3dmet:
description: 3DMET is a database collecting three-dimensional structures of natural
metabolites.
example: B00162
homepage: http://www.3dmet.dna.affrc.go.jp/
mappings:
biocontext: 3DMET
fairsharing: FAIRsharing.5ab0n7
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=$1
4dn.biosource:
description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network
and other reference nucleomics data sets. The 4D Nucleome Network aims to understand
the principles underlying nuclear organization in space and time, the role nuclear
organization plays in gene expression and cellular function, and how changes in
nuclear organization affect normal development as well as various diseases.
example: 4DNSR73BT2A2
homepage: https://data.4dnucleome.org/biosources
mappings:
cellosaurus: 4DN
fairsharing: FAIRsharing.CugtbQ
miriam: 4dn
prefixcommons: 4dn
name: 4D Nucleome Data Portal Biosource
pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
preferred_prefix: 4dn.biosource
synonyms:
- 4DN
uri_format: https://data.4dnucleome.org/biosources/$1
4dn.replicate:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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:
biocontext: AAO
fairsharing: FAIRsharing.mxx5rp
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
fairsharing: FAIRsharing.Z8OKi5
uniprot: ABCD
name: AntiBodies Chemically Defined database
preferred_prefix: abcd
uri_format: https://web.expasy.org/abcd/ABCD_$1
abm:
description: Cell line collections
example: T0599
homepage: https://www.abmgood.com/Cell-Biology.html
mappings:
cellosaurus: ABM
name: Applied Biological Materials cell line products
preferred_prefix: abm
uri_format: https://www.abmgood.com/catalogsearch/result/?cat=&q=$1
abs:
description: The database of Annotated regulatory Binding Sites (from orthologous
promoters), ABS, is a public database of known binding sites identified in promoters
of orthologous vertebrate genes that have been manually curated from bibliography.
example: A0014
homepage: http://genome.crg.es/datasets/abs2005/
mappings:
biocontext: ABS
fairsharing: FAIRsharing.7mnebr
miriam: abs
n2t: abs
prefixcommons: abs
name: Annotated Regulatory Binding Sites
pattern: ^A\d+$
preferred_prefix: abs
uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html
ac:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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#$1
aceview.worm:
description: AceView provides a curated sequence representation of all public mRNA
sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST
and Trace). These are aligned on the genome and clustered into a minimal number
of alternative transcript variants and grouped into genes. In addition, alternative
features such as promoters, and expression in tissues is recorded. This collection
references C. elegans genes and expression.
example: aap-1
homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm
mappings:
biocontext: ACEVIEW.WORM
miriam: aceview.worm
n2t: aceview.worm
prefixcommons: aceview.worm
name: Aceview Worm
pattern: ^[a-z0-9-]+$
preferred_prefix: aceview.worm
uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1
addexbio:
description: Cell line collections
example: C0020004/4992
homepage: https://www.addexbio.com/productshow?id=4
mappings:
cellosaurus: AddexBio
name: AddexBio cell line products
preferred_prefix: addexbio
uri_format: https://www.addexbio.com/productdetail?pid=$1
addgene:
description: Addgene is a non-profit plasmid repository. Addgene facilitates the
exchange of genetic material between laboratories by offering plasmids and their
associated cloning data to not-for-profit laboratories around the world.
example: '50943'
homepage: http://addgene.org/
mappings:
fairsharing: FAIRsharing.8hcczk
miriam: addgene
n2t: addgene
prefixcommons: addgene
name: Addgene Plasmid Repository
pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$
preferred_prefix: addgene
uri_format: http://addgene.org/$1
adw:
banana: ADW
contact:
email: adw_geeks@umich.edu
github: null
name: Animal Diversity Web technical staff
orcid: null
deprecated: true
description: Animal Diversity Web (ADW) is an online database of animal natural
history, distribution, classification, and conservation biology.
example: Lycalopex_vetulus
homepage: http://www.animaldiversity.org
mappings:
biocontext: ADW
bioportal: ADW
fairsharing: FAIRsharing.t9fvdn
miriam: adw
n2t: adw
obofoundry: ADW
name: Animal natural history and life history
pattern: ^[A-Z_a-z]+$
preferred_prefix: ADW
uri_format: https://animaldiversity.org/accounts/$1
aeo:
appears_in:
- ehdaa2
banana: AEO
contact:
email: J.Bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
description: AEO is an ontology of anatomical structures that expands CARO, the
Common Anatomy Reference Ontology
download_obo: https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo
download_owl: http://purl.obolibrary.org/obo/aeo.owl
example: '0001017'
homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
license: CC BY 4.0
mappings:
biocontext: AEO
bioportal: AEO
fairsharing: FAIRsharing.93ee19
obofoundry: AEO
ols: aeo
ontobee: AEO
name: Anatomical Entity Ontology
pattern: ^\d{7}$
preferred_prefix: AEO
repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
synonyms:
- AEO_RETIRED
uri_format: http://purl.obolibrary.org/obo/AEO_$1
version: '2014-12-05'
aero:
banana: AERO
contact:
email: mcourtot@gmail.com
github: null
name: Melanie Courtot
orcid: 0000-0002-9551-6370
deprecated: true
description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at
supporting clinicians at the time of data entry, increasing quality and accuracy
of reported adverse events
download_owl: http://purl.obolibrary.org/obo/aero.owl
example: '0000125'
homepage: http://purl.obolibrary.org/obo/aero
license: CC BY 3.0
mappings:
biocontext: AERO
bioportal: AERO
fairsharing: FAIRsharing.rycy2x
obofoundry: AERO
name: Adverse Event Reporting Ontology
pattern: ^\d{7}$
preferred_prefix: AERO
uri_format: http://purl.obolibrary.org/obo/AERO_$1
affy.probeset:
description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide)
microarray probes designed to measure a single gene or a family of genes as a
unit. Multiple probe sets may be available for each gene under consideration.
example: 243002_at
homepage: http://www.affymetrix.com/
mappings:
biocontext: AFFY.PROBESET
miriam: affy.probeset
n2t: affy.probeset
name: Affymetrix Probeset
pattern: ^\d{4,}((_[asx])?_at)$
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=$1
afo:
description: Allotrope Merged Ontology Suite
download_owl: http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10
homepage: https://www.allotrope.org/
mappings:
bioportal: AFO
fairsharing: FAIRsharing.595710
ols: afo
name: Allotrope Merged Ontology Suite
no_own_terms: true
preferred_prefix: afo
version: '2019-05-10'
aftol.taxonomy:
description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated
to significantly enhancing our understanding of the evolution of the Kingdom Fungi,
which represents one of the major clades of life. There are roughly 80,000 described
species of Fungi, but the actual diversity in the group has been estimated to
be about 1.5 million species.
example: '959'
homepage: https://aftol.umn.edu
mappings:
biocontext: AFTOL.TAXONOMY
miriam: aftol.taxonomy
n2t: aftol.taxonomy
name: Assembling the Fungal Tree of Life - Taxonomy
pattern: ^\d+$
preferred_prefix: aftol.taxonomy
uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1
agilent.probe:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent
design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows
x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows
x 192 cols). Version 2 of this array contains long intergenic non-coding RNA
(lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute,
along with an update of mRNA content when compared to version 1. Probes were designed
using GRCh37 assembly of the human genome. Annotation of probes came from the
following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank
(April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute
TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.'
example: A_24_P98555
homepage: https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt
name: Agilent Probe
pattern: ^A_\d+_.+$
preferred_prefix: agilent.probe
references:
- http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt
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:
biocontext: AGRICOLA
go: AGRICOLA_ID
miriam: agricola
n2t: agricola
name: Agricultural Online Access
pattern: ^\d+$
preferred_prefix: agricola
synonyms:
- AGR
- AGRICOLA_ID
uri_format: https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1
agro:
banana: AGRO
contact:
email: m.a.laporte@cgiar.org
github: marieALaporte
name: Marie-Angélique Laporte
orcid: 0000-0002-8461-9745
depends_on:
- bfo
- envo
- foodon
- go
- iao
- ncbitaxon
- obi
- pato
- peco
- po
- ro
- to
- uo
- xco
description: AgrO is an ontlogy for representing agronomic practices, techniques,
variables and related entities
download_obo: https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo
download_owl: http://purl.obolibrary.org/obo/agro.owl
example: '00020007'
homepage: https://github.com/AgriculturalSemantics/agro
license: CC BY 4.0
mappings:
biocontext: AGRO
bioportal: AGRO
fairsharing: FAIRsharing.m40bhw
obofoundry: AGRO
ols: agro
ontobee: AGRO
name: Agronomy Ontology
pattern: ^\d{8}$
preferred_prefix: AGRO
repository: https://github.com/AgriculturalSemantics/agro
uri_format: http://purl.obolibrary.org/obo/AGRO_$1
version: '2021-11-05'
agrovoc:
description: AGROVOC is a multilingual and controlled vocabulary designed to cover
concepts and terminology under FAO's areas of interest. It is the largest Linked
Open Data set about agriculture available for public use and its greatest impact
is through providing the access and visibility of data across domains and languages.
example: '2842'
homepage: https://data.apps.fao.org/catalog/organization/agrovoc
mappings:
fairsharing: FAIRsharing.anpj91
name: Agronomy Vocabulary
pattern: ^[a-z0-9]+$
preferred_prefix: agrovoc
references:
- http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip
- http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip
- https://en.wikipedia.org/wiki/AGROVOC
uri_format: http://aims.fao.org/aos/agrovoc/c_$1
aism:
appears_in:
- colao
- lepao
banana: AISM
contact:
email: entiminae@gmail.com
github: JCGiron
name: Jennifer C. Girón
orcid: 0000-0002-0851-6883
depends_on:
- bfo
- bspo
- caro
- pato
- ro
- uberon
description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
contains terms used to describe the cuticle - as a single anatomical structure
- and the skeletal muscle system, to be used in insect biodiversity research.
download_json: http://purl.obolibrary.org/obo/aism.json
download_obo: http://purl.obolibrary.org/obo/aism.obo
download_owl: http://purl.obolibrary.org/obo/aism.owl
example: '0000027'
homepage: https://github.com/insect-morphology/aism
license: CC BY 4.0
mappings:
bioportal: AISM
obofoundry: AISM
ols: aism
ontobee: AISM
name: Ontology for the Anatomy of the Insect SkeletoMuscular system
pattern: ^\d{7}$
preferred_prefix: AISM
repository: https://github.com/insect-morphology/aism
uri_format: http://purl.obolibrary.org/obo/AISM_$1
version: '2022-03-17'
allergome:
description: Allergome is a repository of data related to all IgE-binding compounds.
Its purpose is to collect a list of allergenic sources and molecules by using
the widest selection criteria and sources.
example: '1948'
homepage: http://www.allergome.org/
mappings:
biocontext: ALLERGOME
fairsharing: FAIRsharing.w6cxgb
miriam: allergome
n2t: allergome
prefixcommons: allergome
uniprot: Allergome
name: Allergome
pattern: ^\d+$
preferred_prefix: allergome
uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1
alzforum.mutation:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/$1
amoebadb:
description: AmoebaDB is one of the databases that can be accessed through the EuPathDB
(http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: EDI_244000
homepage: http://amoebadb.org/amoeba/
mappings:
biocontext: AMOEBADB
fairsharing: FAIRsharing.swbypy
miriam: amoebadb
n2t: amoebadb
prefixcommons: amoebadb
name: AmoebaDB
pattern: ^EDI_\d+$
preferred_prefix: amoebadb
uri_format: https://amoebadb.org/amoeba/app/record/gene/$1
amphx:
banana: AMPHX
contact:
email: hescriva@obs-banyuls.fr
github: hescriva
name: Hector Escriva
orcid: 0000-0001-7577-5028
depends_on:
- uberon
description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
lanceolatum).
download_obo: http://purl.obolibrary.org/obo/amphx.obo
download_owl: http://purl.obolibrary.org/obo/amphx.owl
example: '1000160'
homepage: https://github.com/EBISPOT/amphx_ontology
license: CC BY 3.0
mappings:
bioportal: AMPHX
obofoundry: AMPHX
ols: amphx
ontobee: AMPHX
name: The Amphioxus Development and Anatomy Ontology
pattern: ^\d+$
preferred_prefix: AMPHX
repository: https://github.com/EBISPOT/amphx_ontology
uri_format: http://purl.obolibrary.org/obo/AMPHX_$1
version: '2020-12-18'
antibodyregistry:
description: The Antibody Registry provides identifiers for antibodies used in publications.
It lists commercial antibodies from numerous vendors, each assigned with a unique
identifier. Unlisted antibodies can be submitted by providing the catalog number
and vendor information.
example: '493771'
homepage: http://antibodyregistry.org/
mappings:
biocontext: ANTIBODYREGISTRY
miriam: antibodyregistry
n2t: antibodyregistry
name: Antibody Registry
pattern: ^\d{6}$
preferred_prefix: antibodyregistry
uri_format: http://antibodyregistry.org/AB_$1
antweb:
description: AntWeb is a website documenting the known species of ants, with records
for each species linked to their geographical distribution, life history, and
includes pictures.
example: casent0106247
homepage: http://www.antweb.org/
mappings:
biocontext: ANTWEB
fairsharing: FAIRsharing.yk38tw
miriam: antweb
n2t: antweb
ncbi: AntWeb
prefixcommons: antweb
name: Ant Database
pattern: ^casent\d+(\-D\d+)?$
preferred_prefix: antweb
uri_format: http://www.antweb.org/specimen.do?name=$1
aop:
description: International repository of Adverse Outcome Pathways.
example: '98'
homepage: https://aopwiki.org/
mappings:
biocontext: AOP
miriam: aop
n2t: aop
name: AOPWiki
pattern: ^\d+$
preferred_prefix: aop
uri_format: https://aopwiki.org/aops/$1
aop.events:
description: International repository of Adverse Outcome Pathways.
example: '3'
homepage: https://aopwiki.org/
mappings:
biocontext: AOP.EVENTS
miriam: aop.events
n2t: aop.events
name: AOPWiki (Key Event)
pattern: ^\d+$
preferred_prefix: aop.events
uri_format: https://aopwiki.org/events/$1
aop.relationships:
description: International repository of Adverse Outcome Pathways.
example: '5'
homepage: https://aopwiki.org/
mappings:
biocontext: AOP.RELATIONSHIPS
miriam: aop.relationships
n2t: aop.relationships
name: AOPWiki (Key Event Relationship)
pattern: ^\d+$
preferred_prefix: aop.relationships
uri_format: https://aopwiki.org/relationships/$1
aop.stressor:
description: International repository of Adverse Outcome Pathways.
example: '9'
homepage: https://aopwiki.org/
mappings:
biocontext: AOP.STRESSOR
miriam: aop.stressor
n2t: aop.stressor
name: AOPWiki (Stressor)
pattern: ^\d+$
preferred_prefix: aop.stressor
uri_format: https://aopwiki.org/stressors/$1
apaonto:
description: Ontology from the APA
example: Abdomen
homepage: https://bioportal.bioontology.org/ontologies/APAONTO
mappings:
bioportal: APAONTO
fairsharing: FAIRsharing.gkw1w8
name: Psychology Ontology
preferred_prefix: apaonto
uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1
apd:
description: The antimicrobial peptide database (APD) provides information on anticancer,
antiviral, antifungal and antibacterial peptides.
example: '01001'
homepage: http://aps.unmc.edu/AP/
mappings:
biocontext: APD
fairsharing: FAIRsharing.ctwd7b
miriam: apd
n2t: apd
prefixcommons: apd
name: Antimicrobial Peptide Database
pattern: ^\d{5}$
preferred_prefix: apd
uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1
aphidbase.transcript:
description: AphidBase is a centralized bioinformatic resource that was developed
to facilitate community annotation of the pea aphid genome by the International
Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed
to organize and distribute genomic data and annotations for a large international
community. This collection references the transcript report, which describes genomic
location, sequence and exon information.
example: ACYPI000159
homepage: http://www.aphidbase.com/aphidbase
mappings:
biocontext: APHIDBASE.TRANSCRIPT
miriam: aphidbase.transcript
n2t: aphidbase.transcript
name: AphidBase Transcript
pattern: ^ACYPI\d{6}(-RA)?$
preferred_prefix: aphidbase.transcript
uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1
apid.interactions:
description: APID (Agile Protein Interactomes DataServer) provides information on
the protein interactomes of numerous organisms, based on the integration of known
experimentally validated protein-protein physical interactions (PPIs). Interactome
data includes a report on quality levels and coverage over the proteomes for
each organism included. APID integrates PPIs from primary databases of molecular
interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally
resolved 3D structures (PDB) where more than two distinct proteins have been identified.
This collection references protein interactors, through a UniProt identifier.
example: P01116
homepage: http://cicblade.dep.usal.es:8080/APID/
mappings:
biocontext: APID.INTERACTIONS
miriam: apid.interactions
n2t: apid.interactions
name: APID Interactomes
pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
preferred_prefix: apid.interactions
provides: uniprot
uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1
apo:
banana: APO
contact:
email: stacia@stanford.edu
github: srengel
name: Stacia R Engel
orcid: 0000-0001-5472-917X
description: A structured controlled vocabulary for the phenotypes of Ascomycete
fungi.
download_obo: http://purl.obolibrary.org/obo/apo.obo
download_owl: http://purl.obolibrary.org/obo/apo.owl
example: 0000184
homepage: http://www.yeastgenome.org/
license: CC BY 4.0
mappings:
biocontext: YPO
bioportal: APO
fairsharing: FAIRsharing.dyqz3y
obofoundry: APO
ols: apo
ontobee: APO
name: Ascomycete phenotype ontology
pattern: ^\d{7}$
preferred_prefix: APO
repository: https://github.com/obophenotype/ascomycete-phenotype-ontology
uri_format: https://www.yeastgenome.org/observable/APO:$1
version: '2022-04-19'
apollosv:
appears_in:
- scdo
banana: APOLLO_SV
contact:
email: hoganwr@ufl.edu
github: hoganwr
name: William Hogan
orcid: 0000-0002-9881-1017
description: Defines terms and relations necessary for interoperation between epidemic
models and public health application software that interface with these models
download_owl: http://purl.obolibrary.org/obo/apollo_sv.owl
example: '00000443'
homepage: https://github.com/ApolloDev/apollo-sv
license: CC BY 4.0
mappings:
bioportal: APOLLO-SV
fairsharing: FAIRsharing.ngv2xx
obofoundry: APOLLO_SV
ols: apollo_sv
ontobee: APOLLO_SV
name: Apollo Structured Vocabulary
pattern: ^\d{8}$
preferred_prefix: APOLLO_SV
repository: https://github.com/ApolloDev/apollo-sv
uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1
version: 4.1.1
arachnoserver:
description: ArachnoServer (www.arachnoserver.org) is a manually curated database
providing information on the sequence, structure and biological activity of protein
toxins from spider venoms. It include a molecular target ontology designed specifically
for venom toxins, as well as current and historic taxonomic information.
example: AS000060
homepage: http://www.arachnoserver.org/
mappings:
biocontext: ARACHNOSERVER
fairsharing: FAIRsharing.c54ywe
miriam: arachnoserver
n2t: arachnoserver
prefixcommons: arachnoserver
uniprot: ArachnoServer
name: ArachnoServer
pattern: ^AS\d{6}$
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=$1
ardb:
description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated
database which characterises genes involved in antibiotic resistance. Each gene
and resistance type is annotated with information, including resistance profile,
mechanism of action, ontology, COG and CDD annotations, as well as external links
to sequence and protein databases. This collection references resistance genes.
example: CAE46076
homepage: http://ardb.cbcb.umd.edu/
mappings:
biocontext: ARDB
miriam: ardb
n2t: ardb
name: Antibiotic Resistance Genes Database
pattern: ^[A-Z_]{3}[0-9]{4,}$
preferred_prefix: ardb
uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1
ark:
banana: ark
description: An Archival Resource Key (ARK) is a Uniform Resource Locator (URL)
that is a multi-purpose persistent identifier for information objects of any type.
example: /12345/fk1234
homepage: http://n2t.net/
mappings:
biocontext: ARK
miriam: ark
n2t: ark
name: Archival Resource Key
namespace_in_lui: true
pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
preferred_prefix: ark
uri_format: http://n2t.net/ark:$1
aro:
appears_in:
- scdo
banana: ARO
contact:
email: mcarthua@mcmaster.ca
github: agmcarthur
name: Andrew G. McArthur
orcid: 0000-0002-1142-3063
description: Antibiotic resistance genes and mutations
download_owl: http://purl.obolibrary.org/obo/aro.owl
example: '1000001'
homepage: https://github.com/arpcard/aro
license: CC BY 4.0
mappings:
biocontext: ARO
bioportal: ARO
obofoundry: ARO
ols: aro
ontobee: ARO
name: Antibiotic Resistance Ontology
pattern: ^\d{7}$
preferred_prefix: ARO
repository: https://github.com/arpcard/aro
uri_format: http://purl.obolibrary.org/obo/ARO_$1
arrayexpress:
description: ArrayExpress is a public repository for microarray data, which is aimed
at storing MIAME-compliant data in accordance with Microarray Gene Expression
Data (MGED) recommendations.
example: E-MEXP-1712
homepage: https://www.ebi.ac.uk/arrayexpress/
mappings:
biocontext: ARRAYEXPRESS
cellosaurus: ArrayExpress
fairsharing: FAIRsharing.6k0kwd
miriam: arrayexpress
n2t: arrayexpress
prefixcommons: arrayexpress
name: ArrayExpress
pattern: ^[AEP]-\w{4}-\d+$
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/$1
arrayexpress.platform:
description: ArrayExpress is a public repository for microarray data, which is aimed
at storing MIAME-compliant data in accordance with Microarray Gene Expression
Data (MGED) recommendations.This collection references the specific platforms
used in the generation of experimental results.
example: A-GEOD-50
homepage: https://www.ebi.ac.uk/arrayexpress/
mappings:
biocontext: ARRAYEXPRESS.PLATFORM
miriam: arrayexpress.platform
n2t: arrayexpress.platform
name: ArrayExpress Platform
pattern: ^[AEP]-\w{4}-\d+$
preferred_prefix: arrayexpress.platform
uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1
arraymap:
description: arrayMap is a collection of pre-processed oncogenomic array data sets
and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation
commonly found in cancer genomes. arrayMap data is assembled from public repositories
and supplemented with additional sources, using custom curation pipelines. This
information has been mapped to multiple editions of the reference human genome.
example: icdom:8500_3
homepage: https://www.arraymap.org
mappings:
biocontext: ARRAYMAP
fairsharing: FAIRsharing.1fbc5y
miriam: arraymap
n2t: arraymap
name: ArrayMap
pattern: ^[\w\-:,]{3,64}$
preferred_prefix: arraymap
uri_format: https://www.arraymap.org/pgx:$1
arxiv:
description: arXiv is an e-print service in the fields of physics, mathematics,
non-linear science, computer science, and quantitative biology.
example: 0807.4956v1
homepage: https://arxiv.org/
mappings:
biocontext: ARXIV
miriam: arxiv
n2t: arxiv
prefixcommons: arxiv
scholia: arxiv
name: arXiv
pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$
preferred_prefix: arxiv
uri_format: https://arxiv.org/abs/$1
asap:
description: ASAP (a systematic annotation package for community analysis of genomes)
stores bacterial genome sequence and functional characterization data. It includes
multiple genome sequences at various stages of analysis, corresponding experimental
data and access to collections of related genome resources.
example: ABE-0009634
homepage: http://asap.ahabs.wisc.edu/asap/home.php
mappings:
biocontext: ASAP
fairsharing: FAIRsharing.anpa6
go: ASAP
miriam: asap
n2t: asap
ncbi: ASAP
prefixcommons: asap
name: A Systematic Annotation Package for Community Analysis of Genomes
pattern: ^[A-Za-z0-9-]+$
preferred_prefix: asap
uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1
ascl:
description: The Astrophysics Source Code Library (ASCL) is a free online registry
for software that have been used in research that has appeared in, or been submitted
to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics
Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable
by using the unique ascl ID assigned to each code. The ascl ID can be used to
link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).
example: '1801.012'
homepage: http://ascl.net/
mappings:
biocontext: ASCL
fairsharing: FAIRsharing.wb0txg
miriam: ascl
n2t: ascl
name: Astrophysics Source Code Library
pattern: ^[0-9\.]+$
preferred_prefix: ascl
uri_format: http://ascl.net/$1
asin:
description: Almost every product on our site has its own ASIN, a unique code we
use to identify it. For books, the ASIN is the same as the ISBN number, but for
all other products a new ASIN is created when the item is uploaded to our catalogue.
example: 0471491039
homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182
mappings:
biocontext: ASIN
miriam: asin
n2t: asin
name: Amazon Standard Identification Number
pattern: ^[0-9]{10}$
preferred_prefix: asin
uri_format: https://amzn.com/$1
aspgd.locus:
description: The Aspergillus Genome Database (AspGD) is a repository for information
relating to fungi of the genus Aspergillus, which includes organisms of clinical,
agricultural and industrial importance. AspGD facilitates comparative genomics
by providing a full-featured genomics viewer, as well as matched and standardized
sets of genomic information for the sequenced aspergilli. This collection references
gene information.
example: ASPL0000349247
homepage: http://www.aspgd.org/
mappings:
biocontext: ASPGD.LOCUS
go: AspGD_LOCUS
miriam: aspgd.locus
n2t: aspgd.locus
name: Aspergillus Genome Database
pattern: ^[A-Za-z_0-9]+$
preferred_prefix: aspgd.locus
uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1
aspgd.protein:
description: The Aspergillus Genome Database (AspGD) is a repository for information
relating to fungi of the genus Aspergillus, which includes organisms of clinical,
agricultural and industrial importance. AspGD facilitates comparative genomics
by providing a full-featured genomics viewer, as well as matched and standardized
sets of genomic information for the sequenced aspergilli. This collection references
protein information.
example: ASPL0000349247
homepage: http://www.aspgd.org/
mappings:
biocontext: ASPGD.PROTEIN
miriam: aspgd.protein
n2t: aspgd.protein
name: AspGD Protein
pattern: ^[A-Za-z_0-9]+$
preferred_prefix: aspgd.protein
uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1
asrp:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/
mappings:
prefixcommons: asrp
name: Arabidopsis Small RNA Project
preferred_prefix: asrp
uri_format: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1
atc:
description: The Anatomical Therapeutic Chemical (ATC) classification system, divides
active substances into different groups according to the organ or system on which
they act and their therapeutic, pharmacological and chemical properties. Drugs
are classified in groups at five different levels; Drugs are divided into fourteen
main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The
3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the
5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC)
classification system and the Defined Daily Dose (DDD) is a tool for exchanging
and comparing data on drug use at international, national or local levels.
example: A10BA02
homepage: http://www.whocc.no/atc_ddd_index/
mappings:
biocontext: ATC
bioportal: ATC
fairsharing: FAIRsharing.1a27h8
miriam: atc
n2t: atc
prefixcommons: atc
wikidata: P267
name: Anatomical Therapeutic Chemical Classification System
pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$
preferred_prefix: atc
synonyms:
- ATC_code
- ATTC
uri_format: http://www.whocc.no/atc_ddd_index/?code=$1
atcc:
description: The American Type Culture Collection (ATCC) is a private, nonprofit
biological resource center whose mission focuses on the acquisition, authentication,
production, preservation, development and distribution of standard reference microorganisms,
cell lines and other materials for research in the life sciences.
example: '11303'
homepage: https://www.lgcstandards-atcc.org
mappings:
biocontext: ATCC
cellosaurus: ATCC
fairsharing: FAIRsharing.j0ezpm
miriam: atcc
n2t: atcc
ncbi: ATCC
name: American Type Culture Collection
pattern: ^([A-Z]+-)?\d+$
preferred_prefix: atcc
synonyms:
- ATCC
- ATCC number
- ATCC(dna)
- ATCC(in host)
uri_format: https://www.atcc.org/products/$1
atcvet:
description: The ATCvet system for the classification of veterinary medicines is
based on the same overall principles as the ATC system for substances used in
human medicine. In ATCvet systems, preparations are divided into groups, according
to their therapeutic use. First, they are divided into 15 anatomical groups (1st
level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic
use.
example: QJ51RV02
homepage: http://www.whocc.no/atcvet/atcvet_index/
mappings:
biocontext: ATCVET
miriam: atcvet
n2t: atcvet
name: Anatomical Therapeutic Chemical Vetinary
pattern: ^Q[A-Z0-9]+$
preferred_prefix: atcvet
uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1
atfdb.family:
description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs
in sequenced animal genomes, as well as collecting the transcription co-factors
and chromatin remodeling factors of those genomes. This collections refers to
transcription factor families, and the species in which they are found.
example: CUT
homepage: http://www.bioguo.org/AnimalTFDB/family_index.php
mappings:
biocontext: ATFDB.FAMILY
miriam: atfdb.family
n2t: atfdb.family
name: Animal TFDB Family
pattern: ^\w+$
preferred_prefix: atfdb.family
uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1
ato:
banana: ATO
contact:
email: david.c.blackburn@gmail.com
github: null
name: David Blackburn
orcid: null
deprecated: true
description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and
genres. It is being integrated into UBERON resource
example: '0000000'
homepage: http://www.amphibanat.org
mappings:
biocontext: ATO
bioportal: ATO
fairsharing: FAIRsharing.ayjdsm
obofoundry: ATO
name: Amphibian taxonomy
pattern: ^\d{7}$
preferred_prefix: ATO
uri_format: http://purl.obolibrary.org/obo/ATO_$1
atol:
description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics
defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide
a reference ontology of phenotypic traits of farm animals for the international
scientificand educational - communities, farmers, etc.; - deliver this reference
ontology in a language which can be used by computers in order to support database
management, semantic analysis and modeling; - represent traits as generic as possible
for livestock vertebrates; - make the ATOL ontology as operational as possible
and closely related to measurement techniques; - structure the ontology in relation
to animal production.'
download_owl: https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl
example: '0002233'
homepage: http://www.atol-ontology.com
mappings:
bioportal: ATOL
fairsharing: FAIRsharing.wsfk5z
ols: atol
name: Animal Trait Ontology for Livestock
pattern: ^\d{7}$
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:
biocontext: AUTDB
miriam: autdb
n2t: autdb
name: AutDB
pattern: ^[A-Z]+[A-Z-0-9]{2,}$
preferred_prefix: autdb
uri_format: http://autism.mindspec.org/GeneDetail/$1
bacdive:
description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked
information on the different aspects of bacterial and archaeal biodiversity.
example: '131392'
homepage: https://bacdive.dsmz.de/
mappings:
fairsharing: FAIRsharing.aSszvY
miriam: bacdive
n2t: bacdive
name: Bacterial Diversity Metadatabase
pattern: ^[0-9]+$
preferred_prefix: bacdive
uri_format: https://bacdive.dsmz.de/strain/$1
bacmap.biog:
description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
to the level of individual genes and each gene is hyperlinked to a richly annotated
gene card. All bacterial genome maps are supplemented with separate prophage genome
maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in
BacMap contains graphs and tables on a variety of gene and protein statistics.
Likewise, every bacterial species entry contains a bacterial 'biography' card,
with taxonomic details, phenotypic details, textual descriptions and images. This
collection references 'biography' information.
example: '1050'
homepage: http://bacmap.wishartlab.com/
mappings:
biocontext: BACMAP.BIOG
miriam: bacmap.biog
n2t: bacmap.biog
name: BacMap Biography
pattern: ^\d+$
preferred_prefix: bacmap.biog
uri_format: http://bacmap.wishartlab.com/organisms/$1
bacmap.map:
description: BacMap is an electronic, interactive atlas of fully sequenced bacterial
genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced
prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed
to the level of individual genes and each gene is hyperlinked to a richly annotated
gene card. All bacterial genome maps are supplemented with separate prophage genome
maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in
BacMap contains graphs and tables on a variety of gene and protein statistics.
Likewise, every bacterial species entry contains a bacterial 'biography' card,
with taxonomic details, phenotypic details, textual descriptions and images. This
collection references genome map information.
example: AP011135
homepage: http://bacmap.wishartlab.com/
mappings:
biocontext: BACMAP.MAP
miriam: bacmap.map
n2t: bacmap.map
name: BacMap Map
pattern: ^\w+(\_)?\d+(\.\d+)?$
preferred_prefix: bacmap.map
uri_format: http://bacmap.wishartlab.com/maps/$1/index.html
bactibase:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
mappings:
fairsharing: FAIRsharing.5f5mfm
prefixcommons: bactibase
name: Bactibase
preferred_prefix: bactibase
uri_format: http://bactibase.hammamilab.org/$1
bams:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: 'BAMS (Brain Architectural Management System) describes vertebrate
neuroinformatics data at four levels of organization: expressed molecules, neuron
types and classes, brain regions, and networks of brain regions.'
homepage: https://bams1.org
name: Brain Architecture Knowledge Management System Neuroanatomical Ontology
preferred_prefix: bams
references:
- https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full
bao:
description: The BioAssay Ontology (BAO) describes chemical biology screening assays
and their results including high-throughput screening (HTS) data for the purpose
of categorizing assays and data analysis.
download_owl: http://www.bioassayontology.org/bao/bao_complete.owl
example: 0002989
homepage: http://bioassayontology.org
mappings:
biocontext: BAO
bioportal: BAO
fairsharing: FAIRsharing.mye76w
miriam: bao
n2t: bao
ols: bao
ontobee: BAO
name: BioAssay Ontology
pattern: ^\d{7}$
preferred_prefix: bao
synonyms:
- BAO
uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1
version: 2.7.2
bbkg:
description: Blue Brain Project's published data as knowledge graphs and Web Studios.
example: topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a
homepage: https://portal.bluebrain.epfl.ch
mappings:
miriam: bbkg
name: Blue Brain Project Knowledge Graph
pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$
preferred_prefix: bbkg
uri_format: https://bbp.epfl.ch/nexus/web/studios/public/$1
bbtp:
description: Input data and analysis results for the paper "Topology of synaptic
connectivity constrains neuronal stimulus representation, predicting two complementary
coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2
).
example: f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a
homepage: https://portal.bluebrain.epfl.ch
mappings:
miriam: bbtp
name: Blue Brain Project Topological sampling Knowledge Graph
pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
preferred_prefix: bbtp
uri_format: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1
bcgo:
banana: BCGO
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
deprecated: true
description: An application ontology built for beta cell genomics studies.
download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl
homepage: https://github.com/obi-bcgo/bcgo
license: CC BY 3.0
mappings:
biocontext: BCGO
bioportal: BCGO
cellosaurus: BCGO
obofoundry: BCGO
ontobee: BCGO
name: Beta Cell Genomics Ontology
preferred_prefix: BCGO
repository: https://github.com/obi-bcgo/bcgo
uri_format: http://purl.obolibrary.org/obo/BCGO_$1
bcio:
description: The Behaviour Change Intervention Ontology is an ontology for all aspects
of human behaviour change interventions and their evaluation.
download_owl: http://humanbehaviourchange.org/ontology/bcio.owl
example: '040000'
homepage: https://www.humanbehaviourchange.org/
mappings:
bioportal: BCI-O
ols: bcio
name: The Behaviour Change Intervention Ontology
pattern: ^\d{6}$
preferred_prefix: bcio
bco:
appears_in:
- fovt
banana: BCO
contact:
email: rlwalls2008@gmail.com
github: ramonawalls
name: Ramona Walls
orcid: 0000-0001-8815-0078
description: An ontology to support the interoperability of biodiversity data, including
data on museum collections, environmental/metagenomic samples, and ecological
surveys.
download_owl: http://purl.obolibrary.org/obo/bco.owl
example: 0000081
homepage: https://github.com/BiodiversityOntologies/bco
license: CC0 1.0
mappings:
biocontext: BCO
bioportal: BCO
fairsharing: FAIRsharing.8ktkqy
obofoundry: BCO
ols: bco
ontobee: BCO
name: Biological Collections Ontology
pattern: ^\d{7}$
preferred_prefix: BCO
repository: https://github.com/BiodiversityOntologies/bco
uri_format: http://purl.obolibrary.org/obo/BCO_$1
version: '2021-11-14'
bcrc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell line collections
example: '60316'
homepage: https://catalog.bcrc.firdi.org.tw
mappings:
cellosaurus: BCRC
name: BCRC Strain Collection Catalog
pattern: ^\d+$
preferred_prefix: bcrc
uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1
bcrj:
description: Cell line collections
example: 0278
homepage: http://bcrj.org.br/celula/bcrj
mappings:
cellosaurus: BCRJ
name: Banco de Celulas do Rio de Janeiro
pattern: ^\d{4}$
preferred_prefix: bcrj
uri_format: http://bcrj.org.br/celula/$1
bdgp.est:
description: The BDGP EST database collects the expressed sequence tags (ESTs) derived
from a variety of tissues and developmental stages for Drosophila melanogaster.
All BDGP ESTs are available at dbEST (NCBI).
example: EY223054.1
has_canonical: dbest
homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html
mappings:
biocontext: BDGP.EST
miriam: bdgp.est
n2t: bdgp.est
ncbi: BDGP_EST
name: Berkeley Drosophila Genome Project EST database
pattern: ^\w+(\.)?(\d+)?$
preferred_prefix: bdgp.est
uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
bdgp.insertion:
description: BDGP gene disruption collection provides a public resource of gene
disruptions of Drosophila genes using a single transposable element.
example: KG09531
homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/
mappings:
biocontext: BDGP.INSERTION
miriam: bdgp.insertion
n2t: bdgp.insertion
name: BDGP insertion DB
pattern: ^\w+$
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/$1
beetlebase:
description: BeetleBase is a comprehensive sequence database and community resource
for Tribolium genetics, genomics and developmental biology. It incorporates information
about genes, mutants, genetic markers, expressed sequence tags and publications.
example: TC010103
homepage: http://beetlebase.org/
mappings:
biocontext: BEETLEBASE
fairsharing: FAIRsharing.h5f091
miriam: beetlebase
n2t: beetlebase
ncbi: BEETLEBASE
prefixcommons: beetlebase
name: Tribolium Genome Database -- Insertion
pattern: ^TC\d+$
preferred_prefix: beetlebase
uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1
begdb:
description: The Benchmark Energy & Geometry Database (BEGDB) collects results of
highly accurate quantum mechanics (QM) calculations of molecular structures, energies
and properties. These data can serve as benchmarks for testing and parameterization
of other computational methods.
example: '4214'
homepage: http://www.begdb.com
mappings:
biocontext: BEGDB
fairsharing: FAIRsharing.nbe4fq
miriam: begdb
n2t: begdb
name: Benchmark Energy & Geometry Database
pattern: ^[0-9]+$
preferred_prefix: begdb
uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1
beiresources:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell line collections
example: MRA-253
homepage: https://www.beiresources.org
mappings:
cellosaurus: BEI_Resources
name: BEI Resources
preferred_prefix: beiresources
synonyms:
- BEI_Resources
uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx
bel:
comment: INDRA uses bel as a catch-all for scomp/sfam
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Biological Expression Language is a domain-specific language for
describing causal, correlative, and associative relationships between a variety
of biological agents.
example: 9-1-1 Complex
homepage: https://biological-expression-language.github.io/
mappings:
fairsharing: FAIRsharing.dp0jvd
name: Biological Expression Language
preferred_prefix: bel
bfo:
appears_in:
- agro
- aism
- cdno
- colao
- duo
- ecocore
- epio
- foodon
- fovt
- hso
- lepao
- mco
- ons
- pcl
- pco
- psdo
- rbo
- xpo
- zp
banana: BFO
contact:
email: phismith@buffalo.edu
github: phismith
name: Barry Smith
orcid: 0000-0003-1384-116X
description: The upper level ontology upon which OBO Foundry ontologies are built.
download_obo: http://purl.obolibrary.org/obo/bfo.obo
download_owl: http://purl.obolibrary.org/obo/bfo.owl
example: '0000001'
homepage: http://ifomis.org/bfo/
license: CC BY 4.0
mappings:
biocontext: BFO
bioportal: BFO
fairsharing: FAIRsharing.wcpd6f
go: BFO
obofoundry: BFO
ols: bfo
ontobee: BFO
name: Basic Formal Ontology
pattern: ^\d{7}$
preferred_prefix: BFO
repository: https://github.com/BFO-ontology/BFO
uri_format: http://purl.obolibrary.org/obo/BFO_$1
version: '2019-08-26'
bgee.family:
description: Bgee is a database of gene expression patterns within particular anatomical
structures within a species, and between different animal species. This collection
refers to expression across species.
example: ENSFM00500000270089
homepage: http://bgee.unil.ch/bgee/bgee
mappings:
biocontext: BGEE.FAMILY
miriam: bgee.family
n2t: bgee.family
name: Bgee family
pattern: ^(ENSFM|ENSGTV:)\d+$
preferred_prefix: bgee.family
uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1
bgee.gene:
description: Bgee is a database to retrieve and compare gene expression patterns
in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in
situ hybridization, and EST data). This collection references genes in Bgee.
example: FBgn0000015
homepage: https://bgee.org/
mappings:
biocontext: BGEE.GENE
miriam: bgee.gene
n2t: bgee.gene
name: Bgee gene
pattern: ^[A-Za-z]+\d+$
preferred_prefix: bgee.gene
uri_format: https://bgee.org/?page=gene&gene_id=$1
bgee.organ:
description: Bgee is a database of gene expression patterns within particular anatomical
structures within a species, and between different animal species. This collection
refers to anatomical structures.
example: EHDAA:2185
homepage: http://bgee.unil.ch/bgee/bgee
mappings:
biocontext: BGEE.ORGAN
miriam: bgee.organ
n2t: bgee.organ
name: Bgee organ
pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$
preferred_prefix: bgee.organ
uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1
bgee.stage:
description: Bgee is a database of gene expression patterns within particular anatomical
structures within a species, and between different animal species. This collection
refers to developmental stages.
example: HsapDO:0000004
homepage: http://bgee.unil.ch/bgee/bgee
mappings:
biocontext: BGEE.STAGE
miriam: bgee.stage
n2t: bgee.stage
name: Bgee stage
pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$
preferred_prefix: bgee.stage
uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1
bigg.compartment:
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
structured genome-scale metabolic network reconstructions. It more published genome-scale
metabolic networks into a single database with a set of stardized identifiers
called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
and metabolites are linked to many external databases (KEGG, PubChem, and many
more). This collection references model compartments.
example: c
homepage: http://bigg.ucsd.edu/compartments/
mappings:
biocontext: BIGG.COMPARTMENT
miriam: bigg.compartment
n2t: bigg.compartment
name: BiGG Compartment
pattern: ^[a-z_A-Z]+$
preferred_prefix: bigg.compartment
uri_format: http://bigg.ucsd.edu/compartments/$1
bigg.metabolite:
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
structured genome-scale metabolic network reconstructions. It more published genome-scale
metabolic networks into a single database with a set of stardized identifiers
called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
and metabolites are linked to many external databases (KEGG, PubChem, and many
more). This collection references individual metabolotes.
example: 12dgr161
homepage: http://bigg.ucsd.edu/universal/metabolites
mappings:
biocontext: BIGG.METABOLITE
miriam: bigg.metabolite
n2t: bigg.metabolite
name: BiGG Metabolite
pattern: ^[a-z_A-Z0-9]+$
preferred_prefix: bigg.metabolite
uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1
bigg.model:
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
structured genome-scale metabolic network reconstructions. It more published genome-scale
metabolic networks into a single database with a set of stardized identifiers
called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
and metabolites are linked to many external databases (KEGG, PubChem, and many
more). This collection references individual models.
example: iECABU_c1320
homepage: http://bigg.ucsd.edu/models
mappings:
biocontext: BIGG.MODEL
miriam: bigg.model
n2t: bigg.model
name: BiGG Model
pattern: ^[a-z_A-Z0-9]+$
preferred_prefix: bigg.model
uri_format: http://bigg.ucsd.edu/models/$1
bigg.reaction:
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
structured genome-scale metabolic network reconstructions. It more published genome-scale
metabolic networks into a single database with a set of stardized identifiers
called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
and metabolites are linked to many external databases (KEGG, PubChem, and many
more). This collection references reactions.
example: 13GS
homepage: http://bigg.ucsd.edu/universal/reactions
mappings:
biocontext: BIGG.REACTION
miriam: bigg.reaction
n2t: bigg.reaction
name: BiGG Reaction
pattern: ^[a-z_A-Z0-9]+$
preferred_prefix: bigg.reaction
uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1
bila:
banana: BILA
deprecated: true
description: This is a record of the Bilateria anatomy terminology and ontology.
