  example: label
  homepage: https://www.w3.org/TR/rdf-schema/
  mappings:
    bioportal: RDFS
    prefixcommons: rdfs
  name: RDF Schema
  preferred_prefix: rdfs
  uri_format: http://www.w3.org/2000/01/rdf-schema#$1
rdo:
  description: Ontologies of diseases that integrates many types of data for Rattus
    Norvegicus, Homo Sapiens, Mus Musculus and other organisms.
  example: '9002859'
  homepage: https://ratmine.mcw.edu/ontology/disease/
  mappings:
    bioportal: RDO
  name: RGD Disease_Ontology
  pattern: ^\d{7}$
  preferred_prefix: rdo
re3data:
  description: Re3data is a global registry of research data repositories that covers
    research data repositories from different academic disciplines.
  example: r3d100010772
  homepage: https://datacite.org
  mappings:
    miriam: re3data
  name: re3data
  pattern: ^r3d\d{9,9}$
  preferred_prefix: re3data
  uri_format: https://www.re3data.org/repository/$1
reactome:
  description: The Reactome project is a collaboration to develop a curated resource
    of core pathways and reactions in human biology.
  example: R-BTA-418592
  homepage: https://www.reactome.org/
  mappings:
    cheminf: '000411'
    go: Reactome
    miriam: reactome
    n2t: reactome
    prefixcommons: REACT
    uniprot: Reactome
    wikidata: P3937
  name: Reactome ID
  pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$
  preferred_prefix: reactome
  providers:
  - code: pathwaycommons
    description: Pathway diagram drawn with Cytoscape
    homepage: https://www.pathwaycommons.org
    name: Pathway Commons
    uri_format: https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1
  synonyms:
  - RE
  - REACT
  uri_format: https://reactome.org/content/detail/$1
reaxys:
  description: Reaxys is a web-based tool for the retrieval of chemistry information
    and data from published literature, including journals and patents. The information
    includes chemical compounds, chemical reactions, chemical properties, related
    bibliographic data, substance data with synthesis planning information, as well
    as experimental procedures from selected journals and patents. It is licensed
    by Elsevier.
  example: '1257009'
  homepage: https://www.reaxys.com
  mappings:
    wikidata: P1579
  name: Reaxys
  preferred_prefix: reaxys
  synonyms:
  - Beilstein
  - Reaxys
rebase:
  description: REBASE is a comprehensive database of information about restriction
    enzymes, DNA methyltransferases and related proteins involved in the biological
    process of restriction-modification (R-M). It contains fully referenced information
    about recognition and cleavage sites, isoschizomers, neoschizomers, commercial
    availability, methylation sensitivity, crystal and sequence data.
  example: '101'
  homepage: http://rebase.neb.com/rebase/
  mappings:
    go: REBASE
    miriam: rebase
    n2t: rebase
    prefixcommons: REBASE
    uniprot: REBASE
  name: REBASE restriction enzyme database
  pattern: ^\d+$
  preferred_prefix: rebase
  uri_format: http://rebase.neb.com/rebase/enz/$1.html
receptome.family:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The human receptor families involved in signaling (with the exception
    of channels) are presented in the Human Plasma Membrane Receptome database.
  example: '5.1'
  homepage: http://www.receptome.org
  name: Human Plasma Membrane Receptome Families
  preferred_prefix: receptome.family
  uri_format: http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1
refseq:
  description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive,
    integrated, non-redundant set of sequences, including genomic DNA, transcript
    (RNA), and protein products.
  example: NP_012345
  has_canonical: ncbiprotein
  homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/
  mappings:
    go: RefSeq
    miriam: refseq
    n2t: refseq
    prefixcommons: RefSeq
    uniprot: RefSeq
  name: Reference Sequence Collection
  pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$
  preferred_prefix: refseq
  synonyms:
  - REFSEQ_PROT
  uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
repeatsdb.protein:
  description: RepeatsDB is a database of annotated tandem repeat protein structures.
    This collection references protein entries in the database.
  example: P29894
  homepage: https://repeatsdb.org/
  mappings:
    miriam: repeatsdb.protein
  name: RepeatsDB Protein
  pattern: ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$
  preferred_prefix: repeatsdb.protein
  uri_format: https://repeatsdb.org/protein/$1
repeatsdb.structure:
  description: RepeatsDB is a database of annotated tandem repeat protein structures.
    This collection references structural entries in the database.
  example: 2gc4E
  homepage: https://repeatsdb.org/
  mappings:
    miriam: repeatsdb.structure
  name: RepeatsDB Structure
  pattern: ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$
  preferred_prefix: repeatsdb.structure
  uri_format: https://repeatsdb.org/structure/$1
reproduceme:
  description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan
    ontology to describe a complete path of a scientific experiment. It expresses
    the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides
    a set of classes and properties to represent a scientific experiment including
    its computational and non-computational steps to track the provenance of results.
    It describes a complete path of a scientific experiment considering the use-case
    of biological imaging and microscopy experiments, computational experiments, including
    Jupyter notebooks and scripts. It describes an experiment and its data, agents,
    activities, plans, steps, variables, instruments, materials, and settings required
    for its reproducibility.
  example: MicrobeamManipulation
  homepage: https://w3id.org/reproduceme/research
  license: CC BY-NC-SA 2.0
  mappings:
    bioportal: REPRODUCE-ME
    ols: reproduceme
  name: REPRODUCE-ME Ontology
  preferred_prefix: reproduceme
  version: '1.1'
resid:
  banana: RESID
  contact:
    email: john.garavelli@ebi.ac.uk
    github: null
    name: John Garavelli
    orcid: null
  deprecated: true
  description: The RESID Database of Protein Modifications is a comprehensive collection
    of annotations and structures for protein modifications including amino-terminal,
    carboxyl-terminal and peptide chain cross-link post-translational modifications.
  example: AA0001
  homepage: http://www.ebi.ac.uk/RESID/
  mappings:
    go: RESID
    miriam: resid
    n2t: resid
    obofoundry: RESID
    prefixcommons: RESID
  name: Protein covalent bond
  pattern: ^AA\d{4}$
  preferred_prefix: RESID
  uri_format: http://pir0.georgetown.edu/cgi-bin/resid?id=$1
reto:
  description: Regulation of Transcription
  homepage: http://www.semantic-systems-biology.org/apo
  mappings:
    bioportal: RETO
    ols: reto
  name: Regulation of Transcription Ontology
  no_own_terms: true
  preferred_prefix: reto
  version: '2019-09-17'
rex:
  banana: REX
  description: An ontology of physico-chemical processes, i.e. physico-chemical changes
    occurring in course of time.
  example: '0000512'
  homepage: https://www.ebi.ac.uk/chebi/
  mappings:
    bioportal: REX
    obofoundry: REX
    ols: rex
    ontobee: REX
    prefixcommons: REX
  name: Physico-chemical process
  part_of: chebi
  preferred_prefix: REX
  uri_format: http://purl.obolibrary.org/obo/REX_$1
  version: '2017-11-19'
rexo:
  description: Regulation of Gene Expression
  homepage: http://www.semantic-systems-biology.org/apo
  mappings:
    bioportal: REXO
    ols: rexo
  name: Regulation of Gene Expression Ontology
  no_own_terms: true
  preferred_prefix: rexo
  version: '2019-04-11'
rfam:
  description: 'The Rfam database is a collection of RNA families, each represented
    by multiple sequence alignments, consensus secondary structures and covariance
    models (CMs). The families in Rfam break down into three broad functional classes:
    non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs.
    Typically these functional RNAs often have a conserved secondary structure which
    may be better preserved than the RNA sequence. The CMs used to describe each family
    are a slightly more complicated relative of the profile hidden Markov models (HMMs)
    used by Pfam. CMs can simultaneously model RNA sequence and the structure in an
    elegant and accurate fashion.'
  example: RF00230
  homepage: https://rfam.xfam.org/
  mappings:
    go: Rfam
    miriam: rfam
    n2t: rfam
    ncbi: RFAM
    prefixcommons: RFAM
  name: Rfam database of RNA families
  pattern: ^RF\d{5}$
  preferred_prefix: rfam
  uri_format: https://rfam.xfam.org/family/$1
rgd:
  description: Rat Genome Database seeks to collect, consolidate, and integrate rat
    genomic and genetic data with curated functional and physiological data and make
    these data widely available to the scientific community. This collection references
    genes.
  example: '7499841'
  homepage: http://rgd.mcw.edu/
  mappings:
    bioportal: RGD
    cellosaurus: RGD
    go: RGD
    miriam: rgd
    n2t: rgd
    ncbi: RGD
    prefixcommons: RGD
    uniprot: RGD
    wikidata: P3853
  name: Rat Genome Database ID
  pattern: ^\d{4,}$
  preferred_prefix: rgd
  providers:
  - code: agr
    description: RGD through the Alliance of Genome Resources
    homepage: https://www.alliancegenome.org
    name: RGD through the Alliance of Genome Resources
    uri_format: https://www.alliancegenome.org/gene/RGD:$1
  synonyms:
  - RGD
  uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1
rgd.qtl:
  description: Rat Genome Database seeks to collect, consolidate, and integrate rat
    genomic and genetic data with curated functional and physiological data and make
    these data widely available to the scientific community. This collection references
    quantitative trait loci (qTLs), providing phenotype and disease descriptions,
    mapping, and strain information as well as links to markers and candidate genes.
  example: '1354581'
  homepage: http://rgd.mcw.edu/
  mappings:
    miriam: rgd.qtl
    n2t: rgd.qtl
    prefixcommons: RGD.QTL
  name: Rat Genome Database qTL
  pattern: ^\d+$
  preferred_prefix: rgd.qtl
  uri_format: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1
rgd.strain:
  description: Rat Genome Database seeks to collect, consolidate, and integrate rat
    genomic and genetic data with curated functional and physiological data and make
    these data widely available to the scientific community. This collection references
    strain reports, which include a description of strain origin, disease, phenotype,
    genetics and immunology.
  example: '5688061'
  homepage: http://rgd.mcw.edu/
  mappings:
    miriam: rgd.strain
    n2t: rgd.strain
    prefixcommons: RGD.STRAIN
  name: Rat Genome Database strain
  pattern: ^\d+$
  preferred_prefix: rgd.strain
  uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1
rhea:
  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.


    Rhea 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.'
  example: '12345'
  homepage: https://www.rhea-db.org/
  mappings:
    go: RHEA
    miriam: rhea
    n2t: rhea
    prefixcommons: RHEA
  name: Rhea, the Annotated Reactions Database
  pattern: ^\d{5}$
  preferred_prefix: rhea
  synonyms:
  - RHEA
  uri_format: https://www.rhea-db.org/rhea/$1
ricegap:
  description: The objective of this project is to provide high quality annotation
    for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated
    with functional annotation including expression data, gene ontologies, and tagged
    lines.
  example: LOC_Os02g13300
  homepage: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml
  mappings:
    miriam: ricegap
    n2t: ricegap
    prefixcommons: RICEGAP
  name: Rice Genome Annotation Project
  pattern: ^LOC\_Os\d{1,2}g\d{5}$
  preferred_prefix: ricegap
  uri_format: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1
ricenetdb.compound:
  description: 'RiceNetDB is currently the most comprehensive regulatory database
    on Oryza Sativa based on genome annotation. It was displayed in three levels:
    GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
    mapping.'
  example: OSC1416
  homepage: http://bis.zju.edu.cn/ricenetdb
  mappings:
    miriam: ricenetdb.compound
    n2t: ricenetdb.compound
    prefixcommons: RICENETDB.COMPOUND
  name: RiceNetDB Compound
  pattern: ^OSC\d{4}$
  preferred_prefix: ricenetdb.compound
  uri_format: http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1
ricenetdb.gene:
  description: 'RiceNetDB is currently the most comprehensive regulatory database
    on Oryza Sativa based on genome annotation. It was displayed in three levels:
    GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
    mapping.'
  example: LOC_Os01g49190.1
  homepage: http://bis.zju.edu.cn/ricenetdb/
  mappings:
    miriam: ricenetdb.gene
    n2t: ricenetdb.gene
    prefixcommons: RICENETDB.GENE
  name: RiceNetDB Gene
  pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$
  preferred_prefix: ricenetdb.gene
  uri_format: http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1
ricenetdb.mirna:
  description: 'RiceNetDB is currently the most comprehensive regulatory database
    on Oryza Sativa based on genome annotation. It was displayed in three levels:
    GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
    mapping.'
  example: osa-miR446
  homepage: http://bis.zju.edu.cn/ricenetdb
  mappings:
    miriam: ricenetdb.mirna
    n2t: ricenetdb.mirna
    prefixcommons: RICENETDB.MIRNA
  name: RiceNetDB miRNA
  pattern: ^osa-miR\d{3,5}[a-z]{0,1}$
  preferred_prefix: ricenetdb.mirna
  uri_format: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1
ricenetdb.protein:
  description: 'RiceNetDB is currently the most comprehensive regulatory database
    on Oryza Sativa based on genome annotation. It was displayed in three levels:
    GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
    mapping.'
  example: LOC_Os01g49190
  homepage: http://bis.zju.edu.cn/ricenetdb/
  mappings:
    miriam: ricenetdb.protein
    n2t: ricenetdb.protein
    prefixcommons: RICENETDB.PROTEIN
  name: RiceNetDB Protein
  pattern: ^LOC\_Os\d{1,2}g\d{5}$
  preferred_prefix: ricenetdb.protein
  uri_format: http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1
ricenetdb.reaction:
  description: 'RiceNetDB is currently the most comprehensive regulatory database
    on Oryza Sativa based on genome annotation. It was displayed in three levels:
    GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
    mapping.'
  example: OSR0818
  homepage: http://bis.zju.edu.cn/ricenetdb
  mappings:
    miriam: ricenetdb.reaction
    n2t: ricenetdb.reaction
    prefixcommons: RICENETDB.REACTION
  name: RiceNetDB Reaction
  pattern: ^OSR\d{4}$
  preferred_prefix: ricenetdb.reaction
  uri_format: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1
rnacentral:
  description: RNAcentral is a public resource that offers integrated access to a
    comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating
    group of Expert Databases.
  example: URS0000759CF4
  homepage: https://rnacentral.org/
  mappings:
    go: RNAcentral
    miriam: rnacentral
    n2t: rnacentral
    ncbi: RNAcentral
    prefixcommons: RNACENTRAL
  name: RNAcentral
  pattern: ^URS[0-9A-F]{10}(\_\d+)?$
  preferred_prefix: rnacentral
  synonyms:
  - LNCRNADB
  uri_format: https://rnacentral.org/rna/$1
rnamod:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A comprehensive listing of post-transcriptionally modified nucleosides
    from RNA -
  example: '051'
  homepage: http://rna.rega.kuleuven.be/rnamods/
  name: The RNA Modification Database
  preferred_prefix: rnamod
  uri_format: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1
rnamods:
  description: The RNA modification database provides a comprehensive listing of post-transcriptionally
    modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides
    of known structure, including those from established sequence positions, as well
    as those detected or characterized from hydrolysates of RNA.
  example: '101'
  homepage: http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm
  mappings:
    go: RNAmods
    miriam: rnamods
    n2t: rnamods
    prefixcommons: RNAMODS
  name: RNA Modification Database
  pattern: ^\d{3}$
  preferred_prefix: rnamods
  uri_format: http://mods.rna.albany.edu/mods/modifications/view/$1
rnao:
  banana: RNAO
  contact:
    email: BatchelorC@rsc.org
    github: null
    name: Colin Batchelor
    orcid: null
  description: Controlled vocabulary pertaining to RNA function and based on RNA sequences,
    secondary and three-dimensional structures.
  example: 0000128
  homepage: https://github.com/bgsu-rna/rnao
  license: CC0 1.0
  mappings:
    bioportal: RNAO
    obofoundry: RNAO
    ols: rnao
    ontobee: RNAO
    prefixcommons: RNAO
  name: RNA ontology
  pattern: ^\d{7}$
  preferred_prefix: RNAO
  uri_format: http://purl.obolibrary.org/obo/RNAO_$1
  version: '2019-04-15'
ro:
  banana: RO
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: null
  description: The OBO Relation Ontology provides consistent and unambiguous formal
    definitions of the relational expressions used in biomedical ontologies.
  example: RO_0002533
  homepage: https://oborel.github.io/
  license: CC0 1.0
  mappings:
    biolink: RO
    bioportal: OBOREL
    go: RO
    miriam: ro
    n2t: ro
    obofoundry: RO
    ols: ro
    ontobee: RO
    prefixcommons: OBO_REL
    wikidata: P3590
  name: Relation Ontology
  pattern: ^RO_\d{7}$
  preferred_prefix: RO
  synonyms:
  - RO_proposed_relation
  - obo_rel
  - oborel
  uri_format: http://purl.obolibrary.org/obo/RO_$1
  version: '2021-10-27'
rouge:
  description: The Rouge protein database contains results from sequence analysis
    of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
  example: mKIAA4200
  homepage: http://www.kazusa.or.jp/rouge/
  mappings:
    miriam: rouge
    n2t: rouge
    prefixcommons: ROUGE
    uniprot: Rouge
  name: Rodent Unidentified Gene-Encoded Large Proteins
  pattern: ^m\w+$
  preferred_prefix: rouge
  uri_format: https://www.kazusa.or.jp/rouge/gfpage/$1
rrid:
  banana: RRID
  description: "The Research Resource Identification Initiative provides RRIDs to\
    \ 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases\
    \ / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\
    \nThe initiative works with participating journals to intercept manuscripts in\
    \ the publication process that use these resources, and allows publication authors\
    \ to incorporate RRIDs within the methods sections. It also provides resolver\
    \ services that access curated data from 10 data sources: the antibody registry\
    \ (a curated catalog of antibodies), the SciCrunch registry (a curated catalog\
    \ of software tools and databases), and model organism nomenclature authority\
    \ databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These\
    \ RRIDs are aggregated and can be searched through SciCrunch."