We have been unable to find any further information about this resource.
mappings:
biocontext: BILA
fairsharing: FAIRsharing.eqgjeq
obofoundry: BILA
name: Bilateria anatomy
preferred_prefix: BILA
uri_format: http://purl.obolibrary.org/obo/BILA_$1
bindingdb:
description: BindingDB is the first public database of protein-small molecule affinity
data.
example: e999
homepage: https://www.bindingdb.org
mappings:
biocontext: BINDINGDB
fairsharing: FAIRsharing.3b36hk
miriam: bindingdb
n2t: bindingdb
prefixcommons: bindingdb
uniprot: BindingDB
name: BindingDB
pattern: ^\w\d+$
preferred_prefix: bindingdb
uri_format: http://www.bindingdb.org/compact/$1
biocarta.pathway:
description: BioCarta is a supplier and distributor of characterized reagents and
assays for biopharmaceutical and academic research. It catalogs community produced
online maps depicting molecular relationships from areas of active research, generating
classical pathways as well as suggestions for new pathways. This collections references
pathway maps.
example: h_aktPathway
homepage: https://www.biocarta.com/
mappings:
biocontext: BIOCARTA.PATHWAY
miriam: biocarta.pathway
n2t: biocarta.pathway
name: BioCarta Pathway
pattern: ^([hm]\_)?\w+Pathway$
preferred_prefix: biocarta.pathway
uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1
biocatalogue.service:
description: The BioCatalogue provides a common interface for registering, browsing
and annotating Web Services to the Life Science community. Registered services
are monitored, allowing the identification of service problems and changes and
the filtering-out of unavailable or unreliable resources. BioCatalogue is free
to use, for all.
example: '614'
homepage: https://www.biocatalogue.org/
mappings:
biocontext: BIOCATALOGUE.SERVICE
miriam: biocatalogue.service
n2t: biocatalogue.service
name: BioCatalogue Service
pattern: ^\d+$
preferred_prefix: biocatalogue.service
uri_format: https://www.biocatalogue.org/services/$1
biocyc:
description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides
an electronic reference source on the genomes and metabolic pathways of sequenced
organisms.
example: ECOLI:CYT-D-UBIOX-CPLX
homepage: http://biocyc.org
mappings:
biocontext: BIOCYC
go: BioCyc
miriam: biocyc
n2t: biocyc
prefixcommons: biocyc
uniprot: BioCyc
name: BioCyc collection of metabolic pathway databases
pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$
preferred_prefix: biocyc
uri_format: http://biocyc.org/getid?id=$1
biogrid:
description: BioGRID is a database of physical and genetic interactions in Saccharomyces
cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
Schizosaccharomyces pombe.
example: '31623'
homepage: http://thebiogrid.org/
mappings:
biocontext: BIOGRID
fairsharing: FAIRsharing.9d5f5r
miriam: biogrid
n2t: biogrid
prefixcommons: biogrid
uniprot: BioGRID
name: BioGRID
pattern: ^\d+$
preferred_prefix: biogrid
uri_format: http://thebiogrid.org/$1
biogrid.interaction:
contact:
email: md.tyers@umontreal.ca
github: null
name: Mike Tyers
orcid: 0000-0002-9713-9994
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: BioGRID is a database of physical and genetic interactions in Saccharomyces
cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
Schizosaccharomyces pombe.
example: '2649230'
homepage: https://thebiogrid.org/
name: BioGRID Interactions
part_of: biogrid
pattern: ^\d+$
preferred_prefix: biogrid.interaction
uri_format: https://thebiogrid.org/interaction/$1
biolegend:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: BioLegend is a life sciences supply vendor.
example: '3403'
homepage: https://www.biolegend.com
name: BioLegend
pattern: ^\d+$
preferred_prefix: biolegend
uri_format: https://www.biolegend.com/Default.aspx?ID=6664&productid=$1
biolink:
description: A high level datamodel of biological entities (genes, diseases, phenotypes,
pathways, individuals, substances, etc) and their associations.
example: Gene
homepage: https://biolink.github.io/biolink-model/
mappings:
biolink: biolink
bioportal: BIOLINK
fairsharing: FAIRsharing.ad9d85
miriam: biolink
name: Biolink Model
pattern: ^\S+$
preferred_prefix: biolink
uri_format: https://w3id.org/biolink/vocab/$1
biominder:
description: Database of the dielectric properties of biological tissues.
example: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3
homepage: https://datalab.rwth-aachen.de/MINDER
mappings:
biocontext: BIOMINDER
miriam: biominder
n2t: biominder
name: Bio-MINDER Tissue Database
pattern: ^[a-z0-9\-]+$
preferred_prefix: biominder
uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1
biomodels.db:
description: BioModels Database is a data resource that allows biologists to store,
search and retrieve published mathematical models of biological interests.
example: BIOMD0000000048
homepage: https://www.ebi.ac.uk/biomodels/
mappings:
biocontext: BIOMODELS.DB
go: BIOMD
miriam: biomodels.db
n2t: biomodels.db
name: BioModels Database
pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
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/$1
biomodels.kisao:
banana: KISAO
contact:
email: jonrkarr@gmail.com
github: jonrkarr
name: Jonathan Karr
orcid: 0000-0002-2605-5080
description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that
describes simulation algorithms and methods used for biological kinetic models,
and the relationships between them. This provides a means to unambiguously refer
to simulation algorithms when describing a simulation experiment.
download_owl: http://purl.obolibrary.org/obo/kisao.owl
example: KISAO_0000057
homepage: https://github.com/SED-ML/KiSAO
license: Artistic License 2.0
mappings:
biocontext: KISAO
bioportal: KISAO
fairsharing: FAIRsharing.jcg19w
miriam: biomodels.kisao
n2t: biomodels.kisao
obofoundry: KISAO
ols: kisao
ontobee: KISAO
prefixcommons: kisao
name: Kinetic Simulation Algorithm Ontology
pattern: ^KISAO_\d+$
preferred_prefix: biomodels.kisao
repository: https://github.com/SED-ML/KiSAO
synonyms:
- kisao
uri_format: http://purl.obolibrary.org/obo/KISAO_$1
version: '2.30'
biomodels.teddy:
description: The Terminology for Description of Dynamics (TEDDY) is an ontology
for dynamical behaviours, observable dynamical phenomena, and control elements
of bio-models and biological systems in Systems Biology and Synthetic Biology.
download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl
example: '0000066'
homepage: http://teddyontology.sourceforge.net/
mappings:
biocontext: BIOMODELS.TEDDY
bioportal: TEDDY
fairsharing: FAIRsharing.w9jvbt
miriam: biomodels.teddy
n2t: biomodels.teddy
ols: teddy
prefixcommons: teddy
name: Terminology for Description of Dynamics
pattern: ^\d+$
preferred_prefix: biomodels.teddy
synonyms:
- teddy
uri_format: https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1
version: '2014-04-24'
biomodels.vocabulary:
description: Vocabulary used in the RDF representation of SBML models.
example: rateRule
homepage: http://biomodels.net/rdf/vocabulary.rdf
mappings:
biocontext: BIOMODELS.VOCABULARY
miriam: biomodels.vocabulary
n2t: biomodels.vocabulary
name: SBML RDF Vocabulary
pattern: ^[A-Za-z]+$
preferred_prefix: biomodels.vocabulary
uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1
bionumbers:
description: BioNumbers is a database of key numberical information that may be
used in molecular biology. Along with the numbers, it contains references to the
original literature, useful comments, and related numeric data.
example: '104674'
homepage: https://bionumbers.hms.harvard.edu
mappings:
biocontext: BIONUMBERS
miriam: bionumbers
n2t: bionumbers
prefixcommons: bionumbers
name: BioNumbers
pattern: ^\d+$
preferred_prefix: bionumbers
uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1
bioportal:
description: BioPortal is an open repository of biomedical ontologies that provides
access via Web services and Web browsers to ontologies developed in OWL, RDF,
OBO format and Protégé frames. BioPortal functionality includes the ability to
browse, search and visualize ontologies.
example: '1046'
homepage: http://bioportal.bioontology.org/
mappings:
biocontext: BIOPORTAL
fairsharing: FAIRsharing.4m97ah
miriam: bioportal
n2t: bioportal
prefixcommons: bioportal
name: BioPortal
pattern: ^\d+$
preferred_prefix: bioportal
uri_format: http://bioportal.bioontology.org/ontologies/$1
bioproject:
description: BioProject provides an organizational framework to access metadata
about research projects and the data from the projects that are deposited into
different databases. It provides information about a project’s scope, material,
objectives, funding source and general relevance categories.
example: PRJDB3
homepage: http://trace.ddbj.nig.ac.jp/bioproject/
mappings:
biocontext: BIOPROJECT
fairsharing: FAIRsharing.aqhv1y
miriam: bioproject
n2t: bioproject
name: BioProject
pattern: ^PRJ[DEN][A-Z]\d+$
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/$1
bioregistry.collection:
contact:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Manually curated collections of resources stored in the bioregistry
example: '0000001'
homepage: https://bioregistry.io/collection
name: Bioregistry Collections
pattern: ^\d{7}$
preferred_prefix: bioregistry.collection
uri_format: https://bioregistry.io/collection/$1
bioregistry.registry:
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's meta-registry
example: miriam
homepage: https://bioregistry.io/metaregistry/
name: Bioregistry Metaregistry
preferred_prefix: bioregistry.registry
uri_format: https://bioregistry.io/metaregistry/$1
bioregistry.schema:
contact:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Schema for the export of the Bioregistry as RDF
example: '0000001'
homepage: https://bioregistry.io/schema
name: Bioregistry Schema
pattern: ^\d{7}$
preferred_prefix: bioregistry.schema
uri_format: https://bioregistry.io/schema/#$1
biorxiv:
description: The bioRxiv is a preprint server for biology
example: 2021.07.23.453588
example_extras:
- 000091
- 000091v1
- 2022.01.24.477526v1
homepage: https://biorxiv.org
mappings:
go: bioRxiv
scholia: biorxiv
name: bioRxiv
pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$
preferred_prefix: biorxiv
uri_format: https://www.biorxiv.org/content/10.1101/$1
biosample:
description: The BioSample Database stores information about biological samples
used in molecular experiments, such as sequencing, gene expression or proteomics.
It includes reference samples, such as cell lines, which are repeatedly used in
experiments. Accession numbers for the reference samples will be exchanged with
a similar database at NCBI, and DDBJ (Japan). Record access may be affected due
to different release cycles and inter-institutional synchronisation.
example: SAMEA2397676
homepage: https://www.ebi.ac.uk/biosamples/
mappings:
biocontext: BIOSAMPLE
cellosaurus: BioSamples
fairsharing: FAIRsharing.qr6pqk
miriam: biosample
n2t: biosample
name: BioSample
pattern: ^SAM[NED](\w)?\d+$
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
synonyms:
- biosamples
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/$1
biosimulators:
description: BioSimulators is a registry of containerized simulation tools that
support a common interface. The containers in BioSimulators support a range of
modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete
kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats
(e.g., BGNL, SBML, SED-ML).
example: vcell
homepage: https://biosimulators.org/
mappings:
fairsharing: FAIRsharing.pwEima
miriam: biosimulators
name: BioSimulators
pattern: ^[a-zA-Z0-9-_]+$
preferred_prefix: biosimulators
uri_format: https://biosimulators.org/simulators/$1
biostudies:
description: The BioStudies database holds descriptions of biological studies, links
to data from these studies in other databases at EMBL-EBI or outside, as well
as data that do not fit in the structured archives at EMBL-EBI. The database can
accept a wide range of types of studies described via a simple format. It also
enables manuscript authors to submit supplementary information and link to it
from the publication.
example: S-EPMC6266652
homepage: https://www.ebi.ac.uk/biostudies/
mappings:
fairsharing: FAIRsharing.mtjvme
miriam: biostudies
n2t: biostudies
name: BioStudies database
pattern: ^S-[A-Z]{4}[A-Z\d\-]+$
preferred_prefix: biostudies
uri_format: https://www.ebi.ac.uk/biostudies/studies/$1
biosystems:
description: The NCBI BioSystems database centralizes and cross-links existing biological
systems databases, increasing their utility and target audience by integrating
their pathways and systems into NCBI resources.
example: '001'
homepage: https://www.ncbi.nlm.nih.gov/biosystems/
mappings:
biocontext: BIOSYSTEMS
fairsharing: FAIRsharing.w2eeqr
miriam: biosystems
n2t: biosystems
prefixcommons: biosystems
name: BioSystems
pattern: ^\d+$
preferred_prefix: biosystems
uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1
biotools:
description: BioTools is a registry of databases and software with tools, services,
and workflows for biological and biomedical research.
example: uniprotkb
homepage: https://bio.tools/
mappings:
biocontext: BIOTOOLS
fairsharing: FAIRsharing.63520c
miriam: biotools
n2t: biotools
name: BioTools
pattern: ^[-A-Za-z0-9\_]*$
preferred_prefix: biotools
uri_format: https://bio.tools/$1
biozil:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/$1
birnlex:
comment: Part of the NeuroLex namespace now
description: The BIRN Project lexicon will provide entities for data and database
annotation for the BIRN project, covering anatomy, disease, data collection, project
management and experimental design.
example: birnlex_2023
homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX
mappings:
bioportal: BIRNLEX
fairsharing: FAIRsharing.jedbbt
name: Biomedical Informatics Research Network Lexicon
preferred_prefix: birnlex
bitbucket:
description: Bitbucket is a Git-based source code repository hosting service owned
by Atlassian.
example: andreadega/systems-biology-compiler
homepage: https://www.atlassian.com/
mappings:
fairsharing: FAIRsharing.fc3431
miriam: bitbucket
name: Bitbucket
pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$
preferred_prefix: bitbucket
uri_format: https://bitbucket.org/$1
bitterdb.cpd:
description: BitterDB is a database of compounds reported to taste bitter to humans.
The compounds can be searched by name, chemical structure, similarity to other
bitter compounds, association with a particular human bitter taste receptor, and
so on. The database also contains information on mutations in bitter taste receptors
that were shown to influence receptor activation by bitter compounds. The aim
of BitterDB is to facilitate studying the chemical features associated with bitterness.
This collection references compounds.
example: '46'
homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
mappings:
biocontext: BITTERDB.CPD
miriam: bitterdb.cpd
n2t: bitterdb.cpd
name: BitterDB Compound
pattern: ^\d+$
preferred_prefix: bitterdb.cpd
uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1
bitterdb.rec:
description: BitterDB is a database of compounds reported to taste bitter to humans.
The compounds can be searched by name, chemical structure, similarity to other
bitter compounds, association with a particular human bitter taste receptor, and
so on. The database also contains information on mutations in bitter taste receptors
that were shown to influence receptor activation by bitter compounds. The aim
of BitterDB is to facilitate studying the chemical features associated with bitterness.
This collection references receptors.
example: '1'
homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php
mappings:
biocontext: BITTERDB.REC
miriam: bitterdb.rec
n2t: bitterdb.rec
name: BitterDB Receptor
pattern: ^\d+$
preferred_prefix: bitterdb.rec
uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1
bko:
comment: This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.
contact:
email: adrienrougny@gmail.com
github: adrienrougny
name: Adrien Rougny
orcid: 0000-0002-2118-035X
contributor:
email: null
github: bgyori
name: Benjamin Gyori
orcid: 0000-0001-9439-5346
description: SBGN bricks represent biomolecular or biological concepts. BKO formally
associates bricks with the concepts they represent. BKO includes terms that describe
concepts, the template bricks representing these concepts, and categories that
gather bricks in a broader way.
example: '0000204'
homepage: http://www.sbgnbricks.org/
mappings:
bioportal: BKO
name: SBGN Bricks data and ontology
pattern: ^\d+$
preferred_prefix: bko
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1
bmrb:
description: BMRB collects, annotates, archives, and disseminates (worldwide in
the public domain) the important spectral and quantitative data derived from NMR
spectroscopic investigations of biological macromolecules and metabolites. The
goal is to empower scientists in their analysis of the structure, dynamics, and
chemistry of biological systems and to support further development of the field
of biomolecular NMR spectroscopy.
example: '15000'
homepage: http://www.bmrb.wisc.edu/
mappings:
fairsharing: FAIRsharing.p06nme
miriam: bmrb
uniprot: BMRB
name: Biological Magnetic Resonance Data Bank
pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$
preferred_prefix: bmrb
uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html
bmrb.restraint:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The NMR Restraints Grid contains the original NMR data as collected
for over 2500 protein and nucleic acid structures with corresponding PDB entries.
In addition to the original restraints, most of the distance, dihedral angle and
RDC restraint data (>85%) were parsed, and those in over 500 entries were converted
and filtered. The converted and filtered data sets constitute the DOCR and FRED
databases respectively.
example: '28789'
homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
name: NMR Restraints Grid
pattern: ^\d+$
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=$1
bold.taxonomy:
description: The Barcode of Life Data System (BOLD) is an informatics workbench
aiding the acquisition, storage, analysis and publication of DNA barcode records.
The associated taxonomy browser shows the progress of DNA barcoding and provides
sample collection site distribution, and taxon occurence information.
example: '27267'
homepage: http://www.boldsystems.org/
mappings:
biocontext: BOLD.TAXONOMY
miriam: bold.taxonomy
n2t: bold.taxonomy
ncbi: BOLD
name: Barcode of Life database
pattern: ^\d+$
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:
biocontext: BOOTSTREP
obofoundry: BOOTSTREP
name: Gene Regulation Ontology
preferred_prefix: BOOTSTREP
uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1
bpdb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'Database of biopesticides maintained by the University of Hertfordshire '
example: '2404'
homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm
name: Bio-Pesticides DataBase
pattern: ^\d+$
preferred_prefix: bpdb
uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm
brenda:
description: BRENDA is a collection of enzyme functional data available to the scientific
community. Data on enzyme function are extracted directly from the primary literature
The database covers information on classification and nomenclature, reaction and
specificity, functional parameters, occurrence, enzyme structure and stability,
mutants and enzyme engineering, preparation and isolation, the application of
enzymes, and ligand-related data.
example: 1.1.1.1
homepage: https://www.brenda-enzymes.org/
mappings:
biocontext: BRENDA
fairsharing: FAIRsharing.etp533
go: BRENDA
miriam: brenda
n2t: brenda
prefixcommons: brenda
uniprot: BRENDA
name: BRENDA, The Comprehensive Enzyme Information System
pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
preferred_prefix: brenda
uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1
brenda.ligand:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Information for ligands in the BRENDA database.
example: '278'
homepage: https://www.brenda-enzymes.de/ligand.php
name: BRENDA Ligand
pattern: ^\d+$
preferred_prefix: brenda.ligand
uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1
brenda.ligandgroup:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Information for ligand groups (chemical classes).
example: '18030'
homepage: https://www.brenda-enzymes.de/ligand.php
name: BRENDA Ligand Group
pattern: ^\d+$
preferred_prefix: brenda.ligandgroup
uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1
broad:
description: Magnaporthe grisea, the causal agent of rice blast disease, is one
of the most devasting threats to food security worldwide and is a model organism
for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe
comparative genomics database provides accesses to multiple fungal genomes from
the Magnaporthaceae family to facilitate the comparative analysis. As part of
the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes
the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies
of Gaeumannomyces graminis var. tritici and M. poae.
example: S7000002168151102
homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/
mappings:
biocontext: BROAD
miriam: broad
n2t: broad
name: Broad Fungal Genome Initiative
pattern: ^S\d+$
preferred_prefix: broad
uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1
bs:
comment: An alernative vocabulary that has been aligned and integrated in Sequence
Ontology (SO).
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: SO is a collaborative ontology project for the definition of sequence
features used in biological sequence annotation. It is part of the Open Biomedical
Ontologies library.
download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo
example: '00042'
homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies
name: Biosapiens Protein Feature Ontology
pattern: ^\d+$
preferred_prefix: bs
repository: https://github.com/The-Sequence-Ontology/SO-Ontologies
bspo:
appears_in:
- aism
- colao
- fovt
- lepao
- zp
banana: BSPO
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
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.
download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo
download_owl: http://purl.obolibrary.org/obo/bspo.owl
example: 0000029
homepage: https://github.com/obophenotype/biological-spatial-ontology
license: CC BY 3.0
mappings:
biocontext: BSPO
bioportal: BSPO
fairsharing: FAIRsharing.newa3z
obofoundry: BSPO
ols: bspo
ontobee: BSPO
name: Biological Spatial Ontology
pattern: ^\d{7}$
preferred_prefix: BSPO
repository: https://github.com/obophenotype/biological-spatial-ontology
uri_format: http://purl.obolibrary.org/obo/BSPO_$1
version: '2021-10-13'
bto:
banana: BTO
contact:
email: c.dudek@tu-braunschweig.de
github: chdudek
name: Christian-Alexander Dudek
orcid: 0000-0001-9117-7909
description: The Brenda tissue ontology is a structured controlled vocabulary eastablished
to identify the source of an enzyme cited in the Brenda enzyme database. It comprises
terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular
organisms.
download_json: http://purl.obolibrary.org/obo/bto.json
download_obo: http://purl.obolibrary.org/obo/bto.obo
download_owl: http://purl.obolibrary.org/obo/bto.owl
example: 0000590
homepage: http://www.brenda-enzymes.org
license: CC BY 4.0
mappings:
biocontext: BTO
bioportal: BTO
cellosaurus: BTO
fairsharing: FAIRsharing.1414v8
go: BTO
miriam: bto
n2t: bto
obofoundry: BTO
ols: bto
ontobee: BTO
prefixcommons: bto
wikidata: P5501
name: BRENDA tissue / enzyme source
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: BTO
repository: https://github.com/BRENDA-Enzymes/BTO
synonyms:
- BTO
uri_format: https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1
version: '2021-10-26'
bugbase.expt:
description: BugBase is a MIAME-compliant microbial gene expression and comparative
genomic database. It stores experimental annotation and multiple raw and analysed
data formats, as well as protocols for bacterial microarray designs. This collection
references microarray experiments.
example: '288'
homepage: http://bugs.sgul.ac.uk/E-BUGS
mappings:
biocontext: BUGBASE.EXPT
miriam: bugbase.expt
n2t: bugbase.expt
name: BugBase Expt
pattern: ^\d+$
preferred_prefix: bugbase.expt
uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view
bugbase.protocol:
description: BugBase is a MIAME-compliant microbial gene expression and comparative
genomic database. It stores experimental annotation and multiple raw and analysed
data formats, as well as protocols for bacterial microarray designs. This collection
references design protocols.
example: '67'
homepage: http://bugs.sgul.ac.uk/E-BUGS
mappings:
biocontext: BUGBASE.PROTOCOL
miriam: bugbase.protocol
n2t: bugbase.protocol
name: BugBase Protocol
pattern: ^\d+$
preferred_prefix: bugbase.protocol
uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view
bykdb:
description: The bacterial tyrosine kinase database (BYKdb) that collects sequences
of putative and authentic bacterial tyrosine kinases, providing structural and
functional information.
example: A0A009E7X8
homepage: https://bykdb.ibcp.fr/BYKdb/
mappings:
biocontext: BYKDB
fairsharing: FAIRsharing.jr30xc
miriam: bykdb
n2t: bykdb
prefixcommons: bykdb
name: Bacterial Tyrosine Kinase Database
pattern: ^[A-Z0-9]+$
preferred_prefix: bykdb
provides: uniprot
uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html
cabri:
description: CABRI (Common Access to Biotechnological Resources and Information)
is an online service where users can search a number of European Biological Resource
Centre catalogues. It lists the availability of a particular organism or genetic
resource and defines the set of technical specifications and procedures which
should be used to handle it.
example: dsmz_mutz-id:ACC 291
homepage: http://www.cabri.org/
mappings:
biocontext: CABRI
fairsharing: FAIRsharing.qx2rvz
miriam: cabri
n2t: cabri
ncbi: CABRI
name: Common Access to Biological Resources and Information Project
pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$
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=$1]
caloha:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: This is a code repository for the SIB - Swiss Institute of Bioinformatics
CALIPHO group neXtProt project, which is a comprehensive human-centric discovery
platform, that offers a integration of and navigation through protein-related
data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies
to help uncover the function of uncharacterized human proteins.
download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo
example: TS-0001
homepage: https://github.com/calipho-sib/controlled-vocabulary
name: CALIPHO Group Ontology of Human Anatomy
pattern: ^TS-\d+$
preferred_prefix: caloha
references:
- https://twitter.com/neXtProt_news/status/1350105997633867781
repository: https://github.com/calipho-sib/controlled-vocabulary
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:
biocontext: CAMEO
fairsharing: FAIRsharing.dq34p2
miriam: cameo
n2t: cameo
name: Continuous Automated Model Evaluation
pattern: ^[0-9\-_]+$
preferred_prefix: cameo
uri_format: https://www.cameo3d.org/sp/targets/target/$1
caps:
description: CAPS-DB is a structural classification of helix-cappings or caps compiled
from protein structures. The regions of the polypeptide chain immediately preceding
or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps
extracted from protein structures have been structurally classified based on geometry
and conformation and organized in a tree-like hierarchical classification where
the different levels correspond to different properties of the caps.
example: '434'
homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home
mappings:
biocontext: CAPS
miriam: caps
n2t: caps
name: CAPS-DB
pattern: ^\d+$
preferred_prefix: caps
uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1
caro:
appears_in:
- aism
- colao
- ehdaa2
- lepao
- pco
banana: CARO
contact:
email: haendel@ohsu.edu
github: mellybelly
name: Melissa Haendel
orcid: 0000-0001-9114-8737
description: None
download_owl: http://purl.obolibrary.org/obo/caro.owl
example: '0000000'
homepage: https://github.com/obophenotype/caro/
license: CC BY 3.0
mappings:
biocontext: CARO
bioportal: CARO
fairsharing: FAIRsharing.3kcgmr
go: CARO
obofoundry: CARO
ols: caro
ontobee: CARO
name: Common Anatomy Reference Ontology
pattern: ^\d{7}$
preferred_prefix: CARO
repository: https://github.com/obophenotype/caro
uri_format: http://purl.obolibrary.org/obo/CARO_$1
version: '2022-02-18'
cas:
description: CAS (Chemical Abstracts Service) is a division of the American Chemical
Society and is the producer of comprehensive databases of chemical information.
example: 50-00-0
homepage: https://commonchemistry.cas.org/
mappings:
biocontext: CAS
cheminf: '000446'
fairsharing: FAIRsharing.r7Kwy7
go: CAS
miriam: cas
n2t: cas
prefixcommons: cas
scholia: cas
wikidata: P231
name: CAS Chemical Registry
pattern: ^\d{1,7}\-\d{2}\-\d$
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=$1
casspc:
comment: Jim Balhoff said that Catalog of Fishes does not publish their data in
a machine readable format, but a long time ago they sent a CSV dump to help in
the development of TTO and VTO. These ontologies are effectively retired and CASSPC
terms are only also used in Phenoscape.
contributor:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
deprecated: true
example: '5359'
homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
mappings:
go: CASSPC
name: Eschmeyer's Catalog of Fishes
pattern: ^\d+$
preferred_prefix: casspc
uri_format: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1
cath:
description: CATH is a classification of protein structural domains. We group protein
domains into superfamilies when there is sufficient evidence they have diverged
from a common ancestor. CATH can be used to predict structural and functional
information directly from protein sequence.
example: 1.10.8.10
homepage: http://www.cathdb.info
mappings:
biocontext: CATH
fairsharing: FAIRsharing.xgcyyn
miriam: cath
n2t: cath
prefixcommons: cath
name: CATH Protein Structural Domain Superfamily
pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$
preferred_prefix: cath
uri_format: http://www.cathdb.info/cathnode/$1
cath.domain:
description: The CATH database is a hierarchical domain classification of protein
structures in the Protein Data Bank. Protein structures are classified using a
combination of automated and manual procedures. There are four major levels in
this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
Architecture (classification based on overall shape), Topology (fold family) and
Homologous superfamily (protein domains which are thought to share a common ancestor).
This colelction is concerned with CATH domains.
example: 1cukA01
homepage: http://www.cathdb.info/
mappings:
biocontext: CATH.DOMAIN
miriam: cath.domain
n2t: cath.domain
name: CATH domain
pattern: ^\w+$
preferred_prefix: cath.domain
uri_format: http://www.cathdb.info/domain/$1
cath.superfamily:
description: The CATH database is a hierarchical domain classification of protein
structures in the Protein Data Bank. Protein structures are classified using a
combination of automated and manual procedures. There are four major levels in
this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
Architecture (classification based on overall shape), Topology (fold family) and Homologous
superfamily (protein domains which are thought to share a common ancestor). This
colelction is concerned with superfamily classification.
example: 1.10.10.200
homepage: http://www.cathdb.info/
mappings:
biocontext: CATH.SUPERFAMILY
miriam: cath.superfamily
n2t: cath.superfamily
name: CATH superfamily
part_of: cath
pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$
preferred_prefix: cath.superfamily
uri_format: http://www.cathdb.info/cathnode/$1
cattleqtldb:
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
designed to house publicly all available QTL and single-nucleotide polymorphism/gene
association data on livestock animal species. This collection references cattle
QTLs.
example: '4685'
homepage: https://www.animalgenome.org/QTLdb
mappings:
biocontext: CATTLEQTLDB
miriam: cattleqtldb
n2t: cattleqtldb
prefixcommons: cattleqtldb
name: Animal Genome Cattle QTL
part_of: qtldb
pattern: ^\d+$
preferred_prefix: cattleqtldb
uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
cazy:
description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized
in enzymes that build and breakdown complex carbohydrates and glycoconjugates.
These enzymes are classified into families based on structural features.
example: GT10
homepage: http://www.cazy.org/
mappings:
biocontext: CAZY
fairsharing: FAIRsharing.ntyq70
go: CAZY
miriam: cazy
n2t: cazy
prefixcommons: cazy
uniprot: CAZy
name: Carbohydrate Active EnZYmes
pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$
preferred_prefix: cazy
uri_format: http://www.cazy.org/$1.html
cba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological
Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available
in MEDLINE.'
example: '375364'
homepage: http://www.cba.ac.cn
name: Chinese Biological Abstracts
pattern: ^\d+$
preferred_prefix: cba
uri_format: https://europepmc.org/article/CBA/$1
cbioportal:
description: The cBioPortal for Cancer Genomics provides visualization, analysis
and download of large-scale cancer genomics data sets.
example: laml_tcga_pub
homepage: http://www.cbioportal.org
mappings:
fairsharing: FAIRsharing.6L6MjA
miriam: cbioportal
n2t: cbioportal
name: The cBioPortal for Cancer Genomics
pattern: ^[a-z0-9\_]+$
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:$1&sid=IDORG
ccds:
description: The Consensus CDS (CCDS) project is a collaborative effort to identify
a core set of human and mouse protein coding regions that are consistently annotated
and of high quality. The CCDS set is calculated following coordinated whole genome
annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal
is to support convergence towards a standard set of gene annotations.
example: CCDS13573.1
homepage: http://www.ncbi.nlm.nih.gov/CCDS/
mappings:
biocontext: CCDS
fairsharing: FAIRsharing.46s4nt
miriam: ccds
n2t: ccds
prefixcommons: ccds
uniprot: CCDS
name: Consensus CDS
pattern: ^CCDS\d+\.\d+$
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 Cells
preferred_prefix: ccle
synonyms:
- ccle.cell
uri_format: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1
cco:
banana: CCO
description: The Cell Cycle Ontology is an application ontology that captures and
integrates detailed knowledge on the cell cycle process.
download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo
download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl
example: '0000003'
homepage: http://www.semantic-systems-biology.org/apo
mappings:
biocontext: CCO
bioportal: CCO
fairsharing: FAIRsharing.xhwrnr
miriam: cco
n2t: cco
ols: cco
prefixcommons: cco
name: Cell Cycle Ontology
namespace_in_lui: true
pattern: ^\w+$
preferred_prefix: cco
uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1
version: '2016-03-23'
ccrid:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell line databases/resources
example: 4201PAT-CCTCC00348
homepage: http://www.cellresource.cn
mappings:
cellosaurus: CCRID
name: National Experimental Cell Resource Sharing Platform
preferred_prefix: ccrid
uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1
cdao:
banana: CDAO
contact:
email: balhoff@renci.org
github: balhoff
name: Jim Balhoff
orcid: 0000-0002-8688-6599
description: The Comparative Data Analysis Ontology (CDAO) provides a framework
for understanding data in the context of evolutionary-comparative analysis. This
comparative approach is used commonly in bioinformatics and other areas of biology
to draw inferences from a comparison of differently evolved versions of something,
such as differently evolved versions of a protein. In this kind of analysis,
the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic
Units). The OTUs can represent biological species, but also may be drawn from
higher or lower in a biological hierarchy, anywhere from molecules to communities. The
features to be compared among OTUs are rendered in an entity-attribute-value model
sometimes referred to as the 'character-state data model'. For a given character,
such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences
between states are understood to emerge by a historical process of evolutionary
transitions in state, represented by a model (or rules) of transitions along with
a phylogenetic tree. CDAO provides the framework for representing OTUs, trees,
transformations, and characters. The representation of characters and transformations
may depend on imported ontologies for a specific type of character.
download_owl: http://purl.obolibrary.org/obo/cdao.owl
example: '0000072'
homepage: https://github.com/evoinfo/cdao
license: CC0 1.0
mappings:
biocontext: CDAO
bioportal: CDAO
fairsharing: FAIRsharing.kay31r
obofoundry: CDAO
ols: cdao
ontobee: CDAO
name: Comparative Data Analysis Ontology
pattern: ^\d{7}$
preferred_prefix: CDAO
repository: https://github.com/evoinfo/cdao
uri_format: http://purl.obolibrary.org/obo/CDAO_$1
version: '2019-06-26'
cdd:
description: The Conserved Domain Database (CDD) is a collection of multiple sequence
alignments and derived database search models, which represent protein domains
conserved in molecular evolution.
example: cd00400
homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd
mappings:
biocontext: CDD
fairsharing: FAIRsharing.ea287c
go: CDD
miriam: cdd
n2t: cdd
ncbi: CDD
prefixcommons: cdd
uniprot: CDD
name: Conserved Domain Database at NCBI
pattern: ^(cd)?\d{5}$
preferred_prefix: cdd
uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
cdno:
banana: CDNO
contact:
email: l.andres.hernandez.18@student.scu.edu.au
github: LilyAndres
name: Liliana Andres Hernandez
orcid: 0000-0002-7696-731X
depends_on:
- bfo
- chebi
- envo
- pato
- ro
description: None
download_obo: http://purl.obolibrary.org/obo/cdno.obo
download_owl: http://purl.obolibrary.org/obo/cdno.owl
example: '0000013'
homepage: https://cdno.info/
license: CC BY 3.0
mappings:
bioportal: CDNO
obofoundry: CDNO
ols: cdno
ontobee: CDNO
name: Compositional Dietary Nutrition Ontology
pattern: ^\d{7}$
preferred_prefix: CDNO
repository: https://github.com/Southern-Cross-Plant-Science/cdno
uri_format: http://purl.obolibrary.org/obo/CDNO_$1
version: '2022-04-06'
cdpd:
description: The Canadian Drug Product Database (DPD) contains product specific
information on drugs approved for use in Canada, and includes human pharmaceutical
and biological drugs, veterinary drugs and disinfectant products. This information
includes 'brand name', 'route of administration' and a Canadian 'Drug Identification
Number' (DIN).
example: '63250'
homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp
mappings:
biocontext: CDPD
miriam: cdpd
n2t: cdpd
name: Canadian Drug Product Database
pattern: ^\d+$
preferred_prefix: cdpd
uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1
cell_biolabs:
description: Cell line collections
example: AKR-270
homepage: https://www.cellbiolabs.com
mappings:
cellosaurus: Cell_Biolabs
name: Cell Biolabs cell line products
preferred_prefix: cell_biolabs
uri_format: https://www.cellbiolabs.com/search?keywords=$1
cell_model_passport:
description: Cell line databases/resources
example: SIDM01262
homepage: https://cellmodelpassports.sanger.ac.uk/
mappings:
cellosaurus: Cell_Model_Passport
name: Sanger Cell Model Passports
preferred_prefix: cell_model_passport
uri_format: https://cellmodelpassports.sanger.ac.uk/passports/$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/$1.html
cellimage:
description: 'The Cell: An Image Library™ is a freely accessible, public repository
of reviewed and annotated images, videos, and animations of cells from a variety
of organisms, showcasing cell architecture, intracellular functionalities, and
both normal and abnormal processes.'
example: '24801'
homepage: http://cellimagelibrary.org/
mappings:
biocontext: CELLIMAGE
fairsharing: FAIRsharing.8t18te
miriam: cellimage
n2t: cellimage
prefixcommons: cellimage
name: Cell Image Library
pattern: ^\d+$
preferred_prefix: cellimage
uri_format: http://cellimagelibrary.org/images/$1
cellopub:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cellosaurus identifeirs for publications, like Pubmed
example: CLPUB00496
homepage: https://web.expasy.org/cellosaurus/
mappings:
cellosaurus: CelloPub
name: Cellosaurus Publication
preferred_prefix: cellopub
uri_format: https://web.expasy.org/cellosaurus/cellopub/$1
cellosaurus:
description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts
to describe all cell lines used in biomedical research. Its scope includes: Immortalized
cell lines; naturally immortal cell lines (example: stem cell lines); finite life
cell lines when those are distributed and used widely; vertebrate cell line with
an emphasis on human, mouse and rat cell lines; and invertebrate (insects and
ticks) cell lines. Its scope does not include primary cell lines (with the exception
of the finite life cell lines described above) and plant cell lines.'
download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo
example: CVCL_0440
homepage: https://web.expasy.org/cellosaurus/
mappings:
biocontext: CELLOSAURUS
cellosaurus: Cellosaurus
fairsharing: FAIRsharing.hkk309
miriam: cellosaurus
n2t: cellosaurus
wikidata: P3289
name: Cellosaurus
pattern: ^CVCL_[A-Z0-9]{4}$
preferred_prefix: cellosaurus
synonyms:
- CVCL
uri_format: https://web.expasy.org/cellosaurus/$1
cellosaurus.resource:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The set of prefixes used in the Cellosaurus resource
example: 4DN
homepage: https://web.expasy.org/cellosaurus/
name: Cellosaurus Registry
preferred_prefix: cellosaurus.resource
uri_format: https://bioregistry.io/metaregistry/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/$1
ceph:
banana: CEPH
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: An anatomical and developmental ontology for cephalopods
download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo
download_owl: http://purl.obolibrary.org/obo/ceph.owl
example: 0000109
homepage: https://github.com/obophenotype/cephalopod-ontology
license: CC BY 3.0
mappings:
biocontext: CEPH
bioportal: CEPH
fairsharing: FAIRsharing.p58bm4
obofoundry: CEPH
ols: ceph
ontobee: CEPH
name: Cephalopod Ontology
pattern: ^\d{7}$
preferred_prefix: CEPH
repository: https://github.com/obophenotype/cephalopod-ontology
uri_format: http://purl.obolibrary.org/obo/CEPH_$1
version: '2016-01-12'
cgd:
description: The Candida Genome Database (CGD) provides access to genomic sequence
data and manually curated functional information about genes and proteins of the
human pathogen Candida albicans. It collects gene names and aliases, and assigns
gene ontology terms to describe the molecular function, biological process, and
subcellular localization of gene products.
example: CAL0003079
homepage: http://www.candidagenome.org/
mappings:
biocontext: CGD
fairsharing: FAIRsharing.j7j53
go: CGD
miriam: cgd
n2t: cgd
ncbi: CGD
prefixcommons: cgd
uniprot: CGD
name: Candida Genome Database
pattern: ^CAL\d{7}$
preferred_prefix: cgd
uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1
cghdb:
description: Cell line databases/resources
example: 300165/p13898_2106T
homepage: http://www.cghtmd.jp/CGHDatabase/index_e.jsp
mappings:
cellosaurus: CGH-DB
name: CGH Data Base
preferred_prefix: cghdb
uri_format: http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en
cgnc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Nomenclature Consortium around Chicken genes (analogous to the HGNC
for humans)
example: '10087'
homepage: http://birdgenenames.org/cgnc/
mappings:
prefixcommons: cgnc
name: Chicken Gene Nomenclature Consortium
pattern: ^\d+$
preferred_prefix: cgnc
synonyms:
- BirdBase
- CGNC
uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1
cgsc:
description: The CGSC Database of E. coli genetic information includes genotypes
and reference information for the strains in the CGSC collection, the names, synonyms,
properties, and map position for genes, gene product information, and information
on specific mutations and references to primary literature.
example: '74'
homepage: http://cgsc.biology.yale.edu/index.php
mappings:
biocontext: CGSC
fairsharing: FAIRsharing.1tbrdz
go: CGSC
miriam: cgsc
n2t: cgsc
prefixcommons: cgsc
name: Coli Genetic Stock Center
pattern: ^\d+$
preferred_prefix: cgsc
uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1
charprot:
description: CharProt is a database of biochemically characterized proteins designed
to support automated annotation pipelines. Entries are annotated with gene name,
symbol and various controlled vocabulary terms, including Gene Ontology terms,
Enzyme Commission number and TransportDB accession.
example: CH_001923
homepage: http://www.jcvi.org/charprotdb
mappings:
biocontext: CHARPROT
miriam: charprot
n2t: charprot
name: CharProt
pattern: ^CH_\d+$
preferred_prefix: charprot
uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1
chebi:
appears_in:
- cdno
- chiro
- cl
- ecocore
- ecto
- envo
- fobi
- foodon
- genepio
- maxo
- mco
- ons
- pcl
- scdo
- uberon
- xpo
banana: CHEBI
contact:
email: amalik@ebi.ac.uk
github: amalik01
name: Adnan Malik
orcid: 0000-0001-8123-5351
description: Chemical Entities of Biological Interest (ChEBI) is a freely available
dictionary of molecular entities focused on 'small' chemical compounds.
download_obo: http://purl.obolibrary.org/obo/chebi.obo
download_owl: http://purl.obolibrary.org/obo/chebi.owl
example: '24867'
homepage: http://www.ebi.ac.uk/chebi
license: CC BY 4.0
mappings:
biocontext: CHEBI
bioportal: CHEBI
cellosaurus: ChEBI
cheminf: '000407'
fairsharing: FAIRsharing.62qk8w
go: CHEBI
miriam: chebi
n2t: chebi
obofoundry: CHEBI
ols: chebi
ontobee: CHEBI
prefixcommons: chebi
wikidata: P683
name: Chemical Entities of Biological Interest
namespace_in_lui: true
pattern: ^\d+$
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
repository: https://github.com/ebi-chebi/ChEBI
synonyms:
- CHEBI
- CHEBIID
- ChEBI
uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
version: '210'
chembl:
description: ChEMBL is a database of bioactive compounds, their quantitative properties
and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
abstracted and curated from the primary scientific literature.
example: CHEMBL4303805
homepage: https://www.ebi.ac.uk/chembl
mappings:
cheminf: '000412'
fairsharing: FAIRsharing.m3jtpg
miriam: chembl
prefixcommons: chembl
uniprot: ChEMBL
name: ChEMBL
pattern: ^CHEMBL\d+$
preferred_prefix: chembl
synonyms:
- ChEMBL
- ChEMBL_ID
- chembl
uri_format: https://www.ebi.ac.uk/chembl/entity/$1
chembl.cell:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Chemistry resources
example: CHEMBL3307800
homepage: https://www.ebi.ac.uk/chembldb
mappings:
cellosaurus: ChEMBL-Cells
name: ChEMBL database of bioactive drug-like small molecules - Cell lines section
part_of: chembl
preferred_prefix: chembl.cell
synonyms:
- ChEMBL-Cells
uri_format: https://www.ebi.ac.uk/chembl/cell_line_report_card/$1
chembl.compound:
description: ChEMBL is a database of bioactive compounds, their quantitative properties
and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
abstracted and curated from the primary scientific literature.
example: CHEMBL465070
homepage: https://www.ebi.ac.uk/chembldb/
mappings:
biocontext: CHEMBL.COMPOUND
miriam: chembl.compound
n2t: chembl.compound
wikidata: P592
name: ChEMBL
part_of: chembl
pattern: ^CHEMBL\d+$
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/$1
chembl.target:
description: ChEMBL is a database of bioactive compounds, their quantitative properties
and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
abstracted and curated from the primary scientific literature.
example: CHEMBL3467
homepage: https://www.ebi.ac.uk/chembldb/
mappings:
biocontext: CHEMBL.TARGET
cellosaurus: ChEMBL-Targets
miriam: chembl.target
n2t: chembl.target
name: ChEMBL target
part_of: chembl
pattern: ^CHEMBL\d+$
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
synonyms:
- ChEMBL-Targets
uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1
chemdb:
description: ChemDB is a chemical database containing commercially available small
molecules, important for use as synthetic building blocks, probes in systems biology
and as leads for the discovery of drugs and other useful compounds.
example: '3966782'
homepage: http://cdb.ics.uci.edu/
mappings:
biocontext: CHEMDB
fairsharing: FAIRsharing.dstf7h
miriam: chemdb
n2t: chemdb
prefixcommons: chemdb
name: ChemDB
pattern: ^\d+$
preferred_prefix: chemdb
uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1
chemidplus:
description: ChemIDplus is a web-based search system that provides access to structure
and nomenclature authority files used for the identification of chemical substances
cited in National Library of Medicine (NLM) databases. It also provides structure
searching and direct links to many biomedical resources at NLM and on the Internet
for chemicals of interest.
example: 57-27-2
homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp
mappings:
biocontext: CHEMIDPLUS
fairsharing: FAIRsharing.5949vn
miriam: chemidplus
n2t: chemidplus
prefixcommons: chemidplus
name: ChemIDplus
pattern: ^\d+\-\d+\-\d+$
preferred_prefix: chemidplus
synonyms:
- ChemIDplus
uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1
cheminf:
banana: CHEMINF
contact:
email: egon.willighagen@gmail.com
github: egonw
name: Egon Willighagen
orcid: 0000-0001-7542-0286
description: Includes terms for the descriptors commonly used in cheminformatics
software applications and the algorithms which generate them.
download_owl: https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl
example: '000410'
homepage: https://github.com/semanticchemistry/semanticchemistry
license: CC BY 4.0
mappings:
biocontext: CHEMINF
bioportal: CHEMINF
fairsharing: FAIRsharing.sjhvyy
obofoundry: CHEMINF
ols: cheminf
ontobee: CHEMINF
name: Chemical Information Ontology
pattern: ^\d{6}$
preferred_prefix: CHEMINF
repository: https://github.com/semanticchemistry/semanticchemistry
uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1
version: '2.0'
chemspider:
description: ChemSpider is a collection of compound data from across the web, which
aggregates chemical structures and their associated information into a single
searchable repository entry. These entries are supplemented with additional properties,
related information and links back to original data sources.
example: '56586'
homepage: http://www.chemspider.com/
mappings:
biocontext: CHEMSPIDER
cheminf: '000405'
fairsharing: FAIRsharing.96f3gm
miriam: chemspider
n2t: chemspider
prefixcommons: chemspider
wikidata: P661
name: ChemSpider
pattern: ^\d+$
preferred_prefix: chemspider
synonyms:
- ChemSpiderID
- Chemspider
uri_format: http://www.chemspider.com/Chemical-Structure.$1.html
chickenqtldb:
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
designed to house publicly all available QTL and single-nucleotide polymorphism/gene
association data on livestock animal species. This collection references chicken
QTLs.
example: '14362'
homepage: https://www.animalgenome.org/QTLdb
mappings:
biocontext: CHICKENQTLDB
miriam: chickenqtldb
n2t: chickenqtldb
prefixcommons: chickenqtldb
name: Animal Genome Chicken QTL
part_of: qtldb
pattern: ^\d+$
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: 0000-0001-5208-3432
depends_on:
- chebi
- go
- hp
- mp
- ncbitaxon
- pr
- uberon
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.
download_obo: http://purl.obolibrary.org/obo/chiro.obo
download_owl: http://purl.obolibrary.org/obo/chiro.owl
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
repository: https://github.com/obophenotype/chiro
uri_format: http://purl.obolibrary.org/obo/CHIRO_$1
version: '2015-11-23'
chmo:
appears_in:
- rbo
- scdo
banana: CHMO
contact:
email: batchelorc@rsc.org
github: batchelorc
name: Colin Batchelor
orcid: 0000-0001-5985-7429
description: CHMO, the chemical methods ontology, describes methods used to collect
data in chemical experiments, such as mass spectrometry and electron microscopy
prepare and separate material for further analysis, such as sample ionisation,
chromatography, and electrophoresis synthesise materials, such as epitaxy and
continuous vapour deposition It also describes the instruments used in these experiments,
such as mass spectrometers and chromatography columns. It is intended to be complementary
to the Ontology for Biomedical Investigations (OBI).
download_owl: http://purl.obolibrary.org/obo/chmo.owl
example: 0002902
homepage: https://github.com/rsc-ontologies/rsc-cmo
license: CC BY 4.0
mappings:
biocontext: CHMO
bioportal: CHMO
fairsharing: FAIRsharing.9j4wh2
obofoundry: CHMO
ols: chmo
ontobee: CHMO
name: Chemical Methods Ontology
pattern: ^\d{7}$
preferred_prefix: CHMO
repository: https://github.com/rsc-ontologies/rsc-cmo
uri_format: http://purl.obolibrary.org/obo/CHMO_$1
version: '2022-04-19'
cido:
banana: CIDO
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven
open-source biomedical ontology in the area of coronavirus infectious disease.
The CIDO is developed to provide standardized human- and computer-interpretable
annotation and representation of various coronavirus infectious diseases, including
their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.
download_owl: http://purl.obolibrary.org/obo/cido.owl
example: '0000005'
homepage: https://github.com/cido-ontology/cido
license: CC BY 4.0
mappings:
bioportal: CIDO
fairsharing: FAIRsharing.aVmpKl
obofoundry: CIDO
ols: cido
ontobee: CIDO
name: Coronavirus Infectious Disease Ontology
pattern: ^\d{7}$
preferred_prefix: CIDO
repository: https://github.com/cido-ontology/cido
uri_format: http://purl.obolibrary.org/obo/CIDO_$1
version: 1.0.326
cio:
banana: CIO
contact:
email: frederic.bastian@unil.ch
github: fbastian
name: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: An ontology to capture confidence information about annotations.
download_obo: http://purl.obolibrary.org/obo/cio.obo
download_owl: http://purl.obolibrary.org/obo/cio.owl
example: '0000040'
homepage: https://github.com/BgeeDB/confidence-information-ontology
license: CC0 1.0
mappings:
biocontext: CIO
bioportal: CIO
fairsharing: FAIRsharing.e3t0yw
obofoundry: CIO
ols: cio
ontobee: CIO
name: Confidence Information Ontology
pattern: ^\d{7}$
preferred_prefix: CIO
repository: https://github.com/BgeeDB/confidence-information-ontology
uri_format: http://purl.obolibrary.org/obo/CIO_$1
version: '2015-03-10'
citexplore:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/
mappings:
fairsharing: FAIRsharing.619eqr
prefixcommons: 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/$1
civic.eid:
description: Evidence Items are the central building block of the Clinical Interpretation
of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece
of information that has been manually curated from trustable medical literature
about a Variant or genomic ‘event’ that has implications in cancer Predisposition,
Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy,
Oncogenicity or protein Function. For example, an Evidence Item might describe
a line of evidence supporting the notion that tumors with a somatic BRAF V600
mutation generally respond well to the drug dabrafenib. A Variant may be a single
nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a
chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc.
Each clinical Evidence statement corresponds to a single citable Source (a publication
or conference abstract).
example: '1199'
homepage: https://civicdb.org/
mappings:
miriam: civic.eid
name: CIViC Evidence
pattern: ^[0-9]+$
preferred_prefix: civic.eid
uri_format: https://civicdb.org/links/evidence/$1
cl:
appears_in:
- clo
- ecao
- ehdaa2
- go
- mco
- pcl
- uberon
- xpo
banana: CL
contact:
email: addiehl@buffalo.edu
github: addiehl
name: Alexander Diehl
orcid: 0000-0001-9990-8331
depends_on:
- chebi
- go
- ncbitaxon
- pato
- pr
- ro
- uberon
description: The Cell Ontology is designed as a structured controlled vocabulary
for cell types. The ontology was constructed for use by the model organism and
other bioinformatics databases, incorporating cell types from prokaryotes to mammals,
and includes plants and fungi.
download_obo: https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo
download_owl: http://purl.obolibrary.org/obo/cl.owl
example: '0000062'
homepage: https://obophenotype.github.io/cell-ontology/
license: CC BY 4.0
mappings:
biocontext: CL
bioportal: CL
cellosaurus: CL
fairsharing: FAIRsharing.j9y503
go: CL
miriam: cl
n2t: cl
obofoundry: CL
ols: cl
ontobee: CL
prefixcommons: cl
wikidata: P7963
name: Cell Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: CL
repository: https://github.com/obophenotype/cell-ontology
uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1
version: '2022-02-16'
clao:
banana: CLAO
contact:
email: lagonzalezmo@unal.edu.co
github: luis-gonzalez-m
name: Luis González-Montaña
orcid: 0000-0002-9136-9932
depends_on:
- ro
description: 'CLAO is an ontology of anatomical terms employed in morphological
descriptions for the Class Collembola (Arthropoda: Hexapoda).'
download_obo: http://purl.obolibrary.org/obo/clao.obo
download_owl: http://purl.obolibrary.org/obo/clao.owl
example: 0000088
homepage: https://github.com/luis-gonzalez-m/Collembola
license: CC0 1.0
mappings:
bioportal: CLAO
obofoundry: CLAO
ols: clao
ontobee: CLAO
name: Collembola Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: CLAO
repository: https://github.com/luis-gonzalez-m/Collembola
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/$1
cldb:
description: The Cell Line Data Base (CLDB) is a reference information source for
human and animal cell lines. It provides the characteristics of the cell lines
and their availability through distributors, allowing cell line requests to be
made from collections and laboratories.
example: cl3603
homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html
mappings:
biocontext: CLDB
cellosaurus: CLDB
miriam: cldb
n2t: cldb
name: Cell Line Database
pattern: ^(cl|tum)\d+$
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=$1
clinicaltrials:
description: ClinicalTrials.gov provides free access to information on clinical
studies for a wide range of diseases and conditions. Studies listed in the database
are conducted in 175 countries
example: NCT00222573
homepage: https://clinicaltrials.gov/
mappings:
biocontext: CLINICALTRIALS
miriam: clinicaltrials
n2t: clinicaltrials
prefixcommons: clinicaltrials
name: ClinicalTrials.gov
pattern: ^NCT\d{8}$
preferred_prefix: clinicaltrials
uri_format: https://clinicaltrials.gov/ct2/show/$1
clinvar:
description: ClinVar archives reports of relationships among medically important
variants and phenotypes. It records human variation, interpretations of the relationship
specific variations to human health, and supporting evidence for each interpretation.
Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
of the same variation and condition from one or more submitters. Submissions for
individual variation/phenotype combinations (SCV identifier) are also collected
and made available separately. This collection references the Variant identifier.
example: '12345'
homepage: http://www.ncbi.nlm.nih.gov/clinvar/
mappings:
biocontext: ClinVar
biolink: CLINVAR
cellosaurus: ClinVar
fairsharing: FAIRsharing.wx5r6f
miriam: clinvar
n2t: clinvar
wikidata: P1929
name: ClinVar Variation
pattern: ^\d+$
preferred_prefix: clinvar
uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1
clinvar.record:
description: ClinVar archives reports of relationships among medically important
variants and phenotypes. It records human variation, interpretations of the relationship
specific variations to human health, and supporting evidence for each interpretation.
Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
of the same variation and condition from one or more submitters. Submissions
for individual variation/phenotype combinations (SCV identifier) are also collected
and made available separately. This collection references the Record Report, based
on RCV accession.
example: RCV000033555.3
homepage: http://www.ncbi.nlm.nih.gov/clinvar/
mappings:
biocontext: CLINVAR.RECORD
miriam: clinvar.record
n2t: clinvar.record
name: ClinVar Record
pattern: ^RCV\d+(\.\d+)?$
preferred_prefix: clinvar.record
uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1
clinvar.submission:
description: ClinVar archives reports of relationships among medically important
variants and phenotypes. It records human variation, interpretations of the relationship
specific variations to human health, and supporting evidence for each interpretation.
Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
of the same variation and condition from one or more submitters. Submissions for
individual variation/phenotype combinations (SCV identifier) are also collected
and made available separately. This collection references submissions, and is
based on SCV accession.
example: SCV000151292
homepage: http://www.ncbi.nlm.nih.gov/clinvar/
mappings:
biocontext: CLINVAR.SUBMISSION
miriam: clinvar.submission
n2t: clinvar.submission
name: ClinVar Submission
pattern: ^SCV\d+(\.\d+)?$
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/$1
clo:
appears_in:
- mco
banana: CLO
contact:
email: siiraa@umich.edu
github: siiraa
name: Sirarat Sarntivijai
orcid: 0000-0002-2548-641X
depends_on:
- cl
- doid
- ncbitaxon
- uberon
description: The Cell Line Ontology (CLO) is a community-based ontology of cell
lines. The CLO is developed to unify publicly available cell line entry data from
multiple sources to a standardized logically defined format based on consensus
design patterns.
download_owl: http://purl.obolibrary.org/obo/clo.owl
example: 0000091
homepage: http://www.clo-ontology.org
license: CC BY 3.0
mappings:
biocontext: CLO
bioportal: CLO
cellosaurus: CLO
fairsharing: FAIRsharing.4dvtcz
obofoundry: CLO
ols: clo
ontobee: CLO
prefixcommons: clo
wikidata: P2158
name: Cell Line Ontology
pattern: ^\d{7}$
preferred_prefix: CLO
repository: https://github.com/CLO-Ontology/CLO
synonyms:
- CLO
uri_format: http://purl.obolibrary.org/obo/CLO_$1
version: 2.1.178
cls:
description: Cell line collections
example: 300108/p3934_A-172
homepage: https://cls.shop/
mappings:
cellosaurus: CLS
name: Cell Lines Service
preferred_prefix: cls
uri_format: https://www.clsgmbh.de/$1.html
clyh:
banana: CLYH
contact:
email: lucas.leclere@obs-vlfr.fr
github: L-Leclere
name: Lucas Leclere
orcid: 0000-0002-7440-0467
depends_on:
- iao
- ro
- uberon
description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish
- of the cnidarian hydrozoan species, Clytia hemiphaerica.
download_obo: http://purl.obolibrary.org/obo/clyh.obo
download_owl: http://purl.obolibrary.org/obo/clyh.owl
example: '1000100'
homepage: https://github.com/EBISPOT/clyh_ontology
license: CC BY 3.0
mappings:
bioportal: CLYH
obofoundry: CLYH
ols: clyh
ontobee: CLYH
name: Clytia hemisphaerica Development and Anatomy Ontology
pattern: ^\d+$
preferred_prefix: CLYH
repository: https://github.com/EBISPOT/clyh_ontology
uri_format: http://purl.obolibrary.org/obo/CLYH_$1
version: '2020-05-29'
cmecs:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Use this database to browse the CMECS classification and to get definitions
for individual CMECS Units. This database contains the units that were published
in the Coastal and Marine Ecological Classification Standard.
example: '595'
homepage: https://cmecscatalog.org/cmecs
name: Costal and Marine Ecological Classification Standard
pattern: ^\d+$
preferred_prefix: cmecs
references:
- http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf
uri_format: https://cmecscatalog.org/cmecs/classification/unit/$1.html
cmf:
banana: CMF
contact:
email: engelsta@ohsu.edu
github: null
name: Mark Engelstad
orcid: 0000-0001-5889-4463
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:
biocontext: CMF
obofoundry: CMF
ontobee: CMF
name: CranioMaxilloFacial ontology
preferred_prefix: CMF
uri_format: http://purl.obolibrary.org/obo/CMF_$1
cmo:
appears_in:
- scdo
banana: CMO
contact:
email: jrsmith@mcw.edu
github: jrsjrs
name: Jennifer Smith
orcid: 0000-0002-6443-9376
description: Morphological and physiological measurement records generated from
clinical and model organism research and health programs.
download_obo: http://purl.obolibrary.org/obo/cmo.obo
download_owl: http://purl.obolibrary.org/obo/cmo.owl
example: '0001350'
homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
license: CC0 1.0
mappings:
biocontext: CMO
bioportal: CMO
fairsharing: FAIRsharing.dq78pn
obofoundry: CMO
ols: cmo
ontobee: CMO
name: Clinical measurement ontology
pattern: ^\d{7}$
preferred_prefix: CMO
repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology
uri_format: http://purl.obolibrary.org/obo/CMO_$1
version: '2019-02-19'
cmpo:
description: CMPO is a species neutral ontology for describing general phenotypic
observations relating to the whole cell, cellular components, cellular processes
and cell populations.
download_owl: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl
example: '0000435'
homepage: http://www.ebi.ac.uk/cmpo
mappings:
bioportal: CMPO
fairsharing: FAIRsharing.knp11s
ols: cmpo
name: Cellular Microscopy Phenotype Ontology
pattern: ^\d{7}$
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
download_owl: https://cropontology.org/ontology/CO_320/Rice/owl
example: 0000618
homepage: https://cropontology.org/ontology/CO_320/Rice
mappings:
fairsharing: FAIRsharing.2jkxp5
ols: co_320
name: Rice ontology
pattern: ^\d{7}$
preferred_prefix: co_320
uri_format: https://www.cropontology.org/rdf/CO_320:$1
version: '2019-10-09'
co_321:
description: July 2018
download_owl: https://cropontology.org/ontology/CO_321/Wheat/owl
example: 0000449
homepage: https://cropontology.org/ontology/CO_321/Wheat
mappings:
fairsharing: FAIRsharing.czzmpg
ols: co_321
name: Wheat ontology
pattern: ^\d{7}$
preferred_prefix: co_321
uri_format: https://www.cropontology.org/rdf/CO_321:$1
version: '2019-10-09'
co_322:
description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016
download_owl: https://cropontology.org/ontology/CO_322/Maize/owl
example: '0000773'
homepage: https://cropontology.org/ontology/CO_322/Maize
mappings:
fairsharing: FAIRsharing.eeyne8
ols: co_322
name: Maize ontology
pattern: ^\d{7}$
preferred_prefix: co_322
uri_format: https://www.cropontology.org/rdf/CO_322:$1
version: '2019-10-09'
co_323:
description: ICARDA - TDv5 - Sept 2018
download_owl: https://cropontology.org/ontology/CO_323/Barley/owl
example: '0000252'
homepage: https://cropontology.org/ontology/CO_323/Barley
mappings:
fairsharing: FAIRsharing.f69084
ols: co_323
name: Barley ontology
pattern: ^\d{7}$
preferred_prefix: co_323
uri_format: https://www.cropontology.org/rdf/CO_323:$1
version: '2019-11-20'
co_324:
description: Sorghum TDv5 - Oct 2019
download_owl: https://cropontology.org/ontology/CO_324/Sorghum/owl
example: '0000111'
homepage: https://cropontology.org/ontology/CO_324/Sorghum
mappings:
fairsharing: FAIRsharing.dxx0c
ols: co_324
name: Sorghum ontology
pattern: ^\d{7}$
preferred_prefix: co_324
uri_format: https://www.cropontology.org/rdf/CO_324:$1
version: '2019-10-09'
co_325:
description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019
download_owl: https://cropontology.org/ontology/CO_325/Banana/owl
example: 0000519
homepage: https://cropontology.org/ontology/CO_325/Banana
mappings:
fairsharing: FAIRsharing.gdszhh
ols: co_325
name: Banana ontology
pattern: ^\d{7}$
preferred_prefix: co_325
uri_format: https://www.cropontology.org/rdf/CO_325:$1
version: '2019-10-09'
co_326:
description: Draft version
download_owl: https://cropontology.org/ontology/CO_326/Coconut/owl
example: '0000254'
homepage: https://cropontology.org/ontology/CO_326/Coconut
mappings:
ols: co_326
name: Coconut ontology
pattern: ^\d{7}$
preferred_prefix: co_326
co_327:
description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April
2016
download_owl: http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl
example: 0000095
homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet
mappings:
fairsharing: FAIRsharing.4e3qh9
ols: co_327
name: Pearl millet ontology
pattern: ^\d{7}$
preferred_prefix: co_327
uri_format: https://www.cropontology.org/rdf/CO_327:$1
co_330:
description: CIP - potato ontology - december 2018
download_owl: https://cropontology.org/ontology/CO_330/Potato/owl
example: '0000106'
homepage: https://cropontology.org/ontology/CO_330/Potato
mappings:
fairsharing: FAIRsharing.4fa657
ols: co_330
name: Potato ontology
pattern: ^\d{7}$
preferred_prefix: co_330
uri_format: https://www.cropontology.org/rdf/CO_330:$1
version: '2019-10-09'
co_331:
description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019
download_owl: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl
example: 0000088
homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato
mappings:
fairsharing: FAIRsharing.4g5qcw
ols: co_331
name: Sweet Potato ontology
pattern: ^\d{7}$
preferred_prefix: co_331
uri_format: https://www.cropontology.org/rdf/CO_331:$1
co_333:
description: 'This ontology was built as part of the AKER project. It describes
variables used in beet phenotyping (experimental properties and measurement scale)
for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez).
Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez)
- First submission in November 2017.'
download_owl: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl
example: '3000045'
homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology
mappings:
fairsharing: FAIRsharing.af5655
ols: co_333
name: Beet Ontology ontology
pattern: ^\d+$
preferred_prefix: co_333
uri_format: https://www.cropontology.org/rdf/CO_333:$1
co_334:
description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated
in February 2016
download_owl: https://cropontology.org/ontology/CO_334/Cassava/owl
example: '0000070'
homepage: https://cropontology.org/ontology/CO_334/Cassava
mappings:
fairsharing: FAIRsharing.v06c4q
ols: co_334
name: Cassava ontology
pattern: ^\d{7}$
preferred_prefix: co_334
uri_format: https://www.cropontology.org/rdf/CO_334:$1
version: '2019-10-09'
co_335:
description: CIAT Common bean trait dictionary - version August 2014
download_owl: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl
example: 0000189
homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean
mappings:
fairsharing: FAIRsharing.a14123
ols: co_335
name: Common Bean ontology
pattern: ^\d{7}$
preferred_prefix: co_335
uri_format: https://www.cropontology.org/rdf/CO_335:$1
co_336:
description: Soybean Trait Dictionary in template v5 - IITA - July 2015
download_owl: https://cropontology.org/ontology/CO_336/Soybean/owl
example: 0000339
homepage: https://cropontology.org/ontology/CO_336/Soybean
mappings:
fairsharing: FAIRsharing.j75srj
ols: co_336
name: Soybean ontology
pattern: ^\d{7}$
preferred_prefix: co_336
uri_format: https://www.cropontology.org/rdf/CO_336:$1
co_337:
description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept
2015
download_owl: https://cropontology.org/ontology/CO_337/Groundnut/owl
example: '0000054'
homepage: https://cropontology.org/ontology/CO_337/Groundnut
mappings:
fairsharing: FAIRsharing.ge8y23
ols: co_337
name: Groundnut ontology
pattern: ^\d{7}$
preferred_prefix: co_337
uri_format: https://www.cropontology.org/rdf/CO_337:$1
version: '2019-10-09'
co_338:
description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015
download_owl: https://cropontology.org/ontology/CO_338/Chickpea/owl
example: 0000138
homepage: https://cropontology.org/ontology/CO_338/Chickpea
mappings:
fairsharing: FAIRsharing.js20q3
ols: co_338
name: Chickpea ontology
pattern: ^\d{7}$
preferred_prefix: co_338
uri_format: https://www.cropontology.org/rdf/CO_338:$1
version: '2019-10-09'
co_339:
description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015
download_owl: https://cropontology.org/ontology/CO_339/Lentil/owl
example: '0000032'
homepage: https://cropontology.org/ontology/CO_339/Lentil
mappings:
fairsharing: FAIRsharing.ry1ezg
ols: co_339
name: Lentil ontology
pattern: ^\d{7}$
preferred_prefix: co_339
uri_format: https://www.cropontology.org/rdf/CO_339:$1
version: '2019-10-09'
co_340:
description: Cowpea Trait Dictionary in template v5 - IITA - August 2015
download_owl: https://cropontology.org/ontology/CO_340/Cowpea/owl
example: 0000639
homepage: https://cropontology.org/ontology/CO_340/Cowpea
mappings:
fairsharing: FAIRsharing.31apg2
ols: co_340
name: Cowpea ontology
pattern: ^\d{7}$
preferred_prefix: co_340
uri_format: https://www.cropontology.org/rdf/CO_340:$1
version: '2019-10-09'
co_341:
description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015
download_owl: https://cropontology.org/ontology/CO_341/Pigeonpea/owl
example: '0000140'
homepage: https://cropontology.org/ontology/CO_341/Pigeonpea
mappings:
fairsharing: FAIRsharing.ehe3yp
ols: co_341
name: Pigeonpea ontology
pattern: ^\d{7}$
preferred_prefix: co_341
uri_format: https://www.cropontology.org/rdf/CO_341:$1
version: '2019-11-18'
co_343:
description: version 2019 - pvs
download_owl: https://cropontology.org/ontology/CO_343/Yam/owl
example: '0100010'
homepage: https://cropontology.org/ontology/CO_343/Yam
mappings:
fairsharing: FAIRsharing.7e9cff
ols: co_343
name: Yam ontology
pattern: ^\d{7}$
preferred_prefix: co_343
uri_format: https://www.cropontology.org/rdf/CO_343:$1
version: '2019-10-09'
co_345:
description: Brachiaria (forages) ontology TD v5 - Version Oct 2016
download_owl: https://cropontology.org/ontology/CO_345/Brachiaria/owl
example: '0000127'
homepage: https://cropontology.org/ontology/CO_345/Brachiaria
mappings:
fairsharing: FAIRsharing.9e9683
ols: co_345
name: Brachiaria ontology
pattern: ^\d{7}$
preferred_prefix: co_345
uri_format: https://www.cropontology.org/rdf/CO_345:$1
version: '2019-10-09'
co_346:
description: oct 2016
download_owl: https://cropontology.org/ontology/CO_346/Mungbean/owl
example: 0000199
homepage: https://cropontology.org/ontology/CO_346/Mungbean
mappings:
fairsharing: FAIRsharing.fgd5gq
ols: co_346
name: Mungbean ontology
pattern: ^\d{7}$
preferred_prefix: co_346
uri_format: https://www.cropontology.org/rdf/CO_346:$1
version: '2019-10-09'
co_347:
description: 'March 2017 version '
download_owl: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl
example: 0000108
homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean
mappings:
fairsharing: FAIRsharing.qrrvyk
ols: co_347
name: Castor bean ontology
pattern: ^\d{7}$
preferred_prefix: co_347
uri_format: https://www.cropontology.org/rdf/CO_347:$1
co_348:
description: Brassica Trait Ontology (BRaTO) hosts trait information to describe
brassica crop data. Terms are collected from various projects including OREGIN,
RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute
(UK), Southern Cross University (Australia) and INRA (France).
download_owl: https://cropontology.org/ontology/CO_348/Brassica/owl
example: '1100107'
homepage: https://cropontology.org/ontology/CO_348/Brassica
mappings:
fairsharing: FAIRsharing.af7a2d
ols: co_348
name: Brassica ontology
pattern: ^\d+$
preferred_prefix: co_348
uri_format: https://www.cropontology.org/rdf/CO_348:$1
version: '2019-11-29'
co_350:
description: Oat trait dictionary started by Oat Global (http://oatglobal.org/)
and improved by NIAB and PepsiCo
download_owl: https://cropontology.org/ontology/CO_350/Oat/owl
example: '0000215'
homepage: https://cropontology.org/ontology/CO_350/Oat
mappings:
fairsharing: FAIRsharing.35e1c3
ols: co_350
name: Oat ontology
pattern: ^\d{7}$
preferred_prefix: co_350
uri_format: https://www.cropontology.org/rdf/CO_350:$1
version: '2019-10-09'
co_356:
description: Grape Ontology including OIV and bioversity descriptors. INRA July
2017
download_owl: https://cropontology.org/ontology/CO_356/Vitis/owl
example: '4000027'
homepage: https://cropontology.org/ontology/CO_356/Vitis
mappings:
fairsharing: FAIRsharing.c7f4d7
ols: co_356
name: Vitis ontology
pattern: ^\d+$
preferred_prefix: co_356
uri_format: https://www.cropontology.org/rdf/CO_356:$1
version: '2019-11-29'
co_357:
description: 'This ontology lists all variables used for woody plant observations.
Terms are collected from various sources (past and ongoing projects at national
and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET)
- Version 2 submitted on Jun 2020 by INRAE.'
download_owl: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl
example: '1000290'
homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology
mappings:
fairsharing: FAIRsharing.2b04ae
ols: co_357
name: Woody Plant Ontology ontology
pattern: ^\d+$
preferred_prefix: co_357
uri_format: https://www.cropontology.org/rdf/CO_357:$1
co_358:
description: Cotton ontology from CottonGen database - June 2019
download_owl: https://cropontology.org/ontology/CO_358/Cotton/owl
example: 0000139
homepage: https://cropontology.org/ontology/CO_358/Cotton
mappings:
ols: co_358
name: Cotton ontology
pattern: ^\d{7}$
preferred_prefix: co_358
uri_format: https://www.cropontology.org/rdf/CO_358:$1
version: '2020-01-03'
co_359:
description: December 2019
download_owl: https://cropontology.org/ontology/CO_359/Sunflower/owl
example: 0000947
homepage: https://cropontology.org/ontology/CO_359/Sunflower
mappings:
ols: co_359
name: Sunflower ontology
pattern: ^\d{7}$
preferred_prefix: co_359
uri_format: https://www.cropontology.org/rdf/CO_359:$1
co_360:
description: Sugar Kelp trait ontology
download_owl: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl
example: '0000071'
homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait
mappings:
fairsharing: FAIRsharing.1c1738
ols: co_360
name: Sugar Kelp trait ontology
pattern: ^\d{7}$
preferred_prefix: co_360
uri_format: https://www.cropontology.org/rdf/CO_360:$1
co_365:
description: developed by ICARDA - Dec 2018
download_owl: https://cropontology.org/ontology/CO_365/Fababean/owl
example: '0000205'
homepage: https://cropontology.org/ontology/CO_365/Fababean
mappings:
ols: co_365
name: Fababean ontology
pattern: ^\d{7}$
preferred_prefix: co_365
uri_format: https://www.cropontology.org/rdf/CO_365:$1
version: '2019-10-15'
co_366:
description: version Dec 2019
download_owl: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl
example: '0000072'
homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut
mappings:
ols: co_366
name: Bambara groundnut ontology
pattern: ^\d{7}$
preferred_prefix: co_366
uri_format: https://www.cropontology.org/rdf/CO_366:$1
cob:
banana: COB
contact:
email: bpeters@lji.org
github: bpeters42
name: Bjoern Peters
orcid: 0000-0002-8457-6693
description: COB brings together key terms from a wide range of OBO projects to
improve interoperability.
download_owl: http://purl.obolibrary.org/obo/cob.owl
example: 0000080
homepage: https://github.com/OBOFoundry/COB
license: CC0 1.0
mappings:
bioportal: COB
obofoundry: COB
ols: cob
ontobee: COB
name: Core Ontology for Biology and Biomedicine
pattern: ^\d{7}$
preferred_prefix: COB
repository: https://github.com/OBOFoundry/COB
uri_format: http://purl.obolibrary.org/obo/COB_$1
version: '2022-05-02'
coconut:
comment: '@mSorok is the dev of the resource, hope I got it right!'
contributor:
email: null
github: adafede
name: Adriano Rutz
orcid: 0000-0003-0443-9902
description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source
project for Natural Products (NPs) storage, search and analysis. It gathers data
from over 50 open NP resources and is available free of charge and without any
restriction. Each entry corresponds to a "flat" NP structure, and is associated,
when available, to their known stereochemical forms, literature, organisms that
produce them, natural geographical presence and diverse pre-computed molecular
properties.
example: CNP0171505
homepage: https://coconut.naturalproducts.net
name: COlleCtion of Open Natural ProdUcTs
pattern: ^CNP\d{7}$
preferred_prefix: coconut
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://coconut.naturalproducts.net/compound/coconut_id/$1
codelink:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray
targets most of the known and predictive genes of the human genome as it is described
today in the public domain. It is comprised of approximately 55,000 30-mer probes
designed to conserved exons across the transcripts of targeted genes. These 55,000
probes represent well annotated, full length, and partial human gene sequences
from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human
Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build
#165, RefSeq database (January 5, 2004 release) and dbEST database (January 8,
2004 release).'
example: GE86325
homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt
name: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
pattern: ^GE\d+$
preferred_prefix: codelink
references:
- https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt
- https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt
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
fairsharing: FAIRsharing.djsbw2
go: COG_Cluster
prefixcommons: cog
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: cthoyt
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/$1
cohd:
comment: not really sure where the source is. this also links to a system called
athena. I was not able to figure out what COHD stands for.