  example: AB_262044
  homepage: https://scicrunch.org/resolver
  mappings:
    miriam: rrid
    n2t: rrid
    prefixcommons: RRID
  name: Research Resource Identification
  namespace_in_lui: true
  pattern: ^[a-zA-Z]+.+$
  preferred_prefix: rrid
  uri_format: https://scicrunch.org/resolver/RRID:$1
rs:
  banana: RS
  contact:
    email: sjwang@mcw.edu
    github: null
    name: Shur-Jen Wang
    orcid: null
  description: Ontology of rat strains
  example: 0001807
  homepage: http://rgd.mcw.edu/rgdweb/search/strains.html
  license: CC BY 4.0
  mappings:
    bioportal: RS
    obofoundry: RS
    ols: rs
    ontobee: RS
    prefixcommons: RS
  name: Rat Strain Ontology
  pattern: ^\d{7}$
  preferred_prefix: RS
  uri_format: http://purl.obolibrary.org/obo/RS_$1
  version: '2019-12-13'
runbiosimulations:
  description: runBioSimulations is a platform for sharing simulation experiments
    and their results. runBioSimulations enables investigators to use a wide range
    of simulation tools to execute a wide range of simulations. runBioSimulations
    permanently saves the results of these simulations, and investigators can share
    results by sharing URLs similar to sharing URLs for files with DropBox and Google
    Drive.
  example: 5fde96bdc5f1aa9ff0cce18a
  homepage: https://icahn.mssm.edu/
  mappings:
    miriam: runbiosimulations
  name: runBioSimulations
  pattern: ^[0-9a-z]{24,24}$
  preferred_prefix: runbiosimulations
  uri_format: https://run.biosimulations.org/simulations/$1
rxno:
  banana: RXNO
  contact:
    email: batchelorc@rsc.org
    github: batchelorc
    name: Colin Batchelor
    orcid: null
  description: "RXNO is the name reaction ontology. It contains more than 500 classes\
    \ representing organic reactions such as the Diels\u2013Alder cyclization."
  example: '0000253'
  homepage: https://github.com/rsc-ontologies/rxno
  license: CC BY 4.0
  mappings:
    bioportal: RXNO
    obofoundry: RXNO
    ols: rxno
    ontobee: RXNO
    prefixcommons: RXNO
    wikidata: P2106
  name: Name Reaction Ontology
  pattern: ^\d{7}$
  preferred_prefix: RXNO
  uri_format: http://purl.obolibrary.org/obo/RXNO_$1
  version: '2021-01-21'
rxnorm:
  description: RxNorm provides normalized names for clinical drugs and links its names
    to many of the drug vocabularies commonly used in pharmacy management and drug
    interaction software, including those of First Databank, Micromedex, and Gold
    Standard Drug Database. By providing links between these vocabularies, RxNorm
    can mediate messages between systems not using the same software and vocabulary.
  example: '221058'
  homepage: https://www.nlm.nih.gov/research/umls/rxnorm/
  mappings:
    biolink: RXCUI
    bioportal: RXNORM
    prefixcommons: RXCUI
    wikidata: P3345
  name: RxNorm
  pattern: ^[0-9]{1,7}$
  preferred_prefix: rxnorm
  synonyms:
  - RXCUI
  uri_format: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1
sabiork.compound:
  description: SABIO-RK is a relational database system that contains information
    about biochemical reactions, their kinetic equations with their parameters, and
    the experimental conditions under which these parameters were measured. The compound
    data set provides information regarding the reactions in which a compound participates
    as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further
    information.
  example: '75'
  homepage: http://sabiork.h-its.org/
  mappings:
    miriam: sabiork.compound
    n2t: sabiork.compound
  name: SABIO-RK Compound
  pattern: ^\d+$
  preferred_prefix: sabiork.compound
  uri_format: http://sabiork.h-its.org/newSearch?q=$1
sabiork.ec:
  description: SABIO-RK is a relational database system that contains information
    about biochemical reactions, their kinetic equations with their parameters, and
    the experimental conditions under which these parameters were measured. The EC
    record provides for a given enzyme classification (EC) the associated list of
    enzyme-catalysed reactions and their corresponding kinetic data.
  example: 2.7.1.1
  homepage: http://sabiork.h-its.org/
  mappings:
    miriam: sabiork.ec
    n2t: sabiork.ec
    prefixcommons: SABIORK.EC
  name: SABIO-RK EC Record
  pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$
  preferred_prefix: sabiork.ec
  uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1
sabiork.kineticrecord:
  description: SABIO-RK is a relational database system that contains information
    about biochemical reactions, their kinetic equations with their parameters, and
    the experimental conditions under which these parameters were measured. The kinetic
    record data set provides information regarding the kinetic law, measurement conditions,
    parameter details and other reference information.
  example: '5046'
  homepage: http://sabiork.h-its.org/
  mappings:
    go: SABIO-RK
    miriam: sabiork.kineticrecord
    n2t: sabiork.kineticrecord
    prefixcommons: SABIORK.KINETICRECORD
  name: SABIO Reaction Kinetics
  pattern: ^\d+$
  preferred_prefix: sabiork.kineticrecord
  uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1
sabiork.reaction:
  description: SABIO-RK is a relational database system that contains information
    about biochemical reactions, their kinetic equations with their parameters, and
    the experimental conditions under which these parameters were measured. The reaction
    data set provides information regarding the organism in which a reaction is observed,
    pathways in which it participates, and links to further information.
  example: '75'
  homepage: http://sabiork.h-its.org/
  mappings:
    miriam: sabiork.reaction
    n2t: sabiork.reaction
    prefixcommons: SABIORK.REACTION
  name: SABIO-RK Reaction
  pattern: ^\d+$
  preferred_prefix: sabiork.reaction
  uri_format: http://sabiork.h-its.org/newSearch?q=sabioreactionid:$1
sael:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
  preferred_prefix: sael
  references:
  - https://pubmed.ncbi.nlm.nih.gov/18629134/
salk:
  comment: spider stuff!
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Scientific research institute for neuroscience, genetics, immunology,
    plant biology and more.
  example: '037727'
  homepage: https://www.salk.edu/
  name: Salk Institute for Biological Studies Accession
  preferred_prefix: salk
  uri_format: https://abrc.osu.edu/stocks/number/SALK_$1
sao:
  banana: SAO
  contact:
    email: slarson@ncmir.ucsd.edu
    github: null
    name: Stephen Larson
    orcid: null
  deprecated: true
  homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html
  mappings:
    bioportal: SAO
    obofoundry: SAO
    prefixcommons: SAO
  name: Subcellular Anatomy Ontology
  preferred_prefix: SAO
  references:
  - http://www.ontobee.org/ontology/SAO
  uri_format: http://purl.obolibrary.org/obo/SAO_$1
sasbdb:
  description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository
    for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and
    derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural
    information on biological macromolecules in solution at a resolution of 1-2 nm.
    SASBDB provides freely accessible and downloadable experimental data, which are
    deposited together with the relevant experimental conditions, sample details,
    derived models and their fits to the data.
  example: SASDAX8
  homepage: http://www.sasbdb.org/
  mappings:
    miriam: sasbdb
    n2t: sasbdb
    prefixcommons: SASBDB
    uniprot: SASBDB
  name: Small Angle Scattering Biological Data Bank
  pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$
  preferred_prefix: sasbdb
  uri_format: http://www.sasbdb.org/data/$1
sbo:
  banana: SBO
  contact:
    email: sheriff@ebi.ac.uk
    github: null
    name: Rahuman Sheriff
    orcid: null
  description: The goal of the Systems Biology Ontology is to develop controlled vocabularies
    and ontologies tailored specifically for the kinds of problems being faced in
    Systems Biology, especially in the context of computational modeling. SBO is a
    project of the BioModels.net effort.
  example: 0000485
  homepage: http://www.ebi.ac.uk/sbo/
  license: Artistic License 2.0
  mappings:
    bioportal: SBO
    miriam: sbo
    n2t: sbo
    obofoundry: SBO
    ols: sbo
    ontobee: SBO
    prefixcommons: SBO
  name: Systems Biology Ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: SBO
  uri_format: https://www.ebi.ac.uk/sbo/main/SBO:$1
  version: '2021-08-28'
scdo:
  banana: SCDO
  contact:
    email: giant.plankton@gmail.com
    github: JadeHotchkiss
    name: Jade Hotchkiss
    orcid: null
  description: An ontology for the standardization of terminology and integration
    of knowledge about Sickle Cell Disease.
  example: 0000728
  homepage: https://scdontology.h3abionet.org/
  license: GPL-3.0
  mappings:
    bioportal: SCDO
    obofoundry: SCDO
    ols: scdo
    ontobee: SCDO
  name: Sickle Cell Disease Ontology
  preferred_prefix: SCDO
  uri_format: http://purl.obolibrary.org/obo/SCDO_$1
  version: '2021-04-15'
schem:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Selventa legacy chemical namespace used with the Biological Expression
    Language
  example: A0001
  homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets
  name: Selventa Chemicals
  pattern: ^A\d{4}$
  preferred_prefix: schem
scomp:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Selventa legacy complex namespace used with the Biological Expression
    Language
  example: C0001
  homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets
  name: Selventa Complexes
  pattern: ^C\d{4}$
  preferred_prefix: scomp
scop:
  description: The SCOP (Structural Classification of Protein) database is a comprehensive
    ordering of all proteins of known structure according to their evolutionary, functional
    and structural relationships. The basic classification unit is the protein domain.
    Domains are hierarchically classified into species, proteins, families, superfamilies,
    folds, and classes.
  example: '47419'
  homepage: http://scop.mrc-lmb.cam.ac.uk/scop/
  mappings:
    miriam: scop
    n2t: scop
    prefixcommons: SCOP
  name: Structural Classification of Protein
  pattern: ^\d+$
  preferred_prefix: scop
  providers:
  - code: CURATOR_REVIEW
    description: SCOP at Berkeley
    homepage: http://scop.berkeley.edu/
    name: SCOP at Berkeley
    uri_format: http://scop.berkeley.edu/sunid=$1
  uri_format: http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$1
scopus:
  description: "Scopus is the largest abstract and citation database of peer-reviewed\
    \ literature: scientific journals, books and conference proceedings. \nDelivering\
    \ a comprehensive overview of the world's research output in  the fields of science,\
    \ technology, medicine, social sciences, and arts \nand humanities, Scopus features\
    \ smart tools to track, analyze and  visualize research."
  example: '56305849200'
  homepage: https://www.scopus.com
  mappings:
    biolink: ScopusID
  name: Scopus Researcher Identifier
  pattern: ^\d+$
  preferred_prefix: scopus
scretf:
  description: ScerTF is a database of position weight matrices (PWMs) for transcription
    factors in Saccharomyces species. It identifies a single matrix for each TF that
    best predicts in vivo data, providing metrics related to the performance of that
    matrix in accurately representing the DNA binding specificity of the annotated
    transcription factor.
  example: RSC3
  homepage: http://stormo.wustl.edu/ScerTF/
  mappings:
    miriam: scretf
    n2t: scretf
    prefixcommons: SCRETF
  name: ScerTF
  pattern: ^\w+$
  preferred_prefix: scretf
  uri_format: http://stormo.wustl.edu/ScerTF/details/$1
sdbs:
  description: The Spectral Database for Organic Compounds (SDBS) is an integrated
    spectral database system for organic compounds. It provides access to 6 different
    types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier
    transform infrared spectrum (FT-IR), and NMR spectra.
  example: '4544'
  homepage: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi
  mappings:
    miriam: sdbs
    n2t: sdbs
    prefixcommons: SDBS
  name: Spectral Database for Organic Compounds
  pattern: ^\d+$
  preferred_prefix: sdbs
  uri_format: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1
sdgio:
  description: An OBO-compliant ontology representing the entities referenced by the
    SDGs, their targets, and indicators.
  example: '00020134'
  homepage: https://github.com/SDG-InterfaceOntology/sdgio
  mappings:
    ols: sdgio
    ontobee: SDGIO
  name: Sustainable Development Goals Interface Ontology
  preferred_prefix: sdgio
  version: '2018-08-10'
sdis:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Selventa legacy disease namespace used with the Biological Expression
    Language
  example: D0001
  homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets
  name: Selventa iseasess
  pattern: ^D\d{4}$
  preferred_prefix: sdis
sedml.format:
  description: Data format that can be used in conjunction with the Simulation Experimental
    Description Markup Language (SED-ML).
  example: csv
  homepage: http://sed-ml.org/
  mappings:
    miriam: sedml.format
  name: SED-ML data format
  pattern: ^[a-z]+(\..*?)?$
  preferred_prefix: sedml.format
  uri_format: https://sed-ml.org/urns.html#format:$1
sedml.language:
  description: Model format that can be used in conjunction with the Simulation Experimental
    Description Markup Language (SED-ML).
  example: sbml.level-3.version-2
  homepage: http://sed-ml.org/
  mappings:
    miriam: sedml.language
  name: SED-ML model format
  pattern: ^[a-z]+(\..*?)?$
  preferred_prefix: sedml.language
  uri_format: https://sed-ml.org/urns.html#language:$1
seed:
  description: This cooperative effort, which includes Fellowship for Interpretation
    of Genomes (FIG), Argonne National Laboratory, and the University of Chicago,
    focuses on the development of the comparative genomics environment called the
    SEED. It is a framework to support comparative analysis and annotation of genomes,
    and the development of curated genomic data (annotation). Curation is performed
    at the level of subsystems by an expert annotator, across many genomes, and not
    on a gene by gene basis. This collection references subsystems.
  example: Biotin_biosynthesis
  homepage: http://seed-viewer.theseed.org/seedviewer.cgi
  mappings:
    go: SEED
    miriam: seed
    n2t: seed
    ncbi: SEED
    prefixcommons: SEED
  name: The SEED;
  pattern: ^\w+$
  preferred_prefix: seed
  uri_format: http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1
seed.compound:
  description: This cooperative effort, which includes Fellowship for Interpretation
    of Genomes (FIG), Argonne National Laboratory, and the University of Chicago,
    focuses on the development of the comparative genomics environment called the
    SEED. It is a framework to support comparative analysis and annotation of genomes,
    and the development of curated genomic data (annotation). Curation is performed
    at the level of subsystems by an expert annotator, across many genomes, and not
    on a gene by gene basis. This collection references subsystems.
  example: cpd15380
  homepage: http://modelseed.org/
  mappings:
    miriam: seed.compound
    n2t: seed.compound
    prefixcommons: SEED.COMPOUND
  name: SEED Compound
  pattern: ^cpd\d+$
  preferred_prefix: seed.compound
  uri_format: http://modelseed.org/biochem/compounds/$1
seed.reaction:
  description: ModelSEED is a platform for creating genome-scale metabolic network
    reconstructions for microbes and plants. As part of the platform, a biochemistry
    database is managed that contains reactions unique to ModelSEED as well as reactions
    aggregated from other databases or from manually-curated genome-scale metabolic
    network reconstructions.
  example: rxn00001
  homepage: http://modelseed.org/biochem/reactions/
  mappings:
    biolink: SEED.REACTION
    miriam: seed.reaction
    n2t: seed.reaction
  name: SEED Reactions
  pattern: ^rxn\d+$
  preferred_prefix: seed.reaction
  uri_format: http://modelseed.org/biochem/reactions/$1
sep:
  banana: SEP
  contact:
    email: psidev-gps-dev@lists.sourceforge.net
    github: null
    name: SEP developers via the PSI and MSI mailing lists
    orcid: null
  deprecated: true
  description: A structured controlled vocabulary for the annotation of sample processing
    and separation techniques in scientific experiments.
  homepage: https://psidev.info/sepcv
  mappings:
    bioportal: SEP
    obofoundry: SEP
    prefixcommons: SEP
  name: Sample processing and separation techniques
  preferred_prefix: SEP
  uri_format: http://purl.obolibrary.org/obo/SEP_$1
sepio:
  banana: SEPIO
  contact:
    email: mhb120@gmail.com
    github: null
    name: Matthew Brush
    orcid: null
  description: An ontology for representing the provenance of scientific claims and
    the evidence that supports them.
  example: 0000048
  homepage: https://github.com/monarch-initiative/SEPIO-ontology
  license: CC BY 3.0
  mappings:
    bioportal: SEPIO
    obofoundry: SEPIO
    ols: sepio
    ontobee: SEPIO
    prefixcommons: SEPIO
  name: Scientific Evidence and Provenance Information Ontology
  preferred_prefix: SEPIO
  uri_format: http://purl.obolibrary.org/obo/SEPIO_$1
  version: $Revision$
sfam:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Selventa legacy protein family namespace used with the Biological Expression
    Language
  example: F0001
  homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets
  name: Selventa Families
  pattern: ^F\d{4}$
  preferred_prefix: sfam
sgd:
  description: The Saccharomyces Genome Database (SGD) project collects information
    and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.
  example: S000002493
  homepage: https://www.yeastgenome.org/
  mappings:
    go: SGD
    miriam: sgd
    n2t: sgd
    ncbi: SGD
    prefixcommons: SGD
    uniprot: SGD
    wikidata: P3406
  name: Saccharomyces Genome Database
  pattern: ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$
  preferred_prefix: sgd
  providers:
  - code: CURATOR_REVIEW
    description: Bio2RDF
    homepage: http://sgd.bio2rdf.org/fct
    name: Bio2RDF
    uri_format: http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$1
  - code: bioentitylink
    description: SGD through BioEntity Link
    homepage: https://bioentity.link/
    name: SGD through BioEntity Link
    uri_format: https://bioentity.link/#/lexicon/public/$1
  - code: agr
    description: SGD through the Alliance of Genome Resources
    homepage: https://www.alliancegenome.org
    name: SGD through the Alliance of Genome Resources
    uri_format: https://www.alliancegenome.org/gene/SGD:$1
  uri_format: https://www.yeastgenome.org/locus/$1
sgd.pathways:
  description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces
    genome database (SGD).
  example: PWY3O-214
  homepage: http://pathway.yeastgenome.org/
  mappings:
    miriam: sgd.pathways
    n2t: sgd.pathways
    prefixcommons: SGD.PATHWAYS
  name: Saccharomyces genome database pathways
  pattern: ^PWY\w{2}\-\d{3}$
  preferred_prefix: sgd.pathways
  uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1
sgn:
  description: The Sol Genomics Network (SGN) is a database and website dedicated
    to the genomic information of the nightshade family, which includes species such
    as tomato, potato, pepper, petunia and eggplant.