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: MIMIC-III is a dataset comprising health-related data associated with
over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess
Medical Center between 2001 and 2012
homepage: https://github.com/MIT-LCP/mimic-omop
name: MIMIC III Database
no_own_terms: true
preferred_prefix: cohd
repository: https://github.com/MIT-LCP/mimic-omop
colao:
banana: COLAO
contact:
email: entiminae@gmail.com
github: JCGiron
name: Jennifer C. Giron
orcid: 0000-0002-0851-6883
depends_on:
- aism
- bfo
- bspo
- caro
- pato
- ro
- uberon
description: The Coleoptera Anatomy Ontology contains terms used for describing
the anatomy and phenotype of beetles in biodiversity research.
download_obo: http://purl.obolibrary.org/obo/colao.obo
download_owl: http://purl.obolibrary.org/obo/colao.owl
example: '0000000'
homepage: https://github.com/insect-morphology/colao
license: CC BY 4.0
mappings:
bioportal: COLAO
obofoundry: COLAO
ols: colao
ontobee: COLAO
name: Coleoptera Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: COLAO
repository: https://github.com/insect-morphology/colao
uri_format: http://purl.obolibrary.org/obo/COLAO_$1
version: '2021-12-14'
colonatlas:
description: Cell line databases/resources
example: ALA
homepage: http://www.coloncanceratlas.org
mappings:
cellosaurus: ColonAtlas
name: Colorectal Cancer Atlas
preferred_prefix: colonatlas
uri_format: http://www.coloncanceratlas.org/search_cell_line?cell_line=$1
combine.specifications:
description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative
to coordinate the development of the various community standards and formats for
computational models, initially in Systems Biology and related fields. This collection
pertains to specifications of the standard formats developed by the Computational
Modeling in Biology Network.
example: sbgn.er.level-1.version-1.2
homepage: https://co.mbine.org/standards/
mappings:
biocontext: COMBINE.SPECIFICATIONS
miriam: combine.specifications
n2t: combine.specifications
name: COMBINE specifications
pattern: ^\w+(\-|\.|\w)*$
preferred_prefix: combine.specifications
uri_format: https://co.mbine.org/specifications/$1
come:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
mappings:
prefixcommons: come
name: The Bioinorganic Motif Database
preferred_prefix: come
uri_format: https://www.flymine.org/come/entry?gn=$1
complexportal:
description: A database that describes manually curated macromolecular complexes
and provides links to details about these complexes in other databases.
example: CPX-263
homepage: https://www.ebi.ac.uk/complexportal
mappings:
biocontext: COMPLEXPORTAL
go: ComplexPortal
miriam: complexportal
n2t: complexportal
uniprot: ComplexPortal
wikidata: P7718
name: Complex Portal
pattern: ^CPX-[0-9]+$
preferred_prefix: complexportal
synonyms:
- ComplexPortal
uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
comptox:
description: The Chemistry Dashboard is a part of a suite of databases and web applications
developed by the US Environmental Protection Agency's Chemical Safety for Sustainability
Research Program. These databases and apps support EPA's computational toxicology
research efforts to develop innovative methods to change how chemicals are currently
evaluated for potential health risks.
example: DTXSID2021028
homepage: https://comptox.epa.gov/dashboard
mappings:
biocontext: COMPTOX
miriam: comptox
n2t: comptox
wikidata: P3117
name: CompTox Chemistry Dashboard
pattern: ^DTXSID\d+$
preferred_prefix: comptox
uri_format: https://comptox.epa.gov/dashboard/$1
compulyeast:
description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis
federated database. This collection references a subset of Uniprot, and contains
general information about the protein record.
example: O08709
homepage: http://compluyeast2dpage.dacya.ucm.es/
mappings:
biocontext: COMPULYEAST
fairsharing: FAIRsharing.rbjs3e
miriam: compulyeast
n2t: compulyeast
name: Compluyeast-2D-DB
pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9])$
preferred_prefix: compulyeast
provides: uniprot
uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1
conoserver:
description: ConoServer is a database specialized in the sequence and structures
of conopeptides, which are peptides expressed by carnivorous marine cone snails.
example: '2639'
homepage: http://www.conoserver.org/
mappings:
biocontext: CONOSERVER
fairsharing: FAIRsharing.y00hz4
miriam: conoserver
n2t: conoserver
uniprot: ConoServer
name: ConoServer
pattern: ^\d+$
preferred_prefix: conoserver
uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1
conso:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology describing phenomena encountered in the literature surrounding
neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's
disease, tauopathies, and related protein aggregation diseases.
example: CONSO00010
homepage: https://pharmacome.github.io/conso/
name: Curation of Neurodegeneration Supporting Ontology
pattern: ^CONSO\d{5}$
preferred_prefix: conso
uri_format: https://pharmacome.github.io/conso/$1
coriell:
description: The Coriell Cell Repositories provide essential research reagents to
the scientific community by establishing, verifying, maintaining, and distributing
cell cultures and DNA derived from cell cultures. These collections, supported
by funds from the National Institutes of Health (NIH) and several foundations,
are extensively utilized by research scientists around the world.
example: GM17027
homepage: http://ccr.coriell.org/
mappings:
biocontext: Coriell
cellosaurus: Coriell
go: CORIELL
miriam: coriell
n2t: coriell
name: Coriell Institute for Medical Research
pattern: ^[A-Z]{2}\d+$
preferred_prefix: coriell
uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1
corrdb:
description: A genetic correlation is the proportion of shared variance between
two traits that is due to genetic causes; a phenotypic correlation is the degree
to which two traits co-vary among individuals in a population. In the genomics
era, while gene expression, genetic association, and network analysis provide
unprecedented means to decode the genetic basis of complex phenotypes, it is important
to recognize the possible effects genetic progress in one trait can have on other
traits. This database is designed to collect all published livestock genetic/phenotypic
trait correlation data, aimed at facilitating genetic network analysis or systems
biology studies.
example: '37232'
homepage: https://www.animalgenome.org
mappings:
fairsharing: FAIRsharing.IziuCK
miriam: corrdb
name: CorrDB
pattern: ^[0-9]+$
preferred_prefix: corrdb
uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1
corum:
description: The CORUM database provides a resource of manually annotated protein
complexes from mammalian organisms. Annotation includes protein complex function,
localization, subunit composition, literature references and more. All information
is obtained from individual experiments published in scientific articles, data
from high-throughput experiments is excluded.
example: '100'
homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/
mappings:
biocontext: CORUM
fairsharing: FAIRsharing.ohbpNw
go: CORUM
miriam: corum
n2t: corum
prefixcommons: corum
uniprot: CORUM
name: Comprehensive Resource of Mammalian protein complexes
pattern: ^\d+$
preferred_prefix: corum
uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1
cosmic:
description: COSMIC is a comprehensive global resource for information on somatic
mutations in human cancer, combining curation of the scientific literature with
tumor resequencing data from the Cancer Genome Project at the Sanger Institute,
U.K. This collection references genes.
example: BRAF
homepage: http://cancer.sanger.ac.uk/cosmic/
mappings:
biocontext: COSMIC
cellosaurus: Cosmic
fairsharing: FAIRsharing.s5zmbp
miriam: cosmic
n2t: cosmic
name: COSMIC Gene
pattern: ^[A-Z0-9]+$
preferred_prefix: cosmic
uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1
cosmic.cell:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's
largest and most comprehensive resource for exploring the impact of somatic mutations
in human cancer
example: '906801'
homepage: https://cancer.sanger.ac.uk/cell_lines/
mappings:
cellosaurus: Cosmic-CLP
name: COSMIC Cell Lines
pattern: ^\d+$
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/$1
covoc:
contact:
email: zmp@ebi.ac.uk
github: zoependlington
name: Zoë May Pendlington
orcid: 0000-0002-4071-8397
description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related
to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity,
gene and gene products, barrier gestures, treatments and more.
download_owl: http://purl.obolibrary.org/obo/covoc/releases/2020-08-28/covoc.owl
example: '0010034'
homepage: https://github.com/EBISPOT/covoc
mappings:
ols: covoc
name: CoVoc Coronavirus Vocabulary
pattern: ^\d{7}$
preferred_prefix: covoc
repository: https://github.com/EBISPOT/covoc
version: '2020-08-28'
cp:
appears_in:
- cl
comment: Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572
contributor:
email: cthoyt@gmail.com
github: cthoyt
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:
biocontext: CPC
fairsharing: FAIRsharing.e08886
miriam: cpc
n2t: 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:
biocontext: gro.cpga
bioportal: GRO-CPGA
obofoundry: GRO
name: Cereal Plant Gross Anatomy
preferred_prefix: GRO
uri_format: http://purl.obolibrary.org/obo/GRO_$1
cpt:
contributor:
email: null
github: sierra-moxon
name: Sierra Moxon
orcid: 0000-0002-8719-7760
description: Current Procedural Terminology, more commonly known as CPT®, refers
to a medical code set created and maintained by the American Medical Association
— and used by physicians, allied health professionals, nonphysician practitioners,
hospitals, outpatient facilities, and laboratories to represent the services and
procedures they perform. No provider of outpatient services gets paid without
reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]
example: '00103'
homepage: https://www.aapc.com
mappings:
biolink: CPT
bioportal: CPT
fairsharing: FAIRsharing.wpxab1
name: Current Procedural Terminology
pattern: ^\d+$
preferred_prefix: cpt
references:
- https://github.com/biopragmatics/bioregistry/issues/357
- https://github.com/biopragmatics/bioregistry/pull/358
- https://github.com/biolink/biolink-model/pull/993
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://www.aapc.com/codes/cpt-codes/$1
credit:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including
14 roles, that can be used to represent the roles typically played by contributors
to scientific scholarly output. The roles describe each contributor’s specific
contribution to the scholarly output.
example: Software
homepage: https://casrai.org/credit/
name: CASRAI Contributor Roles Taxonomy
preferred_prefix: credit
crisprdb:
description: Repeated CRISPR ("clustered regularly interspaced short palindromic
repeats") elements found in archaebacteria and eubacteria are believed to defend
against viral infection, potentially targeting invading DNA for degradation. CRISPRdb
is a database that stores information on CRISPRs that are automatically extracted
from newly released genome sequence data.
example: '551115'
homepage: http://crispr.i2bc.paris-saclay.fr/
mappings:
biocontext: CRISPRDB
fairsharing: FAIRsharing.7sfedh
miriam: crisprdb
n2t: crisprdb
name: CRISPRdb
pattern: ^[0-9]+$
preferred_prefix: crisprdb
uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1
cro:
banana: CRO
contact:
email: whimar@ohsu.edu
github: marijane
name: Marijane White
orcid: 0000-0001-5059-4132
description: A classification of the diverse roles performed in the work leading
to a published research output in the sciences. Its purpose to provide transparency
in contributions to scholarly published work, to enable improved systems of attribution,
credit, and accountability.
download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo
download_owl: http://purl.obolibrary.org/obo/cro.owl
example: 0000038
homepage: https://github.com/data2health/contributor-role-ontology
license: CC BY 2.0
mappings:
biocontext: CRO
bioportal: CRO
obofoundry: CRO
ols: cro
ontobee: CRO
name: Contributor Role Ontology
pattern: ^\d{7}$
preferred_prefix: CRO
repository: https://github.com/data2health/contributor-role-ontology
uri_format: http://purl.obolibrary.org/obo/CRO_$1
version: '2019-12-11'
cryoem:
description: Ontology that describes data types and image processing operations
in Cryo Electron Microscopy of Single Particles
download_owl: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl
example: '0000052'
homepage: http://scipion.i2pc.es/ontology/cryoem
mappings:
bioportal: CRYOEM
ols: cryoem
name: Cryo Electron Microscopy ontology
pattern: ^\d{7}$
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:
biocontext: CRYPTODB
fairsharing: FAIRsharing.t3nprm
miriam: cryptodb
n2t: cryptodb
prefixcommons: cryptodb
name: CryptoDB
pattern: ^\w+$
preferred_prefix: cryptodb
uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1
csa:
description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
for catalytic residues which includes only those residues thought to be directly
involved in some aspect of the reaction catalysed by an enzyme.
example: 1a05
homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/
mappings:
biocontext: CSA
fairsharing: FAIRsharing.2ajtcf
miriam: csa
n2t: csa
prefixcommons: csa
name: Catalytic Site Atlas
pattern: ^[0-9][A-Za-z0-9]{3}$
preferred_prefix: csa
uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1
csd:
description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive
collection of small-molecule crystal structures. Entries curated into the CSD
are identified by a CSD Refcode.
example: PELNAW
homepage: https://www.ccdc.cam.ac.uk/
mappings:
fairsharing: FAIRsharing.vs7865
miriam: csd
name: Cambridge Structural Database
pattern: ^[A-Z]{6}(\d{2})?$
preferred_prefix: csd
uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG
csp:
deprecated: true
example: 2004-2820
homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm
mappings:
bioportal: CRISP
name: Computer Retrieval of Information on Science Projects Thesaurus
preferred_prefix: csp
synonyms:
- CRISP
- CRISP Thesaurus
- CRISP Thesaurus, 2006
- CSP2005
cst:
description: Cell Signaling Technology is a commercial organisation which provides
a pathway portal to showcase their phospho-antibody products. This collection
references pathways.
example: Akt_PKB
homepage: http://www.cellsignal.com/pathways/index.html
mappings:
biocontext: CST
bioportal: CST
fairsharing: FAIRsharing.n8pxvx
miriam: cst
n2t: cst
prefixcommons: cst
name: Cancer Staging Terms
pattern: ^[A-Za-z0-9_-]+$
preferred_prefix: cst
uri_format: http://www.cellsignal.com/reference/pathway/$1.html
cst.ab:
description: Cell Signaling Technology is a commercial organisation which provides
a pathway portal to showcase their phospho-antibody products. This collection
references antibody products.
example: '3305'
homepage: http://www.cellsignal.com/catalog/index.html
mappings:
biocontext: CST.AB
miriam: cst.ab
n2t: cst.ab
name: Cell Signaling Technology Antibody
pattern: ^\d+$
preferred_prefix: cst.ab
uri_format: http://www.cellsignal.com/products/$1.html
ctd.chemical:
description: The Comparative Toxicogenomics Database (CTD) presents scientifically
reviewed and curated information on chemicals, relevant genes and proteins, and
their interactions in vertebrates and invertebrates. It integrates sequence, reference,
species, microarray, and general toxicology information to provide a unique centralized
resource for toxicogenomic research. The database also provides visualization
capabilities that enable cross-species comparisons of gene and protein sequences.
example: D001151
homepage: http://ctdbase.org/
mappings:
biocontext: CTD.CHEMICAL
biolink: CTD.CHEMICAL
miriam: ctd.chemical
n2t: ctd.chemical
name: CTD Chemical
part_of: ctd
pattern: ^[CD]\d+$
preferred_prefix: ctd.chemical
provides: mesh
uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1
ctd.disease:
description: The Comparative Toxicogenomics Database (CTD) presents scientifically
reviewed and curated information on chemicals, relevant genes and proteins, and
their interactions in vertebrates and invertebrates. It integrates sequence, reference,
species, microarray, and general toxicology information to provide a unique centralized
resource for toxicogenomic research. The database also provides visualization
capabilities that enable cross-species comparisons of gene and protein sequences.
example: D053716
homepage: http://ctdbase.org/
mappings:
biocontext: CTD.DISEASE
biolink: CTD.DISEASE
miriam: ctd.disease
n2t: ctd.disease
name: CTD Disease
part_of: ctd
pattern: ^D\d+$
preferred_prefix: ctd.disease
provides: mesh
uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1
ctd.gene:
description: The Comparative Toxicogenomics Database (CTD) presents scientifically
reviewed and curated information on chemicals, relevant genes and proteins, and
their interactions in vertebrates and invertebrates. It integrates sequence, reference,
species, microarray, and general toxicology information to provide a unique centralized
resource for toxicogenomic research. The database also provides visualization
capabilities that enable cross-species comparisons of gene and protein sequences.
example: '101'
homepage: http://ctdbase.org/
mappings:
biocontext: CTD.GENE
biolink: CTD.GENE
miriam: ctd.gene
n2t: ctd.gene
name: CTD Gene
part_of: ctd
pattern: ^\d+$
preferred_prefix: ctd.gene
provides: ncbigene
uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1
cteno:
banana: CTENO
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
depends_on:
- ro
- uberon
description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo
download_owl: http://purl.obolibrary.org/obo/cteno.owl
example: '0000047'
homepage: https://github.com/obophenotype/ctenophore-ontology
license: CC BY 3.0
mappings:
biocontext: CTENO
bioportal: CTENO
fairsharing: FAIRsharing.mgxgza
obofoundry: CTENO
ols: cteno
ontobee: CTENO
name: Ctenophore Ontology
pattern: ^\d{7}$
preferred_prefix: CTENO
repository: https://github.com/obophenotype/ctenophore-ontology
uri_format: http://purl.obolibrary.org/obo/CTENO_$1
version: '2016-10-19'
cto:
banana: CTO
contact:
email: alpha.tom.kodamullil@scai.fraunhofer.de
github: akodamullil
name: Dr. Alpha Tom Kodamullil
orcid: 0000-0001-9896-3531
description: The core Ontology of Clinical Trials (CTO) will serve as a structured
resource integrating basic terms and concepts in the context of clinical trials.
Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to
generate extended versions for specific applications such as annotation of variables
in study documents from clinical trials.
download_owl: http://purl.obolibrary.org/obo/cto.owl
example: '0000022'
homepage: https://github.com/ClinicalTrialOntology/CTO/
license: CC BY 4.0
mappings:
bioportal: CTO
fairsharing: FAIRsharing.qp211a
obofoundry: CTO
ols: cto
ontobee: CTO
name: Clinical Trials Ontology
pattern: ^\d{7}$
preferred_prefix: CTO
repository: https://github.com/ClinicalTrialOntology/CTO
uri_format: http://purl.obolibrary.org/obo/CTO_$1
version: 1.0.0
cubedb:
comment: website down as of 2021-10-04
deprecated: true
description: Cube-DB is a database of pre-evaluated results for detection of functional
divergence in human/vertebrate protein families. It analyzes comparable taxonomical
samples for all paralogues under consideration, storing functional specialisation
at the level of residues. The data are presented as a table of per-residue scores,
and mapped onto related structures where available.
example: AKR
homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html
mappings:
biocontext: CUBEDB
miriam: cubedb
n2t: cubedb
name: Cube db
pattern: ^[A-Za-z_0-9]+$
preferred_prefix: cubedb
uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/
cvdo:
banana: CVDO
contact:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
description: An ontology to describe entities related to cardiovascular diseases
download_owl: http://purl.obolibrary.org/obo/cvdo.owl
example: '0000546'
homepage: https://github.com/OpenLHS/CVDO
license: CC BY 4.0
mappings:
biocontext: CVDO
bioportal: CVDO
fairsharing: FAIRsharing.2basyz
obofoundry: CVDO
ols: cvdo
ontobee: CVDO
name: Cardiovascular Disease Ontology
pattern: ^\d{7}$
preferred_prefix: CVDO
repository: https://github.com/OpenLHS/CVDO
uri_format: http://purl.obolibrary.org/obo/CVDO_$1
version: '2020-03-05'
d1id:
description: DataONE provides infrastructure facilitating long-term access to scientific
research data of relevance to the earth sciences.
example: 00030692-0FE1-4A1B-955E-A2E55D659267
homepage: https://www.dataone.org
mappings:
biocontext: D1ID
miriam: d1id
n2t: d1id
name: DataONE
pattern: ^\S+$
preferred_prefix: d1id
uri_format: https://cn.dataone.org/cn/v2/resolve/{$1}
dailymed:
description: DailyMed provides information about marketed drugs. This information
includes FDA labels (package inserts). The Web site provides a standard, comprehensive,
up-to-date, look-up and download resource of medication content and labeling as
found in medication package inserts. Drug labeling is the most recent submitted
to the Food and Drug Administration (FDA) and currently in use; it may include,
for example, strengthened warnings undergoing FDA review or minor editorial changes.
These labels have been reformatted to make them easier to read.
example: 973a9333-fec7-46dd-8eb5-25738f06ee54
homepage: https://dailymed.nlm.nih.gov/dailymed/
mappings:
biocontext: DAILYMED
miriam: dailymed
n2t: dailymed
prefixcommons: dailymed
name: DailyMed
pattern: ^[A-Za-z0-9-]+$
preferred_prefix: dailymed
uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1
dandi:
description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate
data using community data standards such as NWB and BIDS, and to make data and
software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable,
and Reusable).
DANDI references electrical and optical cellular neurophysiology recordings and
associated MRI and/or optical imaging data.
These data will help scientists uncover and understand cellular level mechanisms
of brain function. Scientists will study the formation of neural networks, how
cells and networks enable functions such as learning and memory, and how these
functions are disrupted in neurological disorders.'
example: '000017'
homepage: https://dandiarchive.org/
mappings:
miriam: dandi
name: Distributed Archives for Neurophysiology Data Integration
pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$
preferred_prefix: dandi
uri_format: https://dandiarchive.org/dandiset/$1
darc:
description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM
(electron microscopy) data and atomic coordinates of ribosomal particles from
the PDB, which are aligned within a common coordinate system. The aligned coordinate
system simplifies direct visualization of conformational changes in the ribosome,
such as subunit rotation and head-swiveling, as well as direct comparison of bound
ligands, such as antibiotics or translation factors.
example: '1250'
homepage: http://darcsite.genzentrum.lmu.de/darc/index.php
mappings:
biocontext: DARC
fairsharing: FAIRsharing.evfe2s
miriam: darc
n2t: darc
name: Database of Aligned Ribosomal Complexes
pattern: ^\d+$
preferred_prefix: darc
uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1
dashr:
description: DASHR reports the annotation, expression and evidence for specific
RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor
and mature sncRNA products across different human tissues and cell types. DASHR
integrates information from multiple existing annotation resources for small non-coding
RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs),
nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs),
and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human
tissues and cell types and were generated for studying or profiling small non-coding
RNAs. This collection references RNA records.
example: hsa-mir-200a
homepage: http://lisanwanglab.org/DASHR/
mappings:
biocontext: DASHR
fairsharing: FAIRsharing.ztvs34
miriam: dashr
n2t: dashr
name: Database of small human noncoding RNAs
pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
preferred_prefix: dashr
uri_format: http://lisanwanglab.org/DASHR/entry/$1
dashr.expression:
description: DASHR reports the annotation, expression and evidence for specific
RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor
and mature sncRNA products across different human tissues and cell types. DASHR
integrates information from multiple existing annotation resources for small non-coding
RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs),
nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs),
and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human
tissues and cell types and were generated for studying or profiling small non-coding
RNAs. This collection references RNA expression.
example: hsa-mir-200a
homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0
mappings:
biocontext: DASHR.EXPRESSION
miriam: dashr.expression
n2t: dashr.expression
name: DASHR expression
pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
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/$1
datf:
deprecated: true
description: DATF contains known and predicted Arabidopsis transcription factors
(1827 genes in 56 families) with the unique information of 1177 cloned sequences
and many other features including 3D structure templates, EST expression information,
transcription factor binding sites and nuclear location signals.
example: AT1G01030.1
homepage: http://datf.cbi.pku.edu.cn/
mappings:
biocontext: DATF
miriam: datf
n2t: datf
prefixcommons: datf
name: Database of Arabidopsis Transcription Factors
pattern: ^AT[1-5]G\d{5}(\.\d+)?$
preferred_prefix: datf
uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1
dbd:
description: The DBD (transcription factor database) provides genome-wide transcription
factor predictions for organisms across the tree of life. The prediction method
identifies sequence-specific DNA-binding transcription factors through homology
using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY.
It does not include basal transcription factors or chromatin-associated proteins.
example: '0045310'
homepage: http://www.transcriptionfactor.org/
mappings:
biocontext: DBD
miriam: dbd
n2t: dbd
prefixcommons: dbd
name: Transcription Factor Database
pattern: ^\d+$
preferred_prefix: dbd
uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD
dbest:
description: The dbEST contains sequence data and other information on "single-pass"
cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
example: BP100000
homepage: https://www.ncbi.nlm.nih.gov/nucest
mappings:
biocontext: DBEST
fairsharing: FAIRsharing.v9fya8
miriam: dbest
n2t: dbest
ncbi: dbEST
prefixcommons: dbest
name: EST database maintained at the NCBI.
pattern: ^([A-Z]+)?\d+(\.\d+)?$
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/$1
dbg2introns:
description: The Database for Bacterial Group II Introns provides a catalogue of
full-length, non-redundant group II introns present in bacterial DNA sequences
in GenBank.
example: Cu.me.I1
homepage: http://webapps2.ucalgary.ca/~groupii/
mappings:
biocontext: DBG2INTRONS
miriam: dbg2introns
n2t: dbg2introns
name: DBG2 Introns
pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
preferred_prefix: dbg2introns
uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1
dbgap:
description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes
the results of studies that have investigated the interaction of genotype and
phenotype.
example: phs000768.v2.p1
homepage: https://www.ncbi.nlm.nih.gov/projects/gap
mappings:
biocontext: DBGAP
fairsharing: FAIRsharing.88v2k0
miriam: dbgap
n2t: dbgap
name: Database of Genotypes and Phenotypes
pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$
preferred_prefix: dbgap
uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1
dbmhc:
appears_in:
- cellosaurus
deprecated: true
description: Cell line databases/resources
example: '48439'
homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/
mappings:
cellosaurus: dbMHC
name: Database of human Major Histocompatibility Complex
pattern: ^\d+$
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:
biocontext: DBPROBE
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=$1
dbsnp:
description: The dbSNP database is a repository for both single base nucleotide
subsitutions and short deletion and insertion polymorphisms.
example: rs121909098
homepage: https://www.ncbi.nlm.nih.gov/snp/
mappings:
biocontext: dbSNP
cellosaurus: dbSNP
fairsharing: FAIRsharing.edxb58
go: dbSNP
miriam: dbsnp
n2t: dbsnp
ncbi: dbSNP
prefixcommons: dbsnp
uniprot: dbSNP
name: NCBI dbSNP
pattern: ^rs\d+$
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
dbvar.study:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Studies in dbVar.
example: nstd102
homepage: https://www.ncbi.nlm.nih.gov/dbvar
name: Database of Genomic Structural Variation - Study
preferred_prefix: dbvar.study
synonyms:
- dbvar.studies
uri_format: https://www.ncbi.nlm.nih.gov/dbvar/studies/$1
dbvar.variant:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Variants in dbVar.
example: nsv3875336
homepage: https://www.ncbi.nlm.nih.gov/dbvar
name: Database of Genomic Structural Variation - Variant
preferred_prefix: dbvar.variant
synonyms:
- dbvar.variants
uri_format: https://www.ncbi.nlm.nih.gov/dbvar/variants/$1
dc:
description: Metadata terms maintained by the Dublin Core Metadata Initiative, including
properties, vocabulary encoding schemes, syntax encoding schemes, and classes.
example: contributor
has_canonical: dcterms
homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
mappings:
biocontext: dc
bioportal: DC
fairsharing: FAIRsharing.3nx7t
name: Dublin Core
preferred_prefix: dc
uri_format: http://purl.org/dc/terms/$1
dc_cl:
banana: DC_CL
contact:
email: Lindsay.Cowell@utsouthwestern.edu
github: null
name: Lindsay Cowell
orcid: 0000-0003-1617-8244
deprecated: true
example: '0000003'
homepage: http://www.dukeontologygroup.org/Projects.html
mappings:
biocontext: DC_CL
obofoundry: DC_CL
name: Dendritic cell
pattern: ^\d{7}$
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:
biocontext: dcat
biolink: dcat
bioportal: DCAT
fairsharing: FAIRsharing.h4j3qm
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:
biocontext: dcterms
biolink: dct
bioportal: DCTERMS
fairsharing: FAIRsharing.9vtwjs
name: Dublin Core Metadata Vocabulary
preferred_prefix: dcterms
synonyms:
- dc.terms
uri_format: http://purl.org/dc/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:
biocontext: dctypes
name: Dublin Core Types
preferred_prefix: dctypes
uri_format: http://purl.org/dc/dcmitype/$1
ddanat:
banana: DDANAT
contact:
email: pfey@northwestern.edu
github: pfey03
name: Petra Fey
orcid: 0000-0002-4532-2703
description: A structured controlled vocabulary of the anatomy of the slime-mold
Dictyostelium discoideum
download_obo: http://purl.obolibrary.org/obo/ddanat.obo
download_owl: http://purl.obolibrary.org/obo/ddanat.owl
example: '0000006'
homepage: http://dictybase.org/
license: CC0 1.0
mappings:
biocontext: DDANAT
bioportal: DDANAT
fairsharing: FAIRsharing.z656ab
go: DDANAT
obofoundry: DDANAT
ols: ddanat
ontobee: DDANAT
prefixcommons: ddanat
name: Dictyostelium discoideum anatomy
pattern: ^\d{7}$
preferred_prefix: DDANAT
repository: https://github.com/dictyBase/migration-data
uri_format: http://purl.obolibrary.org/obo/DDANAT_$1
version: '2020-04-13'
ddpheno:
banana: DDPHENO
contact:
email: pfey@northwestern.edu
github: pfey03
name: Petra Fey
orcid: 0000-0002-4532-2703
description: A structured controlled vocabulary of phenotypes of the slime-mould
Dictyostelium discoideum.
download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo
download_owl: http://purl.obolibrary.org/obo/ddpheno.owl
example: '0001417'
homepage: http://dictybase.org/
license: CC0 1.0
mappings:
biocontext: DDPHENO
bioportal: DDPHENO
fairsharing: FAIRsharing.9c1p18
obofoundry: DDPHENO
ols: ddpheno
ontobee: DDPHENO
name: Dictyostelium discoideum phenotype ontology
pattern: ^\d{7}$
preferred_prefix: DDPHENO
repository: https://github.com/obophenotype/dicty-phenotype-ontology
uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1
version: '2020-06-19'
decipher:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: CNV syndromes in the DECIPHER genomics database that are linked to
Human Phenotype Ontology terms
example: '1'
homepage: https://www.deciphergenomics.org/
mappings:
biocontext: DECIPHER
fairsharing: FAIRsharing.l8Sf5x
name: DECIPHER CNV Syndromes
pattern: ^\d+$
preferred_prefix: decipher
references:
- https://www.deciphergenomics.org/redirect?to=https%3A%2F%2Fdx.doi.org%2F10.1016%2Fj.ajhg.2009.03.010
uri_format: https://www.deciphergenomics.org/syndrome/$1
degradome:
description: The Degradome Database contains information on the complete set of
predicted proteases present in a a variety of mammalian species that have been
subjected to whole genome sequencing. Each protease sequence is curated and, when
necessary, cloned and sequenced.
example: Ax1
homepage: http://degradome.uniovi.es/
mappings:
biocontext: DEGRADOME
miriam: degradome
n2t: degradome
name: Degradome Database
pattern: ^[AMCST][0-9x][0-9]$
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/$1
depod:
description: The human DEPhOsphorylation Database (DEPOD) contains information on
known human active phosphatases and their experimentally verified protein and
nonprotein substrates. Reliability scores are provided for dephosphorylation interactions,
according to the type of assay used, as well as the number of laboratories that
have confirmed such interaction. Phosphatase and substrate entries are listed
along with the dephosphorylation site, bioassay type, and original literature,
and contain links to other resources.
example: PTPN1
homepage: http://www.depod.bioss.uni-freiburg.de
mappings:
biocontext: DEPOD
fairsharing: FAIRsharing.q9j2e3
miriam: depod
n2t: depod
uniprot: DEPOD
name: Human Dephosphorylation Database
pattern: ^[A-Z0-9]+$
preferred_prefix: depod
provides: hgnc.symbol
uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1
dermo:
description: DermO is an ontology with broad coverage of the domain of dermatologic
disease and we demonstrate here its utility for text mining and investigation
of phenotypic relationships between dermatologic disorders
example: '0000000'
homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x
mappings:
bioportal: DERMO
fairsharing: FAIRsharing.k008w7
name: Human Dermatological Disease Ontology
pattern: ^\d{7}$
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:
biocontext: DEV.GA4GHDOS
miriam: dev.ga4ghdos
n2t: 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/$1
dg5b0d:
description: The Blood Profiling Atlas in Cancer (BloodPAC) supports the management,
analysis and sharing of liquid biopsy data for the oncology research community
and aims to accelerate discovery and development of therapies, diagnostic tests,
and other technologies for cancer treatment and prevention. The data commons supports
cross-project analyses by harmonizing data from different projects through the
collaborative development of a data dictionary, providing an API for data queries
and download, and providing a cloud-based analysis workspace with rich tools and
resources.
example: 00000d53-99bc-4d3e-8ed7-6dc358baccb7
homepage: https://data.bloodpac.org/.
mappings:
miriam: dg.5b0d
name: BloodPAC
pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
preferred_prefix: dg5b0d
uri_format: https://data.bloodpac.org/ga4gh/drs/v1/objects/$1
dgrc:
description: Cell line collections
example: '215'
homepage: https://dgrc.bio.indiana.edu/cells/Catalog
mappings:
cellosaurus: DGRC
name: Drosophila Genomics Resource Center
pattern: ^\d+$
preferred_prefix: dgrc
uri_format: https://dgrc.bio.indiana.edu/product/View?product=$1
dhba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
developing human brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo
example: '10153'
homepage: https://www.brainspan.org/
name: Developing Human Brain Atlas
pattern: ^\d+$
preferred_prefix: DHBA
dicom:
description: DICOM Controlled Terminology
download_owl: ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl
example: '109082'
homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html
mappings:
bioportal: DCM
fairsharing: FAIRsharing.b7z8by
ols: dicom
name: DICOM Controlled Terminology
pattern: ^\d+$
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:
biocontext: dictyBase
fairsharing: FAIRsharing.4shj9c
go: dictyBase
ncbi: dictyBase
prefixcommons: dictybase
uniprot: dictyBase
name: dictyBase
preferred_prefix: dictybase
synonyms:
- dictyBase
uri_format: http://dictybase.org/gene/$1
dictybase.est:
description: The dictyBase database provides data on the model organism Dictyostelium
discoideum and related species. It contains the complete genome sequence, ESTs,
gene models and functional annotations. This collection references expressed sequence
tag (EST) information.
example: DDB0016567
homepage: http://dictybase.org/
mappings:
biocontext: DICTYBASE.EST
miriam: dictybase.est
n2t: dictybase.est
name: dictyBase Expressed Sequence Tag
part_of: dictybase
pattern: ^DDB\d+$
preferred_prefix: dictybase.est
uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1
dictybase.gene:
description: The dictyBase database provides data on the model organism Dictyostelium
discoideum and related species. It contains the complete genome sequence, ESTs,
gene models and functional annotations. This collection references gene information.
example: DDB_G0267522
homepage: http://dictybase.org/
mappings:
biocontext: DICTYBASE.GENE
miriam: dictybase.gene
n2t: dictybase.gene
name: Dictybase Gene
part_of: dictybase
pattern: ^DDB_G\d+$
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:$1
dideo:
banana: DIDEO
contact:
email: mbrochhausen@gmail.com
github: mbrochhausen
name: Mathias Brochhausen
orcid: 0000-0003-1834-3856
description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
Evidence Ontology
download_owl: http://purl.obolibrary.org/obo/dideo.owl
example: 00000180
homepage: https://github.com/DIDEO/DIDEO
license: CC BY 4.0
mappings:
biocontext: DIDEO
bioportal: DIDEO
fairsharing: FAIRsharing.9y8f0n
obofoundry: DIDEO
ols: dideo
ontobee: DIDEO
name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
pattern: ^\d{8}$
preferred_prefix: DIDEO
repository: https://github.com/DIDEO/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.
download_owl: http://purl.obolibrary.org/obo/dinto.owl
homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto
license: CC BY 3.0
mappings:
biocontext: DINTO
bioportal: DINTO
obofoundry: DINTO
ontobee: DINTO
name: The Drug-Drug Interactions Ontology
preferred_prefix: DINTO
repository: https://github.com/labda/DINTO
uri_format: http://purl.obolibrary.org/obo/DINTO_$1
dip:
description: The database of interacting protein (DIP) database stores experimentally
determined interactions between proteins. It combines information from a variety
of sources to create a single, consistent set of protein-protein interactions
example: DIP-743N
homepage: https://dip.doe-mbi.ucla.edu/
mappings:
biocontext: DIP
fairsharing: FAIRsharing.qje0v8
miriam: dip
n2t: dip
prefixcommons: dip
uniprot: DIP
name: Database of Interacting Proteins
pattern: ^DIP(\:)?\-\d{1,}[ENXS]$
preferred_prefix: dip
uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1
discoverx:
description: Cell line collections
example: 95-0166C6
homepage: https://www.discoverx.com/products-applications/cell-lines
mappings:
cellosaurus: DiscoverX
name: DiscoverX cell line products
preferred_prefix: discoverx
uri_format: https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact
disdriv:
banana: DISDRIV
contact:
email: lynn.schriml@gmail.com
github: lschriml
name: Lynn Schriml
orcid: 0000-0001-8910-9851
description: Drivers of human diseases including environmental, maternal and social
exposures.
download_owl: http://purl.obolibrary.org/obo/disdriv.owl
example: '0000000'
homepage: http://www.disease-ontology.org
license: CC0 1.0
mappings:
bioportal: DISDRIV
obofoundry: DISDRIV
ols: disdriv
name: Disease Drivers Ontology
pattern: ^\d+$
preferred_prefix: DISDRIV
repository: https://github.com/DiseaseOntology/DiseaseDriversOntology
uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1
diseaseclass:
appears_in:
- efo
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: Legacy disease classes that later became MONDO
download_obo: https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo
example: 0000598
name: Disease Class
pattern: ^\d{7}$
preferred_prefix: diseaseclass
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
pattern: ^\d+$
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:
biocontext: DISPROT
fairsharing: FAIRsharing.dt9z89
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/$1
dmba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
developing mouse brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo
example: '688'
homepage: https://developingmouse.brain-map.org/
name: Developing Mouse Brain Atlas
pattern: ^\d+$
preferred_prefix: DMBA
doi:
comment: 'The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html)
specifies that `https://doi.org/DOI` is the preferred format:
> Users may resolve DOI names that are structured to use the DOI system Proxy
Server (https://doi.org (preferred)). The resolution of the DOI name in this case
depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would
be resolved from the address: "https://doi.org/10.123/456". Any standard browser
encountering a DOI name in this form will be able to resolve it. The proxy service
(both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible
over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**)
as well as HTTP requests.'
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:
biocontext: DOI
biolink: doi
cellosaurus: DOI
fairsharing: FAIRsharing.hFLKCn
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: dx_doi_http
description: An alternate provider from the DOI website using HTTP
homepage: https://www.doi.org
name: Digital Object Identifier
uri_format: http://dx.doi.org/$1
- code: dx_doi_https
description: An alternate provider from the DOI website using HTTPS
homepage: https://www.doi.org
name: Digital Object Identifier
uri_format: https://dx.doi.org/$1
- code: doi_http
description: An alternate provider from the DOI website using HTTP
homepage: https://www.doi.org
name: Digital Object Identifier
uri_format: http://doi.org/$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/doi/$1
references:
- https://github.com/biopragmatics/bioregistry/issues/287
- https://github.com/biopragmatics/bioregistry/pull/316
uri_format: https://doi.org/$1
doid:
appears_in:
- clo
- scdo
banana: DOID
contact:
email: lynn.schriml@gmail.com
github: lschriml
name: Lynn Schriml
orcid: 0000-0001-8910-9851
description: The Disease Ontology has been developed as a standardized ontology
for human disease with the purpose of providing the biomedical community with
consistent, reusable and sustainable descriptions of human disease terms, phenotype
characteristics and related medical vocabulary disease concepts.
download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo
download_owl: http://purl.obolibrary.org/obo/doid.owl
example: 0110974
homepage: http://www.disease-ontology.org
license: CC0 1.0
mappings:
biocontext: DOID
bioportal: DOID
fairsharing: FAIRsharing.8b6wfq
miriam: doid
n2t: doid
obofoundry: DOID
ols: doid
ontobee: DOID
prefixcommons: do
wikidata: P699
name: Human Disease Ontology
namespace_in_lui: true
pattern: ^\d+$
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
repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
synonyms:
- do
uri_format: https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1
version: '2022-04-28'
dommino:
description: DOMMINO is a database of macromolecular interactions that includes
the interactions between protein domains, interdomain linkers, N- and C-terminal
regions and protein peptides.
example: 2GC4
homepage: http://korkinlab.org/dommino
mappings:
biocontext: DOMMINO
miriam: dommino
n2t: dommino
name: Database of Macromolecular Interactions
pattern: ^[0-9][A-Za-z0-9]{3}$
preferred_prefix: dommino
uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1
door:
description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted
operons of all the sequenced prokaryotic genomes. It includes operons for RNA
genes.
example: '1398574'
homepage: http://csbl.bmb.uga.edu/DOOR/operon.php
mappings:
biocontext: DOOR
miriam: door
n2t: door
prefixcommons: door
name: Database for Prokaryotic Operons
pattern: ^\d+$
preferred_prefix: door
uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1
doqcs.model:
description: The Database of Quantitative Cellular Signaling is a repository of
models of signaling pathways. It includes reaction schemes, concentrations, rate
constants, as well as annotations on the models. The database provides a range
of search, navigation, and comparison functions. This datatype provides access
to specific models.
example: '57'
homepage: http://doqcs.ncbs.res.in/
mappings:
biocontext: DOQCS.MODEL
miriam: doqcs.model
n2t: doqcs.model
prefixcommons: doqcs.model
name: 'Database of Quantitative Cellular Signaling: Model'
part_of: doqcs
pattern: ^\d+$
preferred_prefix: doqcs.model
uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1
doqcs.pathway:
description: The Database of Quantitative Cellular Signaling is a repository of
models of signaling pathways. It includes reaction schemes, concentrations, rate
constants, as well as annotations on the models. The database provides a range
of search, navigation, and comparison functions. This datatype provides access
to pathways.
example: '131'
homepage: http://doqcs.ncbs.res.in/
mappings:
biocontext: DOQCS.PATHWAY
miriam: doqcs.pathway
n2t: doqcs.pathway
prefixcommons: doqcs.pathway
name: 'Database of Quantitative Cellular Signaling: Pathway'
part_of: doqcs
pattern: ^\d+$
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: 0000-0002-1373-1705
description: An ontology for the description of Drosophila melanogaster phenotypes.
download_json: http://purl.obolibrary.org/obo/dpo.json
download_obo: http://purl.obolibrary.org/obo/dpo.obo
download_owl: http://purl.obolibrary.org/obo/dpo.owl
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
repository: https://github.com/FlyBase/drosophila-phenotype-ontology
uri_format: http://purl.obolibrary.org/obo/FBcv_$1
version: '2022-04-13'
dpv:
description: Description of Plant Viruses (DPV) provides information about viruses,
viroids and satellites of plants, fungi and protozoa. It provides taxonomic information,
including brief descriptions of each family and genus, and classified lists of
virus sequences. The database also holds detailed information for all sequences
of viruses, viroids and satellites of plants, fungi and protozoa that are complete
or that contain at least one complete gene.
example: '100'
homepage: http://www.dpvweb.net/
mappings:
biocontext: DPV
miriam: dpv
n2t: dpv
name: Description of Plant Viruses
pattern: ^\d+$
preferred_prefix: dpv
uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1
dragondb.allele:
comment: Deprecated because the website is dead
deprecated: true
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
This collection refers to allele information.
example: cho
homepage: http://www.antirrhinum.net/
mappings:
biocontext: DRAGONDB.ALLELE
miriam: dragondb.allele
n2t: dragondb.allele
name: DragonDB Allele
part_of: dragondb
pattern: ^\w+$
preferred_prefix: dragondb.allele
uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele
dragondb.dna:
comment: Deprecated because the website is dead
deprecated: true
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
This collection refers to DNA sequence information.
example: 3hB06
homepage: http://www.antirrhinum.net/
mappings:
biocontext: DRAGONDB.DNA
miriam: dragondb.dna
n2t: dragondb.dna
name: DragonDB DNA
part_of: dragondb
pattern: ^\d\w+$
preferred_prefix: dragondb.dna
uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA
dragondb.locus:
comment: Deprecated because the website is dead
deprecated: true
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
This collection refers to Locus information.
example: DEF
homepage: http://www.antirrhinum.net/
mappings:
biocontext: DRAGONDB.LOCUS
miriam: dragondb.locus
n2t: dragondb.locus
name: DragonDB Locus
part_of: dragondb
pattern: ^\w+$
preferred_prefix: dragondb.locus
uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus
dragondb.protein:
comment: Deprecated because the website is dead
deprecated: true
description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon).
This collection refers to protein sequence information.
example: AMDEFA
homepage: http://www.antirrhinum.net/
mappings:
biocontext: DRAGONDB.PROTEIN
miriam: dragondb.protein
n2t: dragondb.protein
name: DragonDB Protein
part_of: dragondb
pattern: ^\w+$
preferred_prefix: dragondb.protein
uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide
dron:
appears_in:
- scdo
banana: DRON
contact:
email: hoganwr@gmail.com
github: hoganwr
name: William Hogan
orcid: 0000-0002-9881-1017
description: We built this ontology primarily to support comparative effectiveness
researchers studying claims data. They need to be able to query U.S. National
Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade),
physiological effect (diuresis), and therapeutic intent (anti-hypertensive).
download_owl: http://purl.obolibrary.org/obo/dron.owl
example: '00023232'
homepage: https://github.com/ufbmi/dron
license: CC BY 3.0
mappings:
biocontext: DRON
bioportal: DRON
fairsharing: FAIRsharing.w5ntfd
obofoundry: DRON
ols: dron
ontobee: DRON
name: The Drug Ontology
pattern: ^\d{8}$
preferred_prefix: DRON
repository: https://github.com/ufbmi/dron
uri_format: http://purl.obolibrary.org/obo/DRON_$1
version: '2022-04-22'
drsc:
description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of
reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen
results. It maintains a list of Drosophila gene names, identifiers, symbols and
synonyms and provides information for cell-based or in vivo RNAi reagents, other
types of reagents, screen results, etc. corresponding for a given gene.
example: DRSC05221
homepage: http://flyrnai.org/
mappings:
biocontext: DRSC
miriam: drsc
n2t: drsc
name: Drosophila RNAi Screening Center
pattern: ^DRSC\d+$
preferred_prefix: drsc
uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1
drugbank:
description: The DrugBank database is a bioinformatics and chemoinformatics resource
that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
This collection references drug information.
example: DB14938
homepage: http://www.drugbank.ca
mappings:
biocontext: DrugBank
cellosaurus: DrugBank
cheminf: '000406'
fairsharing: FAIRsharing.353yat
miriam: drugbank
n2t: drugbank
prefixcommons: drugbank
uniprot: DrugBank
wikidata: P715
name: DrugBank
pattern: ^DB\d{5}$
preferred_prefix: drugbank
synonyms:
- DRUGBANK_ID
- DrugBank
uri_format: http://www.drugbank.ca/drugs/$1
drugbank.salt:
description: DrugBank is a web-enabled database containing comprehensive molecular
information about drugs, their mechanisms, their interactions and their targets.
example: DBSALT001211
homepage: http://www.drugbank.ca
mappings:
biocontext: DRUGBANK.TARGET
name: DrugBank Salts
part_of: drugbank
pattern: ^DBSALT\d{6}$
preferred_prefix: drugbank.salt
synonyms:
- drugbank.target
uri_format: https://go.drugbank.com/salts/$1
drugbankv4.target:
description: The DrugBank database is a bioinformatics and chemoinformatics resource
that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
This collection references target information from version 4 of the database.
example: BE0000048
homepage: http://www.drugbank.ca/targets
mappings:
biocontext: DRUGBANKV4.TARGET
miriam: drugbankv4.target
n2t: drugbankv4.target
name: DrugBank Target v4
part_of: drugbank
pattern: ^BE\d{7}$
preferred_prefix: drugbankv4.target
uri_format: http://www.drugbank.ca/biodb/bio_entities/$1
drugcentral:
description: DrugCentral provides information on active ingredients chemical entities,
pharmaceutical products, drug mode of action, indications, pharmacologic action.
example: '307'
homepage: http://drugcentral.org
mappings:
biolink: DrugCentral
fairsharing: FAIRsharing.3me82d
uniprot: DrugCentral
name: Drug Central
pattern: ^\d+$
preferred_prefix: drugcentral
synonyms:
- Drug_Central
uri_format: http://drugcentral.org/drugcard/$1
dsmz:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/$1
dto:
appears_in:
- pr
description: 'DTO integrates and harmonizes knowledge of the most important druggable
protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.'
example: '90000018'
homepage: https://github.com/DrugTargetOntology/DTO
mappings:
bioportal: DTO
fairsharing: FAIRsharing.tke3y2
name: Drug Target Ontology
pattern: ^\d+$
preferred_prefix: dto
repository: https://github.com/DrugTargetOntology/DTO
duo:
appears_in:
- scdo
banana: DUO
contact:
email: mcourtot@gmail.com
github: mcourtot
name: Melanie Courtot
orcid: 0000-0002-9551-6370
depends_on:
- bfo
- iao
description: DUO is an ontology which represent data use conditions.
download_owl: http://purl.obolibrary.org/obo/duo.owl
example: '0000046'
homepage: https://github.com/EBISPOT/DUO
license: CC BY 4.0
mappings:
biocontext: DUO
bioportal: DUO
fairsharing: FAIRsharing.5dnjs2
obofoundry: DUO
ols: duo
ontobee: DUO
name: Data Use Ontology
pattern: ^\d{7}$
preferred_prefix: DUO
repository: https://github.com/EBISPOT/DUO
uri_format: http://purl.obolibrary.org/obo/DUO_$1
version: '2021-02-23'
eaglei:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
ebisc:
description: Cell line collections
example: ESi007-A
homepage: https://www.ebisc.org
mappings:
cellosaurus: EBiSC
name: European Bank for induced pluripotent Stem Cells
preferred_prefix: ebisc
uri_format: https://cells.ebisc.org/$1
ecacc:
description: The European Collection of Authenticated Cell Cultures (ECACC) is one
of four Culture Collections of Public Health England. We supply authenticated
and quality controlled cell lines, nucleic acids and induced Pluripotent Stem
Cells (iPSCs).
example: '90062901'
homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx
mappings:
cellosaurus: ECACC
name: European Collection of Authenticated Cell Culture
pattern: ^\d+$
preferred_prefix: ecacc
uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1
ecao:
banana: ECAO
contact:
email: ettensohn@cmu.edu
github: ettensohn
name: Charles Ettensohn
orcid: 0000-0002-3625-0955
depends_on:
- cl
- ro
- uberon
description: None
download_obo: http://purl.obolibrary.org/obo/ecao.obo
download_owl: http://purl.obolibrary.org/obo/ecao.owl
example: 0107180
homepage: https://github.com/echinoderm-ontology/ecao_ontology
license: CC BY 3.0
mappings:
bioportal: ECAO
obofoundry: ECAO
ols: ecao
ontobee: ECAO
name: The Echinoderm Anatomy and Development Ontology
pattern: ^\d{7}$
preferred_prefix: ECAO
repository: https://github.com/echinoderm-ontology/ecao_ontology
uri_format: http://purl.obolibrary.org/obo/ECAO_$1
version: '2020-05-22'
eccode:
description: The Enzyme Classification contains the recommendations of the Nomenclature
Committee of the International Union of Biochemistry and Molecular Biology on
the nomenclature and classification of enzyme-catalysed reactions.
example: 1.1.1.1
example_extras:
- '2'
- '2.3'
- 2.3.1
- 2.3.1.n12
- 3.1.26.n2
homepage: https://www.ebi.ac.uk/intenz/
mappings:
biocontext: EC
fairsharing: FAIRsharing.q1fdkc
go: EC
miriam: ec-code
n2t: ec-code
prefixcommons: intenz
wikidata: P591
name: Enzyme Nomenclature
pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$
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=$1
ecg:
description: The Electrocardiography (ECG) Ontology is a Driving Biological Project
of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms,
their capture method(s) and their waveforms.
example: 000000159
homepage: https://bioportal.bioontology.org/ontologies/ECG
mappings:
bioportal: ECG
fairsharing: FAIRsharing.azr389
name: Electrocardiogram Ontology
pattern: ^\d+$
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:
biocontext: ECHOBASE
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=$1
ecmdb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The ECMDB is an expertly curated database containing extensive metabolomic
data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655).
This database includes significant quantities of “original” data compiled by members
of the Wishart laboratory as well as additional material derived from hundreds
of textbooks, scientific journals, metabolic reconstructions and other electronic
databases. Each metabolite is linked to more than 100 data fields describing the
compound, its ontology, physical properties, reactions, pathways, references,
external links and associated proteins or enzymes.
example: ECMDB00005
homepage: https://ecmdb.ca
name: E. coli Metabolite Database
pattern: ^ECMDB\d+$
preferred_prefix: ecmdb
synonyms:
- ECMDB
uri_format: http://ecmdb.ca/compounds/$1
eco:
banana: ECO
contact:
email: mgiglio@som.umaryland.edu
github: mgiglio99
name: Michelle Giglio
orcid: 0000-0001-7628-5565
description: Evidence codes can be used to specify the type of supporting evidence
for a piece of knowledge. This allows inference of a 'level of support' between
an entity and an annotation made to an entity.
download_obo: http://purl.obolibrary.org/obo/eco.obo
download_owl: http://purl.obolibrary.org/obo/eco.owl
example: 0007807
homepage: https://github.com/evidenceontology/evidenceontology/
license: CC0 1.0
mappings:
biocontext: ECO
bioportal: ECO
fairsharing: FAIRsharing.wvpgwn
go: ECO
miriam: eco
n2t: eco
obofoundry: ECO
ols: eco
ontobee: ECO
prefixcommons: eco
name: Evidence ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: ECO
repository: https://github.com/evidenceontology/evidenceontology
uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1
version: '2022-04-11'
ecocore:
banana: ECOCORE
contact:
email: p.buttigieg@gmail.com
github: pbuttigieg
name: Pier Luigi Buttigieg
orcid: 0000-0002-4366-3088
depends_on:
- bfo
- chebi
- envo
- go
- iao
- pato
- pco
- po
- ro
- uberon
description: Ecocore is a community ontology for the concise and controlled description
of ecological traits of organisms.
download_obo: http://purl.obolibrary.org/obo/ecocore.obo
download_owl: http://purl.obolibrary.org/obo/ecocore.owl
example: '00000001'
homepage: https://github.com/EcologicalSemantics/ecocore
license: CC BY 3.0
mappings:
biocontext: ECOCORE
bioportal: ECOCORE
obofoundry: ECOCORE
ols: ecocore
ontobee: ECOCORE
name: An ontology of core ecological entities
pattern: ^\d+$
preferred_prefix: ECOCORE
repository: https://github.com/EcologicalSemantics/ecocore
uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1
version: '2022-03-09'
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:
fairsharing: FAIRsharing.65dmtr
go: EcoCyc
ncbi: ECOCYC
name: EcoCyc
preferred_prefix: ecocyc
uri_format: https://biocyc.org/gene?id=$1
ecogene:
description: The EcoGene database contains updated information about the E. coli
K-12 genome and proteome sequences, including extensive gene bibliographies. A
major EcoGene focus has been the re-evaluation of translation start sites.
example: EG10173
homepage: http://ecogene.org/
mappings:
biocontext: EcoGene
fairsharing: FAIRsharing.3q3kvn
miriam: ecogene
n2t: ecogene
ncbi: EcoGene
prefixcommons: ecogene
name: Database of Escherichia coli Sequence and Function
pattern: ^EG\d+$
preferred_prefix: ecogene
uri_format: http://www.ecogene.org/gene/$1
ecolexicon:
comment: No resolution - everything is in a single page app
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: EcoLexicon represents the conceptual structure of the specialized domain
of the Environment in the form of a visual thesaurus. This thesaurus has been
elaborated according to the theoretical premises of Frame-Based Terminology.
example: canal
homepage: http://ecolexicon.ugr.es/en/index.htm
name: EcoLexicon
preferred_prefix: ecolexicon
ecoliwiki:
description: EcoliWiki is a wiki-based resource to store information related to
non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This
collection references genes.
example: aaeA
homepage: http://ecoliwiki.net/colipedia/
mappings:
biocontext: ECOLIWIKI
fairsharing: FAIRsharing.tx95wa
go: EcoliWiki
miriam: ecoliwiki
n2t: ecoliwiki
name: EcoliWiki from EcoliHub
pattern: ^[A-Za-z0-9-]+$
preferred_prefix: ecoliwiki
uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene
ecto:
banana: ECTO
contact:
email: annethessen@gmail.com
github: diatomsRcool
name: Anne Thessen
orcid: 0000-0002-2908-3327
depends_on:
- chebi
- envo
- exo
- go
- iao
- maxo
- nbo
- ncbitaxon
- ncit
- pato
- ro
- uberon
- xco
description: ECTO describes exposures to experimental treatments of plants and model
organisms (e.g. exposures to modification of diet, lighting levels, temperature);
exposures of humans or any other organisms to stressors through a variety of routes,
for purposes of public health, environmental monitoring etc, stimuli, natural
and experimental, any kind of environmental condition or change in condition that
can be experienced by an organism or population of organisms on earth. The scope
is very general and can include for example plant treatment regimens, as well
as human clinical exposures (although these may better be handled by a more specialized
ontology).
download_json: http://purl.obolibrary.org/obo/ecto.json
download_obo: http://purl.obolibrary.org/obo/ecto.obo
download_owl: http://purl.obolibrary.org/obo/ecto.owl
example: '0000001'
homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
license: CC0 1.0
mappings:
biolink: ECTO
bioportal: ECTO
obofoundry: ECTO
ols: ecto
ontobee: ECTO
name: Environmental conditions, treatments and exposures ontology
pattern: ^\d{7}$
preferred_prefix: ECTO
repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology
uri_format: http://purl.obolibrary.org/obo/ECTO_$1
version: '2021-08-25'
ecyano.entity:
description: E-cyanobacterium.org is a web-based platform for public sharing, annotation,
analysis, and visualisation of dynamical models and wet-lab experiments related
to cyanobacteria. It allows models to be represented at different levels of abstraction
— as biochemical reaction networks or ordinary differential equations.It provides
concise mappings of mathematical models to a formalised consortium-agreed biochemical
description, with the aim of connecting the world of biological knowledge with
benefits of mathematical description of dynamic processes. This collection references
entities.
example: '23'
homepage: http://www.e-cyanobacterium.org/bcs/entity/
mappings:
biocontext: ECYANO.ENTITY
miriam: ecyano.entity
n2t: ecyano.entity
name: E-cyanobacterium entity
part_of: ecyano
pattern: ^\d+$
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=$1
ecyano.model:
description: E-cyanobacterium.org is a web-based platform for public sharing, annotation,
analysis, and visualisation of dynamical models and wet-lab experiments related
to cyanobacteria. It allows models to be represented at different levels of abstraction
— as biochemical reaction networks or ordinary differential equations.It provides
concise mappings of mathematical models to a formalised consortium-agreed biochemical
description, with the aim of connecting the world of biological knowledge with
benefits of mathematical description of dynamic processes. This collection references
models.
example: '26'
homepage: http://e-cyanobacterium.org/models/
mappings:
biocontext: ECYANO.MODEL
miriam: ecyano.model
n2t: ecyano.model
name: E-cyanobacterium model
pattern: ^\d+$
preferred_prefix: ecyano.model
uri_format: https://e-cyanobacterium.org/models/model/$1
ecyano.rule:
description: E-cyanobacterium.org is a web-based platform for public sharing, annotation,
analysis, and visualisation of dynamical models and wet-lab experiments related
to cyanobacteria. It allows models to be represented at different levels of abstraction
— as biochemical reaction networks or ordinary differential equations.It provides
concise mappings of mathematical models to a formalised consortium-agreed biochemical
description, with the aim of connecting the world of biological knowledge with
benefits of mathematical description of dynamic processes. This collection references
rules.
example: '56'
homepage: http://www.e-cyanobacterium.org/bcs/rule/
mappings:
biocontext: ECYANO.RULE
miriam: ecyano.rule
n2t: ecyano.rule
name: E-cyanobacterium rule
part_of: ecyano
pattern: ^\d+$
preferred_prefix: ecyano.rule
uri_format: https://e-cyanobacterium.org/bcs/rule/$1
edam:
description: 'EDAM is an ontology of general bioinformatics concepts, including
topics, data types, formats, identifiers and operations. EDAM provides a controlled
vocabulary for the description, in semantic terms, of things such as: web services
(e.g. WSDL files), applications, tool collections and packages, work-benches and
workflow software, databases and ontologies, XSD data schema and data objects,
data syntax and file formats, web portals and pages, resource catalogues and documents
(such as scientific publications).'
download_owl: https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl
example: data_1664
homepage: http://edamontology.org
mappings:
biocontext: EDAM
bioportal: EDAM
fairsharing: FAIRsharing.a6r7zs
miriam: edam
n2t: edam
ols: edam
ontobee: EDAM
prefixcommons: edam
name: Bioinformatics operations, data types, formats, identifiers and topics
pattern: ^(data|topic|operation|format)\_\d{4}$
preferred_prefix: edam
uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1
version: '2019-07-17'
edda:
description: Coverage of the terminology appearing in JMLA was extended with terms
from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international
repository for health technology assessment], and Robert Sandieson's synonym ring
for research synthesis. Collected terms were enriched with terms from the NCI
Metathesaurus. Variants include synonyms for preferred terms, singular and plural
forms, and American and British spellings. Definitions, if they exist, are mainly
from MeSH, NCI, Emtree, and medical dictionaries.
example: health_care_quality_assessment
homepage: https://bioportal.bioontology.org/ontologies/EDDA
mappings:
bioportal: EDDA
fairsharing: FAIRsharing.2ffmsb
name: EDDA Study Designs Taxonomy
preferred_prefix: edda
efo:
contact:
email: plwhetzel@gmail.com
github: twhetzel
name: Trish Whetzel
orcid: 0000-0002-3458-4839
description: The Experimental Factor Ontology (EFO) provides a systematic description
of many experimental variables available in EBI databases. It combines parts of
several biological ontologies, such as anatomy, disease and chemical compounds.
The scope of EFO is to support the annotation, analysis and visualization of data
handled by the EBI Functional Genomics Team.
download_obo: http://www.ebi.ac.uk/efo/efo.obo
download_owl: http://www.ebi.ac.uk/efo/releases/v3.42.0/efo.owl
example: '0005147'
homepage: http://www.ebi.ac.uk/efo
mappings:
biocontext: EFO
biolink: EFO
bioportal: EFO
cellosaurus: EFO
fairsharing: FAIRsharing.1gr4tz
miriam: efo
n2t: efo
ols: efo
ontobee: EFO
name: Experimental Factor Ontology
pattern: ^\d{7}$
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
repository: https://github.com/EBISPOT/efo/
uri_format: http://www.ebi.ac.uk/efo/EFO_$1
version: 3.42.0
ega.dataset:
description: The EGA is a service for permanent archiving and sharing of all types
of personally identifiable genetic and phenotypic data resulting from biomedical
research projects. The EGA contains exclusive data collected from individuals
whose consent agreements authorize data release only for specific research use
or to bona fide researchers. Strict protocols govern how information is managed,
stored and distributed by the EGA project. This collection references 'Datasets'.
example: EGAD00000000001
homepage: https://ega-archive.org/
mappings:
biocontext: EGA.DATASET
fairsharing: FAIRsharing.mya1ff
miriam: ega.dataset
n2t: ega.dataset
name: European Genome-phenome Archive Dataset
pattern: ^EGAD\d{11}$
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/$1
ega.study:
description: The EGA is a service for permanent archiving and sharing of all types
of personally identifiable genetic and phenotypic data resulting from biomedical
research projects. The EGA contains exclusive data collected from individuals
whose consent agreements authorize data release only for specific research use
or to bona fide researchers. Strict protocols govern how information is managed,
stored and distributed by the EGA project. This collection references 'Studies'
which are experimental investigations of a particular phenomenon, often drawn
from different datasets.
example: EGAS00000000001
homepage: https://www.ebi.ac.uk/ega/studies
mappings:
biocontext: EGA.STUDY
miriam: ega.study
n2t: ega.study
name: European Genome-phenome Archive Study
pattern: ^EGAS\d{11}$
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/$1
eggnog:
description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
Groups) is a database of orthologous groups of genes. The orthologous groups are
annotated with functional description lines (derived by identifying a common denominator
for the genes based on their various annotations), with functional categories
(i.e derived from the original COG/KOG categories).'
example: veNOG12876
homepage: http://eggnog.embl.de/version_3.0/
mappings:
biocontext: EGGNOG
fairsharing: FAIRsharing.j1wj7d
miriam: eggnog
n2t: eggnog
prefixcommons: eggnog
uniprot: eggNOG
name: eggNOG
pattern: ^\w+$
preferred_prefix: eggnog
uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1
ehda:
banana: EHDA
contact:
email: J.Bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
deprecated: true
example: '1'
homepage: http://genex.hgu.mrc.ac.uk/
mappings:
biocontext: EHDA
bioportal: EHDA
obofoundry: EHDA
prefixcommons: ehda
name: Human developmental anatomy, timed version
pattern: ^\d+$
preferred_prefix: EHDA
uri_format: http://purl.obolibrary.org/obo/EHDA_$1
ehdaa:
banana: EHDAA
contact:
email: J.Bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
deprecated: true
example: '1'
mappings:
biocontext: EHDAA
bioportal: EHDAA
obofoundry: EHDAA
prefixcommons: ehdaa
name: Human developmental anatomy, abstract version
pattern: ^\d+$
preferred_prefix: EHDAA
uri_format: http://purl.obolibrary.org/obo/EHDAA_$1
ehdaa2:
banana: EHDAA2
contact:
email: J.Bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
depends_on:
- aeo
- caro
- cl
description: A structured controlled vocabulary of stage-specific anatomical structures
of the developing human.
download_obo: http://purl.obolibrary.org/obo/ehdaa2.obo
download_owl: http://purl.obolibrary.org/obo/ehdaa2.owl
example: '0000000'
homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology
license: CC BY 4.0
mappings:
biocontext: EHDAA2
bioportal: EHDAA2
fairsharing: FAIRsharing.7zxrs6
obofoundry: EHDAA2
ols: ehdaa2
ontobee: EHDAA2
name: Human developmental anatomy, abstract
pattern: ^\d{7}$
preferred_prefix: EHDAA2
repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
synonyms:
- EHDAA2_RETIRED
- HDAA2
- RETIRED_EHDAA2
uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1
version: '2013-07-04'
elm:
description: Linear motifs are short, evolutionarily plastic components of regulatory
proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif
resource (ELM) is a database of curated motif classes and instances.
example: CLV_MEL_PAP_1
homepage: http://elm.eu.org/
mappings:
biocontext: ELM
fairsharing: FAIRsharing.rj3kj5
miriam: elm
n2t: elm
uniprot: ELM
name: Eukaryotic Linear Motif Resource
pattern: ^[A-Za-z_0-9]+$
preferred_prefix: elm
uri_format: http://elm.eu.org/elms/elmPages/$1.html
emap:
banana: EMAP
contact:
email: Terry.Hayamizu@jax.org
github: tfhayamizu
name: Terry Hayamizu
orcid: 0000-0002-0956-8634
deprecated: true
description: A structured controlled vocabulary of stage-specific anatomical structures
of the mouse (Mus).
download_owl: http://purl.obolibrary.org/obo/emap.owl
example: '1'
homepage: http://emouseatlas.org
mappings:
biocontext: EMAP
bioportal: EMAP
obofoundry: EMAP
name: Mouse gross anatomy and development, timed
pattern: ^\d+$
preferred_prefix: EMAP
uri_format: http://purl.obolibrary.org/obo/EMAP_$1
emapa:
banana: EMAPA
contact:
email: Terry.Hayamizu@jax.org
github: tfhayamizu
name: Terry Hayamizu
orcid: 0000-0002-0956-8634
description: An ontology for mouse anatomy covering embryonic development and postnatal
stages.
download_obo: http://purl.obolibrary.org/obo/emapa.obo
download_owl: http://purl.obolibrary.org/obo/emapa.owl
example: '26753'
homepage: http://www.informatics.jax.org/expression.shtml
license: CC BY 4.0
mappings:
biocontext: EMAPA
bioportal: EMAPA
fairsharing: FAIRsharing.j0fa1d
go: EMAPA
obofoundry: EMAPA
ols: emapa
ontobee: EMAPA
name: Mouse Developmental Anatomy Ontology
pattern: ^\d+$
preferred_prefix: EMAPA
repository: https://github.com/obophenotype/mouse-anatomy-ontology
synonyms:
- EMAPA_RETIRED
uri_format: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1
version: '2021-09-01'
emdb:
description: The Electron Microscopy Data Bank (EMDB) is a public repository for
electron microscopy density maps of macromolecular complexes and subcellular structures.
It covers a variety of techniques, including single-particle analysis, electron
tomography, and electron (2D) crystallography. The EMDB map distribution format
follows the CCP4 definition, which is widely recognized by software packages used
by the structural biology community.
example: EMD-1001
homepage: https://www.ebi.ac.uk/pdbe/emdb/
mappings:
biocontext: EMDB
fairsharing: FAIRsharing.651n9j
miriam: emdb
n2t: emdb
name: Electron Microscopy Data Bank
pattern: ^EMD-\d{4}$
preferred_prefix: emdb
uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1
emolecules:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Catalog of purchasable reagents and building blocks
example: '491187'
homepage: https://reaxys.emolecules.com
name: Reaxys eMolecules
pattern: ^\d+$
preferred_prefix: emolecules
uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1
empiar:
description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource
for raw, 2D electron microscopy images. Here, you can browse, upload and download
the raw images used to build a 3D structure
example: '10595'
homepage: https://www.ebi.ac.uk/pdbe/emdb
mappings:
fairsharing: FAIRsharing.dff3ef
name: Electron Microscopy Public Image Archive
pattern: ^\d+$
preferred_prefix: empiar
uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1
ena.embl:
description: The European Nucleotide Archive (ENA) captures and presents information
relating to experimental workflows that are based around nucleotide sequencing.
ENA is made up of a number of distinct databases that includes EMBL-Bank, the
Sequence Read Archive (SRA) and the Trace Archive each with their own data formats
and standards. This collection references Embl-Bank identifiers.
example: BN000065
homepage: https://www.ebi.ac.uk/ena/
mappings:
biocontext: ENA.EMBL
fairsharing: FAIRsharing.dj8nt8
go: ENA
miriam: ena.embl
n2t: ena.embl
prefixcommons: ena
name: European Nucleotide Archive
pattern: ^[A-Z]+[0-9]+(\.\d+)?$
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/$1
encode:
description: The ENCODE Consortium is integrating multiple technologies and approaches
in a collective effort to discover and define the functional elements encoded
in the human genome, including genes, transcripts, and transcriptional regulatory
regions, together with their attendant chromatin states and DNA methylation patterns.
example: ENCSR163RYW
homepage: https://www.encodeproject.org
mappings:
biocontext: ENCODE
cellosaurus: ENCODE
fairsharing: FAIRsharing.v0hbjs
miriam: encode
n2t: encode
name: Encyclopedia of DNA Elements
pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$
preferred_prefix: encode
uri_format: https://www.encodeproject.org/$1
enm:
description: 'The eNanoMapper project (www.enanomapper.net) is creating a pan-European
computational infrastructure for toxicological data management for ENMs, based
on semantic web standards and ontologies. > This ontology is an application ontology
targeting the full domain of nanomaterial safety assessment. It re-uses several
other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. '
download_owl: http://enanomapper.github.io/ontologies/enanomapper.owl
example: '8000221'
homepage: http://www.enanomapper.net/
mappings:
bioportal: ENM
fairsharing: FAIRsharing.2gpf81
ols: enm
name: eNanoMapper Ontology
pattern: ^\d+$
preferred_prefix: enm
version: '7.3'
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
example_extras:
- ENSG00000049246.14
- ENSG00000109819.9
- ENSG00000132326.12
- ENSG00000179094.16
- ENST00000264867.7
homepage: https://www.ensembl.org/
mappings:
biocontext: ENSEMBL
fairsharing: FAIRsharing.fx0mw7
go: ENSEMBL
miriam: ensembl
n2t: ensembl
ncbi: ENSEMBL
prefixcommons: ensembl
uniprot: Ensembl
wikidata: P594
name: Ensembl Gene
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: opentargets.genetics
description: Open Targets Genetics is a comprehensive tool highlighting variant-centric
statistical evidence to allow both prioritisation of candidate causal variants
at trait-associated loci and identification of potential drug targets.
homepage: https://genetics.opentargets.org
name: OpenTargets Genetics
uri_format: https://genetics.opentargets.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/$1
ensembl.bacteria:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with bacterial
genomes.
example: MU9_3181
homepage: https://bacteria.ensembl.org/
mappings:
biocontext: ENSEMBL.BACTERIA
fairsharing: FAIRsharing.zsgmvd
miriam: ensembl.bacteria
n2t: ensembl.bacteria
prefixcommons: ensembl.bacteria
uniprot: EnsemblBacteria
name: Ensembl Bacteria
pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$
preferred_prefix: ensembl.bacteria
uri_format: https://bacteria.ensembl.org/id/$1
ensembl.fungi:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.
example: CADAFLAT00006211
homepage: https://fungi.ensembl.org/
mappings:
biocontext: ENSEMBL.FUNGI
fairsharing: FAIRsharing.bg5xqs
go: EnsemblFungi
miriam: ensembl.fungi
n2t: ensembl.fungi
prefixcommons: ensembl.fungi
uniprot: EnsemblFungi
name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
pattern: ^[A-Z-a-z0-9]+$
preferred_prefix: ensembl.fungi
uri_format: https://fungi.ensembl.org/id/$1
ensembl.metazoa:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes.
example: FBtr0084214
homepage: https://metazoa.ensembl.org/
mappings:
biocontext: ENSEMBL.METAZOA
fairsharing: FAIRsharing.c23cqq
go: EnsemblMetazoa
miriam: ensembl.metazoa
n2t: ensembl.metazoa
prefixcommons: ensembl.metazoa
uniprot: EnsemblMetazoa
name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from
non-vertebrate metazoa.
pattern: ^\w+(\.)?\d+$
preferred_prefix: ensembl.metazoa
uri_format: https://metazoa.ensembl.org/id/$1
ensembl.plant:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.
example: AT1G73965
homepage: https://plants.ensembl.org/
mappings:
biocontext: ENSEMBL.PLANT
miriam: ensembl.plant
n2t: ensembl.plant
prefixcommons: ensembl.plant
name: Ensembl Plants
pattern: ^\w+(\.\d+)?(\.\d+)?$
preferred_prefix: ensembl.plant
uri_format: https://plants.ensembl.org/id/$1
ensembl.protist:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with protist genomes.
example: PF3D7_1328700
homepage: https://protists.ensembl.org
mappings:
biocontext: ENSEMBL.PROTIST
miriam: ensembl.protist
n2t: ensembl.protist
prefixcommons: ensembl.protist
name: Ensembl Protists
pattern: ^\w+$
preferred_prefix: ensembl.protist
uri_format: https://protists.ensembl.org/id/$1
ensemblglossary:
description: The Ensembl glossary lists the terms, data types and file types that
are used in Ensembl and describes how they are used.
download_owl: http://ensembl.org/glossary/ensembl-glossary/releases/2021-07-14/ensembl-glossary.owl
example: 0000198
homepage: http://ensembl.org/glossary
mappings:
ols: ensemblglossary
name: Ensembl Glossary
pattern: ^\d{7}$
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:
fairsharing: FAIRsharing.g0c5qn
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/$1
envo:
appears_in:
- agro
- cdno
- ecocore
- ecto
- foodon
- ons
- pco
- rbo
- scdo
banana: ENVO
contact:
email: p.buttigieg@gmail.com
github: pbuttigieg
name: Pier Luigi Buttigieg
orcid: 0000-0002-4366-3088
depends_on:
- chebi
- foodon
- go
- ncbitaxon
- pco
- po
- ro
- uberon
description: The Environment Ontology is a resource and research target for the
semantically controlled description of environmental entities. The ontology's
initial aim was the representation of the biomes, environmental features, and
environmental materials pertinent to genomic and microbiome-related investigations.
download_json: http://purl.obolibrary.org/obo/envo.json
download_obo: http://purl.obolibrary.org/obo/envo.obo
download_owl: http://purl.obolibrary.org/obo/envo.owl
example: 09200010
homepage: http://environmentontology.org/
license: CC BY 3.0
mappings:
biocontext: ENVO
bioportal: ENVO
fairsharing: FAIRsharing.azqskx
miriam: envo
n2t: envo
obofoundry: ENVO
ols: envo
ontobee: ENVO
name: Environment Ontology
namespace_in_lui: true
pattern: ^\d{7,8}$
preferred_prefix: ENVO
repository: https://github.com/EnvironmentOntology/envo
uri_format: https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1
version: '2021-05-14'
enzo:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/$1
eo:
appears_in:
- foodon
banana: EO
contact:
email: jaiswalp@science.oregonstate.edu
github: jaiswalp
name: Pankaj Jaiswal
orcid: 0000-0002-1005-8383
deprecated: true
description: The Plant Environment Ontology is a set of standardized controlled
vocabularies to describe various types of treatments given to an individual plant
/ a population or a cultured tissue and/or cell type sample to evaluate the response
on its exposure. It also includes the study types, where the terms can be used
to identify the growth study facility. Each growth facility such as field study,
growth chamber, green house etc is a environment on its own it may also involve
instances of biotic and abiotic environments as supplemental treatments used in
these studies.
download_obo: http://purl.obolibrary.org/obo/eo.obo
download_owl: http://purl.obolibrary.org/obo/eo.owl
example: '0007404'
homepage: http://planteome.org/
license: CC BY 4.0
mappings:
biocontext: EO
miriam: eo
n2t: eo
obofoundry: EO
prefixcommons: eo
name: Plant Environment Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: EO
repository: https://github.com/Planteome/plant-environment-ontology
uri_format: http://archive.gramene.org/db/ontology/search?query=EO:$1
eol:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The EOL ontology describes environmental conditions of livestock farms.
More specifically, it describes the feeding modalities, the environment, the structure
of livestock farms and rearing systems.
download_owl: https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl
example: 0001927
homepage: http://www.atol-ontology.com
mappings:
bioportal: EOL
fairsharing: FAIRsharing.w7bw2y
ols: eol
name: Environment Ontology for Livestock
pattern: ^\d{7}$
preferred_prefix: eol
version: '2018-09-13'
eolife:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A collaborative project intended to create an encyclopedia documenting
all living species known to science
example: '1044544'
homepage: https://eol.org
mappings:
fairsharing: FAIRsharing.3J6NYn
wikidata: P830
name: Encyclopedia of Life
pattern: ^\d+$
preferred_prefix: eolife
uri_format: https://eol.org/pages/$1
epcc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Collection of European paediatric cardiac coding files
homepage: https://www.aepc.org/european-paediatric-cardiac-coding
name: European Paediatric Cardiac Codes
preferred_prefix: epcc
proprietary: true
references:
- https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE
epd:
description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant
collection of eukaryotic POL II promoters, for which the transcription start site
has been determined experimentally. Access to promoter sequences is provided by
pointers to positions in nucleotide sequence entries. The annotation part of an
entry includes description of the initiation site mapping data, cross-references
to other databases, and bibliographic references. EPD is structured in a way that
facilitates dynamic extraction of biologically meaningful promoter subsets for
comparative sequence analysis.
example: TA_H3
homepage: http://epd.vital-it.ch/
mappings:
biocontext: EPD
fairsharing: FAIRsharing.sym4ne
miriam: epd
n2t: epd
ncbi: EPD
uniprot: EPD
name: Eukaryotic Promoter Database
pattern: ^[A-Z-_0-9]+$
preferred_prefix: epd
uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1
epio:
banana: EPIO
contact:
email: alpha.tom.kodamullil@scai.fraunhofer.de
github: akodamullil
name: Alpha Tom Kodamullil
orcid: 0000-0001-9896-3531
depends_on:
- bfo
description: A application driven Epilepsy Ontology with official terms from the
ILAE.
download_owl: http://purl.obolibrary.org/obo/epio.owl
example: '0000011'
homepage: https://github.com/SCAI-BIO/EpilepsyOntology
license: CC BY 4.0
mappings:
bioportal: EPIO
obofoundry: EPIO
ontobee: EPIO
name: Epilepsy Ontology
pattern: ^\d{7}$
preferred_prefix: EPIO
repository: https://github.com/SCAI-BIO/EpilepsyOntology
uri_format: http://purl.obolibrary.org/obo/EPIO_$1
epo:
banana: EPO
deprecated: true
description: An ontology designed to support the semantic annotation of epidemiology
resources
download_owl: https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl
homepage: https://code.google.com/p/epidemiology-ontology/
mappings:
biocontext: EPO
bioportal: EPO
obofoundry: EPO
ontobee: EPO
name: Epidemiology Ontology
preferred_prefix: EPO
uri_format: http://purl.obolibrary.org/obo/EPO_$1
epso:
description: 'The Epilepsy and Seizure Ontology (EpSO) is an application ontology
developed to support epilepsy focused informatics tools for patient care and clinical
research. '
example: '0000400'
homepage: http://prism.case.edu/prism/index.php/EpilepsyOntology
mappings:
bioportal: EPSO
fairsharing: FAIRsharing.ttprgy
ontobee: EPSO
name: Epilepsy and Seizure Ontology
pattern: ^\d{7}$
preferred_prefix: epso
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#$1
ero:
banana: ERO
contact:
email: Marc_Ciriello@hms.harvard.edu
github: null
name: Marc Ciriello
orcid: null
deprecated: true
description: An ontology of research resources such as instruments. protocols, reagents,
animal models and biospecimens.
download_owl: http://purl.obolibrary.org/obo/ero.owl
example: '0001655'
homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
license: CC BY 2.0
mappings:
biocontext: ERO
bioportal: ERO
fairsharing: FAIRsharing.nwgynk
obofoundry: ERO
ols: ero
ontobee: ERO
name: eagle-i resource ontology
pattern: ^\d{7}$
preferred_prefix: ERO
uri_format: http://purl.obolibrary.org/obo/ERO_$1
version: '2016-07-27'
erv:
description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a
typical mammalian genome contains tens to hundreds of thousands of ERV elements.