  example: '0001'
  homepage: http://solgenomics.net/
  mappings:
    go: SGN
    miriam: sgn
    n2t: sgn
    ncbi: SGN
    prefixcommons: SGN
  name: Sol Genomics Network
  pattern: ^\d+$
  preferred_prefix: sgn
  uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1
sheepqtldb:
  description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
    designed to house publicly all available QTL and single-nucleotide polymorphism/gene
    association data on livestock animal species. This collection references sheep
    QTLs.
  example: '19803'
  homepage: https://www.animalgenome.org/QTLdb
  mappings:
    miriam: sheepqtldb
    n2t: sheepqtldb
    prefixcommons: SHEEPQTLDB
  name: Animal Genome Sheep QTL
  part_of: qtldb
  pattern: ^\d+$
  preferred_prefix: sheepqtldb
  uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
sibo:
  banana: SIBO
  contact:
    email: cjmungall@lbl.gov
    github: null
    name: Chris Mungall
    orcid: null
  description: Social Behavior in insects
  example: 0000509
  homepage: https://github.com/obophenotype/sibo
  license: CC BY 3.0
  mappings:
    bioportal: SIBO
    obofoundry: SIBO
    ols: sibo
    ontobee: SIBO
    prefixcommons: SIBO
  name: Social Insect Behavior Ontology
  pattern: ^\d{7}$
  preferred_prefix: SIBO
  uri_format: http://purl.obolibrary.org/obo/SIBO_$1
  version: '2015-06-15'
sider.drug:
  description: SIDER (Side Effect Resource) is a public, computer-readable side effect
    resource that connects drugs to side effect terms. It aggregates dispersed public
    information on side effects. This collection references drugs in SIDER.
  example: '2244'
  homepage: http://sideeffects.embl.de/
  mappings:
    miriam: sider.drug
    n2t: sider.drug
    prefixcommons: SIDER.DRUG
  name: SIDER Drug
  pattern: ^\d+$
  preferred_prefix: sider.drug
  uri_format: http://sideeffects.embl.de/drugs/$1
sider.effect:
  description: SIDER (Side Effect Resource) is a public, computer-readable side effect
    resource that connects drugs to side effect terms. It aggregates dispersed public
    information on side effects. This collection references side effects of drugs
    as referenced in SIDER.
  example: C0017565
  homepage: http://sideeffects.embl.de/
  mappings:
    miriam: sider.effect
    n2t: sider.effect
    prefixcommons: SIDER.EFFECT
  name: SIDER Side Effect
  pattern: ^C\d+$
  preferred_prefix: sider.effect
  provides: umls
  uri_format: http://sideeffects.embl.de/se/$1
sigmaaldirch:
  description: Sigma Aldrich is a life sciences supply vendor.
  example: HPA000698
  homepage: https://www.sigmaaldrich.com
  name: Sigma Aldrich
  preferred_prefix: sigmaaldirch
  uri_format: https://www.sigmaaldrich.com/US/en/product/sigma/$1
signaling-gateway:
  description: The Signaling Gateway provides  information on  mammalian proteins
    involved in cellular signaling.
  example: A001094
  homepage: http://www.signaling-gateway.org/molecule
  mappings:
    miriam: signaling-gateway
    n2t: signaling-gateway
    prefixcommons: SIGNALING-GATEWAY
  name: Signaling Gateway
  pattern: ^A\d{6}$
  preferred_prefix: signaling-gateway
  uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1
signor:
  description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in
    a structured format signaling information published in the scientific literature.
  example: SIGNOR-C41
  homepage: https://signor.uniroma2.it/
  mappings:
    miriam: signor
    uniprot: SIGNOR
  name: Signaling Network Open Resource
  pattern: ^SIGNOR\-[A-Z]+\d+$
  preferred_prefix: signor
  synonyms:
  - SIGNOR
  uri_format: https://signor.uniroma2.it/relation_result.php?id=$1
signor.relation:
  comment: Currently, you can put a SIGNOR relation ID into the main page search box
    and it will resolve, but there is not currently a way to resolve them via a URL
    pattern
  contributor:
    email: benjamin_gyori@hms.harvard.edu
    github: null
    name: Benjamin M. Gyori
    orcid: 0000-0001-9439-5346
  description: Identifiers for relationships between proteins and complexes, along
    with their type and provenance
  example: SIGNOR-252737
  homepage: https://signor.uniroma2.it
  name: SIGNOR Relation
  part_of: signor
  pattern: ^SIGNOR-\d+$
  preferred_prefix: signor.relation
  reviewer:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
sio:
  description: The semanticscience integrated ontology (SIO) provides a simple, integrated
    upper level ontology (types, relations) for consistent knowledge representation
    across physical, processual and informational entities.
  example: 000912
  homepage: https://github.com/micheldumontier/semanticscience
  license: CC BY 4.0
  mappings:
    biolink: SIO
    bioportal: SIO
    miriam: sio
    ols: sio
    ontobee: SIO
    prefixcommons: SIO
  name: Semanticscience Integrated Ontology
  pattern: ^\d{6}$
  preferred_prefix: sio
  uri_format: https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1
  version: '1.53'
sisu:
  description: The Sequencing Initiative Suomi (SISu) project is an international
    collaboration to harmonize and aggregate whole genome and exome sequence data
    from Finnish samples, providing data for researchers and clinicians. The SISu
    project allows for the search of variants to determine their attributes and occurrence
    in Finnish cohorts, and provides summary data on single nucleotide variants and
    indels from exomes, sequenced in disease-specific and population genetic studies.
  example: 17:41223048
  homepage: http://www.sisuproject.fi/
  mappings:
    miriam: sisu
    n2t: sisu
    prefixcommons: SISU
  name: Sequencing Initiative Suomi
  pattern: ^[0-9]+:[0-9]+$
  preferred_prefix: sisu
  uri_format: http://search.sisuproject.fi/#/variant/$1
sitex:
  description: SitEx is a database containing information on eukaryotic protein functional
    sites. It stores the amino acid sequence positions in the functional site, in
    relation to the exon structure of encoding gene This can be used to detect the
    exons involved in shuffling in protein evolution, or to design protein-engineering
    experiments.
  example: '1000'
  homepage: http://www-bionet.sscc.ru/sitex/
  mappings:
    miriam: sitex
    n2t: sitex
    prefixcommons: SITEX
  name: SitEx
  pattern: ^\d+$
  preferred_prefix: sitex
  uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1
skip:
  description: SKIP is aiming to promote the exchange of information and joint research
    between researchers by aggregating various information of stem cells (iPS cells,
    iPS cells derived from patients, etc.) to stimulate research on disease and regenerative
    medicine.
  example: SKIP001214
  homepage: https://skip.stemcellinformatics.org/en/
  mappings:
    cellosaurus: SKIP
  name: Stemcell Knowledge and Information Portal
  preferred_prefix: skip
  uri_format: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1
skos:
  description: SKOS is an area of work developing specifications and standards to
    support the use of knowledge organization systems (KOS) such as thesauri, classification
    schemes, subject heading lists and taxonomies within the framework of the Semantic
    Web
  example: prefLabel
  homepage: https://www.w3.org/2004/02/skos/
  mappings:
    prefixcommons: skos
  name: Simple Knowledge Organization System
  preferred_prefix: skos
  uri_format: http://www.w3.org/2004/02/skos/core#$1
smart:
  description: The Simple Modular Architecture Research Tool (SMART) is an online
    tool for the identification and annotation of protein domains, and the analysis
    of domain architectures.
  example: SM00015
  homepage: http://smart.embl-heidelberg.de/
  mappings:
    go: SMART
    miriam: smart
    n2t: smart
    prefixcommons: SMART
    uniprot: SMART
  name: Simple Modular Architecture Research Tool
  pattern: ^SM\d{5}$
  preferred_prefix: smart
  uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1
smid:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'SMIDs (Small Molecule Identifiers) represent gene-style identifiers
    for small molecules newly identified in C. elegans and other nematodes. SMIDs
    aim to make life easier for describing biogenic small molecules in metabolomic
    and genomic applications.     '
  example: '137'
  homepage: https://smid-db.org/
  name: C. elegans Small Molecule Identifier Database
  preferred_prefix: smid
  synonyms:
  - SMID-DB
  uri_format: https://smid-db.org/smid/$1
smiles:
  description: Documentation of SMILES (Simplified Molecular Input Line Entry System),
    a line notation (a typographical method using printable characters) for entering
    and representing molecules and reactions.
  example: COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1
  homepage: https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
  mappings:
    wikidata: P233
  name: Simplified molecular-input line-entry system
  preferred_prefix: smiles
smpdb:
  description: The Small Molecule Pathway Database (SMPDB) contains small molecule
    pathways found in humans, which are presented visually. All SMPDB pathways include
    information on the relevant organs, subcellular compartments, protein cofactors,
    protein locations, metabolite locations, chemical structures and protein quaternary
    structures. Accompanying data includes detailed descriptions and references, providing
    an overview of the pathway, condition or processes depicted in each diagram.
  example: SMP0000219
  homepage: https://smpdb.ca/
  mappings:
    biolink: PathWhiz
    miriam: smpdb
    n2t: smpdb
    prefixcommons: SMPDB
  name: Small Molecule Pathway Database
  pattern: ^SMP\d+$
  preferred_prefix: smpdb
  synonyms:
  - SMP
  uri_format: https://smpdb.ca/view/$1
snap:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Theoretical explanation of a purely spatial ontology supporting snapshot
    views of the world at successive instants of time, as part of a modular ontology
    of the dynamic features of reality.
  example: Quality
  homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf
  name: Snapshot
  preferred_prefix: snap
snomedct:
  description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms),
    is a systematically organized computer processable collection of medical terminology
    covering most areas of clinical information such as diseases, findings, procedures,
    microorganisms, pharmaceuticals, etc.
  example: '284196006'
  homepage: http://www.snomedbrowser.com/
  mappings:
    biolink: SNOMEDCT
    bioportal: SNOMEDCT
    miriam: snomedct
    n2t: snomedct
    ols: snomed
    prefixcommons: SNOMED
    wikidata: P5806
  name: SNOMED CT (International Edition)
  pattern: ^(\w+)?\d+$
  preferred_prefix: snomedct
  synonyms:
  - SCTID
  - SCTID_2010_1_31
  - SNOMECT
  - SNOMED
  - SNOMEDCT
  - SNOMEDCTCT
  - SNOMEDCTCT_2018_03_01
  - SNOMEDCTCT_2019_03_01
  - SNOMEDCT_2010_1_31
  - SNOMEDCT_US
  - SNOMEDCT_US_2018_03_01
  - SNOMEDCT_US_2018_09_01
  - SNOMEDCT_US_2019_03_01
  - SNOMEDCT_US_2019_09_01
  - SNOMEDCT_US_2020_03_01
  - SNOMEDCT_US_2020_09_01
  - SNOMED_CT
  - SNOMED_CT_US_2018_03_01
  - SNOWMEDCT
  - SNOWMEDCT_US
  - SNOWMEDCT_US_2018_03_01
  uri_format: http://www.snomedbrowser.com/Codes/Details/$1
  version: '2020-01-31'
snornabase:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'A comprehensive database of


    human H/ACA and C/D box snoRNAs.'
  example: SR0000178
  homepage: https://www-snorna.biotoul.fr/
  name: snoRNABase
  preferred_prefix: snornabase
snp2tfbs:
  description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect
    transcription factor binding (TFB) in the Human genome.
  example: rs11603840
  homepage: https://ccg.epfl.ch/snp2tfbs/
  mappings:
    miriam: snp2tfbs
  name: SNP to Transcription Factor Binding Sites
  pattern: ^rs[0-9]+$
  preferred_prefix: snp2tfbs
  provides: dbsnp
  uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1
so:
  banana: SO
  contact:
    email: keilbeck@genetics.utah.edu
    github: null
    name: Karen Eilbeck
    orcid: null
  description: The Sequence Ontology (SO) is a structured controlled vocabulary for
    the parts of a genomic annotation. It provides a common set of terms and definitions
    to facilitate the exchange, analysis and management of genomic data.
  example: '0001157'
  homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies
  license: CC BY 4.0
  mappings:
    bioportal: SO
    go: SO
    miriam: so
    n2t: so
    obofoundry: SO
    ols: so
    ontobee: SO
    prefixcommons: SO
  name: Sequence types and features ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: SO
  uri_format: http://www.sequenceontology.org/miso/current_release/term/SO:$1
  version: '2021-11-22'
sopharm:
  banana: SOPHARM
  contact:
    email: Adrien.Coulet@loria.fr
    github: null
    name: Adrien Coulet
    orcid: null
  deprecated: true
  homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php
  mappings:
    bioportal: SOPHARM
    obofoundry: SOPHARM
    prefixcommons: SOPHARM
  name: Suggested Ontology for Pharmacogenomics
  preferred_prefix: SOPHARM
  uri_format: http://purl.obolibrary.org/obo/SOPHARM_$1
soybase:
  description: SoyBase is a repository for curated genetics, genomics and related
    data resources for soybean.
  example: BARC-013845-01256
  homepage: http://soybase.org/
  mappings:
    miriam: soybase
    n2t: soybase
    ncbi: SoyBase
    prefixcommons: SOYBASE
  name: Glycine max Genome Database
  pattern: ^\w+(\-)?\w+(\-)?\w+$
  preferred_prefix: soybase
  uri_format: http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1
span:
  comment: see also snap. This ontology only exists in description in the paper and
    does not have an associated web resource
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Theoretical explanation of to a purely spatiotemporal ontology of change
    and process, as part of a modular ontology of the dynamic features of reality.
  homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf
  name: Span
  preferred_prefix: span
spd:
  banana: SPD
  contact:
    email: ramirez@macn.gov.ar
    github: null
    name: Martin Ramirez
    orcid: null
  description: An ontology for spider comparative biology including anatomical parts
    (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk,
    web, borrow).
  example: '0000001'
  homepage: http://research.amnh.org/atol/files/
  license: CC BY 3.0
  mappings:
    bioportal: SPD
    obofoundry: SPD
    ols: spd
    ontobee: SPD
    prefixcommons: SPD
    wikidata: P4537
  name: Spider Ontology
  pattern: ^\d{7}$
  preferred_prefix: SPD
  uri_format: http://purl.obolibrary.org/obo/SPD_$1
  version: '2019-02-27'
spdx:
  description: The SPDX License List is a list of commonly found licenses and exceptions
    used in free and open source and other collaborative software or documentation.
    The purpose of the SPDX License List is to enable easy and efficient identification
    of such licenses and exceptions in an SPDX document, in source files or elsewhere.
    The SPDX License List includes a standardized short identifier, full name, vetted
    license text including matching guidelines markup as appropriate, and a canonical
    permanent URL for each license and exception.
  example: CC-BY-1.0
  homepage: https://spdx.org/licenses
  mappings:
    miriam: spdx
    n2t: spdx
  name: Software Package Data Exchange License
  pattern: ^[0-9A-Za-z\-.]+$
  preferred_prefix: spdx
  uri_format: https://spdx.org/licenses/$1
spike.map:
  description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository
    that can store, organise and allow retrieval of pathway information in a way that
    will be useful for the research community. The database currently focuses primarily
    on pathways describing DNA damage response, cell cycle, programmed cell death
    and hearing related pathways. Pathways are regularly updated, and additional pathways
    are gradually added. The complete database and the individual maps are freely
    exportable in several formats. This collection references pathway maps.
  example: spike00001
  homepage: http://www.cs.tau.ac.il/~spike/
  mappings:
    miriam: spike.map
    n2t: spike.map
    prefixcommons: SPIKE.MAP
  name: SPIKE Map
  pattern: ^spike\d{5}$
  preferred_prefix: spike.map
  uri_format: http://www.cs.tau.ac.il/~spike/maps/$1.html
splash:
  description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier
    for spectra, and is independent of how the spectra were acquired or processed.