Most ERVs are evolutionarily old and have accumulated multiple mutations, playing
important roles in physiology and disease processes. The Human Endogenous Retrovirus
Database (hERV) is compiled from the human genome nucleotide sequences obtained
from Human Genome Projects, and screens those sequences for hERVs, whilst continuously
improving classification and characterization of retroviral families. It provides
access to individual reconstructed HERV elements, their sequence, structure and
features.
example: THE1B
homepage: https://herv.img.cas.cz/
mappings:
biocontext: ERV
miriam: erv
n2t: erv
name: Human Endogenous Retrovirus Database
pattern: ^[A-Za-z0-9\-\_]+$
preferred_prefix: erv
uri_format: https://herv.img.cas.cz/s/$1
estdab:
comment: Website is dead
deprecated: true
description: Cell line databases/resources
example: '046'
homepage: https://www.ebi.ac.uk/ipd/estdab/
mappings:
cellosaurus: ESTDAB
name: European Searchable Tumour Line Database
pattern: ^\d{3}$
preferred_prefix: estdab
uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1
eu89h:
description: The JRC Data Catalogue gives access to the multidisciplinary data produced
and maintained by the Joint Research Centre, the European Commission's in-house
science service providing independent scientific advice and support to policies
of the European Union.
example: jrc-eurl-ecvam-chemagora
homepage: http://data.jrc.ec.europa.eu/
mappings:
biocontext: EU89H
miriam: eu89h
n2t: eu89h
name: JRC Data Catalogue
pattern: ^[a-z0-9\-_]+$
preferred_prefix: eu89h
uri_format: http://data.europa.eu/89h/$1
euclinicaltrials:
description: "The EU Clinical Trials Register contains information on clinical trials\
\ conducted in the European Union (EU), or the European Economic Area (EEA) which\
\ started after 1 May 2004.\r\nIt also includes trials conducted outside these\
\ areas if they form part of a paediatric investigation plan (PIP), or are sponsored\
\ by a marketing authorisation holder, and involve the use of a medicine in the\
\ paediatric population."
example: 2008-005144-16
homepage: https://www.clinicaltrialsregister.eu/
mappings:
biocontext: EUCLINICALTRIALS
miriam: euclinicaltrials
n2t: euclinicaltrials
name: EU Clinical Trials
pattern: ^\d{4}\-\d{6}\-\d{2}$
preferred_prefix: euclinicaltrials
uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1
eupath:
appears_in:
- scdo
banana: EUPATH
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
description: The VEuPathDB ontology is an application ontology developed to encode
our understanding of what data is about in the public resources developed and
maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB;
https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB
ontology prior to EuPathDB joining with VectorBase.The ontology was built based
on the Ontology of Biomedical Investigations (OBI) with integration of other OBO
ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the
VEuPath ontology is primarily intended to be used for support of the VEuPathDB
sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will
be submitted to OBO Foundry ontologies for subsequent import and replacement of
those terms when they are available.
download_owl: http://purl.obolibrary.org/obo/eupath.owl
example: '0010316'
homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
license: CC BY 4.0
mappings:
biocontext: EUPATH
bioportal: EUPATH
fairsharing: FAIRsharing.9rhr9j
obofoundry: EUPATH
ols: eupath
ontobee: EUPATH
name: VEuPathDB ontology
pattern: ^\d{7}$
preferred_prefix: EUPATH
repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
uri_format: http://purl.obolibrary.org/obo/EUPATH_$1
version: '2022-02-15'
eurofir:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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:
appears_in:
- cl
banana: EV
contact:
email: evoc@sanbi.ac.za
github: null
name: eVOC mailing list
orcid: null
deprecated: true
homepage: http://www.evocontology.org/
mappings:
biocontext: EV
obofoundry: 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_$1
evm:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
name: eVOC mouse development stage
preferred_prefix: evm
references:
- https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229
exac.gene:
description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
sequencing projects, and to make summary data available for the wider scientific
community. The data pertains to unrelated individuals sequenced as part of various
disease-specific and population genetic studies and serves as a reference set
of allele frequencies for severe disease studies. This collection references gene
information.
example: ENSG00000169174
homepage: http://exac.broadinstitute.org/
mappings:
biocontext: EXAC.GENE
miriam: exac.gene
n2t: exac.gene
name: ExAC Gene
pattern: ^ENSG\d{11}$
preferred_prefix: exac.gene
uri_format: http://exac.broadinstitute.org/gene/$1
exac.transcript:
description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
sequencing projects, and to make summary data available for the wider scientific
community. The data pertains to unrelated individuals sequenced as part of various
disease-specific and population genetic studies and serves as a reference set
of allele frequencies for severe disease studies. This collection references transcript
information.
example: ENST00000407236
homepage: http://exac.broadinstitute.org/
mappings:
biocontext: EXAC.TRANSCRIPT
miriam: exac.transcript
n2t: exac.transcript
name: ExAC Transcript
pattern: ^ENST\d{11}$
preferred_prefix: exac.transcript
uri_format: http://exac.broadinstitute.org/transcript/$1
exac.variant:
description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
sequencing projects, and to make summary data available for the wider scientific
community. The data pertains to unrelated individuals sequenced as part of various
disease-specific and population genetic studies and serves as a reference set
of allele frequencies for severe disease studies. This collection references variant
information.
example: 22-46615880-T-C
homepage: http://exac.broadinstitute.org/
mappings:
biocontext: EXAC.VARIANT
miriam: exac.variant
n2t: exac.variant
name: ExAC Variant
pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$
preferred_prefix: exac.variant
uri_format: http://exac.broadinstitute.org/variant/$1
exo:
appears_in:
- ecto
- scdo
banana: ExO
contact:
email: annethessen@gmail.com
github: diatomsRcool
name: Anne Thessen
orcid: 0000-0002-2908-3327
description: ExO is intended to bridge the gap between exposure science and diverse
environmental health disciplines including toxicology, epidemiology, disease surveillance,
and epigenetics.
download_obo: http://purl.obolibrary.org/obo/exo.obo
download_owl: http://purl.obolibrary.org/obo/exo.owl
example: 0000078
homepage: https://github.com/CTDbase/exposure-ontology
license: CC BY 4.0
mappings:
biocontext: EXO
biolink: ExO
bioportal: EXO
fairsharing: FAIRsharing.6hna78
obofoundry: ExO
ols: exo
ontobee: ExO
name: Exposure ontology
pattern: ^\d{7}$
preferred_prefix: ExO
repository: https://github.com/CTDbase/exposure-ontology
synonyms:
- ExO
uri_format: http://purl.obolibrary.org/obo/EXO_$1
version: '2020-03-10'
fabio:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for
describing entities that are published or potentially publishable (e.g., journal
articles, conference papers, books), and that contain or are referred to by bibliographic
references.
example: d4e2515
homepage: https://github.com/sparontologies/fabio
mappings:
biolink: fabio
fairsharing: FAIRsharing.2f3180
name: FaBiO, the FRBR-aligned Bibliographic Ontology
preferred_prefix: fabio
repository: https://github.com/sparontologies/fabio
uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1
facebase:
description: FaceBase is a collaborative NIDCR-funded consortium to generate data
in support of advancing research into craniofacial development and malformation.
It serves as a community resource by generating large datasets of a variety of
types and making them available to the wider research community via this website.
Practices emphasize a comprehensive and multidisciplinary approach to understanding
the developmental processes that create the face. The data offered spotlights
high-throughput genetic, molecular, biological, imaging and computational techniques.
One of the missions of this consortium is to facilitate cooperation and collaboration
between projects.
example: FB00000917
homepage: https://www.facebase.org
mappings:
biocontext: FACEBASE
fairsharing: FAIRsharing.mqvqde
miriam: facebase
n2t: facebase
name: FaceBase Data Repository
pattern: ^FB\d{8}$
preferred_prefix: facebase
uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1
fairsharing:
description: The web-based FAIRSharing catalogues aim to centralize bioscience data
policies, reporting standards and links to other related portals. This collection
references bioinformatics data exchange standards, which includes 'Reporting Guidelines',
Format Specifications and Terminologies.
example: bsg-000052
homepage: https://fairsharing.org/
mappings:
biocontext: FAIRSHARING
fairsharing: FAIRsharing.2abjs5
miriam: fairsharing
n2t: fairsharing
name: FAIRsharing
pattern: ^bsg-[dscp]?\d{6}$
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:
biocontext: faldo
bioportal: FALDO
fairsharing: FAIRsharing.haxp7g
name: 'Feature Annotation Location Description Ontology '
preferred_prefix: faldo
uri_format: http://biohackathon.org/resource/faldo#$1
fao:
banana: FAO
contact:
email: vw253@cam.ac.uk
github: ValWood
name: Val Wood
orcid: 0000-0001-6330-7526
description: A structured controlled vocabulary for the anatomy of fungi.
download_obo: http://purl.obolibrary.org/obo/fao.obo
download_owl: http://purl.obolibrary.org/obo/fao.owl
example: '0000001'
homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
license: CC0 1.0
mappings:
biocontext: FAO
bioportal: FAO
fairsharing: FAIRsharing.xs6t67
obofoundry: FAO
ols: fao
ontobee: FAO
prefixcommons: fao
name: Fungal gross anatomy
pattern: ^\d{7}$
preferred_prefix: FAO
repository: https://github.com/obophenotype/fungal-anatomy-ontology
uri_format: http://purl.obolibrary.org/obo/FAO_$1
version: '2020-05-07'
fbbi:
banana: FBbi
contact:
email: wawong@gmail.com
github: wawong
name: Willy Wong
orcid: 0000-0002-8841-5870
description: A structured controlled vocabulary of sample preparation, visualization
and imaging methods used in biomedical research.
download_owl: http://purl.obolibrary.org/obo/fbbi.owl
example: 00000268
homepage: http://cellimagelibrary.org/
license: CC BY 4.0
mappings:
biocontext: FBbi
bioportal: FBbi
fairsharing: FAIRsharing.ny3z9j
obofoundry: FBbi
ols: fbbi
ontobee: FBBI
prefixcommons: fbbi
name: Biological Imaging Methods Ontology
pattern: ^\d+$
preferred_prefix: FBbi
repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology
synonyms:
- FBbi
uri_format: http://purl.obolibrary.org/obo/FBbi_$1
version: '2020-11-06'
fbbt:
banana: FBbt
contact:
email: cp390@cam.ac.uk
github: Clare72
name: Clare Pilgrim
orcid: 0000-0002-1373-1705
description: An ontology of Drosophila melanogaster anatomy.
download_json: http://purl.obolibrary.org/obo/fbbt.json
download_obo: http://purl.obolibrary.org/obo/fbbt.obo
download_owl: http://purl.obolibrary.org/obo/fbbt.owl
example: 00007294
homepage: http://purl.obolibrary.org/obo/fbbt
license: CC BY 3.0
mappings:
biocontext: FBbt
bioportal: FB-BT
fairsharing: FAIRsharing.y2qkst
go: FBbt
obofoundry: FBbt
ols: fbbt
ontobee: FBBT
prefixcommons: fbbt
name: Drosophila gross anatomy
part_of: flybase
pattern: ^\d{8}$
preferred_prefix: FBbt
repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology
synonyms:
- FBbt
- FBbt_root
uri_format: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1
version: '2022-04-13'
fbcv:
appears_in:
- ontoavida
banana: FBcv
contact:
email: cp390@cam.ac.uk
github: Clare72
name: Clare Pilgrim
orcid: 0000-0002-1373-1705
description: A miscellaneous ontology of terms used for curation in FlyBase, including
the DPO.
download_json: http://purl.obolibrary.org/obo/fbcv.json
download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo
download_owl: http://purl.obolibrary.org/obo/fbcv.owl
example: 0000586
homepage: http://purl.obolibrary.org/obo/fbcv
license: CC BY 3.0
mappings:
biocontext: FBcv
bioportal: FB-CV
fairsharing: FAIRsharing.6tgyxf
obofoundry: FBcv
ols: fbcv
ontobee: FBCV
prefixcommons: fbcv
name: FlyBase Controlled Vocabulary
part_of: flybase
pattern: ^\d{7}$
preferred_prefix: FBcv
repository: https://github.com/FlyBase/flybase-controlled-vocabulary
synonyms:
- FBcv
uri_format: http://purl.obolibrary.org/obo/FBcv_$1
version: '2022-04-14'
fbdv:
banana: FBdv
contact:
email: cp390@cam.ac.uk
github: Clare72
name: Clare Pilgrim
orcid: 0000-0002-1373-1705
description: An ontology of Drosophila melanogaster developmental stages.
download_json: http://purl.obolibrary.org/obo/fbdv.json
download_obo: http://purl.obolibrary.org/obo/fbdv.obo
download_owl: http://purl.obolibrary.org/obo/fbdv.owl
example: '00000000'
homepage: http://purl.obolibrary.org/obo/fbdv
license: CC BY 3.0
mappings:
biocontext: FBdv
bioportal: FB-DV
fairsharing: FAIRsharing.p52pzj
obofoundry: FBdv
ols: fbdv
ontobee: FBdv
prefixcommons: fbdv
name: Drosophila development
pattern: ^\d{8}$
preferred_prefix: FBdv
repository: https://github.com/FlyBase/drosophila-developmental-ontology
synonyms:
- FBdv
uri_format: http://purl.obolibrary.org/obo/FBdv_$1
version: '2022-04-12'
fbol:
comment: Website down, checked on 2021-10-07
deprecated: true
description: DNA barcoding is the use of short standardised segments of the genome
for identification of species in all the Kingdoms of Life. The goal of the Fungal
Barcoding site is to promote the DNA barcoding of fungi and other fungus-like
organisms.
example: '2224'
homepage: http://www.fungalbarcoding.org/
mappings:
biocontext: FBOL
miriam: fbol
n2t: fbol
ncbi: FBOL
name: International Fungal Working Group Fungal Barcoding.
pattern: ^\d+$
preferred_prefix: fbol
uri_format: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T
fbql:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
example: '00005254'
name: FlyBase Qualifiers
pattern: ^\d+$
preferred_prefix: fbql
fbrf:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
pattern: ^\d{7}$
preferred_prefix: fbrf
uri_format: https://flybase.org/reports/FBrf$1
fbsp:
banana: FBSP
contact:
email: cp390@cam.ac.uk
github: Clare72
name: Clare Pilgrim
orcid: 0000-0002-1373-1705
deprecated: true
description: The taxonomy of the family Drosophilidae (largely after Baechli)
and of other taxa referred to in FlyBase.
download_owl: http://purl.obolibrary.org/obo/fbsp.owl
example: '00000000'
homepage: http://www.flybase.org/
mappings:
biocontext: FBSP
bioportal: FB-SP
obofoundry: FBSP
name: Fly taxonomy
part_of: flybase
pattern: ^\d{8}$
preferred_prefix: FBSP
uri_format: http://purl.obolibrary.org/obo/FBSP_$1
fbtc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The cell line vocabulary inside FlyBase
example: 0000190
homepage: https://flybase.org
name: Flybase Cell Line
part_of: flybase
pattern: ^\d{7}$
preferred_prefix: fbtc
uri_format: https://flybase.org/reports/FBtc$1
fcb:
description: 'Created by researchers and data managers professionals, the FAIR Cookbook
is an online resource for the Life Sciences with recipes that help you to make
and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).
'
example: FCB005
homepage: https://w3id.org
mappings:
miriam: fcb
name: the FAIR Cookbook
pattern: ^FCB\d{3}$
preferred_prefix: fcb
uri_format: https://w3id.org/faircookbook/$1
fcsfree:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell line databases/resources
example: 240-17-488-3-4-12
homepage: https://fcs-free.org
mappings:
cellosaurus: FCS-free
name: Fetal Calf Serum-Free Database
preferred_prefix: fcsfree
uri_format: https://fcs-free.org/fcs-database?$1
fideo:
banana: FIDEO
contact:
email: georgeta.bordea@u-bordeaux.fr
github: getbordea
name: Georgeta Bordea
orcid: 0000-0001-9921-8234
description: The Food Interactions with Drugs Evidence Ontology (FIDEO) represents
Food-Drug Interactions and underlying interaction mechanisms described in scientific
publications, drug and adverse effects databases, and drug interactions compendia.
The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO
ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo,
and requests for changes or additions should be filed at the issue tracker there.
download_owl: http://purl.obolibrary.org/obo/fideo.owl
example: '00000021'
homepage: https://gitub.u-bordeaux.fr/erias/fideo
license: CC0 1.0
mappings:
bioportal: FIDEO
obofoundry: FIDEO
ols: fideo
ontobee: FIDEO
name: Food Interactions with Drugs Evidence Ontology
pattern: ^\d{8}$
preferred_prefix: FIDEO
repository: https://github.com/getbordea/fideo
uri_format: http://purl.obolibrary.org/obo/FIDEO_$1
fishbase.species:
description: 'Global biodiversity database on finfishes. It offers a wide range
of information on all species currently known in the world: taxonomy, biology,
trophic ecology, life history, and uses, as well as historical data reaching back
to 250 years.'
example: '6472'
homepage: http://fishbase.org
mappings:
wikidata: P938
name: FishBase
pattern: ^\d+$
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.
download_obo: http://purl.obolibrary.org/obo/fix.obo
download_owl: http://purl.obolibrary.org/obo/fix.owl
example: 0000390
homepage: https://www.ebi.ac.uk/chebi/
mappings:
biocontext: FIX
bioportal: FIX
fairsharing: FAIRsharing.wwy1ns
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_$1
version: '2020-04-13'
flopo:
banana: FLOPO
contact:
email: robert.hoehndorf@kaust.edu.sa
github: leechuck
name: Robert Hoehndorf
orcid: 0000-0001-8149-5890
description: Traits and phenotypes of flowering plants occurring in digitized Floras
download_owl: http://purl.obolibrary.org/obo/flopo.owl
example: '0005250'
homepage: https://github.com/flora-phenotype-ontology/flopoontology
license: CC0 1.0
mappings:
biocontext: FLOPO
bioportal: FLOPO
fairsharing: FAIRsharing.ny9vnm
obofoundry: FLOPO
ols: flopo
ontobee: FLOPO
name: Flora Phenotype Ontology
pattern: ^\d{7}$
preferred_prefix: FLOPO
repository: https://github.com/flora-phenotype-ontology/flopoontology
uri_format: http://purl.obolibrary.org/obo/FLOPO_$1
version: '2019-09-09'
flowrepository:
description: FlowRepository is a database of flow cytometry experiments where you
can query and download data collected and annotated according to the MIFlowCyt
standard. It is primarily used as a data deposition place for experimental findings
published in peer-reviewed journals in the flow cytometry field.
example: FR-FCM-ZYGW
homepage: https://flowrepository.org/
mappings:
fairsharing: FAIRsharing.veg2d6
miriam: flowrepository
n2t: flowrepository
name: FlowRepository
pattern: ^FR\-FCM\-\w{4}$
preferred_prefix: flowrepository
uri_format: https://flowrepository.org/id/$1
flu:
banana: FLU
contact:
email: burkesquires@gmail.com
github: null
name: Burke Squires
orcid: null
deprecated: true
download_owl: http://purl.obolibrary.org/obo/flu.owl
example: '0000404'
homepage: http://purl.obolibrary.org/obo/flu/
mappings:
biocontext: FLU
bioportal: FLU
obofoundry: FLU
name: Influenza Ontology
pattern: ^\d{7}$
preferred_prefix: FLU
uri_format: http://purl.obolibrary.org/obo/FLU_$1
flybase:
description: FlyBase is the database of the Drosophila Genome Projects and of associated
literature.
example: FBgn0011293
homepage: http://flybase.org/
mappings:
biocontext: FlyBase
cellosaurus: FlyBase
fairsharing: FAIRsharing.wrvze3
go: FB
miriam: fb
n2t: fb
ncbi: FLYBASE
prefixcommons: flybase
uniprot: FlyBase
wikidata: P3852
name: FlyBase Gene
pattern: ^FB\w{2}\d{7}$
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/$1
flybrain.ndb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A database of fly neurons and pathways with an associated 3D viewer.
example: '10531'
homepage: https://flybrain-ndb.virtualflybrain.org
name: FlyBrain Neuron Database
pattern: ^\d+$
preferred_prefix: flybrain.ndb
uri_format: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html
fma:
banana: FMA
contact:
email: mejino@u.washington.edu
github: null
name: Onard Mejino
orcid: null
description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics
ontology. It is concerned with the representation of classes or types and relationships
necessary for the symbolic representation of the phenotypic structure of the human
body. Specifically, the FMA is a domain ontology that represents a coherent body
of explicit declarative knowledge about human anatomy.
download_owl: http://purl.obolibrary.org/obo/fma.owl
example: '63189'
homepage: http://si.washington.edu/projects/fma
license: CC BY 3.0
mappings:
biocontext: FMA
bioportal: FMA
fairsharing: FAIRsharing.x56jsy
go: FMA
miriam: fma
n2t: fma
obofoundry: FMA
ols: fma
ontobee: FMA
prefixcommons: fma
name: Foundational Model of Anatomy
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: FMA
repository: https://bitbucket.org/uwsig/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:
biocontext: foaf
biolink: foaf
bioportal: FOAF
name: Friend of a Friend
preferred_prefix: foaf
uri_format: http://xmlns.com/foaf/0.1/$1
fobi:
banana: FOBI
contact:
email: polcaes@gmail.com
github: pcastellanoescuder
name: Pol Castellano Escuder
orcid: 0000-0001-6466-877X
depends_on:
- chebi
- foodon
description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake
data and associate it with metabolomic data
download_owl: http://purl.obolibrary.org/obo/fobi.owl
example: 030719
homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
license: CC BY 3.0
mappings:
bioportal: FOBI
obofoundry: FOBI
ols: fobi
ontobee: FOBI
name: Food-Biomarker Ontology
pattern: ^\d{6}$
preferred_prefix: FOBI
repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
uri_format: http://purl.obolibrary.org/obo/FOBI_$1
foodb.compound:
description: FooDB is resource on food and its constituent compounds. It includes
data on the compound’s nomenclature, its description, information on its structure,
chemical class, its physico-chemical data, its food source(s), its color, its
aroma, its taste, its physiological effect, presumptive health effects (from published
studies), and concentrations in various foods. This collection references compounds.
example: FDB002100
homepage: https://foodb.ca/
mappings:
biocontext: FOODB.COMPOUND
biolink: foodb.compound
miriam: foodb.compound
n2t: foodb.compound
name: FooDB Compound
pattern: ^FDB\d+$
preferred_prefix: foodb.compound
synonyms:
- foodb
uri_format: http://foodb.ca/compounds/$1
foodon:
appears_in:
- agro
- envo
- fobi
- maxo
- one
- ons
banana: FOODON
contact:
email: damion_dooley@sfu.ca
github: ddooley
name: Damion Dooley
orcid: 0000-0002-8844-9165
depends_on:
- bfo
- chebi
- envo
- eo
- ncbitaxon
- obi
- ro
- uberon
description: FoodOn is a comprehensive and easily accessible global farm-to-fork
ontology about food that accurately and consistently describes foods commonly
known in cultures from around the world. It is a consortium-driven project built
to interoperate with the The Open Biological and Biomedical Ontology Foundry library
of ontologies.
download_owl: http://purl.obolibrary.org/obo/foodon.owl
example: 03307879
homepage: https://foodon.org/
license: CC BY 3.0
mappings:
biocontext: FOODON
bioportal: FOODON
fairsharing: FAIRsharing.dzxae
miriam: foodon
n2t: foodon
obofoundry: FOODON
ols: foodon
ontobee: FOODON
name: The Food Ontology
namespace_in_lui: true
pattern: ^[0-9]{8}$
preferred_prefix: FOODON
repository: https://github.com/FoodOntology/foodon
uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1
version: '2022-02-01'
fovt:
banana: FOVT
contact:
email: meghan.balk@gmail.com
github: megbalk
name: Meghan Balk
orcid: 0000-0003-2699-3066
depends_on:
- bco
- bfo
- bspo
- iao
- oba
- pato
- ro
- uberon
description: None
download_obo: http://purl.obolibrary.org/obo/fovt.obo
download_owl: http://purl.obolibrary.org/obo/fovt.owl
example: 0000009
homepage: https://github.com/futres/fovt
license: CC0 1.0
mappings:
bioportal: FOVT
obofoundry: FOVT
ols: fovt
ontobee: FOVT
name: FuTRES Ontology of Vertebrate Traits
pattern: ^\d{7}$
preferred_prefix: FOVT
repository: https://github.com/futres/fovt
uri_format: http://purl.obolibrary.org/obo/FOVT_$1
version: '2021-11-10'
fplx:
description: FamPlex is a collection of resources for grounding biological entities
from text and describing their hierarchical relationships.
example: GPIb_IX_V
homepage: https://sorgerlab.github.io/famplex/
mappings:
biocontext: FPLX
bioportal: FPLX
miriam: fplx
n2t: fplx
name: FamPlex
pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$
preferred_prefix: fplx
synonyms:
- famplex
uri_format: https://sorgerlab.github.io/famplex/$1
fsnp:
description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates
information obtained from databases about the functional effects of SNPs. These
effects are predicted and indicated at the splicing, transcriptional, translational
and post-translational level. In particular, users can retrieve SNPs that disrupt
genomic regions known to be functional, including splice sites and transcriptional
regulatory regions. Users can also identify non-synonymous SNPs that may have
deleterious effects on protein structure or function, interfere with protein translation
or impede post-translational modification.
example: rs17852708
homepage: http://compbio.cs.queensu.ca/F-SNP/
mappings:
biocontext: FSNP
miriam: fsnp
n2t: fsnp
prefixcommons: fsnp
name: F-SNP
pattern: ^rs\d+$
preferred_prefix: fsnp
uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1
ftt:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Types of named geographic features. Applicable also to many unnamed
features but reflects the level of detail traditionally shown on maps, so some
feature types specified in scientific studies may not be well represented here.
Not highly specific.
example: '273'
homepage: https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3
name: Feature Type Thesaurus
pattern: ^\d+$
preferred_prefix: ftt
references:
- https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200
- https://github.com/EnvironmentOntology/envo/issues/1130
uri_format: https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1
funcbase.fly:
description: Computational gene function prediction can serve to focus experimental
resources on high-priority experimental tasks. FuncBase is a web resource for
viewing quantitative machine learning-based gene function annotations. Quantitative
annotations of genes, including fungal and mammalian genes, with Gene Ontology
terms are accompanied by a community feedback system. Evidence underlying function
annotations is shown. FuncBase provides links to external resources, and may be
accessed directly or via links from species-specific databases. This collection
references Drosophila data.
example: '10194'
homepage: http://func.mshri.on.ca/fly
mappings:
biocontext: FUNCBASE.FLY
miriam: funcbase.fly
n2t: funcbase.fly
name: FuncBase Fly
pattern: ^\d+$
preferred_prefix: funcbase.fly
uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1
funcbase.human:
description: Computational gene function prediction can serve to focus experimental
resources on high-priority experimental tasks. FuncBase is a web resource for
viewing quantitative machine learning-based gene function annotations. Quantitative
annotations of genes, including fungal and mammalian genes, with Gene Ontology
terms are accompanied by a community feedback system. Evidence underlying function
annotations is shown. FuncBase provides links to external resources, and may be
accessed directly or via links from species-specific databases. This collection
references human data.
example: '119514'
homepage: http://func.mshri.on.ca/human/
mappings:
biocontext: FUNCBASE.HUMAN
miriam: funcbase.human
n2t: funcbase.human
name: FuncBase Human
pattern: ^\d+$
preferred_prefix: funcbase.human
uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1
funcbase.mouse:
description: Computational gene function prediction can serve to focus experimental
resources on high-priority experimental tasks. FuncBase is a web resource for
viewing quantitative machine learning-based gene function annotations. Quantitative
annotations of genes, including fungal and mammalian genes, with Gene Ontology
terms are accompanied by a community feedback system. Evidence underlying function
annotations is shown. FuncBase provides links to external resources, and may be
accessed directly or via links from species-specific databases. This collection
references mouse.
example: '1351341'
homepage: http://func.mshri.on.ca/mouse/
mappings:
biocontext: FUNCBASE.MOUSE
miriam: funcbase.mouse
n2t: funcbase.mouse
name: FuncBase Mouse
pattern: ^\d+$
preferred_prefix: funcbase.mouse
uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1
funcbase.yeast:
description: Computational gene function prediction can serve to focus experimental
resources on high-priority experimental tasks. FuncBase is a web resource for
viewing quantitative machine learning-based gene function annotations. Quantitative
annotations of genes, including fungal and mammalian genes, with Gene Ontology
terms are accompanied by a community feedback system. Evidence underlying function
annotations is shown. FuncBase provides links to external resources, and may be
accessed directly or via links from species-specific databases. This collection
references yeast.
example: '2701'
homepage: http://func.mshri.on.ca/yeast
mappings:
biocontext: FUNCBASE.YEAST
miriam: funcbase.yeast
n2t: funcbase.yeast
name: FuncBase Yeast
pattern: ^\d+$
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/$1
fungidb:
description: FungiDB is a genomic resource for fungal genomes. It contains contains
genome sequence and annotation from several fungal classes, including the Ascomycota
classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota
orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage
Mucormycotina.
example: CNBG_0001
homepage: https://fungidb.org/fungidb
mappings:
biocontext: FUNGIDB
fairsharing: FAIRsharing.xf30yc
miriam: fungidb
n2t: fungidb
name: FungiDB
pattern: ^[A-Za-z_0-9]+$
preferred_prefix: fungidb
uri_format: https://fungidb.org/fungidb/app/record/gene/$1
fyeco:
comment: Rather than admitting FYECO to the OBO foundry, we secure the prefix here
at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere
you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to
other OBO ontologies, but this is way ahead in the future.
contact:
email: vw253@cam.ac.uk
github: ValWood
name: Val Wood
orcid: 0000-0001-6330-7526
contributor:
email: vw253@cam.ac.uk
github: ValWood
name: Val Wood
orcid: 0000-0001-6330-7526
description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO
contains experimental conditions relevant to fission yeast biology. The FYECO
namespace shows up in data ingests from PomBase.
example: '0000003'
homepage: https://github.com/pombase/fypo
mappings:
biolink: FYECO
name: Fission Yeast Experimental Conditions Ontology
pattern: ^\d{7}$
preferred_prefix: FYECO
repository: https://github.com/pombase/fypo
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
fyler:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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: vw253@cam.ac.uk
github: ValWood
name: Val Wood
orcid: 0000-0001-6330-7526
description: A formal ontology of phenotypes observed in fission yeast.
download_obo: http://purl.obolibrary.org/obo/fypo.obo
download_owl: http://purl.obolibrary.org/obo/fypo.owl
example: '0001707'
homepage: https://github.com/pombase/fypo
license: CC BY 4.0
mappings:
biocontext: FYPO
biolink: FYPO
bioportal: FYPO
fairsharing: FAIRsharing.4vr0ys
go: FYPO
obofoundry: FYPO
ols: fypo
ontobee: FYPO
name: Fission Yeast Phenotype Ontology
pattern: ^\d{7}$
preferred_prefix: FYPO
repository: https://github.com/pombase/fypo
uri_format: http://purl.obolibrary.org/obo/FYPO_$1
version: '2022-04-28'
ga4ghdos:
description: Assists in resolving data across cloud resources.
example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d
homepage: http://github.com/ga4gh/data-object-service-schemas
mappings:
biocontext: GA4GHDOS
miriam: ga4ghdos
n2t: ga4ghdos
name: Data Object Service
pattern: ^[a-zA-Z0-9\-:#/\.]+$
preferred_prefix: ga4ghdos
uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1
gabi:
description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database)
constitutes a repository for a wide array of heterogeneous data from high-throughput
experiments in several plant species. These data (i.e. genomics, transcriptomics,
proteomics and metabolomics), originating from different model or crop species,
can be accessed through a central gene 'Green Card'.
example: '2679240'
homepage: http://www.gabipd.org/
mappings:
biocontext: GABI
miriam: gabi
n2t: gabi
ncbi: GABI
prefixcommons: gabi
name: Network of Different Plant Genomic Research Projects
pattern: ^\w+$
preferred_prefix: gabi
uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject
galen:
comment: I really tried, but could not figure out what GALEN stands for
deprecated: true
example: MagnitudeValueType
homepage: https://www.opengalen.org
mappings:
bioportal: GALEN
name: GALEN
preferred_prefix: galen
gard:
description: Database of rare diseases and related terms, including symptoms, healthcare
resources, and organizations supporting research of the disease.
example: '6038'
homepage: https://rarediseases.info.nih.gov/diseases
mappings:
wikidata: P4317
name: Genetic and Rare Diseases Information Center
pattern: ^\d+$
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/$1
gaz:
appears_in:
- scdo
banana: GAZ
contact:
email: lschriml@som.umaryland.edu
github: lschriml
name: Lynn Schriml
orcid: 0000-0001-8910-9851
description: A gazetteer constructed on ontological principles
download_obo: http://purl.obolibrary.org/obo/gaz.obo
download_owl: http://purl.obolibrary.org/obo/gaz.owl
example: '00620027'
homepage: http://environmentontology.github.io/gaz/
license: CC0 1.0
mappings:
biocontext: GAZ
bioportal: GAZ
fairsharing: FAIRsharing.wkdjpb
obofoundry: GAZ
ols: gaz
ontobee: GAZ
wikidata: P6778
name: Gazetteer
pattern: ^\d{8}$
preferred_prefix: GAZ
repository: https://github.com/EnvironmentOntology/gaz
uri_format: http://purl.obolibrary.org/obo/GAZ_$1
gbif:
description: "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity\
\ Information Facility—is international network and data infrastructure funded\
\ by the world's governments and aimed at providing anyone, anywhere, open access\
\ to data about all types of life on Earth."
example: '4238'
homepage: https://www.gbif.org/species
mappings:
fairsharing: FAIRsharing.zv11j3
wikidata: P846
name: Global Biodiversity Information Facility
pattern: ^\d+$
preferred_prefix: gbif
uri_format: https://www.gbif.org/species/$1
gc:
comment: 'see comment here: https://github.com/obophenotype/ncbitaxon/issues/47'
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Genetic code, mitochontrial genetic code, and other linked information
to NCBI taxonomy entries.
example: '11'
homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html
name: Genetic Code
pattern: ^\d+$
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/$1
gdc:
description: The GDC Data Portal is a robust data-driven platform that allows cancer
researchers and bioinformaticians to search and download cancer data for analysis.
example: ae8c77fe-e6c8-44d5-8265-4a38c637bbef
homepage: https://gdc.cancer.gov
mappings:
biocontext: GDC
miriam: gdc
n2t: gdc
name: Genomic Data Commons Data Portal
pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$
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/$1
gecko:
banana: GECKO
contact:
email: rbca.jackson@gmail.com
github: beckyjackson
name: Rebecca Jackson
orcid: 0000-0003-4871-5569
description: An ontology to represent genomics cohort attributes.
download_owl: http://purl.obolibrary.org/obo/gecko.owl
example: '0000044'
homepage: https://github.com/IHCC-cohorts/GECKO
license: CC BY 4.0
mappings:
bioportal: GECKO
fairsharing: FAIRsharing.3da56b
obofoundry: GECKO
ols: gecko
ontobee: GECKO
name: Genomics Cohorts Knowledge Ontology
pattern: ^\d{7}$
preferred_prefix: GECKO
repository: https://github.com/IHCC-cohorts/GECKO
uri_format: http://purl.obolibrary.org/obo/GECKO_$1
version: '2021-01-18'
gemet:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The European Environment Information and Observation Network (Eionet)
is a partnership network of the European Environment Agency (EEA) and its 38 member
and cooperating countries. The EEA is responsible for developing Eionet and coordinating
its activities together with National Focal Points (NFPs) in the countries. This
terminology supports those efforts.
example: '627'
homepage: https://www.eionet.europa.eu/gemet/en/themes/
name: General Multilingual Environmental Thesaurus
pattern: ^\d+$
preferred_prefix: gemet
uri_format: https://www.eionet.europa.eu/gemet/en/concept/$1
genatlas:
description: GenAtlas is a database containing information on human genes, markers
and phenotypes.
example: HBB
homepage: http://genatlas.medecine.univ-paris5.fr/
mappings:
biocontext: GENATLAS
fairsharing: FAIRsharing.pmg2vd
miriam: genatlas
n2t: genatlas
prefixcommons: genatlas
uniprot: GenAtlas
name: Genatlas
pattern: ^\w+$
preferred_prefix: genatlas
uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1
genbank:
description: GenBank ® 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:
biocontext: GenBank
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/$1
genecards:
description: The GeneCards human gene database stores gene related transcriptomic,
genetic, proteomic, functional and disease information. It uses standard nomenclature
and approved gene symbols. GeneCards presents a complete summary for each human
gene.
example: ABL1
homepage: http://www.genecards.org/
mappings:
biocontext: GENECARDS
fairsharing: FAIRsharing.g7jbvn
miriam: genecards
n2t: genecards
prefixcommons: genecards
uniprot: GeneCards
name: GeneCards
pattern: ^[A-Za-z-0-9_]+(\@)?$
preferred_prefix: genecards
uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1
genedb:
deprecated: true
description: GeneDB is a genome database for prokaryotic and eukaryotic organisms
and provides a portal through which data generated by the "Pathogen Genomics"
group at the Wellcome Trust Sanger Institute and other collaborating sequencing
centres can be accessed.
example: LinJ.20.0070
homepage: https://www.genedb.org/
mappings:
biocontext: GENEDB
fairsharing: FAIRsharing.j7esqq
go: GeneDB
miriam: genedb
n2t: genedb
ncbi: GeneDB
prefixcommons: genedb
uniprot: GeneDB
wikidata: P3382
name: GeneDB
pattern: ^[\w\d\.-]*$
preferred_prefix: genedb
uri_format: https://www.genedb.org/gene/$1
genefarm:
description: GeneFarm is a database whose purpose is to store traceable annotations
for Arabidopsis nuclear genes and gene products.
example: '4892'
homepage: http://urgi.versailles.inra.fr/Genefarm/
mappings:
biocontext: GENEFARM
fairsharing: FAIRsharing.2mayq0
miriam: genefarm
n2t: genefarm
prefixcommons: genefarm
name: GeneFarm
pattern: ^\d+$
preferred_prefix: genefarm
uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1
genepio:
banana: GENEPIO
contact:
email: damion_dooley@sfu.ca
github: ddooley
name: Damion Dooley
orcid: 0000-0002-8844-9165
depends_on:
- chebi
- ncbitaxon
- po
- ro
- uberon
description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary
to identify, document and research foodborne pathogens and associated outbreaks.
download_owl: http://purl.obolibrary.org/obo/genepio.owl
example: 0001885
homepage: http://genepio.org/
license: CC BY 3.0
mappings:
biocontext: GENEPIO
fairsharing: FAIRsharing.y1mmbv
obofoundry: GENEPIO
ols: genepio
ontobee: GENEPIO
name: Genomic Epidemiology Ontology
pattern: ^\d{7}$
preferred_prefix: GENEPIO
repository: https://github.com/GenEpiO/genepio
uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1
version: '2022-02-06'
genetree:
description: Genetree displays the maximum likelihood phylogenetic (protein) trees
representing the evolutionary history of the genes. These are constructed using
the canonical protein for every gene in Ensembl.
example: ENSGT00550000074763
homepage: http://www.ensembl.org/
mappings:
biocontext: GENETREE
miriam: genetree
n2t: genetree
prefixcommons: genetree
uniprot: GeneTree
name: GeneTree
pattern: ^ENSGT\d+$
preferred_prefix: genetree
uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1
genewiki:
description: The Gene Wiki is project which seeks to provide detailed information
on human genes. Initial 'stub' articles are created in an automated manner, with
further information added by the community. Gene Wiki can be accessed in wikipedia
using Gene identifiers from NCBI.
example: '1017'
homepage: http://en.wikipedia.org/wiki/Gene_Wiki
mappings:
biocontext: GENEWIKI
fairsharing: FAIRsharing.t3snf
miriam: genewiki
n2t: genewiki
uniprot: GeneWiki
name: Gene Wiki
pattern: ^\d+$
preferred_prefix: genewiki
uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1
geno:
banana: GENO
contact:
email: mhb120@gmail.com
github: mbrush
name: Matthew Brush
orcid: 0000-0002-1048-5019
description: "GENO is an OWL model of genotypes, their more fundamental sequence\
\ components, and links to related biological and experimental entities. At present\
\ many parts of the model are exploratory and set to undergo refactoring. In\
\ addition, many classes and properties have GENO URIs but are place holders for\
\ classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI,\
\ etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype\
\ associations. This will support description of asserted and inferred relationships\
\ between a genotypes, phenotypes, and environments, and the evidence/provenance\
\ behind these associations. \n\nDocumentation is under development as well, and\
\ for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"
download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo
download_owl: http://purl.obolibrary.org/obo/geno.owl
example: '0000632'
homepage: https://github.com/monarch-initiative/GENO-ontology/
license: CC BY-SA 2.0
mappings:
biocontext: GENO
bioportal: GENO
fairsharing: FAIRsharing.kpbna7
obofoundry: GENO
ols: geno
ontobee: GENO
name: Genotype Ontology
pattern: ^\d{7}$
preferred_prefix: GENO
repository: https://github.com/monarch-initiative/GENO-ontology
uri_format: http://purl.obolibrary.org/obo/GENO_$1
version: '2022-03-05'
genpept:
description: The GenPept database is a collection of sequences based on translations
from annotated coding regions in GenBank.
example: CAA71118.1
homepage: https://www.ncbi.nlm.nih.gov/protein
mappings:
biocontext: GENPEPT
miriam: genpept
n2t: genpept
name: GenPept
pattern: ^\w{3}\d{5}(\.\d+)?$
preferred_prefix: genpept
uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept
genprop:
description: Genome properties is an annotation system whereby functional attributes
can be assigned to a genome, based on the presence of a defined set of protein
signatures within that genome.
example: GenProp0699
homepage: https://www.ebi.ac.uk/interpro/genomeproperties/
mappings:
biocontext: GENPROP
miriam: genprop
n2t: genprop
name: Genome Properties
pattern: ^GenProp\d+$
preferred_prefix: genprop
uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1
geo:
description: The Gene Expression Omnibus (GEO) is a gene expression repository providing
a curated, online resource for gene expression data browsing, query and retrieval.
example: GDS1234
homepage: https://www.ncbi.nlm.nih.gov/geo/
mappings:
biocontext: GEO
cellosaurus: GEO
fairsharing: FAIRsharing.27rndz
go: GEO
miriam: geo
n2t: geo
prefixcommons: geo
name: NCBI Gene Expression Omnibus
pattern: ^G(PL|SM|SE|DS)\d+$
preferred_prefix: geo
uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1
geogeo:
banana: GEO
contact:
email: hoganwr@gmail.com
github: null
name: Bill Hogan
orcid: null
description: An ontology and inventory of geopolitical entities such as nations
and their components (states, provinces, districts, counties) and the actual physical
territories over which they have jurisdiction. We thus distinguish and assign
different identifiers to the US in "The US declared war on Germany" vs. the US
in "The plane entered US airspace".
download_owl: http://purl.obolibrary.org/obo/geo.owl
example: '000000021'
homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki
license: CC BY 4.0
mappings:
biocontext: GEO
bioportal: GEO
miriam: geogeo
obofoundry: GEO
ols: geo
ontobee: GEO
name: Geographical Entity Ontology
pattern: ^\d{9}$
preferred_prefix: GEOGEO
repository: https://github.com/ufbmi/geographical-entity-ontology
uri_format: http://purl.obolibrary.org/obo/GEO_$1
version: '2016-03-26'
geonames:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The GeoNames geographical database covers all countries and contains
over eleven million placenames that are available for download free of charge.
example: ADM1
homepage: https://www.geonames.org
mappings:
fairsharing: FAIRsharing.56a0Uj
name: GeoNames
preferred_prefix: geonames
synonyms:
- Geomames
- Geonamaes
uri_format: https://www.geonames.org/recent-changes/featurecode/$1/
gexo:
description: Gene Expression Ontology
download_obo: https://www.bio.ntnu.no/ontology/GeXO/gexo.obo
download_owl: https://www.bio.ntnu.no/ontology/GeXO/gexo.owl
homepage: http://www.semantic-systems-biology.org/apo
mappings:
bioportal: GEXO
fairsharing: FAIRsharing.3e0sn4
ols: gexo
name: Gene Expression Ontology
no_own_terms: true
preferred_prefix: gexo
version: '2019-09-18'
ghr:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/$1
giardiadb:
description: GiardiaDB is one of the databases that can be accessed through the
EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: GL50803_102438
homepage: https://giardiadb.org/giardiadb/
mappings:
biocontext: GIARDIADB
fairsharing: FAIRsharing.e7skwg
miriam: giardiadb
n2t: giardiadb
prefixcommons: giardiadb
name: GiardiaDB
pattern: ^\w+$
preferred_prefix: giardiadb
uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1
github:
description: GitHub is an online host of Git source code repositories.
example: biopragmatics/bioregistry
example_extras:
- biopragmatics
- cthoyt
homepage: https://github.com/
mappings:
fairsharing: FAIRsharing.c55d5e
miriam: github
name: github
pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$
preferred_prefix: github
uri_format: https://github.com/$1
gitlab:
description: GitLab is The DevOps platform that empowers organizations to maximize
the overall return on software development by delivering software faster and efficiently,
while strengthening security and compliance. With GitLab, every team in your organization
can collaboratively plan, build, secure, and deploy software to drive business
outcomes faster with complete transparency, consistency and traceability.
example: morpheus.lab/morpheus
homepage: https://gitlab.com/
mappings:
fairsharing: FAIRsharing.530e61
miriam: gitlab
name: GitLab
pattern: ^.*/.*$
preferred_prefix: gitlab
uri_format: https://gitlab.com/$1
glida.gpcr:
description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic
database that is primarily focused on the correlation of information between GPCRs
and their ligands. It provides correlation data between GPCRs and their ligands,
along with chemical information on the ligands. This collection references G-protein
coupled receptors.
example: ACM1_HUMAN
homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
mappings:
biocontext: GLIDA.GPCR
miriam: glida.gpcr
n2t: glida.gpcr
name: GLIDA GPCR
pattern: ^[A-Z-_0-9]+$
preferred_prefix: glida.gpcr
uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1
glida.ligand:
description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic
database that is primarily focused on the correlation of information between GPCRs
and their ligands. It provides correlation data between GPCRs and their ligands,
along with chemical information on the ligands. This collection references ligands.
example: L000001
homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
mappings:
biocontext: GLIDA.LIGAND
miriam: glida.ligand
n2t: glida.ligand
name: GLIDA Ligand
pattern: ^L\d+$
preferred_prefix: glida.ligand
uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1
glycoepitope:
description: GlycoEpitope is a database containing useful information about carbohydrate
antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can
be used to analyze their expression. This collection references Glycoepitopes.
example: EP0311
homepage: https://www.glycoepitope.jp/epitopes/
mappings:
biocontext: GLYCOEPITOPE
miriam: glycoepitope
n2t: glycoepitope
name: GlycoEpitope
pattern: ^EP\d{4}$
preferred_prefix: glycoepitope
uri_format: https://www.glycoepitope.jp/epitopes/$1
glycomedb:
comment: this is exactly the same as glytoucan. Idk why there are two different
ones
description: GlycomeDB is the result of a systematic data integration effort, and
provides an overview of all carbohydrate structures available in public databases,
as well as cross-links.
example: G77500AY
has_canonical: glytoucan
homepage: https://glytoucan.org/
mappings:
biocontext: GLYCOMEDB
fairsharing: FAIRsharing.k5k0yh
miriam: glycomedb
n2t: glycomedb
prefixcommons: glycomedb
name: GlycomeDB
pattern: ^\w+$
preferred_prefix: glycomedb
uri_format: https://glytoucan.org/Structures/Glycans/$1
glyconavi:
description: GlycoNAVI is a website for carbohydrate research. It consists of the
"GlycoNAVI Database" that provides information such as existence ratios and names
of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI
tools" such as editing of 2D structures of glycans, glycan structure viewers,
and conversion tools.
example: GN_G03681DA
example_extras:
- GN_GlyTouCan_G03681DA
homepage: https://www.noguchi.or.jp/
mappings:
fairsharing: FAIRsharing.wvp1t7
miriam: glyconavi
name: GlycoNAVI
pattern: ^GN_[A-Za-z0-9_:]+$
preferred_prefix: glyconavi
uri_format: https://glyconavi.org/hub/?id=$1
glycopost:
description: GlycoPOST is a mass spectrometry data repository for glycomics and
glycoproteomics. Users can release their "raw/processed" data via this site with
a unique identifier number for the paper publication. Submission conditions are
in accordance with the Minimum Information Required for a Glycomics Experiment
(MIRAGE) guidelines.
example: GPST000024
homepage: https://glycopost.glycosmos.org
mappings:
fairsharing: FAIRsharing.2y1KMt
miriam: glycopost
name: GlycoPOST
pattern: ^GPST[0-9]{6}$
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:
fairsharing: FAIRsharing.aI1J5W
uniprot: GlyGen
name: Computational and Informatics Resources for Glycoscience
preferred_prefix: glygen
uri_format: https://glygen.org/glycan/$1
glytoucan:
description: GlyTouCan is the single worldwide registry of glycan (carbohydrate
sugar chain) data.
example: G00054MO
homepage: https://glytoucan.org
mappings:
biocontext: GLYTOUCAN
miriam: glytoucan
n2t: glytoucan
name: GlyTouCan
pattern: ^G[0-9]{5}[A-Z]{2}$
preferred_prefix: glytoucan
uri_format: https://glytoucan.org/Structures/Glycans/$1
gmd:
description: Golm Metabolome Database (GMD) provides public access to custom mass
spectral libraries, metabolite profiling experiments as well as additional information
and tools. This collection references metabolite information, relating the biologically
active substance to metabolic pathways or signalling phenomena.
example: 68513255-fc44-4041-bc4b-4fd2fae7541d
homepage: http://gmd.mpimp-golm.mpg.de/
mappings:
biocontext: GMD
fairsharing: FAIRsharing.jykmkw
miriam: gmd
n2t: gmd
name: Golm Metabolome Database
pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
preferred_prefix: gmd
uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx
gmd.analyte:
description: Golm Metabolome Database (GMD) provides public access to custom mass
spectral libraries, metabolite profiling experiments as well as additional information
and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically
converted, i.e. derivatised into less polar and volatile compounds, so called
analytes. This collection references analytes.
example: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80
homepage: http://gmd.mpimp-golm.mpg.de/
mappings:
biocontext: GMD.ANALYTE
miriam: gmd.analyte
n2t: gmd.analyte
name: Golm Metabolome Database Analyte
pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
preferred_prefix: gmd.analyte
uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1
gmd.gcms:
description: Golm Metabolome Database (GMD) provides public access to custom mass
spectral libraries, metabolite profiling experiments as well as additional information
and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer,
which records the mass spectrum and the retention time linked to an analyte. This
collection references GC-MS spectra.
example: 53d583d8-40c6-40e1-9296-23f821cd77a5
homepage: http://gmd.mpimp-golm.mpg.de/
mappings:
biocontext: GMD.GCMS
miriam: gmd.gcms
n2t: gmd.gcms
name: Golm Metabolome Database GC-MS spectra
pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
preferred_prefix: gmd.gcms
uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1
gmd.profile:
description: Golm Metabolome Database (GMD) provides public access to custom mass
spectral libraries, metabolite profiling experiments as well as additional information
and tools. GMD's metabolite profiles provide relative metabolite concentrations
normalised according to fresh weight (or comparable quantitative data, such as
volume, cell count, etc.) and internal standards (e.g. ribotol) of biological
reference conditions and tissues.
example: 10b38aaf-b977-4950-85b8-f4775f66658d
homepage: http://gmd.mpimp-golm.mpg.de/
mappings:
biocontext: GMD.PROFILE
miriam: gmd.profile
n2t: gmd.profile
name: Golm Metabolome Database Profile
pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
preferred_prefix: gmd.profile
uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1
gmd.ref:
description: Golm Metabolome Database (GMD) provides public access to custom mass
spectral libraries, metabolite profiling experiments as well as additional information
and tools. Since metabolites often cannot be obtained in their respective native
biological state, for example organic acids may be only acquirable as salts, the
concept of reference substance was introduced. This collection references reference
substances.
example: 8cf84adb-b4db-4807-ac98-0004247c35df
homepage: http://gmd.mpimp-golm.mpg.de/
mappings:
biocontext: GMD.REF
miriam: gmd.ref
n2t: gmd.ref
name: Golm Metabolome Database Reference Substance
pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
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: 0000-0001-5168-3196
description: An ontology for glycans based on GlyTouCan, but organized by subsumption.
download_json: http://purl.obolibrary.org/obo/gno.json
download_obo: http://purl.obolibrary.org/obo/gno.obo
download_owl: http://purl.obolibrary.org/obo/gno.owl
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
repository: https://github.com/glygen-glycan-data/GNOme
uri_format: http://purl.obolibrary.org/obo/GNO_$1
version: 1.10.0
gnpis:
description: GnpIS is an integrative information system focused on plants and fungal
pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers,
single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g.
genomic sequences, physical maps, genome annotation and expression data) for species
of agronomical interest.
example: AY109603
homepage: https://urgi.versailles.inra.fr/gnpis/
mappings:
biocontext: GNPIS
fairsharing: FAIRsharing.dw22y3
miriam: gnpis
n2t: gnpis
name: GnpIS
pattern: ^[A-Za-z0-9]+$
preferred_prefix: gnpis
uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1
go:
appears_in:
- agro
- chiro
- cl
- ecocore
- ecto
- envo
- maxo
- pcl
- pco
- planp
- uberon
- xpo
- zp
banana: GO
contact:
email: suzia@stanford.edu
github: suzialeksander
name: Suzi Aleksander
orcid: 0000-0001-6787-2901
depends_on:
- cl
- ncbitaxon
- ro
- uberon
description: The Gene Ontology project provides a controlled vocabulary to describe
gene and gene product attributes in any organism.
download_json: http://purl.obolibrary.org/obo/go.json
download_obo: http://purl.obolibrary.org/obo/go.obo
download_owl: http://purl.obolibrary.org/obo/go.owl
example: '0032571'
homepage: http://geneontology.org/
license: CC BY 4.0
mappings:
biocontext: GO
bioportal: GO
fairsharing: FAIRsharing.6xq0ee
go: GO
miriam: go
n2t: go
ncbi: GO
obofoundry: GO
ols: go
ontobee: GO
prefixcommons: go
uniprot: GO
wikidata: P686
name: Gene Ontology
namespace_in_lui: true
pattern: ^\d{7}$
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
repository: https://github.com/geneontology/go-ontology
synonyms:
- gobp
- gobpid
- gocc
- goccid
- gomf
- gomfid
uri_format: http://amigo.geneontology.org/amigo/term/GO:$1
version: '2022-03-10'
go.model:
description: GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking
multiple GO annotations into larger models of biological function (such as “pathways”)
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:$1
go.ref:
banana: GO_REF
description: The GO reference collection is a set of abstracts that can be cited
in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files
(in the Reference column). It provides two types of reference; It can be used
to provide details of why specific Evidence codes (see http://identifiers.org/eco/)
are assigned, or to present abstract-style descriptions of "GO content" meetings
at which substantial changes in the ontologies are discussed and made.
example: '0000041'
homepage: http://www.geneontology.org/cgi-bin/references.cgi
mappings:
biocontext: GO_REF
go: GO_REF
miriam: go_ref
n2t: go.ref
name: Gene Ontology Database references
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: go.ref
uri_format: https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md
go.resource:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A database-specific registry supporting curation in the Gene Ontology
example: CHEBI
homepage: http://geneontology.org/
name: Gene Ontology Registry
preferred_prefix: go.resource
uri_format: https://bioregistry.io/metaregistry/go/$1
goa:
description: The GOA (Gene Ontology Annotation) project provides high-quality Gene
Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB)
and International Protein Index (IPI). This involves electronic annotation and
the integration of high-quality manual GO annotation from all GO Consortium model
organism groups and specialist groups.
example: P12345
homepage: https://www.ebi.ac.uk/GOA/
mappings:
biocontext: GOA
fairsharing: FAIRsharing.7zffgc
miriam: goa
n2t: goa
ncbi: GOA
prefixcommons: goa
name: Gene Ontology Annotation Database
pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$
preferred_prefix: goa
provides: uniprot
uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1
goche:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Represent chemical entities having particular CHEBI roles
download_owl: https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl
example: '25512'
homepage: https://github.com/geneontology/go-ontology
name: GO Chemicals
pattern: ^\d+$
preferred_prefix: GOCHE
references:
- https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400
- https://github.com/geneontology/go-ontology/issues/19535
repository: https://github.com/geneontology/go-ontology
synonyms:
- go.chebi
- go.chemical
- go.chemicals
goeco:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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:
fairsharing: FAIRsharing.5q1p14
miriam: gold
prefixcommons: gold
name: Genomes Online Database
pattern: ^[A-Z][a-z][0-9]+$
preferred_prefix: gold
uri_format: https://gold.jgi.doe.gov/resolver?id=$1
gold.genome:
description: '- DEPRECATION NOTE -
Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix
at https://registry.identifiers.org/registry/gold, and this namespace is kept
here for support to already existing citations, new ones would need to use the
pointed ‘gold’ namespace.
The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of
genome and metagenome projects worldwide. It stores information on complete and
ongoing projects, along with their associated metadata. This collection references
the sequencing status of individual genomes.'
example: Gi07796
homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
mappings:
biocontext: GOLD.GENOME
miriam: gold.genome
n2t: gold.genome
name: GOLD genome
pattern: ^(Gi|Gc)\d+$
preferred_prefix: gold.genome
uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1
gold.meta:
description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\
\ been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold,\
\ and this namespace is kept here for support to already existing citations, new\
\ ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine\
\ Database)is a resource for centralized monitoring of genome and metagenome projects\
\ worldwide. It stores information on complete and ongoing projects, along with\
\ their associated metadata. This collection references metadata associated with\
\ samples."
example: Gm00047
homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
mappings:
biocontext: GOLD.META
miriam: gold.meta
n2t: gold.meta
name: GOLD metadata
pattern: ^Gm\d+$
preferred_prefix: gold.meta
uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1
google.patent:
description: Google Patents covers the entire collection of granted patents and
published patent applications from the USPTO, EPO, and WIPO. US patent documents
date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using
patent number, inventor, classification, and filing date.
example: US4145692
homepage: https://www.google.com/patents/
mappings:
biocontext: GOOGLE.PATENT
cellosaurus: Patent
miriam: google.patent
n2t: google.patent
name: Google Patents
pattern: ^[A-Z]{2}\d+([A-Z])?$
preferred_prefix: google.patent
synonyms:
- patent
uri_format: https://www.google.com/patents/$1
google.scholar:
description: 'Google Scholar provides a simple way to broadly search for scholarly
literature. You can search across many disciplines and sources: articles, theses,
books, abstracts and court opinions, from academic publishers, professional societies,
online repositories, universities and other web sites.'
example: PjrpzUIAAAAJ
homepage: https://scholar.google.com/
mappings:
biolink: GSID
name: Google Scholar Researcher
preferred_prefix: google.scholar
gorel:
description: Documentation of GO that provides a description of some of the commonly
used relationships and conventions in GO.
download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl
example: '0002005'
homepage: http://geneontology.org/docs/ontology-relations/
mappings:
biolink: GOREL
go: GOREL
name: GO Relations
pattern: ^\d{7}$
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:
biocontext: GPCRDB
fairsharing: FAIRsharing.e4n3an
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/$1
gpmdb:
description: The Global Proteome Machine Database was constructed to utilize the
information obtained by GPM servers to aid in the difficult process of validating
peptide MS/MS spectra as well as protein coverage patterns.
example: GPM32310002988
homepage: http://gpmdb.thegpm.org/
mappings:
biocontext: GPMDB
fairsharing: FAIRsharing.fhcmwq
miriam: gpmdb
n2t: gpmdb
name: Global Proteome Machine Database
pattern: ^GPM\d+$
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
graingenes.reference:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A database for Triticeae and Avena references.
example: WGS-95-1333
homepage: http://wheat.pw.usda.gov
name: GrainGenes
preferred_prefix: graingenes.reference
uri_format: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1
graingenes.symbol:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A database for Triticeae and Avena gene symbols.
example: 1-FEH+w3
homepage: http://wheat.pw.usda.gov
name: GrainGenes
preferred_prefix: graingenes.symbol
uri_format: http://wheat.pw.usda.gov/report?class=gene;name=$1
gramene.gene:
description: Gramene is a comparative genome mapping database for grasses and crop
plants. It combines a semi-automatically generated database of cereal genomic
and expressed sequence tag sequences, genetic maps, map relations, quantitative
trait loci (QTL), and publications, with a curated database of mutants (genes
and alleles), molecular markers, and proteins. This datatype refers to genes in
Gramene.
example: GR:0080039
homepage: http://www.gramene.org/
mappings:
biocontext: GRAMENE.GENE
go: GR_GENE
miriam: gramene.gene
n2t: gramene.gene
name: Gramene Gene
pattern: ^GR\:\d+$
preferred_prefix: gramene.gene
synonyms:
- GR_GENE
uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1
gramene.growthstage:
banana: gramene.growthstage:GRO\
description: Gramene is a comparative genome mapping database for grasses and crop
plants. It combines a semi-automatically generated database of cereal genomic
and expressed sequence tag sequences, genetic maps, map relations, quantitative
trait loci (QTL), and publications, with a curated database of mutants (genes
and alleles), molecular markers, and proteins. This collection refers to growth
stage ontology information in Gramene.
example: '0007133'
homepage: http://www.gramene.org/
mappings:
biocontext: GRAMENE.GROWTHSTAGE
miriam: gramene.growthstage
n2t: gramene.growthstage
name: Gramene Growth Stage Ontology
pattern: ^\d{7}$
preferred_prefix: gramene.growthstage
uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1
gramene.protein:
description: Gramene is a comparative genome mapping database for grasses and crop
plants. It combines a semi-automatically generated database of cereal genomic
and expressed sequence tag sequences, genetic maps, map relations, quantitative
trait loci (QTL), and publications, with a curated database of mutants (genes
and alleles), molecular markers, and proteins. This datatype refers to proteins
in Gramene.
example: '78073'
homepage: http://www.gramene.org/
mappings:
biocontext: GRAMENE.PROTEIN
go: GR_PROTEIN
miriam: gramene.protein
n2t: gramene.protein
name: Gramene protein
pattern: ^\d+$
preferred_prefix: gramene.protein
synonyms:
- GR_PROTEIN
uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1
gramene.qtl:
description: Gramene is a comparative genome mapping database for grasses and crop
plants. It combines a semi-automatically generated database of cereal genomic
and expressed sequence tag sequences, genetic maps, map relations, quantitative
trait loci (QTL), and publications, with a curated database of mutants (genes
and alleles), molecular markers, and proteins. This datatype refers to quantitative
trait loci identified in Gramene.
example: CQG5
homepage: http://www.gramene.org/
mappings:
biocontext: GRAMENE.QTL
go: GR_QTL
miriam: gramene.qtl
n2t: gramene.qtl
name: Gramene QTL
pattern: ^\w+$
preferred_prefix: gramene.qtl
synonyms:
- GR_QTL
uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1
gramene.reference:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Literature references in Gramene
example: '6200'
homepage: http://www.gramene.org
name: Gramene Reference
pattern: ^\d+$
preferred_prefix: gramene.reference
synonyms:
- gramene.ref
uri_format: http://www.gramene.org/db/literature/pub_search?ref_id=$1
gramene.taxonomy:
description: Gramene is a comparative genome mapping database for grasses and crop
plants. It combines a semi-automatically generated database of cereal genomic
and expressed sequence tag sequences, genetic maps, map relations, quantitative
trait loci (QTL), and publications, with a curated database of mutants (genes
and alleles), molecular markers, and proteins. This datatype refers to taxonomic
information in Gramene.
example: GR_tax:013681
homepage: http://www.gramene.org/
mappings:
biocontext: GRAMENE.TAXONOMY
miriam: gramene.taxonomy
n2t: gramene.taxonomy
name: Gramene Taxonomy
pattern: ^GR\_tax\:\d+$
preferred_prefix: gramene.taxonomy
uri_format: http://www.gramene.org/db/ontology/search?id=$1
grassbase:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: GrassBase provides an interactive guide to nomenclature for the whole
grass family. It provides lists of over 60,000 names for any given genus, geographical
region or genus within a geographical region, helps find the accepted name, synonyms
and distribution for any given name, and gives a desription for each species.
example: imp10873
homepage: https://www.kew.org/data/grasses-syn/index.htm
name: GrassBase
pattern: ^(imp|gen)\d{5}$
preferred_prefix: grassbase
uri_format: https://www.kew.org/data/grasses-db/www/$1
greengenes:
description: A 16S rRNA gene database which provides chimera screening, standard
alignment, and taxonomic classification using multiple published taxonomies.
example: '100000'
homepage: http://greengenes.lbl.gov/
mappings:
biocontext: GREENGENES
fairsharing: FAIRsharing.bpxgb6
miriam: greengenes
n2t: greengenes
ncbi: Greengenes
prefixcommons: greengenes
name: 16S rRNA gene database
pattern: ^\d+$
preferred_prefix: greengenes
uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1
grid:
description: International coverage of the world's leading research organisations,
indexing 92% of funding allocated globally.
example: grid.225360.0
homepage: https://www.grid.ac/
mappings:
biocontext: GRID
fairsharing: FAIRsharing.0pUMYW
miriam: grid
n2t: grid
name: Global Research Identifier Database
pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$
preferred_prefix: grid
uri_format: https://www.grid.ac/institutes/$1
grin.taxonomy:
description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants
provides information on scientific and common names, classification, distribution,
references, and economic impact.
example: '19333'
homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en
mappings:
biocontext: GRIN.TAXONOMY
go: GRIN
miriam: grin.taxonomy
n2t: grin.taxonomy
ncbi: GRIN
name: Germplasm Resources Information Network
pattern: ^\d+$
preferred_prefix: grin.taxonomy
uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1
gro:
deprecated: true
mappings:
bioportal: GRO
name: Gene Regulation Ontology
preferred_prefix: gro
grsdb:
description: GRSDB is a database of G-quadruplexes and contains information on composition
and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped
in the eukaryotic pre-mRNA sequences, including those that are alternatively processed
(alternatively spliced or alternatively polyadenylated). The data stored in the
GRSDB is based on computational analysis of NCBI Entrez Gene entries and their
corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.
example: '10142'
homepage: http://bioinformatics.ramapo.edu/GRSDB2/
mappings:
biocontext: GRSDB
miriam: grsdb
n2t: grsdb
prefixcommons: grsdb
name: G-Rich Sequences Database
pattern: ^\d+$
preferred_prefix: grsdb
uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1
gsfa:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995)
sets forth the conditions under which permitted food additives may be used in
all foods, whether or not they have previously been standardized by Codex. The
Preamble of the GSFA contains additional information for interpreting the data.
Users are encouraged to consult the Preamble when using this database.
example: '174'
homepage: http://www.fao.org/gsfaonline
name: General Standard for Food Additives Online Database
pattern: ^\d+$
preferred_prefix: gsfa
synonyms:
- FAO/WHO_standards
uri_format: http://www.fao.org/gsfaonline/additives/details.html?id=$1
gsso:
appears_in:
- ontoavida
- scdo
banana: GSSO
contact:
email: kronkcj@mail.uc.edu
github: Superraptor
name: Clair Kronk
orcid: 0000-0001-8397-8810
description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary
ontology connecting terms from biology, medicine, psychology, sociology, and gender
studies, aiming to bridge gaps between linguistic variations inside and outside
of the health care environment. A large focus of the ontology is its consideration
of LGBTQIA+ terminology.
download_json: http://purl.obolibrary.org/obo/gsso.json
download_obo: http://purl.obolibrary.org/obo/gsso.obo
download_owl: http://purl.obolibrary.org/obo/gsso.owl
example: 002368
homepage: https://gsso.research.cchmc.org/
license: Apache 2.0 License
mappings:
bioportal: GSSO
miriam: gsso
obofoundry: GSSO
ols: gsso
ontobee: GSSO
name: Gender, Sex, and Sexual Orientation Ontology
namespace_in_lui: true
pattern: ^\d{6}$
preferred_prefix: GSSO
repository: https://github.com/Superraptor/GSSO
uri_format: http://purl.obolibrary.org/obo/GSSO_$1
version: 2.0.5
gtex:
description: The Genotype-Tissue Expression (GTEx) project aims to provide to the
scientific community a resource with which to study human gene expression and
regulation and its relationship to genetic variation.
example: BRIP1
homepage: https://www.gtexportal.org
mappings:
biocontext: GTEX
biolink: GTEx
miriam: gtex
n2t: gtex
name: Genotype-Tissue Expression
pattern: ^\w.+$
preferred_prefix: gtex
uri_format: https://www.gtexportal.org/home/gene/$1
gtr:
appears_in:
- mondo
comment: Identifiers appearing in MONDO don't match any of the resources apparent
endpoints
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Genetic Testing Registry (GTR®) 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
synonyms:
- medgen.gtr
uri_format: https://www.ncbi.nlm.nih.gov/gtr/conditions/$1
gudmap:
description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is
a consortium of laboratories working to provide the scientific and medical community
with tools to facilitate research on the GenitoUrinary (GU) tract.
example: Q-2958
homepage: http://www.gudmap.org/
mappings:
biocontext: GUDMAP
fairsharing: FAIRsharing.910c39
miriam: gudmap
n2t: gudmap
name: Genitourinary Development Molecular Anatomy Project
pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
preferred_prefix: gudmap
uri_format: https://gudmap.org/id/$1
gwascentral.marker:
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
information) is a database of summary level findings from genetic association
studies, both large and small. It gathers datasets from public domain projects,
and accepts direct data submission. It is based upon Marker information encompassing
SNP and variant information from public databases, to which allele and genotype
frequency data, and genetic association findings are additionally added. A Study
(most generic level) contains one or more Experiments, one or more Sample Panels
of test subjects, and one or more Phenotypes. This collection references a GWAS
Central Marker.
example: HGVM15354
homepage: https://www.gwascentral.org/markers
mappings:
biocontext: GWASCENTRAL.MARKER
miriam: gwascentral.marker
n2t: gwascentral.marker
name: GWAS Central Marker
pattern: ^HGVM\d+$
preferred_prefix: gwascentral.marker
uri_format: https://www.gwascentral.org/marker/$1
gwascentral.phenotype:
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
information) is a database of summary level findings from genetic association
studies, both large and small. It gathers datasets from public domain projects,
and accepts direct data submission. It is based upon Marker information encompassing
SNP and variant information from public databases, to which allele and genotype
frequency data, and genetic association findings are additionally added. A Study
(most generic level) contains one or more Experiments, one or more Sample Panels
of test subjects, and one or more Phenotypes. This collection references a GWAS
Central Phenotype.
example: HGVPM623
homepage: https://www.gwascentral.org/phenotypes
mappings:
biocontext: GWASCENTRAL.PHENOTYPE
miriam: gwascentral.phenotype
n2t: gwascentral.phenotype
name: GWAS Central Phenotype
pattern: ^HGVPM\d+$
preferred_prefix: gwascentral.phenotype
uri_format: https://www.gwascentral.org/phenotype/$1
gwascentral.study:
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
information) is a database of summary level findings from genetic association
studies, both large and small. It gathers datasets from public domain projects,
and accepts direct data submission. It is based upon Marker information encompassing
SNP and variant information from public databases, to which allele and genotype
frequency data, and genetic association findings are additionally added. A Study
(most generic level) contains one or more Experiments, one or more Sample Panels
of test subjects, and one or more Phenotypes. This collection references a GWAS
Central Study.
example: HGVST1828
homepage: https://www.gwascentral.org/studies
mappings:
biocontext: GWASCENTRAL.STUDY
miriam: gwascentral.study
n2t: gwascentral.study
name: GWAS Central Study
pattern: ^HGVST\d+$
preferred_prefix: gwascentral.study
uri_format: https://www.gwascentral.org/study/$1
gxa.expt:
description: The Gene Expression Atlas (GXA) is a semantically enriched database
of meta-analysis based summary statistics over a curated subset of ArrayExpress
Archive, servicing queries for condition-specific gene expression patterns as
well as broader exploratory searches for biologically interesting genes/samples.
This collection references experiments.
example: E-MTAB-2037
homepage: https://www.ebi.ac.uk/gxa/
mappings:
biocontext: GXA.EXPT
miriam: gxa.expt
n2t: gxa.expt
name: GXA Expt
pattern: ^[AEP]-\w{4}-\d+$
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/$1
gxa.gene:
description: The Gene Expression Atlas (GXA) is a semantically enriched database
of meta-analysis based summary statistics over a curated subset of ArrayExpress
Archive, servicing queries for condition-specific gene expression patterns as
well as broader exploratory searches for biologically interesting genes/samples.
This collection references genes.
example: AT4G01080
homepage: https://www.ebi.ac.uk/gxa/
mappings:
biocontext: GXA.GENE
miriam: gxa.gene
n2t: gxa.gene
name: GXA Gene
pattern: ^\w+$
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: 0000-0001-6512-3296
deprecated: true
homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html
mappings:
biocontext: HABRONATTUS
obofoundry: HABRONATTUS
name: Habronattus courtship
preferred_prefix: HABRONATTUS
uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1
hamap:
description: HAMAP is a system that identifies and semi-automatically annotates
proteins that are part of well-conserved and orthologous microbial families or
subfamilies. These are used to build rules which are used to propagate annotations
to member bacterial, archaeal and plastid-encoded protein entries.
example: MF_01400
homepage: https://hamap.expasy.org/
mappings:
biocontext: HAMAP
fairsharing: FAIRsharing.63m4ss
go: HAMAP
miriam: hamap
n2t: hamap
prefixcommons: hamap
uniprot: HAMAP
name: High-quality Automated and Manual Annotation of microbial Proteomes
pattern: ^MF_\d+$
preferred_prefix: hamap
uri_format: https://hamap.expasy.org/unirule/$1
hancestro:
banana: HANCESTRO
contact:
email: danielle.welter@uni.lu
github: daniwelter
name: Danielle Welter
orcid: 0000-0003-1058-2668
description: Human ancestry ontology for the NHGRI GWAS Catalog
download_owl: http://purl.obolibrary.org/obo/hancestro.owl
example: 0290
homepage: https://github.com/EBISPOT/ancestro
license: CC BY 4.0
mappings:
biolink: HANCESTRO
bioportal: HANCESTRO
fairsharing: FAIRsharing.rja8qp
obofoundry: HANCESTRO
ols: hancestro
ontobee: HANCESTRO
name: Human Ancestry Ontology
pattern: ^\d{4}$
preferred_prefix: HANCESTRO
repository: https://github.com/EBISPOT/ancestro
uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1
version: '2.5'
hao:
banana: HAO
contact:
email: diapriid@gmail.com
github: mjy
name: Matt Yoder
orcid: 0000-0002-5640-5491
description: A structured controlled vocabulary of the anatomy of the Hymenoptera
(bees, wasps, and ants)
download_obo: http://purl.obolibrary.org/obo/hao.obo
download_owl: http://purl.obolibrary.org/obo/hao.owl
example: 0000187
homepage: http://hymao.org
license: CC0 1.0
mappings:
biocontext: HAO
bioportal: HAO
fairsharing: FAIRsharing.kj3m5n
obofoundry: HAO
ols: hao
ontobee: HAO
name: Hymenoptera Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: HAO
repository: https://github.com/hymao/hao
uri_format: http://purl.obolibrary.org/obo/HAO_$1
version: '2021-03-05'
hba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
human brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo
example: '4005'
example_extras:
- '265504410'
homepage: https://human.brain-map.org
name: Human Brain Atlas
pattern: ^\d+$
preferred_prefix: HBA
hcao:
description: Application ontology for human cell types, anatomy and development
stages for the Human Cell Atlas.
download_owl: http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2022-04-19/hcao.owl
homepage: https://www.humancellatlas.org
mappings:
ols: hcao
name: Human Cell Atlas Ontology
no_own_terms: true
preferred_prefix: hcao
version: '2022-04-19'
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
fairsharing: FAIRsharing.x81wz8
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:
biocontext: HCVDB
miriam: hcvdb
n2t: hcvdb
name: Hepatitis C Virus Database
pattern: ^M\d{5}$
preferred_prefix: hcvdb
uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1
hdr:
description: The Homeodomain Resource is a curated collection of sequence, structure,
interaction, genomic and functional information on the homeodomain family. It
contains sets of curated homeodomain sequences from fully sequenced genomes, including
experimentally derived homeodomain structures, homeodomain protein-protein interactions,
homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic
disorders.
example: '63'
homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/
mappings:
biocontext: HDR
miriam: hdr
n2t: hdr
prefixcommons: hdr
name: Homeodomain Research
pattern: ^\d+$
preferred_prefix: hdr
uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1
hgmd:
description: The Human Gene Mutation Database (HGMD) collates data on germ-line
mutations in nuclear genes associated with human inherited disease. It includes
information on single base-pair substitutions in coding, regulatory and splicing-relevant
regions; micro-deletions and micro-insertions; indels; triplet repeat expansions
as well as gross deletions; insertions; duplications; and complex rearrangements.
Each mutation entry is unique, and includes cDNA reference sequences for most
genes, splice junction sequences, disease-associated and functional polymorphisms,
as well as links to data present in publicly available online locus-specific mutation
databases.
example: CALM1
homepage: http://www.hgmd.cf.ac.uk/ac/index.php
mappings:
biocontext: HGMD
miriam: hgmd
n2t: hgmd
name: Human Gene Mutation Database
pattern: ^[A-Z_0-9]+$
preferred_prefix: hgmd
uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1
hgnc:
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
name and symbol (short-form abbreviation) for each known human gene. All approved
symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers
refer to records in the HGNC symbol database.
example: '16793'
homepage: http://www.genenames.org
mappings:
biocontext: HGNC
bioportal: HGNC
cellosaurus: HGNC
fairsharing: FAIRsharing.amcv1e
go: HGNC
miriam: hgnc
n2t: hgnc
ncbi: HGNC
prefixcommons: hgnc
uniprot: HGNC
wikidata: P354
name: HUGO Gene Nomenclature Committee
pattern: ^((HGNC|hgnc):)?\d{1,5}$
preferred_prefix: hgnc
providers:
- code: indra
description: A large scale database of biomedical statements.
homepage: https://db.indra.bio
name: INDRA Database
uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC
- code: gencc
description: The GenCC DB provides information pertaining to the validity of gene-disease
relationships, with a current focus on Mendelian diseases. Curated gene-disease
relationships are submitted by GenCC member organizations. The GenCC comprises
organizations that currently provide online resources (e.g. ClinGen, DECIPHER,
Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P),
as well as diagnostic laboratories that have committed to sharing their internal
curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s
Health, Mass General Brigham Laboratory for Molecular Medicine).
homepage: https://thegencc.org
name: The Gene Curation Coalition
uri_format: https://search.thegencc.org/genes/HGNC:$1
uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
hgnc.genefamily:
deprecated: true
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
name and symbol (short-form abbreviation) for each known human gene. All approved
symbols are stored in the HGNC database, and each symbol is unique. In addition,
HGNC also provides symbols for both structural and functional gene families. This
collection refers to records using the HGNC family symbol.
example: '2029'
has_canonical: hgnc.genegroup
homepage: http://www.genenames.org
mappings:
biocontext: HGNC.GENEFAMILY
miriam: hgnc.family
n2t: hgnc.genefamily
name: HGNC Family
pattern: ^[A-Z0-9-]+(#[A-Z0-9-]+)?$
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/$1
hgnc.symbol:
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
name and symbol (short-form abbreviation) for each known human gene. All approved
symbols are stored in the HGNC database, and each symbol is unique. This collection
refers to records using the HGNC symbol.
example: DAPK1
homepage: https://www.genenames.org/
mappings:
biocontext: HGNC.SYMBOL
miriam: hgnc.symbol
n2t: hgnc.symbol
name: HGNC Symbol
pattern: ^[A-Za-z-0-9_]+(\@)?$
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=$1
hinv.locus:
description: H-Invitational Database (H-InvDB) is an integrated database of human
genes and transcripts. It provides curated annotations of human genes and transcripts
including gene structures, alternative splicing isoforms, non-coding functional
RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
repeats), relation with diseases, gene expression profiling, molecular evolutionary
features, protein-protein interactions (PPIs) and gene families/groups. This datatype
provides access to the 'Locus' view.
example: HIX0004394
homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
mappings:
biocontext: HINV.LOCUS
miriam: hinv.locus
n2t: hinv.locus
name: H-InvDb Locus
pattern: ^HIX\d{7}(\.\d+)?$
preferred_prefix: hinv.locus
uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1
hinv.protein:
description: H-Invitational Database (H-InvDB) is an integrated database of human
genes and transcripts. It provides curated annotations of human genes and transcripts
including gene structures, alternative splicing isoforms, non-coding functional
RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
repeats), relation with diseases, gene expression profiling, molecular evolutionary
features, protein-protein interactions (PPIs) and gene families/groups. This datatype
provides access to the 'Protein' view.
example: HIP000030660
homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
mappings:
biocontext: HINV.PROTEIN
miriam: hinv.protein
n2t: hinv.protein
name: H-InvDb Protein
pattern: ^HIP\d{9}(\.\d+)?$
preferred_prefix: hinv.protein
uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1
hinv.transcript:
description: H-Invitational Database (H-InvDB) is an integrated database of human
genes and transcripts. It provides curated annotations of human genes and transcripts
including gene structures, alternative splicing isoforms, non-coding functional
RNAs, protein functions, functional domains, sub-cellular localizations, metabolic
pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite
repeats), relation with diseases, gene expression profiling, molecular evolutionary
features, protein-protein interactions (PPIs) and gene families/groups. This datatype
provides access to the 'Transcript' view.
example: HIT000195363
homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp
mappings:
biocontext: HINV.TRANSCRIPT
miriam: hinv.transcript
n2t: hinv.transcript
name: H-InvDb Transcript
pattern: ^HIT\d{9}(\.\d+)?$
preferred_prefix: hinv.transcript
uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1
hipsci:
description: Cell line databases/resources
example: HPSI0114i-bezi_1
homepage: http://www.hipsci.org
mappings:
cellosaurus: HipSci
name: Human Induced Pluripotent Stem Cells Initiative
preferred_prefix: hipsci
uri_format: http://www.hipsci.org/lines/#/lines/$1
hivreagentprogram:
description: Cell line collections
example: ARP-1513
homepage: https://www.hivreagentprogram.org/Home.aspx
mappings:
cellosaurus: HIVReagentProgram
name: NIH HIV Reagent Program
preferred_prefix: hivreagentprogram
uri_format: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx
hmdb:
description: The Human Metabolome Database (HMDB) is a database containing detailed
information about small molecule metabolites found in the human body.It contains
or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
example: HMDB00001
homepage: http://www.hmdb.ca/
mappings:
biocontext: HMDB
cheminf: 000408
fairsharing: FAIRsharing.sye5js
miriam: hmdb
n2t: hmdb
prefixcommons: hmdb
wikidata: P2057
name: Human Metabolome Database
pattern: ^HMDB\d+$
preferred_prefix: hmdb
synonyms:
- HMDB
uri_format: http://www.hmdb.ca/metabolites/$1
hms.lincs.compound:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/$1
hog:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Documentation of HOGS (Homologous Organs Groups). Contains links to
HOGs download, HOGs onthology, HOGs creation, composition, etc.