    It can be easily calculated for a wide range of spectra, including Mass spectroscopy,  infrared
    spectroscopy, ultraviolet and nuclear magnetic resonance.
  example: splash10-0zq2000000-77302b0326a418630a84
  homepage: http://mona.fiehnlab.ucdavis.edu/
  mappings:
    miriam: splash
    n2t: splash
    prefixcommons: SPLASH
  name: Spectra Hash Code
  pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$
  preferred_prefix: splash
  uri_format: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1
spp:
  description: The Signaling Pathways Project is an integrated 'omics knowledgebase
    based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets
    involving genetic and small molecule manipulations of cellular receptors, enzymes
    and transcription factors. Our goal is to create a resource where scientists can
    routinely generate research hypotheses or validate bench data relevant to cellular
    signaling pathways.
  example: 10.1621/vwN2g2HaX3
  homepage: https://www.signalingpathways.org/index.jsf
  mappings:
    miriam: spp
  name: Signaling Pathways Project
  pattern: ^10.\w{4}/\w{10}$
  preferred_prefix: spp
  uri_format: https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1
srao:
  description: The FAIRsharing Subject Ontology (SRAO) is an application ontology
    for the categorization of research disciplines across all research domains, from
    the humanities to the natural sciences. It utilizes multiple external vocabularies.
  example: '0000400'
  homepage: https://github.com/FAIRsharing/subject-ontology
  mappings:
    ols: srao
  name: FAIRsharing Subject Ontology
  preferred_prefix: srao
  version: 0.3.0
ssbd.dataset:
  description: Systems Science of Biological Dynamics database (SSBD:database) is
    an added-value database for biological dynamics. It provides a rich set of open
    resources for analyzing quantitative data and microscopy images of biological
    objects, such as single-molecule, cell, tissue, individual, etc., and software
    tools for analysis. Quantitative biological data and microscopy images are collected
    from a variety of species, sources, and methods. These include data obtained from
    both experiments and computational simulations.
  example: '1'
  homepage: https://ssbd.riken.jp
  mappings:
    fairsharing: FAIRsharing.we2r5a
  name: System Science of Biological Dynamics dataset
  preferred_prefix: ssbd.dataset
  uri_format: https://ssbd.riken.jp/database/dataset/$1
ssbd.project:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Systems Science of Biological Dynamics database (SSBD:database) is
    an added-value database for biological dynamics. It provides a rich set of open
    resources for analyzing quantitative data and microscopy images of biological
    objects, such as single-molecule, cell, tissue, individual, etc., and software
    tools for analysis. Quantitative biological data and microscopy images are collected
    from a variety of species, sources, and methods. These include data obtained from
    both experiments and computational simulations.
  example: '1'
  homepage: https://ssbd.riken.jp
  name: System Science of Biological Dynamics project
  preferred_prefix: ssbd.project
  uri_format: https://ssbd.riken.jp/database/project/$1
stap:
  description: STAP (Statistical Torsional Angles Potentials) was developed since,
    according to several studies, some nuclear magnetic resonance (NMR) structures
    are of lower quality, are less reliable and less suitable for structural analysis
    than high-resolution X-ray crystallographic structures. The refined NMR solution
    structures (statistical torsion angle potentials; STAP) in the database are refined
    from the Protein Data Bank (PDB).
  example: 1a24
  homepage: http://psb.kobic.re.kr/STAP/refinement/
  mappings:
    miriam: stap
    n2t: stap
    prefixcommons: STAP
  name: Statistical Torsional Angles Potentials
  pattern: ^[0-9][A-Za-z0-9]{3}$
  preferred_prefix: stap
  uri_format: http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1
stato:
  banana: STATO
  contact:
    email: alejandra.gonzalez.beltran@gmail.com
    github: null
    name: Alejandra Gonzalez-Beltran
    orcid: null
  description: STATO is the statistical methods ontology. It contains concepts and
    properties related to statistical methods, probability distributions and other
    concepts related to statistical analysis, including relationships to study designs
    and plots.
  example: 0000288
  homepage: http://stato-ontology.org/
  license: CC BY 3.0
  mappings:
    bioportal: STATO
    obofoundry: STATO
    ols: stato
    ontobee: STATO
    prefixcommons: STATO
  name: The Statistical Methods Ontology
  preferred_prefix: STATO
  uri_format: http://purl.obolibrary.org/obo/STATO_$1
  version: RC1.4
stitch:
  description: STITCH is a resource to explore known and predicted interactions of
    chemicals and proteins. Chemicals are linked to other chemicals and proteins by
    evidence derived from experiments, databases and the literature.
  example: BQJCRHHNABKAKU
  homepage: http://stitch.embl.de/
  mappings:
    miriam: stitch
    n2t: stitch
    prefixcommons: STITCH
  name: Search Tool for Interactions of Chemicals
  pattern: ^\w{14}$
  preferred_prefix: stitch
  uri_format: http://stitch.embl.de/interactions/$1
storedb:
  banana: STOREDB
  description: STOREDB database is a repository for data used by the international
    radiobiology community, archiving and sharing primary data outputs from research
    on low dose radiation. It also provides a directory of bioresources and databases
    for radiobiology projects containing information and materials that investigators
    are willing to share. STORE supports the creation of a low dose radiation research
    commons.
  example: STUDY1040
  homepage: https://www.storedb.org/
  mappings:
    miriam: storedb
    n2t: storedb
    prefixcommons: STOREDB
  name: Store DB
  pattern: ^(STUDY|FILE|DATASET)\d+$
  preferred_prefix: storedb
  uri_format: https://www.storedb.org/?$1
string:
  description: "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is\
    \ a database of known and predicted protein interactions.\r\nThe interactions\
    \ include direct (physical) and indirect (functional) associations; they are derived\
    \ from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression,\
    \ Previous Knowledge. STRING quantitatively integrates interaction data from these\
    \ sources for a large number of organisms, and transfers information between these\
    \ organisms where applicable."
  example: P53350
  homepage: http://string.embl.de/
  mappings:
    miriam: string
    n2t: string
    prefixcommons: STRING
    uniprot: STRING
  name: Search Tool for Retrieval of Interacting Genes/Proteins
  pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
    0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$
  preferred_prefix: string
  providers:
  - code: CURATOR_REVIEW
    description: STRING Mirror at Heidelberg
    homepage: http://string-db.org/
    name: STRING Mirror at Heidelberg
    uri_format: http://string-db.org/interactions/$1
  uri_format: http://string.embl.de/interactions/$1
sty:
  description: UMLS Semantic Network The Semantic Network consists of (1) a set of
    broad subject categories, or Semantic Types, that provide a consistent categorization
    of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful
    and important relationships, or Semantic Relations, that exist between Semantic
    Types.
  example: T039
  homepage: https://lhncbc.nlm.nih.gov/semanticnetwork/
  mappings:
    biolink: STY
    bioportal: STY
  name: Semantic Types Ontology
  pattern: ^T\d{3}$
  preferred_prefix: sty
  uri_format: http://purl.bioontology.org/ontology/STY/$1
subtilist:
  description: "SubtiList serves to collate and integrate various aspects of the genomic\
    \ information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\
    \nSubtiList provides a complete dataset of DNA and protein sequences derived from\
    \ the paradigm strain B. subtilis 168, linked to the relevant annotations and\
    \ functional assignments."
  example: BG11523
  homepage: http://genolist.pasteur.fr/SubtiList/
  mappings:
    miriam: subtilist
    n2t: subtilist
    ncbi: SubtiList
    prefixcommons: SUBTILIST
  name: Bacillus subtilis genome sequencing project
  pattern: ^BG\d+$
  preferred_prefix: subtilist
  uri_format: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1
subtiwiki:
  description: "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis.\
    \ It provides comprehensive information on all genes and their proteins and RNA\
    \ products, as well as information related to the current investigation of the\
    \ gene/protein. \r\nNote: Currently, direct access to RNA products is restricted.\
    \ This is expected to be rectified soon."
  example: BSU29180
  homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page
  mappings:
    miriam: subtiwiki
    n2t: subtiwiki
    prefixcommons: SUBTIWIKI
  name: SubtiWiki
  pattern: ^BSU\d{5}$
  preferred_prefix: subtiwiki
  uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1
sugarbind:
  description: The SugarBind Database captures knowledge of glycan binding of human
    pathogen lectins and adhesins, where each glycan-protein binding pair is associated
    with at least one published reference. It provides information on the pathogen
    agent, the lectin/adhesin involved, and the human glycan ligand. This collection
    provides information on ligands.
  example: lectins/172
  homepage: http://sugarbind.expasy.org/
  mappings:
    miriam: sugarbind
    n2t: sugarbind
    prefixcommons: SUGARBIND
  name: SugarBind
  pattern: ^[A-Za-z]+\/[0-9]+$
  preferred_prefix: sugarbind
  uri_format: http://sugarbind.expasy.org/$1
supfam:
  description: SUPERFAMILY provides structural, functional and evolutionary information
    for proteins from all completely sequenced genomes, and large sequence collections
    such as UniProt.
  example: SSF57615
  homepage: http://supfam.org/SUPERFAMILY/
  mappings:
    miriam: supfam
    n2t: supfam
    prefixcommons: SUPFAM
    uniprot: SUPFAM
  name: SUPERFAMILY
  pattern: ^\w+$
  preferred_prefix: supfam
  uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1
swh:
  banana: swh
  description: Software Heritage is the universal archive of software source code.
  example: 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d
  homepage: https://archive.softwareheritage.org
  mappings:
    miriam: swh
    n2t: swh
    prefixcommons: SWH
  name: Software Heritage
  namespace_in_lui: true
  pattern: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$
  preferred_prefix: swh
  uri_format: https://archive.softwareheritage.org/browse/swh:$1
swiss-model:
  description: The SWISS-MODEL Repository is a database of 3D protein structure models
    generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein
    sequences.
  example: P23298
  homepage: https://swissmodel.expasy.org
  mappings:
    miriam: swiss-model
    n2t: swiss-model
    prefixcommons: SWISS-MODEL
  name: SWISS-MODEL Repository
  pattern: ^\w+$
  preferred_prefix: swiss-model
  uri_format: https://swissmodel.expasy.org/repository/uniprot/$1
swisslipid:
  banana: SLM
  description: SwissLipids is a curated resource that provides information about known
    lipids, including lipid structure, metabolism, interactions, and subcellular and
    tissue localization. Information is curated from peer-reviewed literature and
    referenced using established ontologies, and provided with full provenance and
    evidence codes for curated assertions.
  example: '000000341'
  homepage: http://www.swisslipids.org/#/
  mappings:
    miriam: slm
    n2t: swisslipid
    prefixcommons: SWISSLIPID
    uniprot: SwissLipids
    wikidata: P8691
  name: SwissLipid
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: swisslipid
  synonyms:
  - slm
  - swisslipids
  uri_format: https://www.swisslipids.org/#/entity/SLM:$1
swissregulon:
  description: A database of genome-wide annotations of regulatory sites. It contains
    annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers
    an intuitive interface showing genomic information in a graphical form.
  example: AHR
  homepage: http://swissregulon.unibas.ch
  mappings:
    miriam: swissregulon
    n2t: swissregulon
    prefixcommons: SWISSREGULON
  name: SwissRegulon
  pattern: ^[A-Za-z0-9]+$
  preferred_prefix: swissregulon
  uri_format: http://swissregulon.unibas.ch/query/$1
swo:
  banana: SWO
  contact:
    email: allyson.lister@oerc.ox.ac.uk
    github: allysonlister
    name: Allyson Lister
    orcid: null
  description: The Software Ontology (SWO) is a resource for describing software tools,
    their types, tasks, versions, provenance and associated data. It contains detailed
    information on licensing and formats as well as software applications themselves,
    mainly (but not limited) to the bioinformatics community.
  example: '0000144'
  homepage: https://github.com/allysonlister/swo
  license: CC BY 4.0
  mappings:
    bioportal: SWO
    obofoundry: SWO
    ols: swo
    ontobee: SWO
    prefixcommons: SWO
  name: Software ontology
  pattern: ^\d{7}$
  preferred_prefix: SWO
  uri_format: http://purl.obolibrary.org/obo/SWO_$1
  version: '1.7'
symp:
  banana: SYMP
  contact:
    email: lynn.schriml@gmail.com
    github: null
    name: Lynn Schriml
    orcid: null
  description: The Symptom Ontology has been developed as a standardized ontology
    for symptoms of human diseases.
  example: 0019171
  homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page
  license: CC0 1.0
  mappings:
    bioportal: SYMP
    obofoundry: SYMP
    ols: symp
    ontobee: SYMP
    prefixcommons: SYMP
    wikidata: P8656
  name: Symptom Ontology
  pattern: ^\d{7}$
  preferred_prefix: SYMP
  synonyms:
  - SYMP
  uri_format: http://purl.obolibrary.org/obo/SYMP_$1
  version: '2020-08-04'
syoid:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Gemina Symptom Ontology Identifier
  preferred_prefix: syoid
  references:
  - https://github.com/DiseaseOntology/SymptomOntology/issues/7#event-4223716562
t3db:
  description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource
    that combines detailed toxin data with comprehensive toxin target information.
  example: T3D0001
  homepage: http://www.t3db.org/
  mappings:
    miriam: t3db
    n2t: t3db
    prefixcommons: T3DB
  name: Toxin and Toxin Target Database
  pattern: ^T3D\d+$
  preferred_prefix: t3db
  uri_format: http://www.t3db.org/toxins/$1
tads:
  banana: TADS
  contact:
    email: dsonensh@odu.edu
    github: null
    name: Daniel Sonenshine
    orcid: null
  description: 'The anatomy of the Tick, <i>Families: Ixodidae, Argassidae</i>'
  example: '0000547'
  homepage: https://www.vectorbase.org/ontology-browser
  license: CC BY 4.0
  mappings:
    bioportal: TADS
    obofoundry: TADS
    ols: tads
    ontobee: TADS
    prefixcommons: TADS
  name: Tick Anatomy Ontology
  pattern: ^\d{7}$
  preferred_prefix: TADS
  uri_format: http://purl.obolibrary.org/obo/TADS_$1
  version: '2015-08-20'
tahe:
  banana: TAHE
  contact:
    email: pierre.sprumont@unifr.ch
    github: null
    name: Pierre Sprumont
    orcid: null
  deprecated: true
  mappings:
    obofoundry: TAHE
    prefixcommons: TAHE
  name: Terminology of Anatomy of Human Embryology
  preferred_prefix: TAHE
  uri_format: http://purl.obolibrary.org/obo/TAHE_$1
tahh:
  banana: TAHH
  contact:
    email: pierre.sprumont@unifr.ch
    github: null
    name: Pierre Sprumont
    orcid: null
  deprecated: true
  mappings:
    obofoundry: TAHH
    prefixcommons: TAHH
  name: Terminology of Anatomy of Human Histology
  preferred_prefix: TAHH
  uri_format: http://purl.obolibrary.org/obo/TAHH_$1
tair.gene:
  description: The Arabidopsis Information Resource (TAIR) maintains a database of
    genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
    This is the reference gene model for a given locus.
  example: '2200934'
  homepage: http://arabidopsis.org/index.jsp
  mappings:
    miriam: tair.gene
    n2t: tair.gene
    prefixcommons: TAIR.GENE
  name: TAIR Gene
  pattern: ^\d{7}$
  preferred_prefix: tair.gene
  uri_format: http://arabidopsis.org/servlets/TairObject?accession=Gene:$1
tair.locus:
  description: The Arabidopsis Information Resource (TAIR) maintains a database of
    genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
    The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
  example: '2200950'
  homepage: http://arabidopsis.org/index.jsp
  mappings:
    go: TAIR
    miriam: tair.locus
    n2t: tair.locus
    ncbi: TAIR
    prefixcommons: TAIR.LOCUS
  name: The Arabidopsis Information Resource
  pattern: ^\d{7}$
  preferred_prefix: tair.locus
  uri_format: http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1
tair.protein:
  description: The Arabidopsis Information Resource (TAIR) maintains a database of
    genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
    This provides protein information for a given gene model and provides links to
    other sources such as UniProtKB and GenPept
  example: '1009107926'
  homepage: http://arabidopsis.org/index.jsp
  mappings:
    miriam: tair.protein
    n2t: tair.protein
    prefixcommons: TAIR.PROTEIN
  name: TAIR Protein
  pattern: ^\d{10}$
  preferred_prefix: tair.protein
  uri_format: http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1
tao:
  banana: TAO
  contact:
    email: wasila.dahdul@usd.edu
    github: null
    name: Wasila Dahdul
    orcid: null
  deprecated: true
  description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but
    intended to cover terms relevant to other taxa
  example: 0000086
  homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology
  license: CC0 1.0
  mappings:
    bioportal: TAO
    obofoundry: TAO
    prefixcommons: TAO
  name: Teleost Anatomy Ontology
  preferred_prefix: TAO
  synonyms:
  - TAO_RETIRED
  uri_format: http://purl.obolibrary.org/obo/TAO_$1
tarbase:
  description: "TarBase stores microRNA (miRNA) information for miRNA\u2013gene interactions,\
    \ as well as miRNA- and gene-related facts to information specific to the interaction\
    \ and the experimental validation methodologies used."
  example: hsa-let-7a-2-3p
  homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
  mappings:
    miriam: tarbase
    n2t: tarbase
    prefixcommons: TARBASE
  name: TarBase
  pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)$
  preferred_prefix: tarbase
  uri_format: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1
taxrank:
  banana: TAXRANK
  contact:
    email: balhoff@renci.org
    github: balhoff
    name: Jim Balhoff
    orcid: null
  description: A vocabulary of taxonomic ranks (species, family, phylum, etc)
  example: '0000001'
  homepage: https://github.com/phenoscape/taxrank
  license: CC0 1.0
  mappings:
    bioportal: TAXRANK
    obofoundry: TAXRANK
    ols: taxrank
    ontobee: TAXRANK
    prefixcommons: TAXRANK
  name: Taxonomic rank vocabulary
  pattern: ^\d{7}$
  preferred_prefix: TAXRANK
  uri_format: http://purl.obolibrary.org/obo/TAXRANK_$1
  version: '2016-04-15'
tcdb:
  description: The database details a comprehensive  IUBMB approved classification
    system for membrane transport proteins known as the Transporter Classification
    (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for
    classification of enzymes, but incorporates phylogenetic information additionally.
  example: 5.A.1.1.1
  homepage: https://www.tcdb.org
  mappings:
    go: TC
    miriam: tcdb
    n2t: tcdb
    prefixcommons: TCDB
    uniprot: TCDB
    wikidata: P7260
  name: Transporter Classification Database ID
  pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$
  preferred_prefix: tcdb
  synonyms:
  - TC
  uri_format: http://www.tcdb.org/search/result.php?tc=$1
te:
  description: The Terminologia Embryologica (TE) is a standardized list of words
    used in the description of human embryologic and fetal structures. It was produced
    by the Federative International Committee on Anatomical Terminology on behalf
    of the International Federation of Associations of Anatomists and posted on the
    Internet since 2010. [wikipedia]
  example: E5.11.2.0.0.0.4
  homepage: https://ifaa.unifr.ch/
  mappings:
    wikidata: P1693
  name: Terminologia Embryologica
  preferred_prefix: te
  references:
  - https://en.wikipedia.org/wiki/Terminologia_Embryologica
tfclass:
  description: TFClass is a classification of eukaryotic transcription factors based
    on the characteristics of their DNA-binding domains. It comprises four general
    levels (superclass, class, family, subfamily) and two levels of instantiation
    (genus and molecular species). Two of them (subfamily and factor species) are
    optional. More detailed explanations about the classification scheme and its criteria
    are given here..
  example: 2.1.1
  homepage: http://tfclass.bioinf.med.uni-goettingen.de
  mappings:
    go: TFClass
  name: Classification of Transcription Factors in Mammalia
  preferred_prefix: tfclass
  uri_format: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1
tgd:
  description: The Tetrahymena Genome Database (TGD) Wiki is a database of information
    about the Tetrahymena thermophila genome sequence. It provides information curated
    from the literature about each published gene, including a standardized gene name,
    a link to the genomic locus, gene product annotations utilizing the Gene Ontology,
    and links to published literature.
  example: TTHERM_00648910
  homepage: http://ciliate.org/index.php/
  mappings:
    go: TGD
    miriam: tgd
    n2t: tgd
    prefixcommons: TGD
  name: Tetrahymena Genome Database
  pattern: ^TTHERM\_\d+$
  preferred_prefix: tgd
  uri_format: http://ciliate.org/index.php/feature/details/$1
tgma:
  banana: TGMA
  contact:
    email: topalis@imbb.forth.gr
    github: null
    name: Pantelis Topalis
    orcid: null
  description: A structured controlled vocabulary of the anatomy of mosquitoes.
  example: 0000984
  homepage: https://www.vectorbase.org/ontology-browser
  license: CC0 1.0
  mappings:
    bioportal: TGMA
    obofoundry: TGMA
    ols: tgma
    ontobee: TGMA
    prefixcommons: TGMA
  name: Mosquito gross anatomy ontology
  pattern: ^\d{7}$
  preferred_prefix: TGMA
  uri_format: http://purl.obolibrary.org/obo/TGMA_$1
  version: '2013-06-03'
th:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The Terminologia Histologica (TH) is the controlled vocabulary for
    use in cytology and histology. It was intended to replace Nomina Histologica.
    [wikipedia]
  example: H3.03.00.0.00007
  homepage: https://ifaa.unifr.ch/
  name: Terminologia Histologica
  preferred_prefix: th
  references:
  - https://en.wikipedia.org/wiki/Terminologia_Histologica
thermofisher:
  description: ThermoFisher is a life sciences supply vendor.
  example: OSR00185W
  homepage: https://www.thermofisher.com
  name: Thermo Fisher Scientific
  preferred_prefix: thermofisher
  uri_format: https://www.thermofisher.com/antibody/product/$1
tigrfam:
  description: TIGRFAMs is a resource consisting of curated multiple sequence alignments,
    Hidden Markov Models (HMMs) for protein sequence classification, and associated
    information designed to support automated annotation of (mostly prokaryotic) proteins.
  example: TIGR00010
  homepage: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi
  mappings:
    miriam: tigrfam
    n2t: tigrfam
    ncbi: TIGRFAM
    prefixcommons: TIGRFAM
  name: TIGR protein families
  pattern: ^TIGR\d+$
  preferred_prefix: tigrfam
  uri_format: http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$1
tkg:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Collection of cell lines by Tohoku University. This includes transplantable
    animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series)
    cell lines as well as human, murine cell lines and hybridoma cells.
  example: '0221'
  homepage: http://www2.idac.tohoku.ac.jp/dep/ccr/
  mappings:
    cellosaurus: TKG
  name: Tohoku University cell line catalog
  pattern: ^\d+$
  preferred_prefix: tkg
  uri_format: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html
to:
  banana: TO
  contact:
    email: jaiswalp@science.oregonstate.edu
    github: null
    name: Pankaj Jaiswal
    orcid: null
  description: A controlled vocabulary to describe phenotypic traits in plants.
  example: '0000630'
  homepage: http://browser.planteome.org/amigo
  license: CC BY 4.0
  mappings:
    bioportal: PTO
    obofoundry: TO
    ols: to
    ontobee: TO
    prefixcommons: TO
  name: Plant Trait Ontology
  pattern: ^\d{7}$
  preferred_prefix: TO
  uri_format: http://purl.obolibrary.org/obo/TO_$1
  version: '2021-04-06'
tol:
  description: "The Tree of Life Web Project (ToL) is a collaborative effort of biologists\
    \ and nature enthusiasts from around the world. On more than 10,000 World Wide\
    \ Web pages, the project provides information about biodiversity, the characteristics\
    \ of different groups of organisms, and their evolutionary history (phylogeny).\
    \ \r\n\r\nEach page contains information about a particular group, with pages\
    \ linked one to another hierarchically, in the form of the evolutionary tree of\
    \ life. Starting with the root of all Life on Earth and moving out along diverging\
    \ branches to individual species, the structure of the ToL project thus illustrates\
    \ the genetic connections between all living things."
  example: '98034'
  homepage: http://tolweb.org/tree/
  mappings:
    miriam: tol
    n2t: tol
    prefixcommons: TOL
  name: Tree of Life
  pattern: ^\d+$
  preferred_prefix: tol
  uri_format: http://tolweb.org/$1
topdb:
  description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection
    of transmembrane protein datasets containing experimentally derived topology information.
    It contains information gathered from the literature and from public databases
    availableon transmembrane proteins. Each record in TOPDB also contains information
    on the given protein sequence, name, organism and cross references to various
    other databases.
  example: AP00378
  homepage: http://topdb.enzim.hu/
  mappings:
    miriam: topdb
    n2t: topdb
    prefixcommons: TOPDB
  name: Topology Data Bank of Transmembrane Proteins
  pattern: ^[A-Z0-9]+$
  preferred_prefix: topdb
  uri_format: http://topdb.enzim.hu/?m=show&id=$1
topfind:
  description: 'TopFIND is a database of protein termini, terminus modifications and
    their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis
    thaliana, Saccharomyces cerevisiae and Escherichia coli.'
  example: Q9UKQ2
  homepage: https://topfind.clip.msl.ubc.ca
  mappings:
    miriam: topfind
    n2t: topfind
    prefixcommons: TOPFIND
  name: TopFind
  pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
    0-9][A-Z, 0-9][0-9])$
  preferred_prefix: topfind
  uri_format: http://clipserve.clip.ubc.ca/topfind/proteins/$1
toxoplasma:
  description: ToxoDB is one of the databases that can be accessed through the EuPathDB
    (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
    the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
    Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
    database built upon the same infrastructure, the EuPathDB portal offers an entry
    point to all these resources, and the opportunity to leverage orthology for searches
    across genera.
  example: TGME49_053730
  homepage: http://toxodb.org/toxo/
  mappings:
    miriam: toxoplasma
    n2t: toxoplasma
    prefixcommons: TOXOPLASMA
  name: ToxoDB
  pattern: ^\w+$
  preferred_prefix: toxoplasma
  uri_format: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
trans:
  banana: TRANS
  contact:
    email: lynn.schriml@gmail.com
    github: null
    name: Lynn Schriml
    orcid: null
  description: The Pathogen Transmission Ontology describes the tranmission methods
    of human disease pathogens describing how a pathogen is transmitted from one host,
    reservoir, or source to another host. The pathogen transmission may occur either
    directly or indirectly and may involve animate vectors or inanimate vehicles.
  example: '0000024'
  homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology
  license: CC0 1.0
  mappings:
    bioportal: TRANS
    obofoundry: TRANS
    ols: trans
    ontobee: TRANS
    prefixcommons: TRANS
  name: Pathogen Transmission Ontology
  pattern: ^\d{7}$
  preferred_prefix: TRANS
  uri_format: http://purl.obolibrary.org/obo/TRANS_$1
  version: '2020-08-04'
transyt:
  description: The Transport Systems Tracker (TranSyT) is a tool to identify transport
    systems and the compounds carried across membranes.
  example: TR0000001
  homepage: https://www.bio.di.uminho.pt/
  mappings:
    miriam: transyt
  name: Transport Systems Tracker
  pattern: ^T[A-Z]\d{7}$
  preferred_prefix: transyt
  uri_format: https://transyt.bio.di.uminho.pt/reactions/$1
treebase:
  description: TreeBASE is a relational database designed to manage and explore information
    on phylogenetic relationships. It includes phylogenetic trees and data matrices,
    together with information about the relevant publication, taxa, morphological
    and sequence-based characters, and published analyses. Data in TreeBASE are exposed
    to the public if they are used in a publication that is in press or published
    in a peer-reviewed scientific journal, etc.
  example: TB2:S1000
  homepage: http://treebase.org/
  mappings:
    miriam: treebase
    n2t: treebase
    prefixcommons: TREEBASE
  name: TreeBASE
  pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$
  preferred_prefix: treebase
  uri_format: http://purl.org/phylo/treebase/phylows/study/$1?format=html
treefam:
  description: TreeFam is a database of phylogenetic trees of gene families found
    in animals. Automatically generated trees are curated, to create a curated resource
    that presents the accurate evolutionary history of all animal gene families, as
    well as reliable ortholog and paralog assignments.
  example: TF101014
  homepage: http://www.treefam.org/
  mappings:
    miriam: treefam
    n2t: treefam
    prefixcommons: TREEFAM
    uniprot: TreeFam
  name: TreeFam
  pattern: ^\w{1,2}\d+$
  preferred_prefix: treefam
  uri_format: http://www.treefam.org/family/$1
trichdb:
  description: TrichDB is one of the databases that can be accessed through the EuPathDB
    (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
    the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
    Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
    database built upon the same infrastructure, the EuPathDB portal offers an entry
    point to all these resources, and the opportunity to leverage orthology for searches
    across genera.
  example: TVAG_386080
  homepage: http://trichdb.org/trichdb/
  mappings:
    miriam: trichdb
    n2t: trichdb
    prefixcommons: TRICHDB
  name: TrichDB
  pattern: ^\w+$
  preferred_prefix: trichdb
  uri_format: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
tritrypdb:
  description: TriTrypDB is one of the databases that can be accessed through the
    EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
    of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
    Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
    database built upon the same infrastructure, the EuPathDB portal offers an entry
    point to all these resources, and the opportunity to leverage orthology for searches
    across genera.
  example: Tb927.8.620
  homepage: http://tritrypdb.org/tritrypdb/
  mappings:
    miriam: tritrypdb
    n2t: tritrypdb
    prefixcommons: TRITRYPDB
  name: TriTrypDB
  pattern: ^\w+(\.)?\w+(\.)?\w+$
  preferred_prefix: tritrypdb
  uri_format: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
ttd.drug:
  description: The Therapeutic Target Database (TTD) is designed to provide information
    about the known therapeutic protein and nucleic acid targets described in the
    literature, the targeted disease conditions, the pathway information and the corresponding
    drugs/ligands directed at each of these targets. Cross-links to other databases
    allow the access to information about the sequence, 3D structure, function, nomenclature,
    drug/ligand binding properties, drug usage and effects, and related literature
    for each target.
  example: DAP000773
  homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp
  mappings:
    miriam: ttd.drug
    n2t: ttd.drug
    prefixcommons: TTD.DRUG
  name: TTD Drug
  pattern: ^DAP\d+$
  preferred_prefix: ttd.drug
  uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1
ttd.target:
  description: The Therapeutic Target Database (TTD) is designed to provide information
    about the known therapeutic protein and nucleic acid targets described in the
    literature, the targeted disease conditions, the pathway information and the corresponding
    drugs/ligands directed at each of these targets. Cross-links to other databases
    are also introduced to facilitate the access of information about the sequence,
    3D structure, function, nomenclature, drug/ligand binding properties, drug usage
    and effects, and related literature for each target.
  example: TTDS00056
  homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp
  mappings:
    miriam: ttd.target
    n2t: ttd.target
    prefixcommons: TTD.TARGET
  name: TTD Target
  pattern: ^TTDS\d+$
  preferred_prefix: ttd.target
  uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1
tto:
  banana: TTO
  contact:
    email: balhoff@renci.org
    github: balhoff
    name: Jim Balhoff
    orcid: null
  description: An ontology covering the taxonomy of teleosts (bony fish)
  example: '1058367'
  homepage: https://github.com/phenoscape/teleost-taxonomy-ontology
  license: CC0 1.0
  mappings:
    bioportal: TTO
    obofoundry: TTO
    ols: tto
    ontobee: TTO
    prefixcommons: TTO
  name: Teleost taxonomy ontology
  pattern: ^\d+$
  preferred_prefix: TTO
  uri_format: http://purl.obolibrary.org/obo/TTO_$1
  version: '2018-03-26'
txpo:
  banana: TXPO
  contact:
    email: y-yamagata@nibiohn.go.jp
    github: txpo-ontology
    name: Yuki Yamagata
    orcid: null
  description: 'Elucidating the mechanism of toxicity is crucial in drug safety evaluations.
    TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity
    courses and processes. The first version of TXPO focuses on liver toxicity.


    The TXPO contains an is-a hierarchy that is organized into three layers: the top
    layer contains general terms, mostly derived from the Basic Formal Ontology. The
    intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell
    Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID
    and Relational ontology (RO). The lower layer contains toxicological terms.


    In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe
    knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which
    facilitates capturing the comprehensive picture for understanding toxicity mechanisms.
    A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp'
  example: '0002066'
  homepage: https://toxpilot.nibiohn.go.jp/
  license: CC BY 3.0
  mappings:
    bioportal: TXPO
    obofoundry: TXPO
    ols: txpo
    ontobee: TXPO
  name: Toxic Process Ontology
  preferred_prefix: TXPO
  uri_format: http://purl.obolibrary.org/obo/TXPO_$1
  version: '2020-07-09'
uberon:
  banana: UBERON
  contact:
    email: cjmungall@lbl.gov
    github: cmungall
    name: Chris Mungall
    orcid: null
  description: Uberon is an integrated cross-species anatomy ontology representing
    a variety of entities classified according to traditional anatomical criteria
    such as structure, function and developmental lineage. The ontology includes comprehensive
    relationships to taxon-specific anatomical ontologies, allowing integration of
    functional, phenotype and expression data.
  example: '2005080'
  homepage: http://uberon.org
  license: CC BY 3.0
  mappings:
    bioportal: UBERON
    go: UBERON
    miriam: uberon
    n2t: uberon
    obofoundry: UBERON
    ols: uberon
    ontobee: UBERON
    prefixcommons: UBERON
    wikidata: P1554
  name: Uber Anatomy Ontology
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: UBERON
  synonyms:
  - UBERON
  - Uber-anatomy ontology
  - Uberon
  uri_format: http://purl.obolibrary.org/obo/UBERON_$1
  version: '2021-11-28'
ubio.namebank:
  description: NameBank is a "biological name server" focused on storing names and
    objectively-derived nomenclatural attributes. NameBank is a repository for all
    recorded names including scientific names, vernacular (or common names), misspelled
    names, as well as ad-hoc nomenclatural labels that may have limited context.
  example: '2555646'
  homepage: http://www.ubio.org
  mappings:
    miriam: ubio.namebank
    n2t: ubio.namebank
    prefixcommons: UBIO.NAMEBANK
  name: uBio NameBank
  pattern: ^\d+$
  preferred_prefix: ubio.namebank
  uri_format: http://www.ubio.org/browser/details.php?namebankID=$1
ubprop:
  comment: All of these are typedefs in uberon now
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: Uberon Property
  preferred_prefix: ubprop
ucsc:
  description: The UCSC Genome Browser is an on-line, and downloadable, genome browser
    hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive
    website offering access to genome sequence data from a variety of vertebrate and
    invertebrate species and major model organisms, integrated with a large collection
    of aligned annotations.
  example: uc001rvw.5
  homepage: https://genome.ucsc.edu/
  mappings:
    prefixcommons: UCSC
    uniprot: UCSC
    wikidata: P2576
  name: UCSC Genome Browser
  preferred_prefix: ucsc
  uri_format: ftp://hgdownload.cse.ucsc.edu/goldenPath/$1
umbbd.compound:
  description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
    contains information on microbial biocatalytic reactions and biodegradation pathways
    for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide
    information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    This collection refers to compound information.
  example: c0001
  homepage: http://umbbd.ethz.ch/
  mappings:
    miriam: umbbd.compound
    n2t: umbbd.compound
    prefixcommons: UMBBD.COMPOUND
    wikidata: P8121
  name: UM-BBD Compound
  pattern: ^c\d+$
  preferred_prefix: umbbd.compound
  synonyms:
  - UM-BBD_compID
  uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1
umbbd.enzyme:
  description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
    contains information on microbial biocatalytic reactions and biodegradation pathways
    for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide
    information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    This collection refers to enzyme information.
  example: e0333
  homepage: http://umbbd.ethz.ch/
  mappings:
    go: UM-BBD_enzymeID
    miriam: umbbd.enzyme
    n2t: umbbd.enzyme
    prefixcommons: UMBBD.ENZYME
  name: EAWAG Biocatalysis/Biodegradation Database
  pattern: ^e\d+$
  preferred_prefix: umbbd.enzyme
  synonyms:
  - UM-BBD_enzymeID
  uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1
umbbd.pathway:
  description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
    contains information on microbial biocatalytic reactions and biodegradation pathways
    for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide
    information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    This collection refers to pathway information.
  example: ala
  homepage: http://umbbd.ethz.ch/
  mappings:
    go: UM-BBD_pathwayID
    miriam: umbbd.pathway
    n2t: umbbd.pathway
    prefixcommons: UMBBD.PATHWAY
  name: EAWAG Biocatalysis/Biodegradation Database
  pattern: ^\w+$
  preferred_prefix: umbbd.pathway
  synonyms:
  - UM-BBD_pathwayID
  uri_format: http://eawag-bbd.ethz.ch/$1/$1_map.html
umbbd.reaction:
  description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
    contains information on microbial biocatalytic reactions and biodegradation pathways
    for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide
    information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    This collection refers to reaction information.
  example: r0001
  homepage: http://umbbd.ethz.ch/
  mappings:
    go: UM-BBD_reactionID
    miriam: umbbd.reaction
    n2t: umbbd.reaction
    prefixcommons: UMBBD.REACTION
  name: EAWAG Biocatalysis/Biodegradation Database
  pattern: ^r\d+$
  preferred_prefix: umbbd.reaction
  synonyms:
  - UM-BBD_reactionID
  uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1
umbbd.rule:
  description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
    contains information on microbial biocatalytic reactions and biodegradation pathways
    for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System
    (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base,
    and atom-to-atom mapping. The PPS recognizes organic functional groups found in
    a compound and predicts transformations based on biotransformation rules. These
    rules are based on reactions found in the UM-BBD database. This collection references
    those rules.
  example: bt0001
  homepage: http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules
  mappings:
    go: UM-BBD_ruleID
    miriam: umbbd.rule
    n2t: umbbd.rule
    prefixcommons: UMBBD.RULE
  name: EAWAG Biocatalysis/Biodegradation Database
  pattern: ^bt\d+$
  preferred_prefix: umbbd.rule
  synonyms:
  - UM-BBD_ruleID
  uri_format: http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1
umls:
  description: The Unified Medical Language System is a repository of biomedical vocabularies.
    Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene
    Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist
    Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also
    be linked to external resources such as GenBank.
  example: C2584994
  homepage: http://linkedlifedata.com/
  mappings:
    miriam: umls
    n2t: umls
    prefixcommons: UMLS
    wikidata: P2892
  name: Unified Medical Language System
  pattern: ^C\d+$
  preferred_prefix: umls
  synonyms:
  - UMLS
  - UMLS CUI
  - UMLS_CUI
  uri_format: http://linkedlifedata.com/resource/umls/id/$1
unigene:
  description: A UniGene entry is a set of transcript sequences that appear to come
    from the same transcription locus (gene or expressed pseudogene), together with
    information on protein similarities, gene expression, cDNA clone reagents, and
    genomic location.
  example: '4900'
  homepage: http://www.ncbi.nlm.nih.gov/unigene
  mappings:
    miriam: unigene
    n2t: unigene
    prefixcommons: UNIGENE
  name: UniGene
  pattern: ^\d+$
  preferred_prefix: unigene
  uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1
unii:
  description: "The purpose of the joint FDA/USP Substance Registration System (SRS)\
    \ is to support health information technology initiatives by generating unique\
    \ ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and\
    \ devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic,\
    \ alphanumeric identifier based on a substance\u2019s molecular structure and/or\
    \ descriptive information."
  example: 3G6A5W338E
  homepage: http://fdasis.nlm.nih.gov/srs/
  mappings:
    cheminf: '000563'
    miriam: unii
    n2t: unii
    prefixcommons: UNII
    wikidata: P652
  name: Unique Ingredient Identifier
  pattern: ^[A-Z0-9]+$
  preferred_prefix: unii
  uri_format: http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1
unimod:
  description: Unimod is a public domain database created to provide a community supported,
    comprehensive database of protein modifications for mass spectrometry applications.
    That is, accurate and verifiable values, derived from elemental compositions,
    for the mass differences introduced by all types of natural and artificial modifications.
    Other important information includes any mass change, (neutral loss), that occurs
    during MS/MS analysis, and site specificity, (which residues are susceptible to
    modification and any constraints on the position of the modification within the
    protein or peptide).
  example: '1200'
  homepage: http://www.unimod.org/
  mappings:
    miriam: unimod
    n2t: unimod
    ols: unimod
    prefixcommons: UNIMOD
  name: Unimod protein modification database for mass spectrometry
  pattern: ^\d+$
  preferred_prefix: unimod
  uri_format: http://www.unimod.org/modifications_view.php?editid1=$1
  version: '2019-11-21'
uniparc:
  description: The UniProt Archive (UniParc) is a  database containing non-redundant
    protein sequence information from many sources. Each unique sequence is given
    a stable and unique identifier (UPI) making it possible to identify the same protein
    from different source databases.
  example: UPI000000000A
  homepage: https://www.ebi.ac.uk/uniparc/
  mappings:
    go: UniParc
    miriam: uniparc
    n2t: uniparc
    prefixcommons: UNIPARC
  name: UniProt Archive
  pattern: ^UPI[A-F0-9]{10}$
  preferred_prefix: uniparc
  providers:
  - code: CURATOR_REVIEW
    description: UniParc through UniProt
    homepage: http://www.uniprot.org/uniparc/
    name: UniParc through UniProt
    uri_format: https://www.uniprot.org/uniparc/$1
  uri_format: https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1
unipathway.compound:
  description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous
    chemical reactions. It provides a hierarchical representation of metabolic pathways
    and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data
    are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and
    MetaCyc. This collection references compounds.
  example: UPC04349
  homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
  mappings:
    miriam: unipathway.compound
    n2t: unipathway.compound
    prefixcommons: UNIPATHWAY.COMPOUND
  name: UniPathway Compound
  pattern: ^UPC\d{5}$
  preferred_prefix: unipathway.compound
  uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1
unipathway.reaction:
  description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous
    chemical reactions. It provides a hierarchical representation of metabolic pathways
    and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data
    are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and
    MetaCyc. This collection references individual reactions.
  example: UCR00226
  homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
  mappings:
    miriam: unipathway.reaction
    n2t: unipathway.reaction
    prefixcommons: UNIPATHWAY.REACTION
  name: UniPathway Reaction
  pattern: ^UCR\d{5}$
  preferred_prefix: unipathway.reaction
  uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1
uniprot:
  description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for
    protein sequence and functional information with extensive cross-references to
    more than 120 external databases. Besides amino acid sequence and a description,
    it also provides taxonomic data and citation information.
  example: P0DP23
  homepage: http://www.uniprot.org
  mappings:
    cellosaurus: UniProtKB
    go: UniProtKB
    miriam: uniprot
    n2t: uniprot
    ncbi: UniProt
    prefixcommons: UniProtKB
    scholia: uniprot
    wikidata: P352
  name: UniProt protein ID
  pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
    0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
  preferred_prefix: uniprot
  providers:
  - code: omnipath
    description: Molecular interations endpoint from OmniPathDB
    homepage: https://omnipathdb.org/
    name: OmniPathDB
    uri_format: https://omnipathdb.org/interactions/?fields=sources,references&partners=$1
  - code: iptmnet
    description: Protein post translational modification information
    homepage: https://research.bioinformatics.udel.edu/iptmnet
    name: iPTMnet
    uri_format: https://research.bioinformatics.udel.edu/iptmnet/entry/$1
  - code: ncbi
    description: UniProt through NCBI
    homepage: https://www.ncbi.nlm.nih.gov/protein/
    name: UniProt through NCBI
    uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
  synonyms:
  - SwissProt
  - UP
  - UniProt
  - UniProtKB
  - uniprot/swiss-prot
  uri_format: http://purl.uniprot.org/uniprot/$1
uniprot.chain:
  description: This collection is a subset of UniProtKB that provides a means to reference
    the proteolytic cleavage products of a precursor protein.
  example: PRO_0000016681
  homepage: https://www.uniprot.org
  mappings:
    miriam: uniprot.chain
  name: UniProt Chain
  pattern: ^PRO_[0-9]{10}$
  preferred_prefix: uniprot.chain
  synonyms:
  - UPPRO
  uri_format: http://purl.uniprot.org/annotation/$1
uniprot.disease:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: The human diseases in which proteins are involved are described in
    UniProtKB entries with a controlled vocabulary.
  example: '04240'
  homepage: https://www.uniprot.org/diseases/
  name: UniProt Diseases
  preferred_prefix: uniprot.disease
  synonyms:
  - DI
  uri_format: https://www.uniprot.org/diseases/DI-$1
uniprot.isoform:
  description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for
    protein sequence and functional information with extensive cross-references to
    more than 120 external databases. This collection is a subset of UniProtKB, and
    provides a means to reference isoform information.
  example: Q5BJF6-3
  homepage: http://www.uniprot.org/
  mappings:
    miriam: uniprot.isoform
    n2t: uniprot.isoform
    prefixcommons: UNIPROT.ISOFORM
  name: UniProt Isoform
  pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
    0-9][A-Z, 0-9][0-9])(\-\d+)$
  preferred_prefix: uniprot.isoform
  providers:
  - code: CURATOR_REVIEW
    description: UniProt Isoform through Universal Protein Resource using Persistent
      URL system
    homepage: http://purl.uniprot.org/
    name: UniProt Isoform through Universal Protein Resource using Persistent URL
      system
    uri_format: http://purl.uniprot.org/uniprot/$1
  - code: CURATOR_REVIEW
    description: UniProt Isoform through UniParc
    homepage: http://www.uniprot.org/uniparc/
    name: UniProt Isoform through UniParc
    uri_format: http://www.uniprot.org/uniparc/?query=$1
  synonyms:
  - UPISO
  uri_format: http://www.uniprot.org/uniprot/$1
uniprot.keyword:
  description: UniProtKB entries are tagged with keywords that can be used to retrieve
    particular subsets of entries.
  example: KW-1273
  homepage: http://www.uniprot.org/keywords/
  mappings:
    go: UniProtKB-KW
  name: UniProt Keywords
  preferred_prefix: uniprot.keyword
  synonyms:
  - UniProtKB-KW
  uri_format: https://www.uniprot.org/keywords/$1
uniprot.location:
  description: The subcellular locations in which a protein is found are described
    in UniProtKB entries with a controlled vocabulary, which includes also membrane
    topology and orientation terms.
  example: '0002'
  homepage: https://www.uniprot.org/locations/
  mappings:
    go: UniProtKB-SubCell
  name: UniProt Subcellular Locations
  pattern: ^\d+$
  preferred_prefix: uniprot.location
  synonyms:
  - UPLOC
  - UniProtKB-SubCell
  uri_format: https://www.uniprot.org/locations/SL-$1
uniprot.tissue:
  description: The UniProt Tissue List is a controlled vocabulary of terms used to
    annotate biological tissues. It also contains cross-references to other ontologies
    where tissue types are specified.
  example: TS-0285
  homepage: https://www.uniprot.org/docs/tisslist.txt
  mappings:
    miriam: tissuelist
    n2t: tissuelist
    prefixcommons: TISSUELIST
  name: Tissue List
  pattern: ^TS-\d{4}$
  preferred_prefix: uniprot.tissue
  uri_format: https://www.uniprot.org/tissues/$1
uniprot.var:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: 'The purpose of the UniProtKB/Swiss-Prot variant pages is: to display
    the variant related information extracted from UniProtKB/Swiss-Prot, and to provide
    useful additional information such as the conservation of the modified residues
    across orthologous species.'
  example: VAR_068078
  homepage: https://web.expasy.org/variant_pages
  name: UniProt Variants
  pattern: ^VAR_\d+$
  preferred_prefix: uniprot.var
  synonyms:
  - UniProtKB_VAR
  uri_format: https://web.expasy.org/variant_pages/$1.html
uniref:
  description: The UniProt Reference Clusters (UniRef) provide clustered sets of sequences
    from the UniProt Knowledgebase (including isoforms) and selected UniParc records
    in order to obtain complete coverage of the sequence space at several resolutions
    while hiding redundant sequences (but not their descriptions) from view.
  example: UniRef90_P00750
  homepage: https://www.uniprot.org/
  mappings:
    miriam: uniref
  name: UniRef
  pattern: ^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$
  preferred_prefix: uniref
  uri_format: https://www.uniprot.org/uniref/$1
unirule:
  description: Rules are devised and tested by experienced curators using experimental
    data from manually annotated entries as templates. UniRule rules can annotate
    protein properties such as the protein name, function, catalytic activity, pathway
    membership, and subcellular location, along with sequence specific information,
    such as the positions of post-translational modifications and active sites.
  example: UR000124451
  homepage: https://www.uniprot.org/unirule/
  mappings:
    go: UniRule
  name: UniRule
  preferred_prefix: unirule
  uri_format: https://www.uniprot.org/unirule/$1
unists:
  description: UniSTS is a comprehensive database of sequence tagged sites (STSs)
    derived from STS-based maps and other experiments. STSs are defined by PCR primer
    pairs and are associated with additional information such as genomic position,
    genes, and sequences.
  example: '456789'
  homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists
  mappings:
    miriam: unists
    n2t: unists
    ncbi: UniSTS
    prefixcommons: UNISTS
  name: Database of Sequence Tagged Sites
  pattern: ^\d+$
  preferred_prefix: unists
  uri_format: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1
unite:
  description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database.
    It focuses on high-quality ITS sequences generated from fruiting bodies collected
    and identified by experts and deposited in public herbaria. Entries may be supplemented
    with metadata on describing locality, habitat, soil, climate, and interacting
    taxa.
  example: UDB000691
  homepage: http://unite.ut.ee/
  mappings:
    miriam: unite
    n2t: unite
    ncbi: UNITE
    prefixcommons: UNITE
  name: Molecular database for the identification of fungi
  pattern: ^UDB\d{6}$
  preferred_prefix: unite
  uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1
unpd:
  comment: The website is dead, there are no places to get the source information
    except inside https://oolonek.github.io/ISDB/.
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  homepage: http://pkuxxj.pku.edu.cn/UNPD/
  name: Universal Natural Products Database
  preferred_prefix: unpd
  references:
  - http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database
  - https://pharmacognosy.in/the-universal-natural-products-database-unpd/
  - https://pubs.acs.org/doi/abs/10.1021/acs.jnatprod.6b01093
  - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062839
  - https://oolonek.github.io/ISDB/
uo:
  banana: UO
  contact:
    email: g.gkoutos@gmail.com
    github: null
    name: George Gkoutos
    orcid: null
  description: Ontology of standardized units
  example: 0000080
  homepage: https://github.com/bio-ontology-research-group/unit-ontology
  license: CC BY 3.0
  mappings:
    bioportal: UO
    miriam: uo
    n2t: uo
    obofoundry: UO
    ols: uo
    ontobee: UO
    prefixcommons: UO
  name: Units of measurement ontology
  namespace_in_lui: true
  pattern: ^\d{7}$
  preferred_prefix: UO
  uri_format: https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1
  version: '2020-03-10'
upa:
  banana: UPA
  contact:
    email: Anne.Morgat@sib.swiss
    github: amorgat
    name: Anne Morgat
    orcid: null
  deprecated: true
  description: A manually curated resource for the representation and annotation of
    metabolic pathways
  example: UCR00513
  homepage: https://github.com/geneontology/unipathway
  license: CC BY 3.0
  mappings:
    bioportal: UPA
    go: UniPathway
    obofoundry: UPA
    ols: upa
    ontobee: UPA
    prefixcommons: UNIPATHWAY
    uniprot: UniPathway
  name: Unipathway
  pattern: ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$
  preferred_prefix: UPA
  synonyms:
  - UPa
  - unipathway
  uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1
  version: '2018-12-12'
upheno:
  banana: UPHENO
  contact:
    email: vasilevs@ohsu.edu
    github: nicolevasilevsky
    name: Nicole Vasilevsky
    orcid: null
  description: The uPheno ontology integrates multiple phenotype ontologies into a
    unified cross-species phenotype ontology.
  homepage: https://github.com/obophenotype/upheno
  license: CC0 1.0
  mappings:
    bioportal: UPHENO
    obofoundry: UPHENO
    ols: upheno
    ontobee: UPHENO
    prefixcommons: UPHENO
  name: Unified Phenotype Ontology
  no_own_terms: true
  preferred_prefix: UPHENO
  uri_format: http://purl.obolibrary.org/obo/UPHENO_$1
  version: '2017-10-31'
uspto:
  description: The United States Patent and Trademark Office (USPTO) is the federal
    agency for granting U.S. patents and registering trademarks. As a mechanism that
    protects new ideas and investments in innovation and creativity, the USPTO is
    at the cutting edge of the nation's technological progress and achievement.
  example: '4145692'
  homepage: http://patft.uspto.gov/netahtml/PTO/index.html
  mappings:
    miriam: uspto
    n2t: uspto
    prefixcommons: USPTO
  name: United States Patent and Trademark Office
  pattern: ^(D|PP|R|T|H|X|AI)?\d+$
  preferred_prefix: uspto
  uri_format: http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1
validatordb:
  description: Database of validation results for ligands and non-standard residues
    in the Protein Data Bank.
  example: 2h6o
  homepage: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/
  mappings:
    miriam: validatordb
    n2t: validatordb
    prefixcommons: VALIDATORDB
  name: ValidatorDB
  pattern: ^[A-Za-z0-9\/]+$
  preferred_prefix: validatordb
  provides: pdb
  uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1
vandf:
  description: 'The National Drug File (NDF) is produced by the U.S. Department of
    Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained
    electronic drug list used by the VHA hospitals and clinics. Facilities use the
    NDF to check drug interactions, to manage orders, and to send outpatient prescriptions
    to regional automated mail-out pharmacies. NDF includes information on clinical
    drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. '
  example: '4019477'
  homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF
  mappings:
    biolink: VANDF
    bioportal: VANDF
  name: Veterans Administration National Drug File
  preferred_prefix: vandf
  references:
  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244318/
vario:
  banana: VariO
  contact:
    email: mauno.vihinen@med.lu.se
    github: null
    name: Mauno Vihinen
    orcid: null
  description: The Variation Ontology (VariO) is an ontology for the standardized,
    systematic description of effects, consequences and mechanisms of variations.
    It describes the effects of variations at the DNA, RNA and/or protein level.
  example: '0376'
  homepage: http://variationontology.org
  mappings:
    bioportal: VARIO
    miriam: vario
    n2t: vario
    obofoundry: VariO
    ols: vario
    ontobee: VariO
    prefixcommons: VARIO
  name: Variation Ontology
  namespace_in_lui: true
  pattern: ^\d+$
  preferred_prefix: VariO
  providers:
  - code: CURATOR_REVIEW
    description: VariO at Lund University
    homepage: http://www.variationontology.org/
    name: VariO at Lund University
    uri_format: http://www.ontobee.org/search?ontology=VariO&keywords=VariO_$1&submit=Search+terms
  uri_format: http://purl.obolibrary.org/obo/VARIO_$1
  version: '2018-11-09'
vbase2:
  description: The database VBASE2 provides germ-line sequences of human and mouse
    immunoglobulin variable (V) genes.
  example: humIGHV025
  homepage: http://www.vbase2.org/vbase2.php
  mappings:
    miriam: vbase2
    n2t: vbase2
    ncbi: VBASE2
    prefixcommons: VBASE2
  name: Integrative database of germ-line V genes from the immunoglobulin loci of
    human and mouse
  pattern: ^\w+$
  preferred_prefix: vbase2
  uri_format: http://www.vbase2.org/vgene.php?id=$1
vbrc:
  description: The VBRC provides bioinformatics resources to support scientific research
    directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae,
    Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center
    consists of a relational database and web application that support the data storage,
    annotation, analysis, and information exchange goals of this work. Each data release
    contains the complete genomic sequences for all viral pathogens and related strains
    that are available for species in the above-named families. In addition to sequence
    data, the VBRC provides a curation for each virus species, resulting in a searchable,
    comprehensive mini-review of gene function relating genotype to biological phenotype,
    with special emphasis on pathogenesis.
  example: '35742'
  homepage: http://vbrc.org/
  mappings:
    miriam: vbrc
    n2t: vbrc
    prefixcommons: VBRC
  name: Viral Bioinformatics Resource Center
  pattern: ^\d+$
  preferred_prefix: vbrc
  uri_format: http://vbrc.org/gene_detail.asp?gene_id=$1
vectorbase:
  description: 'VectorBase is an NIAID-funded Bioinformatic Resource Center focused
    on invertebrate vectors of human pathogens. VectorBase annotates and curates vector
    genomes providing a web accessible integrated resource for the research community.
    Currently, VectorBase contains genome information for three mosquito species:
    Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus
    humanus and a tick species Ixodes scapularis.'
  example: ISCW007415
  homepage: https://www.vectorbase.org/
  mappings:
    miriam: vectorbase
    n2t: vectorbase
    ncbi: VectorBase
    prefixcommons: VECTORBASE
  name: Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
  pattern: ^\D{4}\d{6}(\-\D{2})?$
  preferred_prefix: vectorbase
  uri_format: https://vectorbase.org/vectorbase/app/record/gene/$1
vega:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: A repository for high-quality gene models produced by the manual annotation
    of vertebrate genomes.
  example: OTTHUMG00000169812
  homepage: https://vega.archive.ensembl.org/index.html
  name: Vertebrate Genome Annotation Database
  preferred_prefix: vega
  synonyms:
  - VEGA
vegbank:
  description: 'VegBank is the vegetation plot database of the Ecological Society
    of America''s Panel on Vegetation Classification. VegBank consists of three linked
    databases that contain (1) vegetation plot records, (2) vegetation types recognized
    in the U.S. National Vegetation Classification and other vegetation types submitted
    by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other
    plant taxa recorded in plot records. Vegetation records, community types and plant
    taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated,
    revised, interpreted, downloaded, and cited. '
  example: VB.Ob.3736.GRSM125
  homepage: http://vegbank.org/
  mappings:
    miriam: vegbank
  name: VegBank
  pattern: ^VB\.[A-Za-z][A-Za-z]\..*$
  preferred_prefix: vegbank
  uri_format: http://vegbank.org/cite/$1
vfb:
  description: An interactive tool for neurobiologists to explore the detailed neuroanatomy,
    neuron connectivity and gene expression of the Drosophila melanogaster.
  example: '00000001'
  homepage: https://VirtualFlyBrain.org
  mappings:
    miriam: vfb
    n2t: vfb
  name: Virtual Fly Brain
  pattern: ^[0-9a-zA-Z]{8}$
  preferred_prefix: vfb
  uri_format: http://virtualflybrain.org/reports/$1
vfdb.gene:
  description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This
    collection references VF genes.
  example: VFG2154
  homepage: http://www.mgc.ac.cn/VFs/
  mappings:
    miriam: vfdb.gene
    n2t: vfdb.gene
    prefixcommons: VFDB.GENE
  name: VFDB Gene
  pattern: ^\w+$
  preferred_prefix: vfdb.gene
  uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1
vfdb.genus:
  description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This
    collection references VF information by Genus.
  example: Chlamydia
  homepage: http://www.mgc.ac.cn/VFs/
  mappings:
    miriam: vfdb.genus
    n2t: vfdb.genus
    prefixcommons: VFDB.GENUS
  name: VFDB Genus
  pattern: ^\w+$
  preferred_prefix: vfdb.genus
  uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1
vgnc:
  description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of
    the established HGNC (HUGO Gene Nomenclature Committee) project that names human
    genes. VGNC is responsible for assigning standardized names to genes in vertebrate
    species that currently lack a nomenclature committee.
  example: VGNC:3792
  homepage: https://vertebrate.genenames.org
  mappings:
    cellosaurus: VGNC
    miriam: vgnc
    ncbi: VGNC
    uniprot: VGNC
  name: Vertebrate Gene Nomenclature Committee
  pattern: ^((VGNC|vgnc):)?\d{1,9}$
  preferred_prefix: vgnc
  uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1
vhog:
  banana: VHOG
  deprecated: true
  example: '0000411'
  mappings:
    bioportal: VHOG
    obofoundry: VHOG
    prefixcommons: VHOG
  name: Vertebrate Homologous Organ Group Ontology
  preferred_prefix: VHOG
  synonyms:
  - VHOG_RETIRED
  uri_format: http://purl.obolibrary.org/obo/VHOG_$1
viaf:
  description: "The VIAF\xAE (Virtual International Authority File) combines multiple\
    \ name authority files into a single OCLC-hosted name authority service. The goal\
    \ of the service is to lower the cost and increase the utility of library authority\
    \ files by matching and linking widely-used authority files and making that information\
    \ available on the Web."
  example: '75121530'
  homepage: http://viaf.org
  mappings:
    miriam: viaf
    n2t: viaf
    scholia: viaf
  name: Virtual International Authority File
  pattern: ^\d+$
  preferred_prefix: viaf
  uri_format: http://viaf.org/viaf/$1
vido:
  description: The Virus Infectious Disease Ontology (IDO Virus) is an extension of
    the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines,
    employs the Basic Formal Ontology as its starting point, and covers epidemiology,
    classification, pathogenesis, and treatment of terms used by Virologists, i.e.
    virus, prion, satellite, viroid, etc.
  example: '0001114'
  homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus
  license: CC BY 4.0
  mappings:
    bioportal: VIDO
    ols: vido
  name: The Virus Infectious Disease Ontology
  preferred_prefix: vido
  version: '2020-08-25'
vipr:
  description: The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics
    workflows for a broad range of human virus pathogens and other related viruses.
    It provides access to sequence records, gene and protein annotations, immune epitopes,
    3D structures,  and host factor data. This collection references viral strain
    information.
  example: BeAn 70563
  homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr
  mappings:
    miriam: vipr
    n2t: vipr
    ncbi: ViPR
    prefixcommons: VIPR
  name: Virus Pathogen Resource
  pattern: ^[A-Za-z 0-9]+$
  preferred_prefix: vipr
  uri_format: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena
viralzone:
  description: ViralZone is a resource bridging textbook knowledge with genomic and
    proteomic sequences. It provides fact sheets on all known virus families/genera
    with easy access to sequence data. A selection of reference strains (RefStrain)
    provides annotated standards to circumvent the exponential increase of virus sequences.
    Moreover ViralZone offers a complete set of detailed and accurate virion pictures.
  example: '992'
  homepage: http://www.expasy.org/viralzone/
  mappings:
    miriam: viralzone
    n2t: viralzone
    prefixcommons: VIRALZONE
  name: ViralZone
  pattern: ^\d+$
  preferred_prefix: viralzone
  uri_format: http://viralzone.expasy.org/all_by_protein/$1.html
virsirna:
  description: The VIRsiRNA database contains details of siRNA/shRNA which target
    viral genome regions. It provides efficacy information where available, as well
    as the siRNA sequence, viral target and subtype, as well as the target genomic
    region.
  example: virsi1909
  homepage: http://crdd.osdd.net/servers/virsirnadb
  mappings:
    miriam: virsirna
    n2t: virsirna
    prefixcommons: VIRSIRNA
  name: VIRsiRNA
  pattern: ^virsi\d+$
  preferred_prefix: virsirna
  uri_format: http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1
vmc:
  deprecated: true
  mappings:
    biolink: VMC
  name: Variation Modelling Collaboration
  preferred_prefix: vmc
  references:
  - https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z
  - https://github.com/ga4gh/vr-spec
vmhgene:
  description: The Virtual Metabolic Human (VMH) is a resource that combines human
    and gut microbiota metabolism with nutrition and disease.
  example: '8639.1'
  homepage: https://www.vmh.life/
  mappings:
    miriam: vmhgene
  name: VMH Gene
  pattern: ^[0-9]+\.[0-9]+$
  preferred_prefix: vmhgene
  uri_format: https://www.vmh.life/#gene/$1
vmhmetabolite:
  description: The Virtual Metabolic Human (VMH) is a resource that combines human
    and gut microbiota metabolism with nutrition and disease.
  example: h2o
  homepage: https://www.vmh.life/
  mappings:
    miriam: vmhmetabolite
    n2t: vmhmetabolite
    prefixcommons: VMHMETABOLITE
  name: VMH metabolite
  pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$
  preferred_prefix: vmhmetabolite
  uri_format: https://www.vmh.life/#metabolite/$1
vmhreaction:
  description: The Virtual Metabolic Human (VMH) is a resource that combines human
    and gut microbiota metabolism with nutrition and disease.
  example: HEX1
  homepage: https://www.vmh.life/
  mappings:
    miriam: vmhreaction
    n2t: vmhreaction
    prefixcommons: VMHREACTION
  name: VMH reaction
  pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$
  preferred_prefix: vmhreaction
  uri_format: https://www.vmh.life/#reaction/$1
vo:
  banana: VO
  contact:
    email: yongqunh@med.umich.edu
    github: yongqunh
    name: Yongqunh He
    orcid: null
  description: The Vaccine Ontology (VO) is a biomedical ontology in the domain of
    vaccine and vaccination. VO aims to standardize vaccine annotation, integrate
    various vaccine data, and support computer-assisted reasoning. VO supports basic
    vaccine R&D and clincal vaccine usage. VO is being developed as a community-based
    ontology with support and collaborations from the vaccine and bio-ontology communities.
  example: 0000093
  homepage: http://www.violinet.org/vaccineontology
  license: CC BY 3.0
  mappings:
    bioportal: VO
    obofoundry: VO
    ols: vo
    ontobee: VO
    prefixcommons: VO
  name: Vaccine Ontology
  preferred_prefix: VO
  uri_format: http://purl.obolibrary.org/obo/VO_$1
  version: 1.1.171
void:
  description: The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary
    for expressing metadata about RDF datasets. It is intended as a bridge between
    the publishers and users of RDF data, with applications ranging from data discovery
    to cataloging and archiving of datasets. This document provides a formal definition
    of the new RDF classes and properties introduced for VoID. It is a companion to
    the main specification document for VoID, Describing Linked Datasets with the
    VoID Vocabulary.
  example: feature
  homepage: http://vocab.deri.ie/void
  mappings:
    prefixcommons: void
  name: Vocabulary of Interlinked Datasets
  preferred_prefix: void
  uri_format: http://rdfs.org/ns/void#$1
vsao:
  banana: VSAO
  contact:
    email: wasila.dahdul@usd.edu
    github: null
    name: Wasila Dahdul
    orcid: null
  deprecated: true
  description: Vertebrate skeletal anatomy ontology.
  homepage: https://www.nescent.org/phenoscape/Main_Page
  mappings:
    bioportal: VSAO
    obofoundry: VSAO
    prefixcommons: VSAO
  name: Vertebrate Skeletal Anatomy Ontology
  preferred_prefix: VSAO
  synonyms:
  - VSAO_RETIRED
  uri_format: http://purl.obolibrary.org/obo/VSAO_$1
vsdb:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Veterinary pharmaceuticals are biologically active and potentially
    persistent substances which are recognised as a continuing threat to environmental
    quality. Whilst the environmental risk of agricultural pesticides has had considerable
    attention in recent decades, risks assessments for veterinary pharmaceuticals
    have only relatively recently began to be addressed. Risk assessments and risk
    modelling tend to be inherently data hungry processes and one of the main obstacles
    to consistent, accurate and efficient assessments is the need for a reliable,
    quality and comprehensive data source.
  example: '1868'
  homepage: https://sitem.herts.ac.uk/aeru/vsdb
  name: Veterinary Substances DataBase
  preferred_prefix: vsdb
  uri_format: https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm
vt:
  banana: VT
  contact:
    email: caripark@iastate.edu
    github: null
    name: Carissa Park
    orcid: null
  description: An ontology of traits covering vertebrates
  example: 0000685
  homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology
  license: CC BY 4.0
  mappings:
    bioportal: VT
    obofoundry: VT
    ols: vt
    ontobee: VT
    prefixcommons: VT
  name: Vertebrate trait ontology
  pattern: ^\d{7}$
  preferred_prefix: VT
  uri_format: http://purl.obolibrary.org/obo/VT_$1
  version: '2019-06-07'
vto:
  banana: VTO
  contact:
    email: balhoff@renci.org
    github: balhoff
    name: Jim Balhoff
    orcid: null
  description: Comprehensive hierarchy of extinct and extant vertebrate taxa.
  example: '9008500'
  homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology
  license: CC0 1.0
  mappings:
    bioportal: VTO
    obofoundry: VTO
    ols: vto
    ontobee: VTO
    prefixcommons: VTO
  name: Vertebrate Taxonomy Ontology
  pattern: ^\d{7}$
  preferred_prefix: VTO
  uri_format: http://purl.obolibrary.org/obo/VTO_$1
  version: '2020-11-13'
vuid:
  comment: The example corresponds to acetaminophen
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "The Veterans Health Administration is America\u2019s largest integrated\
    \ health care system, providing care at 1,293 health care facilities, including\
    \ 171 medical centers and 1,112 outpatient sites of care of varying complexity\
    \ (VHA outpatient clinics), serving 9 million enrolled Veterans each year."
  example: '4007166'
  homepage: https://www.va.gov/health
  name: Veterans Health Administration (VHA) unique identifier
  preferred_prefix: vuid
  references:
  - https://academic.oup.com/jamia/article/17/4/432/866953
vz:
  description: ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for
    all viral genus and families, providing general molecular and epidemiological
    information, along with virion and genome figures. Each virus or family page gives
    an easy access to UniProtKB/Swiss-Prot viral protein entries.
  example: '886'
  homepage: http://viralzone.expasy.org/
  mappings:
    go: VZ
  name: ViralZone
  preferred_prefix: vz
  uri_format: https://viralzone.expasy.org/$1
wb.rnai:
  description: WormBase is an online bioinformatics database of the biology and genome
    of the model organism Caenorhabditis elegans and related nematodes. It is used
    by the C. elegans research community both as an information resource and as a
    mode to publish and distribute their results. This collection references RNAi
    experiments, detailing target and phenotypes.
  example: WBRNAi00086878
  homepage: https://www.wormbase.org/
  mappings:
    miriam: wb.rnai
    n2t: wb.rnai
    prefixcommons: WB.RNAI
  name: WormBase RNAi
  pattern: ^WBRNAi\d{8}$
  preferred_prefix: wb.rnai
  uri_format: https://www.wormbase.org/species/c_elegans/rnai/$1
wbbt:
  banana: WBbt
  contact:
    email: raymond@caltech.edu
    github: null
    name: Raymond Lee
    orcid: null
  description: Ontology about the gross anatomy of the C. elegans
  example: 0001290
  homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
  license: CC BY 4.0
  mappings:
    bioportal: WB-BT
    go: WBbt
    obofoundry: WBbt
    ols: wbbt
    ontobee: WBbt
    prefixcommons: WBBT
  name: C. elegans Gross Anatomy Ontology
  pattern: ^\d{7}$
  preferred_prefix: WBbt
  synonyms:
  - WBbt
  uri_format: http://purl.obolibrary.org/obo/WBBT_$1
  version: '2021-09-27'
wbls:
  banana: WBls
  contact:
    email: cgrove@caltech.edu
    github: null
    name: Chris Grove
    orcid: null
  description: Ontology about the development and life stages of the C. elegans
  example: 0000690
  homepage: https://github.com/obophenotype/c-elegans-development-ontology
  license: CC BY 4.0
  mappings:
    bioportal: WB-LS
    go: WBls
    obofoundry: WBls
    ols: wbls
    ontobee: WBLS
    prefixcommons: WBLS
  name: C. elegans development ontology
  part_of: wormbase
  pattern: ^\d{7}$
  preferred_prefix: WBls
  synonyms:
  - WBls
  uri_format: http://www.wormbase.org/get?name=$1
  version: '2021-07-06'
wbphenotype:
  banana: WBPhenotype
  contact:
    email: cgrove@caltech.edu
    github: null
    name: Chris Grove
    orcid: null
  description: Ontology about C. elegans and other nematode phenotypes
  example: 0000983
  homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology
  license: CC BY 4.0
  mappings:
    bioportal: WB-PHENOTYPE
    go: WBPhenotype
    obofoundry: WBPhenotype
    ols: wbphenotype
    ontobee: WBPhenotype
    prefixcommons: WBPhenotype
  name: C. elegans phenotype
  part_of: wormbase
  pattern: ^\d{7}$
  preferred_prefix: WBPhenotype
  synonyms:
  - WBPhenotype
  uri_format: http://www.wormbase.org/get?name=$1
  version: '2021-10-25'
webelements:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: Browser for the periodic table of the elements
  example: chromium
  homepage: https://www.webelements.com/
  name: Web Elements
  pattern: ^\w+$
  preferred_prefix: webelements
  uri_format: https://www.webelements.com/$1
wgs84:
  description: A vocabulary for representing latitude, longitude and altitude information
    in the WGS84 geodetic reference datum
  example: latitude
  homepage: https://www.w3.org/2003/01/geo/wgs84_pos
  mappings:
    biolink: wgs
  name: WGS84 Geo Positioning
  preferred_prefix: wgs84
  uri_format: http://www.w3.org/2003/01/geo/wgs84_pos#$1
wikidata:
  description: Wikidata is a collaboratively edited knowledge base operated by the
    Wikimedia Foundation. It is intended to provide a common source of certain types
    of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions
    as a document-oriented database, centred on individual items. Items represent
    topics, for which basic information is stored that identifies each topic.
  example: Q2207226
  homepage: https://www.wikidata.org/
  mappings:
    biolink: WIKIDATA
    cellosaurus: Wikidata
    cheminf: '000567'
    miriam: wikidata
    n2t: wikidata
    prefixcommons: WD_Entity
  name: Wikidata
  pattern: ^(Q|P)\d+$
  preferred_prefix: wikidata
  providers:
  - code: scholia
    description: Scholia can generally resolve many Wikidata entries in the biomedical
      and bibliometric domains
    homepage: https://scholia.toolforge.org
    name: Scholia
    uri_format: https://scholia.toolforge.org/$1
  synonyms:
  - WD_Entity
  - wd
  uri_format: http://www.wikidata.org/entity/$1
wikidata.property:
  description: 'Wikidata is a free and open knowledge base that can be read and edited
    by both humans and machines.

    Wikidata acts as central storage for the structured data of its Wikimedia sister
    projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. '
  example: P4355
  homepage: https://www.wikidata.org
  mappings:
    biolink: WIKIDATA_PROPERTY
    prefixcommons: WD_Prop
  name: Wikidata Property
  preferred_prefix: wikidata.property
  providers:
  - code: scholia
    description: Scholia can generally resolve many Wikidata entries in the biomedical
      and bibliometric domains
    homepage: https://scholia.toolforge.org
    name: Scholia
    uri_format: https://scholia.toolforge.org/$1
  uri_format: https://www.wikidata.org/wiki/Property:$1
wikigenes:
  description: WikiGenes is a collaborative knowledge resource for the life sciences,
    which is based on the general wiki idea but employs specifically developed technology
    to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide
    a platform for the scientific community to collect, communicate and evaluate knowledge
    about genes, chemicals, diseases and other biomedical concepts in a bottom-up
    process.
  example: '3771877'
  homepage: http://www.wikigenes.org/
  mappings:
    miriam: wikigenes
    n2t: wikigenes
    prefixcommons: WIKIGENES
  name: WikiGenes
  pattern: ^\d+$
  preferred_prefix: wikigenes
  provides: ncbigene
  uri_format: http://www.wikigenes.org/e/gene/e/$1.html
wikipathways:
  description: "WikiPathways is a resource providing an open and public collection\
    \ of  pathway maps created and curated by the community in a Wiki like style.\r\
    \nAll content is under the Creative Commons Attribution 3.0 Unported license."
  example: WP732
  homepage: http://www.wikipathways.org/
  mappings:
    bioportal: WIKIPATHWAYS
    miriam: wikipathways
    n2t: wikipathways
    prefixcommons: WIKIPATHWAYS
    scholia: wikipathways
    wikidata: P2410
  name: WikiPathways ID
  pattern: ^WP\d{1,5}(\_r\d+)?$
  preferred_prefix: wikipathways
  providers:
  - code: 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/
    name: Scholia
    uri_format: https://scholia.toolforge.org/wikipathways/$1
  uri_format: http://www.wikipathways.org/instance/$1
wikipedia.en:
  description: Wikipedia is a multilingual, web-based, free-content encyclopedia project
    based on an openly editable model. It is written collaboratively by largely anonymous
    Internet volunteers who write without pay.
  example: SM_UB-81
  homepage: http://en.wikipedia.org/wiki/Main_Page
  mappings:
    go: Wikipedia
    miriam: wikipedia.en
    n2t: wikipedia.en
    prefixcommons: WIKIPEDIA.EN
  name: Wikipedia
  pattern: ^[A-Za-z-0-9_]+$
  preferred_prefix: wikipedia.en
  providers:
  - code: CURATOR_REVIEW
    description: Wikipedia structured content through DBpedia
    homepage: http://wiki.dbpedia.org/
    name: Wikipedia structured content through DBpedia
    uri_format: http://dbpedia.org/page/$1
  synonyms:
  - wikipedia
  uri_format: http://en.wikipedia.org/wiki/$1
worfdb:
  description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete
    set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis
    elegans. This collection describes experimentally defined transcript structures
    of unverified genes through RACE (Rapid Amplification of cDNA Ends).
  example: T01B6.1
  homepage: http://worfdb.dfci.harvard.edu/
  mappings:
    miriam: worfdb
    n2t: worfdb
    ncbi: WorfDB
    prefixcommons: WORFDB
  name: C. elegans ORFeome cloning project
  pattern: ^\w+(\.\d+)$
  preferred_prefix: worfdb
  uri_format: http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1
wormbase:
  description: WormBase is an online bioinformatics database of the biology and genome
    of the model organism Caenorhabditis elegans and other nematodes. It is used by
    the C. elegans research community both as an information resource and as a mode
    to publish and distribute their results. This collection references WormBase-accessioned
    entities.
  example: WBGene00000001
  homepage: https://www.wormbase.org/
  mappings:
    biolink: WBVocab
    go: WB_REF
    miriam: wb
    n2t: wb
    ncbi: WormBase
    prefixcommons: WormBase
    uniprot: WormBase
    wikidata: P3860
  name: WormBase database of nematode biology
  pattern: ^WB[A-Z][a-z]+\d+$
  preferred_prefix: WormBase
  providers:
  - code: bioentitylink
    description: WormBase through BioEntity Link
    homepage: https://bioentity.link/
    name: WormBase through BioEntity Link
    uri_format: https://bioentity.link/#/lexicon/public/$1
  - code: agr
    description: WormBase through the Alliance of Genome Resources
    homepage: https://www.alliancegenome.org
    name: WormBase through the Alliance of Genome Resources
    uri_format: https://www.alliancegenome.org/gene/WB:$1
  synonyms:
  - WB_REF
  - wb
  - wormbase
  uri_format: https://www.wormbase.org/get?name=$1
wormpep:
  description: Wormpep contains the predicted proteins from the Caenorhabditis elegans
    genome sequencing project.
  example: CE28239
  homepage: https://www.wormbase.org/db/seq/protein
  mappings:
    miriam: wormpep
    n2t: wormpep
    prefixcommons: WORMPEP
  name: Wormpep
  pattern: ^CE\d{5}$
  preferred_prefix: wormpep
  uri_format: https://www.wormbase.org/db/seq/protein?name=$1
worms:
  description: The World Register of Marine Species (WoRMS) provides an authoritative
    and comprehensive list of names of marine organisms. It includes synonyms for
    valid taxonomic names allowing a more complete interpretation of taxonomic literature.
    The content of WoRMS is administered by taxonomic experts.
  example: '146421'
  homepage: http://www.marinespecies.org/
  mappings:
    miriam: worms
    n2t: worms
    prefixcommons: WORMS
  name: World Register of Marine Species
  pattern: ^\d+$
  preferred_prefix: worms
  uri_format: http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1
wwf.ecoregion:
  comment: ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658
  contributor:
    email: cjmungall@lbl.gov
    github: null
    name: Chris Mungall
    orcid: 0000-0002-6601-2165
  description: WWF ecoregions are large unit of land or water containing a geographically
    distinct assemblage of species, natural communities, and environmental conditions.
  example: AT1402
  homepage: https://www.worldwildlife.org/biomes
  mappings:
    wikidata: P1294
  name: World Wildlife Fund Ecoregion
  pattern: ^AT\d+$
  preferred_prefix: wwf.ecoregion
  reviewer:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  uri_format: https://www.worldwildlife.org/ecoregions/$1
xao:
  banana: XAO
  contact:
    email: esegerd3@gmail.com
    github: seger
    name: Erik Segerdell
    orcid: null
  description: XAO represents the anatomy and development of the African frogs Xenopus
    laevis and tropicalis.
  example: 0004486
  homepage: http://www.xenbase.org/anatomy/xao.do?method=display
  license: CC BY 3.0
  mappings:
    bioportal: XAO
    obofoundry: XAO
    ols: xao
    ontobee: XAO
    prefixcommons: XAO
    wikidata: P4495
  name: Xenopus Anatomy Ontology
  pattern: ^\d{7}$
  preferred_prefix: XAO
  uri_format: http://purl.obolibrary.org/obo/XAO_$1
  version: '2021-03-04'
xco:
  banana: XCO
  contact:
    email: jrsmith@mcw.edu
    github: null
    name: Jennifer Smith
    orcid: null
  description: Conditions under which physiological and morphological measurements
    are made both in the clinic and in studies involving humans or model organisms.
  example: 0000780
  homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000
  license: CC0 1.0
  mappings:
    bioportal: XCO
    obofoundry: XCO
    ols: xco
    ontobee: XCO
    prefixcommons: XCO
  name: Experimental condition ontology
  pattern: ^\d{7}$
  preferred_prefix: XCO
  uri_format: http://purl.obolibrary.org/obo/XCO_$1
  version: '2019-12-18'
xenbase:
  description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana)
    tropicalis. It contains genomic, development data and community information for
    Xenopus research. it includes gene expression patterns that incorporates image
    data from the literature, large scale screens and community submissions.
  example: XB-GENE-922462
  homepage: https://www.xenbase.org/
  mappings:
    biolink: Xenbase
    go: Xenbase
    miriam: xenbase
    n2t: xenbase
    ncbi: Xenbase
    prefixcommons: Xenbase
    uniprot: Xenbase
  name: Xenbase
  pattern: ^XB\-\w+\-\d+$
  preferred_prefix: xenbase
  uri_format: https://www.xenbase.org/common/xsearch.do?exactSearch=true&searchIn=7&searchValue=$1
xl:
  deprecated: true
  description: A structured controlled vocabulary for cross-linking reagents used
    with proteomics mass spectrometry.
  homepage: http://www.psidev.info/groups/controlled-vocabularies
  mappings:
    ols: xl
    prefixcommons: XL
  name: Cross-linker reagents ontology
  preferred_prefix: xl
  uri_format: http://purl.obolibrary.org/obo/XL_$1
xlmod:
  banana: XLMOD
  contact:
    email: gerhard.mayer@rub.de
    github: null
    name: Gerhard Mayer
    orcid: null
  description: A structured controlled vocabulary for cross-linking reagents used
    with proteomics mass spectrometry.
  example: '00050'
  homepage: http://www.psidev.info/groups/controlled-vocabularies
  license: CC BY 3.0
  mappings:
    bioportal: XLMOD
    obofoundry: XLMOD
    ols: xlmod
  name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
  pattern: ^\d{5}$
  preferred_prefix: XLMOD
  uri_format: http://purl.obolibrary.org/obo/XLMOD_$1
xpo:
  banana: XPO
  contact:
    email: esegerd3@gmail.com
    github: seger
    name: Erik Segerdell
    orcid: null
  description: XPO represents anatomical, cellular, and gene function phenotypes occurring
    throughout the development of the African frogs Xenopus laevis and tropicalis.
  example: '0100002'
  homepage: https://github.com/obophenotype/xenopus-phenotype-ontology
  license: CC BY 3.0
  mappings:
    biolink: XPO
    bioportal: XPO
    obofoundry: XPO
    ols: xpo
    ontobee: XPO
  name: Xenopus Phenotype Ontology
  pattern: ^\d+$
  preferred_prefix: XPO
  uri_format: http://purl.obolibrary.org/obo/XPO_$1
  version: '2021-03-05'
xsd:
  description: This document describes the XML Schema namespace. It also contains
    a directory of links to these related resources, using Resource Directory Description
    Language.
  example: decimal
  homepage: http://www.w3.org/2001/XMLSchema
  mappings:
    prefixcommons: xsd
  name: XML Schema Definition
  preferred_prefix: xsd
  uri_format: http://www.w3.org/2001/XMLSchema#$1
xuo:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  deprecated: true
  name: XUO
  preferred_prefix: xuo
ydpm:
  description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial
    Proteomics Project. The project aims to increase the understanding of mitochondrial
    function and biogenesis in the context of the cell. In the Deletion Project, strains
    from the deletion collection were monitored under 9 different media conditions
    selected for the study of mitochondrial function. The YDPM database contains both
    the raw data and growth rates calculated for each strain in each media condition.
  example: YAL001C
  homepage: http://www-deletion.stanford.edu/YDPM/
  mappings:
    miriam: ydpm
    n2t: ydpm
    prefixcommons: YDPM
  name: Yeast Deletion and the Mitochondrial Proteomics Project
  pattern: ^Y[A-Z]{2}\d+[CW]$
  preferred_prefix: ydpm
  uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1
yeastintron:
  description: The YEast Intron Database (version 4.3) contains information on the
    spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression
    data that relates to the efficiency of splicing relative to other processes in
    strains of yeast lacking nonessential splicing factors. The data are displayed
    on each intron page. This is an updated version of the previous dataset, which
    can be accessed through [MIR:00000460].
  example: SNR17A
  homepage: http://intron.ucsc.edu/yeast4.3/
  mappings:
    miriam: yeastintron
    n2t: yeastintron
    prefixcommons: YEASTINTRON
  name: Yeast Intron Database v4.3
  pattern: ^[A-Z0-9]+$
  preferred_prefix: yeastintron
  uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&amp;orfName=$1
yetfasco:
  description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is
    a database of transcription factor specificities for the yeast Saccharomyces cerevisiae
    in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.
  example: YOR172W_571.0
  homepage: http://yetfasco.ccbr.utoronto.ca/
  mappings:
    miriam: yetfasco
    n2t: yetfasco
    prefixcommons: YETFASCO
  name: YeTFasCo
  pattern: ^\w+\_\d+(\.\d+)?$
  preferred_prefix: yetfasco
  uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1
yid:
  description: The YEast Intron Database (version 3) contains information on the spliceosomal
    introns of the yeast Saccharomyces cerevisiae. It includes expression data that
    relates to the efficiency of splicing relative to other processes in strains of
    yeast lacking nonessential splicing factors.  The data are displayed on each intron
    page. An updated version of the database is available through [MIR:00000521].
  example: SNR17A
  homepage: http://compbio.soe.ucsc.edu/yeast_introns.html
  mappings:
    miriam: yid
    n2t: yid
    prefixcommons: YID
  name: Yeast Intron Database v3
  pattern: ^[A-Z0-9]+$
  preferred_prefix: yid
  uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1
ymdb:
  contributor:
    email: cthoyt@gmail.com
    github: null
    name: Charles Tapley Hoyt
    orcid: 0000-0003-4423-4370
  description: "The Yeast Metabolome Database (YMDB) is a manually curated database\
    \ of small molecule metabolites found in or produced by Saccharomyces cerevisiae\
    \ (also known as Baker\u2019s yeast and Brewer\u2019s yeast)."
  example: YMDB00001
  homepage: http://www.ymdb.ca
  name: Yeast Metabolome Database
  pattern: ^YMDB\d+$
  preferred_prefix: ymdb
  uri_format: http://www.ymdb.ca/compounds/$1
yrcpdr:
  description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as
    a single point of access for the experimental data produced from many collaborations
    typically studying Saccharomyces cerevisiae (baker's yeast). The experimental
    data include large amounts of mass spectrometry results from protein co-purification
    experiments, yeast two-hybrid interaction experiments, fluorescence microscopy
    images and protein structure predictions.
  example: '2673500'
  homepage: http://www.yeastrc.org/pdr/
  mappings:
    miriam: yrcpdr
    n2t: yrcpdr
    prefixcommons: YRCPDR
  name: YRC PDR
  pattern: ^\d+$
  preferred_prefix: yrcpdr
  uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1
zea:
  banana: ZEA
  contact:
    email: Leszek@missouri.edu
    github: null
    name: Leszek Vincent
    orcid: null
  deprecated: true
  homepage: http://www.maizemap.org/
  mappings:
    bioportal: ZEA
    obofoundry: ZEA
    prefixcommons: ZEA
  name: Maize gross anatomy
  preferred_prefix: ZEA
  uri_format: http://purl.obolibrary.org/obo/ZEA_$1
zeco:
  banana: ZECO
  contact:
    email: ybradford@zfin.org
    github: ybradford
    name: Yvonne Bradford
    orcid: null
  description: Ontology of Zebrafish Experimental Conditions
  example: '0000171'
  homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
  license: CC BY 3.0
  mappings:
    bioportal: ZECO
    obofoundry: ZECO
    ols: zeco
    ontobee: ZECO
    prefixcommons: ZECO
  name: Zebrafish Experimental Conditions Ontology
  pattern: ^\d{7}$
  preferred_prefix: ZECO
  uri_format: http://purl.obolibrary.org/obo/ZECO_$1
  version: '2021-06-04'
zfa:
  banana: ZFA
  contact:
    email: van_slyke@zfin.org
    github: cerivs
    name: Ceri Van Slyke
    orcid: null
  description: A structured controlled vocabulary of the anatomy and development of
    the Zebrafish
  example: 0005926
  homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
  license: CC BY 3.0
  mappings:
    bioportal: ZFA
    obofoundry: ZFA
    ols: zfa
    ontobee: ZFA
    prefixcommons: ZFA
  name: Zebrafish anatomy and development ontology
  pattern: ^\d{7}$
  preferred_prefix: ZFA
  synonyms:
  - ZFA_RETIRED
  uri_format: http://purl.obolibrary.org/obo/ZFA_$1
  version: '2020-04-14'
zfin:
  description: ZFIN serves as the zebrafish model organism database. This collection
    references all zebrafish biological entities in ZFIN.
  example: ZDB-GENE-041118-11
  homepage: http://zfin.org
  mappings:
    go: ZFIN
    miriam: zfin
    n2t: zfin
    ncbi: ZFIN
    prefixcommons: ZFIN
    uniprot: ZFIN
    wikidata: P3870
  name: ZFIN Gene ID
  pattern: ^ZDB\-\w+\-\d+\-\d+$
  preferred_prefix: zfin
  providers:
  - code: bioentitylink
    description: ZFIN through BioEntity Link
    homepage: https://bioentity.link/
    name: ZFIN through BioEntity Link
    uri_format: https://bioentity.link/#/lexicon/public/$1
  - code: agr
    description: ZFIN through the Alliance of Genome Resources
    homepage: https://www.alliancegenome.org
    name: ZFIN through the Alliance of Genome Resources
    uri_format: https://test.alliancegenome.org/gene/ZFIN:$1
  synonyms:
  - ZFIN
  uri_format: http://zfin.org/$1
zfs:
  banana: ZFS
  contact:
    email: van_slyke@zfin.org
    github: null
    name: Ceri Van Slyke
    orcid: null
  description: Developmental stages of the Zebrafish
  example: '0000050'
  homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
  license: CC BY 3.0
  mappings:
    bioportal: ZFS
    obofoundry: ZFS
    ols: zfs
    ontobee: ZFS
    prefixcommons: ZFS
  name: Zebrafish developmental stages ontology
  pattern: ^\d{7}$
  preferred_prefix: ZFS
  uri_format: http://purl.obolibrary.org/obo/ZFS_$1
  version: '2020-03-10'
zinc:
  description: ZINC is a free public resource for ligand discovery. The database contains
    over twenty million commercially available molecules in biologically relevant
    representations that may be downloaded in popular ready-to-dock formats and subsets.
    The Web site enables searches by structure, biological activity, physical property,
    vendor, catalog number, name, and CAS number.
  example: ZINC1084
  homepage: http://zinc15.docking.org/
  mappings:
    miriam: zinc
    n2t: zinc
    prefixcommons: ZINC
    wikidata: P2084
  name: ZINC is not Commercial
  pattern: ^(ZINC)?\d+$
  preferred_prefix: zinc
  uri_format: http://zinc15.docking.org/substances/$1
zp:
  banana: ZP
  contact:
    email: ybradford@zfin.org
    github: ybradford
    name: Yvonne Bradford
    orcid: null
  description: The Zebrafish Phenotype Ontology formally defines all phenotypes of
    the Zebrafish model organism.
  example: 0019030
  homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology
  license: CC BY 3.0
  mappings:
    bioportal: ZP
    obofoundry: ZP
    ols: zp
    ontobee: ZP
    prefixcommons: ZP
  name: Zebrafish Phenotype Ontology
  pattern: ^\d+$
  preferred_prefix: ZP
  uri_format: http://purl.obolibrary.org/obo/ZP_$1
  version: '2020-08-02'