download_obo: ftp://ftp.bgee.org/general/ontologies/HOG.obo
example: '0000255'
homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships
name: Homologous Organ Groups
pattern: ^\d{7}$
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:
biocontext: HOGENOM
fairsharing: FAIRsharing.qe8tz8
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=$1
hom:
banana: HOM
contact:
email: bgee@sib.swiss
github: fbastian
name: Frederic Bastian
orcid: 0000-0002-9415-5104
description: This ontology represents concepts related to homology, as well as other
concepts used to describe similarity and non-homology.
download_owl: http://purl.obolibrary.org/obo/hom.owl
example: 0000049
homepage: https://github.com/BgeeDB/homology-ontology
license: CC0 1.0
mappings:
biocontext: HOM
bioportal: HOM
fairsharing: FAIRsharing.efv7gw
obofoundry: HOM
ols: hom
ontobee: HOM
name: Homology Ontology
pattern: ^\d{7}$
preferred_prefix: HOM
repository: https://github.com/BgeeDB/homology-ontology
uri_format: http://purl.obolibrary.org/obo/HOM_$1
version: '2015-01-07'
homd.seq:
description: The Human Oral Microbiome Database (HOMD) provides a site-specific
comprehensive database for the more than 600 prokaryote species that are present
in the human oral cavity. It contains genomic information based on a curated 16S
rRNA gene-based provisional naming scheme, and taxonomic information. This datatype
contains genomic sequence information.
example: SEQF1003
homepage: http://www.homd.org/index.php
mappings:
biocontext: HOMD.SEQ
miriam: homd.seq
n2t: homd.seq
prefixcommons: homd.seq
name: HOMD Sequence Metainformation
pattern: ^SEQF\d+$
preferred_prefix: homd.seq
uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1
homd.taxon:
description: The Human Oral Microbiome Database (HOMD) provides a site-specific
comprehensive database for the more than 600 prokaryote species that are present
in the human oral cavity. It contains genomic information based on a curated 16S
rRNA gene-based provisional naming scheme, and taxonomic information. This datatype
contains taxonomic information.
example: '811'
homepage: http://www.homd.org/index.php
mappings:
biocontext: HOMD.TAXON
miriam: homd.taxon
n2t: homd.taxon
prefixcommons: homd.taxon
name: HOMD Taxonomy
pattern: ^\d+$
preferred_prefix: homd.taxon
uri_format: www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1
homologene:
description: HomoloGene is a system for automated detection of homologs among the
annotated genes of several completely sequenced eukaryotic genomes.
example: '1000'
homepage: https://www.ncbi.nlm.nih.gov/homologene/
mappings:
biocontext: HOMOLOGENE
fairsharing: FAIRsharing.mzc066
miriam: homologene
n2t: homologene
prefixcommons: homologene
wikidata: P593
name: HomoloGene
pattern: ^\d+$
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
horizon_discovery:
description: Cell line collections
example: HD+118-001
homepage: https://horizondiscovery.com/
mappings:
cellosaurus: Horizon_Discovery
name: Horizon Discovery cell line collection
preferred_prefix: horizon_discovery
uri_format: https://horizondiscovery.com/en/search?searchterm=$1
hovergen:
description: HOVERGEN is a database of homologous vertebrate genes that allows one
to select sets of homologous genes among vertebrate species, and to visualize
multiple alignments and phylogenetic trees.
example: HBG004341
homepage: https://pbil.univ-lyon1.fr/databases/hovergen.php
mappings:
biocontext: HOVERGEN
fairsharing: FAIRsharing.dg1f0e
miriam: hovergen
n2t: hovergen
prefixcommons: hovergen
name: Homologous Vertebrate Genes Database
pattern: ^HBG\d+$
preferred_prefix: hovergen
uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN
hp:
appears_in:
- chiro
- scdo
banana: HP
contact:
email: dr.sebastian.koehler@gmail.com
github: drseb
name: Sebastian Koehler
orcid: 0000-0002-5316-1399
description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary
of phenotypic abnormalities encountered in human disease. Each term in the HPO
describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently
being developed using the medical literature, Orphanet, DECIPHER, and OMIM.
download_obo: http://purl.obolibrary.org/obo/hp.obo
download_owl: http://purl.obolibrary.org/obo/hp.owl
example: '0011140'
homepage: http://www.human-phenotype-ontology.org/
license: hpo
mappings:
biocontext: HPO
bioportal: HP
fairsharing: FAIRsharing.kbtt7f
miriam: hp
n2t: hp
obofoundry: HP
ols: hp
ontobee: HP
wikidata: P3841
name: Human Phenotype Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: HP
repository: https://github.com/obophenotype/human-phenotype-ontology
synonyms:
- hpo
uri_format: https://hpo.jax.org/app/browse/term/HP:$1
version: '2022-04-14'
hpa:
description: The Human Protein Atlas (HPA) is a publicly available database with
high-resolution images showing the spatial distribution of proteins in different
normal and cancer human cell lines. Primary access to this collection is through
Ensembl Gene identifiers.
example: ENSG00000026508
homepage: http://www.proteinatlas.org/
mappings:
biocontext: HPA
fairsharing: FAIRsharing.j0t0pe
go: HPA
miriam: hpa
n2t: hpa
prefixcommons: hpa
uniprot: HPA
name: Human Protein Atlas tissue profile information
pattern: ^ENSG\d{11}$
preferred_prefix: hpa
uri_format: http://www.proteinatlas.org/$1
hpath:
description: An ontology of histopathological morphologies used by pathologists
to classify/categorise animal lesions observed histologically during regulatory
toxicology studies. The ontology was developed using real data from over 6000
regulatory toxicology studies donated by 13 companies spanning nine species.
download_owl: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo
example: '2000191'
homepage: https://github.com/Novartis/hpath
mappings:
ols: hpath
name: Histopathology Ontology
pattern: ^\d+$
preferred_prefix: hpath
repository: https://github.com/Novartis/hpath
synonyms:
- MC
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:
biocontext: HPM.PEPTIDE
miriam: hpm.peptide
n2t: hpm.peptide
name: Human Proteome Map Peptide
pattern: ^\d+$
preferred_prefix: hpm.peptide
uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1
hpm.protein:
description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
result from the draft map of the human proteome project. The project was based
on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
mass spectrometry. The HPM contains direct evidence of translation of a number
of protein products derived from human genes, based on peptide identifications
of multiple organs/tissues and cell types from individuals with clinically defined
healthy tissues. The HPM portal provides data on individual proteins, as well
as on individual peptide spectra. This collection references proteins.
example: '1968'
homepage: http://www.humanproteomemap.org/index.php
mappings:
biocontext: HPM.PROTEIN
miriam: hpm.protein
n2t: hpm.protein
name: Human Proteome Map Protein
pattern: ^\d+$
preferred_prefix: hpm.protein
uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1
hprd:
description: The Human Protein Reference Database (HPRD) represents a centralized
platform to visually depict and integrate information pertaining to domain architecture,
post-translational modifications, interaction networks and disease association
for each protein in the human proteome.
example: '00001'
homepage: http://www.hprd.org/
mappings:
biocontext: HPRD
fairsharing: FAIRsharing.y2qws7
miriam: hprd
n2t: hprd
prefixcommons: hprd
name: Human Protein Reference Database
pattern: ^\d+$
preferred_prefix: hprd
uri_format: http://www.hprd.org/protein/$1
hpscreg:
description: hPSCreg is a freely accessible global registry for human pluripotent
stem cell lines (hPSC-lines).
example: BCRTi001-A
homepage: https://hpscreg.eu/
mappings:
cellosaurus: hPSCreg
fairsharing: FAIRsharing.7C0aVE
miriam: hpscreg
n2t: hpscreg
name: Human Pluripotent Stem Cell Registry
pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$
preferred_prefix: hpscreg
uri_format: https://hpscreg.eu/cell-line/$1
hsapdv:
appears_in:
- scdo
banana: HsapDv
contact:
email: frederic.bastian@unil.ch
github: fbastian
name: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: Life cycle stages for Human
download_obo: http://purl.obolibrary.org/obo/hsapdv.obo
download_owl: http://purl.obolibrary.org/obo/hsapdv.owl
example: 0000194
homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
license: CC BY 3.0
mappings:
biocontext: HSAPDV
biolink: HsapDv
bioportal: HSAPDV
fairsharing: FAIRsharing.c6vhm3
obofoundry: HsapDv
ols: hsapdv
ontobee: HSAPDV
name: Human Developmental Stages
pattern: ^\d{7}$
preferred_prefix: HsapDv
repository: https://github.com/obophenotype/developmental-stage-ontologies
synonyms:
- HsapDv
uri_format: http://purl.obolibrary.org/obo/HSAPDV_$1
version: '2020-03-10'
hsdb:
description: The Hazardous Substances Data Bank (HSDB) is a toxicology database
that focuses on the toxicology of potentially hazardous chemicals. It provides
information on human exposure, industrial hygiene, emergency handling procedures,
environmental fate, regulatory requirements, nanomaterials, and related areas.
example: '5621'
homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb
mappings:
wikidata: P2062
name: Hazardous Substances Data Bank
pattern: ^\d+$
preferred_prefix: hsdb
uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1
hso:
banana: HSO
contact:
email: fernanda.dorea@sva.se
github: nandadorea
name: Fernanda Dorea
orcid: 0000-0001-8638-8525
depends_on:
- bfo
- ncbitaxon
- obi
- ro
- uberon
description: The health Surveillance Ontology (HSO) focuses on "surveillance system
level data", that is, data outputs from surveillance activities, such as number
of samples collected, cases observed, etc. It aims to support One-Health surveillance,
covering animal health, public health and food safety surveillance.
download_owl: http://purl.obolibrary.org/obo/hso.owl
example: '0000062'
homepage: https://w3id.org/hso
license: CC BY 3.0
mappings:
bioportal: HSO
obofoundry: HSO
ols: hso
ontobee: HSO
name: Health Surveillance Ontology
pattern: ^\d{7}$
preferred_prefix: HSO
repository: https://github.com/SVA-SE/HSO
uri_format: http://purl.obolibrary.org/obo/HSO_$1
version: '2021-12-13'
hssp:
description: HSSP (homology-derived structures of proteins) is a derived database
merging structural (2-D and 3-D) and sequence information (1-D). For each protein
of known 3D structure from the Protein Data Bank, the database has a file with
all sequence homologues, properly aligned to the PDB protein.
example: 102l
homepage: http://swift.cmbi.kun.nl/swift/hssp/
mappings:
biocontext: HSSP
miriam: hssp
n2t: hssp
ncbi: HSSP
prefixcommons: hssp
name: Database of homology-derived secondary structure of proteins
pattern: ^\w{4}$
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/$1.hssp.bz2
htn:
banana: HTN
contact:
email: aellenhicks@gmail.com
github: aellenhicks
name: Amanda Hicks
orcid: 0000-0002-1795-5570
description: An ontology for representing clinical data about hypertension, intended
to support classification of patients according to various diagnostic guidelines
download_owl: http://purl.obolibrary.org/obo/htn.owl
example: '00000014'
homepage: https://github.com/aellenhicks/htn_owl
license: CC BY 4.0
mappings:
bioportal: HTN
obofoundry: HTN
ols: htn
ontobee: HTN
name: Hypertension Ontology
pattern: ^\d{8}$
preferred_prefix: HTN
repository: https://github.com/aellenhicks/htn_owl
uri_format: http://purl.obolibrary.org/obo/HTN_$1
version: '2019-06-10'
huge:
description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results
from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa
cDNA sequencing project.
example: KIAA0001
homepage: http://www.kazusa.or.jp/huge/
mappings:
biocontext: HUGE
fairsharing: FAIRsharing.zx2ztd
miriam: huge
n2t: huge
prefixcommons: huge
uniprot: HUGE
name: Human Unidentified Gene-Encoded
pattern: ^KIAA\d{4}$
preferred_prefix: huge
uri_format: https://www.kazusa.or.jp/huge/gfpage/$1
iao:
appears_in:
- agro
- clyh
- duo
- ecocore
- ecto
- fovt
- labo
- maxo
- pco
- psdo
- xpo
banana: IAO
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
description: An ontology of information entities, originally driven by work by the
Ontology of Biomedical Investigation (OBI) digital entity and realizable information
entity branch.
download_owl: http://purl.obolibrary.org/obo/iao.owl
example: '0000030'
homepage: https://github.com/information-artifact-ontology/IAO/
license: CC BY 4.0
mappings:
biocontext: IAO
bioportal: IAO
fairsharing: FAIRsharing.gq1xtx
go: IAO
miriam: iao
n2t: iao
obofoundry: IAO
ols: iao
ontobee: IAO
name: Information Artifact Ontology
pattern: ^\d{7}$
preferred_prefix: IAO
repository: https://github.com/information-artifact-ontology/IAO
uri_format: http://purl.obolibrary.org/obo/IAO_$1
version: '2020-12-09'
icd10:
description: The International Classification of Diseases is the international standard
diagnostic classification for all general epidemiological and many health management
purposes.
example: C34
homepage: https://icd.who.int/browse10
mappings:
biocontext: ICD
biolink: ICD10
bioportal: ICD10
fairsharing: FAIRsharing.nj16g
miriam: icd
n2t: icd
prefixcommons: icd
wikidata: P494
name: International Classification of Diseases, 10th Revision
pattern: ^[A-Z]\d+(\.[-\d+])?$
preferred_prefix: icd10
references:
- https://icdcodelookup.com/icd-10/codes/A01.1
synonyms:
- ICD
- ICD-10
- ICD10
uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1
icd10cm:
description: ICD-10-CM is the official system of assigning codes to diagnoses and
procedures associated with hospital utilization in the United States.
example: F4521
homepage: https://www.icd10data.com/ICD10CM
mappings:
bioportal: ICD10CM
fairsharing: FAIRsharing.hpvbxb
wikidata: P4229
name: International Classification of Diseases, 10th Revision, Clinical Modification
preferred_prefix: icd10cm
synonyms:
- ICD10CM
uri_format: https://icd.codes/icd10cm/$1
icd10pcs:
description: 'ICD-10-PCS is being developed as the successor to Volume 3 of the
International Classification of Diseases, Ninth Revision, Clinical Modification
(ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.
ICD-10-PCS will be the official system of assigning codes to procedures associated
with hospital utilization in the United States. ICD-10-PCS codes will support
data collection, payment and electronic health records.'
example: 01N50ZZ
homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS
mappings:
bioportal: ICD10PCS
fairsharing: FAIRsharing.85k1jm
wikidata: P1690
name: International Classification of Diseases, 10th Revision, Procedure Coding
System
preferred_prefix: icd10pcs
uri_format: https://www.findacode.com/code.php?set=ICD10PCS&c=$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:
fairsharing: FAIRsharing.97805c
wikidata: P7807
name: International Classification of Diseases, 11th Revision
preferred_prefix: icd11
synonyms:
- ICD-11
uri_format: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1
icd9:
description: The International Classification of Diseases (ICD) is designed to promote
international comparability in the collection, processing, classification, and
presentation of mortality statistics.
example: '277.9'
homepage: https://www.cdc.gov/nchs/icd/icd9.htm
mappings:
biolink: ICD9
wikidata: P493
name: International Classification of Diseases, 9th Revision
preferred_prefix: icd9
synonyms:
- ICD9
- ICD9_2005
- MTHICD9_2006
uri_format: http://www.icd9data.com/getICD9Code.ashx?icd9=$1
icd9cm:
description: ICD-9-CM is the official system of assigning codes to diagnoses and
procedures associated with hospital utilization in the United States.
example: '784'
homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm
mappings:
bioportal: ICD9CM
fairsharing: FAIRsharing.10zsxb
wikidata: P1692
name: International Classification of Diseases, 9th Revision, Clinical Modification
pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$
preferred_prefix: icd9cm
synonyms:
- IC9CM
- ICD9CM
- ICD9CM_2005
- ICD9CM_2006
- ICDCM_2005
uri_format: http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1
icdc:
description: The Integrated Canine Data Commons is one of several repositories within
the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure
that provides secure access to a large, comprehensive, and expanding collection
of cancer research data. The ICDC was established to further research on human
cancers by enabling comparative analysis with canine cancer.
example: 000009
homepage: https://caninecommons.cancer.gov/#/
mappings:
fairsharing: FAIRsharing.d95034
miriam: icdc
name: Integrated Canine Data Commons
pattern: ^\d{6}$
preferred_prefix: icdc
uri_format: https://caninecommons.cancer.gov/#/study/$1
icdo:
description: The International Classification of Diseases for Oncology (ICD-O) is
a domain-specific extension of the International Statistical Classification of
Diseases and Related Health Problems for tumor diseases
example: 9861/3
homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/
mappings:
prefixcommons: icdo
wikidata: P563
name: International Classification of Diseases for Oncology
pattern: ^[8-9]\d{3}(/[0-3])?$
preferred_prefix: icdo
synonyms:
- ICD-O
- ICDO
uri_format: http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1
iceberg.element:
description: ICEberg (Integrative and conjugative elements) is a database of integrative
and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
elements that can integrate into and excise from a host chromosome, and can carry
likely virulence determinants, antibiotic-resistant factors and/or genes coding
for other beneficial traits. It contains details of ICEs found in representatives
bacterial species, and which are organised as families. This collection references
ICE elements.
example: '100'
homepage: http://db-mml.sjtu.edu.cn/ICEberg/
mappings:
biocontext: ICEBERG.ELEMENT
miriam: iceberg.element
n2t: iceberg.element
name: ICEberg element
pattern: ^\d+$
preferred_prefix: iceberg.element
uri_format: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1
iceberg.family:
description: ICEberg (Integrative and conjugative elements) is a database of integrative
and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
elements that can integrate into and excise from a host chromosome, and can carry
likely virulence determinants, antibiotic-resistant factors and/or genes coding
for other beneficial traits. It contains details of ICEs found in representatives
bacterial species, and which are organised as families. This collection references
ICE families.
example: '1'
homepage: http://db-mml.sjtu.edu.cn/ICEberg/
mappings:
biocontext: ICEBERG.FAMILY
miriam: iceberg.family
n2t: iceberg.family
name: ICEberg family
pattern: ^\d+$
preferred_prefix: iceberg.family
uri_format: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1
iceo:
banana: ICEO
contact:
email: liumeng94@sjtu.edu.cn
github: Lemon-Liu
name: Meng LIU
orcid: 0000-0003-3781-6962
description: A biological ontology to standardize and integrate Integrative and
Conjugative Element (ICE) information and to support computer-assisted reasoning.
download_owl: http://purl.obolibrary.org/obo/iceo.owl
example: '0000712_1'
example_extras:
- '0000712'
homepage: https://github.com/ontoice/ICEO
license: CC BY 4.0
mappings:
bioportal: ICEO
obofoundry: ICEO
ols: iceo
ontobee: ICEO
name: Integrative and Conjugative Element Ontology
pattern: ^\d{7}(_\d)?$
preferred_prefix: ICEO
repository: https://github.com/ontoice/ICEO
uri_format: http://purl.obolibrary.org/obo/ICEO_$1
version: '2.1'
icepo:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The Ion Channel Electrophysiology Ontology supports the capture of
voltage-gated ion channel electrophysiological data from the literature in a structured
manner and thus enables other applications such as querying and reasoning tools. '
download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo
example: '0000002'
homepage: https://download.nextprot.org/pub/current_release/controlled_vocabularies/
name: Ion Channel Electrophysiology Ontology
pattern: ^\d{7}$
preferred_prefix: icepo
references:
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823818/
iclc:
description: Cell line collections
example: ATL98012
homepage: http://www.iclc.it
mappings:
cellosaurus: ICLC
name: Interlab Cell Line Collection
preferred_prefix: iclc
uri_format: http://www.iclc.it/details/det_list.php?line_id=$1
ico:
appears_in:
- scdo
banana: ICO
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: The Informed Consent Ontology (ICO) is an ontology for the informed
consent and informed consent process in the medical field.
download_owl: http://purl.obolibrary.org/obo/ico.owl
example: '0000066'
homepage: https://github.com/ICO-ontology/ICO
license: CC BY 3.0
mappings:
biocontext: ICO
bioportal: ICO
fairsharing: FAIRsharing.b9znd5
obofoundry: ICO
ols: ico
ontobee: ICO
name: Informed Consent Ontology
pattern: ^\d{7}$
preferred_prefix: ICO
repository: https://github.com/ICO-ontology/ICO
uri_format: http://purl.obolibrary.org/obo/ICO_$1
version: 1.0.187
ideal:
description: IDEAL provides a collection of knowledge on experimentally verified
intrinsically disordered proteins. It contains manual annotations by curators
on intrinsically disordered regions, interaction regions to other molecules, post-translational
modification sites, references and structural domain assignments.
example: IID00001
homepage: https://www.ideal-db.org
mappings:
biocontext: IDEAL
fairsharing: FAIRsharing.h3y42f
miriam: ideal
n2t: ideal
uniprot: IDEAL
name: Intrinsically Disordered proteins with Extensive Annotations and Literature
pattern: ^IID\d+$
preferred_prefix: ideal
uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1
ido:
appears_in:
- scdo
banana: IDO
contact:
email: Lindsay.Cowell@utsouthwestern.edu
github: lgcowell
name: Lindsay Cowell
orcid: 0000-0003-1617-8244
description: Infectious Disease Ontology holds entities relevant to both biomedical
and clinical aspects of most infectious diseases.
download_owl: http://purl.obolibrary.org/obo/ido.owl
example: '0000504'
homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
license: CC BY 3.0
mappings:
biocontext: IDO
bioportal: IDO
fairsharing: FAIRsharing.aae3v6
miriam: ido
n2t: ido
obofoundry: IDO
ols: ido
ontobee: IDO
name: Infectious Disease Ontology
pattern: ^[0-9]+$
preferred_prefix: IDO
repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology
uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1
version: '2017-11-03'
idocovid19:
contact:
email: johnbeverley2021@u.northwestern.edu
github: johnbeve
name: John Beverly
orcid: 0000-0002-1118-1738
description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension
of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology
(VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal
Ontology as its starting point, and covers epidemiology, classification, pathogenesis,
and treatment of terms used to represent infection by the SARS-CoV-2 virus strain,
and the associated COVID-19 disease.
download_owl: http://purl.obolibrary.org/obo/2020-21-07/ido-covid-19.owl
example: 0001191
homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
mappings:
bioportal: IDO-COVID-19
ols: idocovid19
name: The COVID-19 Infectious Disease Ontology
pattern: ^\d{7}$
preferred_prefix: idocovid19
repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
version: '2020-07-21'
idoden:
description: An ontology for dengue fever.
example: '0003463'
homepage: https://bioportal.bioontology.org/ontologies/IDODEN
mappings:
bioportal: IDODEN
fairsharing: FAIRsharing.askzq4
name: Dengue Fever Ontology
pattern: ^\d{7}$
preferred_prefix: idoden
references:
- https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479
idomal:
appears_in:
- scdo
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.
download_obo: http://purl.obolibrary.org/obo/idomal.obo
download_owl: http://purl.obolibrary.org/obo/idomal.owl
example: '0002350'
homepage: https://www.vectorbase.org/ontology-browser
license: CC0 1.0
mappings:
biocontext: IDOMAL
bioportal: IDOMAL
fairsharing: FAIRsharing.2q8c28
obofoundry: IDOMAL
ols: idomal
ontobee: IDOMAL
name: Malaria Ontology
pattern: ^\d{7}$
preferred_prefix: IDOMAL
repository: https://github.com/VEuPathDB-ontology/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#$1
idot:
description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful
terms for describing datasets.
example: identifierPattern
homepage: http://biomodels.net/vocab/idot.rdf
mappings:
biocontext: IDOT
miriam: idot
n2t: idot
name: Identifiers.org Terms
pattern: ^[A-Za-z]+$
preferred_prefix: idot
uri_format: https://biomodels.net/vocab/idot.rdf#$1
idpo:
contact:
email: f.quaglia@ibiom.cnr.it
github: federicaquaglia
name: Federica Quaglia
orcid: 0000-0002-0341-4888
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions
and functions directly associated with their disordered state. GO is used to describe
functional aspects of an IDP/IDR.
example: '00056'
homepage: https://www.disprot.org/ontology
name: Intrinsically Disordered Proteins Ontology
pattern: ^\d{5}$
preferred_prefix: idpo
uri_format: https://www.disprot.org/idpo/IDPO:$1
idr:
description: Image Data Resource (IDR) is an online, public data repository that
seeks to store, integrate and serve image datasets from published scientific studies.
We have collected and are continuing to receive existing and newly created “reference
image" datasets that are valuable resources for a broad community of users, either
because they will be frequently accessed and cited or because they can serve as
a basis for re-analysis and the development of new computational tools.
example: '0001'
homepage: https://idr.openmicroscopy.org
mappings:
fairsharing: FAIRsharing.6wf1zw
miriam: idr
name: Image Data Resource
pattern: ^[0-9]{4}$
preferred_prefix: idr
uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1
iedb:
description: The Immune Epitope Database (IEDB) is a freely available resource funded
by NIAID. It catalogs experimental data on antibody and T cell epitopes studied
in humans, non-human primates, and other animal species in the context of infectious
disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools
to assist in the prediction and analysis of epitopes.
example: '1038233'
homepage: https://www.lji.org/
mappings:
fairsharing: FAIRsharing.c886cd
miriam: iedb
name: Immune Epitope Database
pattern: ^[0-9]+$
preferred_prefix: iedb
uri_format: https://www.iedb.org/reference/$1
iev:
banana: IEV
deprecated: true
example: '0000000'
homepage: http://www.inoh.org
mappings:
biocontext: IEV
obofoundry: IEV
prefixcommons: iev
name: Event (INOH pathway ontology)
pattern: ^\d{7}$
preferred_prefix: IEV
uri_format: http://purl.obolibrary.org/obo/IEV_$1
igrhcellid:
description: Cell line databases/resources
example: ACHN
homepage: http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi
mappings:
cellosaurus: IGRhCellID
name: Integrated Genomic Resources of human Cell Lines for Identification
preferred_prefix: igrhcellid
uri_format: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1
igsn:
description: IGSN is a globally unique and persistent identifier for material samples
and specimens. IGSNs are obtained from IGSN e.V. Agents.
example: AU124
homepage: http://www.geosamples.org/
mappings:
fairsharing: FAIRsharing.Yvc76F
miriam: igsn
n2t: igsn
name: International Geo Sample Number
pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$
preferred_prefix: igsn
uri_format: http://igsn.org/$1
igsr:
description: 'The International Genome Sample Resource (IGSR) was established to
ensure the ongoing usability of data generated by the 1000 Genomes Project and
to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating
the largest public catalogue of human variation and genotype data. As the project
ended, the Data Coordination Centre at EMBL-EBI has received continued funding
from the Wellcome Trust to maintain and expand the resource. IGSR was set up to
do this and has the following aims: ensure the future access to and usability
of the 1000 Genomes reference data; incorporate additional published genomic data
on the 1000 Genomes samples; and expand the data collection to include new populations
not represented in the 1000 Genomes Project.'
example: NA06985
homepage: https://www.internationalgenome.org/
mappings:
cellosaurus: IGSR
fairsharing: FAIRsharing.4Vs9VM
name: International Genome Sample Resource
preferred_prefix: igsr
uri_format: https://www.internationalgenome.org/data-portal/sample/$1
ihw:
description: The International Histocompatibility Working Group provides a comprehensive
inventory of HLA reference genes to support worldwide research in immunogenetics.
We also offer selected cell lines and DNA from our substantial DNA Bank of more
than 1,000 cell lines from selected families, as well as individuals with diverse
ethnicity and immunologic characteristics.
example: IHW09326
homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html
mappings:
cellosaurus: IHW
name: International Histocompatibility Workshop cell lines
pattern: ^IHW\d+$
preferred_prefix: ihw
illumina.probe:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Illumina probe identifiers for microarrays, such as those in Illumina
HumanRef-6 v2.0 expression beadchip.
example: ILMN_129894
homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt
name: Illumina Probe Identifier
pattern: ^ILMN_\d+$
preferred_prefix: illumina.probe
references:
- https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt
imanis:
description: Cell line collections
example: CL070
homepage: https://www.imanislife.com/collections/cell-lines/
mappings:
cellosaurus: Imanis
name: Imanis Life Sciences cell line products
preferred_prefix: imanis
uri_format: https://www.imanislife.com/?s=$1
imdrf:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The International Medical Device Regulators Forum (IMDRF) is a forum
of voluntary medical device regulators from around the world who have come together
to build on the strong foundational work of the Global Harmonization Task Force
on Medical Devices (GHTF), and to accelerate international medical device regulatory
harmonization and convergence.
homepage: http://www.imdrf.org/
name: International Medical Device Regulators Forum
no_own_terms: true
preferred_prefix: imdrf
references:
- https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes
imex:
description: The International Molecular Exchange (IMEx) is a consortium of molecular
interaction databases which collaborate to share manual curation efforts and provide
accessibility to multiple information sources.
example: IM-19210-3
homepage: https://www.imexconsortium.org/
mappings:
biocontext: IMEX
miriam: imex
n2t: imex
prefixcommons: imex
name: International Molecular Exchange
pattern: ^IM-\d+(-?)(\d+?)$
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=$1
img.gene:
description: The integrated microbial genomes (IMG) system is a data management,
analysis and annotation platform for all publicly available genomes. IMG contains
both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
with all other publicly available genomes from all three domains of life, together
with a large number of plasmids and viruses. This datatype refers to gene information.
example: '638309541'
homepage: http://img.jgi.doe.gov/
mappings:
biocontext: IMG.GENE
miriam: img.gene
n2t: img.gene
prefixcommons: img.gene
name: Integrated Microbial Genomes Gene
pattern: ^\d+$
preferred_prefix: img.gene
uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1
img.taxon:
description: The integrated microbial genomes (IMG) system is a data management,
analysis and annotation platform for all publicly available genomes. IMG contains
both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
with all other publicly available genomes from all three domains of life, together
with a large number of plasmids and viruses. This datatype refers to taxon information.
example: '648028003'
homepage: http://img.jgi.doe.gov/
mappings:
biocontext: IMG.TAXON
miriam: img.taxon
n2t: img.taxon
prefixcommons: img.taxon
name: Integrated Microbial Genomes Taxon
pattern: ^\d+$
preferred_prefix: img.taxon
uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1
imgt.hla:
description: IMGT, the international ImMunoGeneTics project, is a collection of
high-quality integrated databases specialising in Immunoglobulins, T cell receptors
and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA
is a database for sequences of the human MHC, referred to as HLA. It includes
all the official sequences for the WHO Nomenclature Committee For Factors of the
HLA System. This collection references allele information through the WHO nomenclature.
example: A*01:01:01:01
homepage: https://www.ebi.ac.uk/imgt/hla/allele.html
mappings:
biocontext: IMGT.HLA
cellosaurus: IPD-IMGT/HLA
fairsharing: FAIRsharing.e28v7g
go: IMGT_HLA
miriam: imgt.hla
n2t: imgt.hla
ncbi: IMGT/HLA
prefixcommons: imgthla
name: IMGT/HLA human major histocompatibility complex sequence database
pattern: ^[A-Z0-9*:]+$
preferred_prefix: imgt.hla
synonyms:
- IPD-IMGT/HLA
uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1
imgt.ligm:
description: IMGT, the international ImMunoGeneTics project, is a collection of
high-quality integrated databases specialising in Immunoglobulins, T cell receptors
and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM
is a comprehensive database of fully annotated sequences of Immunoglobulins and
T cell receptors from human and other vertebrates.
example: M94112
homepage: http://www.imgt.org/
mappings:
biocontext: IMGT.LIGM
go: IMGT_LIGM
miriam: imgt.ligm
n2t: imgt.ligm
ncbi: IMGT/LIGM
prefixcommons: imgt.ligm
name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors
pattern: ^M\d+$
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=$1
imr:
banana: IMR
contact:
email: curator@inoh.org
github: null
name: INOH curators
orcid: null
deprecated: true
example: '0000001'
homepage: http://www.inoh.org
mappings:
biocontext: IMR
obofoundry: IMR
prefixcommons: imr
name: Molecule role (INOH Protein name/family name ontology)
pattern: ^\d{7}$
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:
biocontext: INCHI
fairsharing: FAIRsharing.ddk9t9
miriam: inchi
n2t: 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/$1
inchikey:
description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383)
is an identifier for chemical substances, and is derived solely from a structural
representation of that substance. Since these can be quite unwieldly, particularly
for web use, the InChIKey was developed. These are of a fixed length (25 character)
and were created as a condensed, more web friendly, digital representation of
the InChI.
example: RYYVLZVUVIJVGH-UHFFFAOYSA-N
homepage: http://www.chemspider.com/
mappings:
biocontext: INCHIKEY
miriam: inchikey
n2t: inchikey
scholia: inchikey
wikidata: P235
name: InChIKey
pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])$
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
inhand:
comment: This nomenclature is available via email. Truly a disgrace.
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The standard reference for nomenclature and diagnostic criteria in
toxicologic pathology.
homepage: https://www.goreni.org/gr3_nomenclature.php
mappings:
fairsharing: FAIRsharing.9gqfpm
name: The International Harmonization of Nomenclature and Diagnostic criteria
preferred_prefix: inhand
proprietary: true
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=$1
ino:
banana: INO
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: he Interaction Network Ontology (INO) is an ontology in the domain
of interactions and interaction networks. INO represents general and species-neutral
types of interactions and interaction networks, and their related elements and
relations. INO is a community-driven ontology, aligns with BFO, and is developed
by following the OBO Foundry principles.
download_owl: http://purl.obolibrary.org/obo/ino.owl
example: '0000003'
homepage: https://github.com/INO-ontology/ino
license: CC BY 3.0
mappings:
biolink: INO
bioportal: INO
fairsharing: FAIRsharing.mm72as
obofoundry: INO
ols: ino
ontobee: INO
name: Interaction Network Ontology
pattern: ^\d{7}$
preferred_prefix: INO
repository: https://github.com/INO-ontology/ino
uri_format: http://purl.obolibrary.org/obo/INO_$1
version: 1.0.112
insdc:
description: The International Nucleotide Sequence Database Collaboration (INSDC)
consists of a joint effort to collect and disseminate databases containing DNA
and RNA sequences.
example: X58356
homepage: https://www.ncbi.nlm.nih.gov/Genbank/
mappings:
biocontext: INSDC
miriam: insdc
n2t: insdc
prefixcommons: insdc
name: Nucleotide Sequence Database
pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
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/$1
insdc.cds:
description: The coding sequence or protein identifiers as maintained in INSDC.
example: AAA35559
has_canonical: ncbiprotein
homepage: http://getentry.ddbj.nig.ac.jp
mappings:
biocontext: INSDC.CDS
miriam: insdc.cds
n2t: insdc.cds
name: INSDC CDS
pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
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/$1
insdc.gca:
description: The genome assembly database contains detailed information about genome
assemblies for eukaryota, bacteria and archaea. The scope of the genome collections
database does not extend to viruses, viroids and bacteriophage.
example: GCA_000155495.1
homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database
mappings:
biocontext: INSDC.GCA
miriam: insdc.gca
n2t: insdc.gca
name: Genome assembly database
pattern: ^GC[AF]_[0-9]{9}\.[0-9]+$
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/$1
insdc.run:
comment: 'https://www.insdc.org/ is the authoritative source for INSDC. However,
confusingly, they don''t mention runs in this table. I think we should ask them
to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html
Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | --'
contributor:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: An experimental run, served thrugh the ENA
example: ERR436051
has_canonical: ena.embl
homepage: https://www.insdc.org/
name: International Nucleotide Sequence Database Collaboration (INSDC) Run
pattern: ^(E|D|S)RR[0-9]{6,}$
preferred_prefix: insdc.run
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
insdc.sra:
description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the
next generation of sequencing platforms Data submitted to SRA. It is organized
using a metadata model consisting of six objects: study, sample, experiment, run,
analysis and submission. The SRA study contains high-level information including
goals of the study and literature references, and may be linked to the INSDC BioProject
database.'
example: SRX000007
homepage: https://www.ncbi.nlm.nih.gov/sra
mappings:
biocontext: INSDC.SRA
fairsharing: FAIRsharing.g7t2hv
miriam: insdc.sra
n2t: insdc.sra
name: Sequence Read Archive
pattern: ^[SED]R[APRSXZ]\d+$
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/$1
intact:
description: IntAct provides a freely available, open source database system and
analysis tools for protein interaction data.
example: EBI-2307691
homepage: https://www.ebi.ac.uk/intact/
mappings:
biocontext: INTACT
fairsharing: FAIRsharing.d05nwx
go: IntAct
miriam: intact
n2t: intact
prefixcommons: intact
uniprot: IntAct
name: IntAct protein interaction database
pattern: ^EBI\-[0-9]+$
preferred_prefix: intact
uri_format: https://www.ebi.ac.uk/intact/interaction/$1
intact.molecule:
description: IntAct provides a freely available, open source database system and
analysis tools for protein interaction data. This collection references interactor
molecules.
example: EBI-366083
homepage: https://www.ebi.ac.uk/intact/
mappings:
biocontext: INTACT.MOLECULE
miriam: intact.molecule
n2t: intact.molecule
name: IntAct Molecule
pattern: ^EBI\-[0-9]+$
preferred_prefix: intact.molecule
uri_format: https://www.ebi.ac.uk/intact/molecule/$1
interlex:
description: 'InterLex is a dynamic lexicon, initially built on the foundation of
NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed
to help improve the way that biomedical scientists communicate about their data,
so that information systems can find data more easily and provide more powerful
means of integrating data across distributed resources and datasets. InterLex
allows for the association of data fields and data values to common data elements
and terminologies enabling the crowdsourcing of data-terminology mappings within
and across communities. InterLex provides a stable layer on top of the many other
existing terminologies, lexicons, ontologies, and common data element collections
and provides a set of inter-lexical and inter-data-lexical mappings. '
example: 0101963
homepage: https://www.fdilab.org
mappings:
fairsharing: FAIRsharing.67sssf
miriam: ilx
name: InterLex
pattern: ^[0-9]+$
preferred_prefix: interlex
references:
- https://github.com/AllenInstitute/nomenclature
synonyms:
- ILX
uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1
interpro:
contact:
email: interhelp@ebi.ac.uk
github: null
name: InterPro Help
orcid: null
description: InterPro is a database of protein families, domains and functional
sites in which identifiable features found in known proteins can be applied to
unknown protein sequences.
example: IPR016380
homepage: http://www.ebi.ac.uk/interpro/index.html
mappings:
biocontext: IPR
biolink: interpro
fairsharing: FAIRsharing.pda11d
go: InterPro
miriam: interpro
n2t: interpro
ncbi: InterPro
obofoundry: IPR
prefixcommons: interpro
uniprot: InterPro
wikidata: P2926
name: InterPro
pattern: ^IPR\d{6}$
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/$1
ird.segment:
description: Influenza Research Database (IRD) contains information related to influenza
virus, including genomic sequence, strain, protein, epitope and bibliographic
information. The Segment Details page contains descriptive information and annotation
data about a particular genomic segment and its encoded product(s).
example: CY077097
homepage: http://www.fludb.org/
mappings:
biocontext: IRD.SEGMENT
miriam: ird.segment
n2t: ird.segment
prefixcommons: ird.segment
name: IRD Segment Sequence
pattern: ^\w+(\_)?\d+(\.\d+)?$
preferred_prefix: ird.segment
uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1
irefweb:
description: 'iRefWeb is an interface to a relational database containing the latest
build of the interaction Reference Index (iRefIndex) which integrates protein
interaction data from ten different interaction databases: BioGRID, BIND, CORUM,
DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates
interactions with the PubMed record from which they are derived.'
example: '617102'
homepage: http://wodaklab.org/iRefWeb/
mappings:
biocontext: IREFWEB
fairsharing: FAIRsharing.t31wcb
miriam: irefweb
n2t: irefweb
prefixcommons: irefweb
name: iRefWeb
pattern: ^\d+$
preferred_prefix: irefweb
uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1
iro:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
example: 0000008
name: Insect Resistance Ontology
pattern: ^\d{7}$
preferred_prefix: iro
uri_format: https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1
isbn:
description: The International Standard Book Number (ISBN) is for identifying printed
books.
example: '9781584885658'
homepage: http://isbndb.com/
mappings:
biocontext: ISBN-13
biolink: isbn
go: ISBN
miriam: isbn
n2t: isbn
prefixcommons: isbn
name: International Standard Book Number
pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[
-]?(\d|X)$
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=$1
isfinder:
description: ISfinder is a database of bacterial insertion sequences (IS). It assigns
IS nomenclature and acts as a repository for ISs. Each IS is annotated with information
such as the open reading frame DNA sequence, the sequence of the ends of the element
and target sites, its origin and distribution together with a bibliography, where
available.
example: ISA1083-2
homepage: http://www-is.biotoul.fr/i
mappings:
biocontext: ISFINDER
fairsharing: FAIRsharing.xhpc3h
miriam: isfinder
n2t: isfinder
ncbi: ISFinder
prefixcommons: isfinder
name: Insertion sequence elements database
pattern: ^IS\w+(\-\d)?$
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/$1
issn:
description: The International Standard Serial Number (ISSN) is a unique eight-digit
number used to identify a print or electronic periodical publication, rather than
individual articles or books.
example: 0745-4570
homepage: https://portal.issn.org
mappings:
biocontext: ISSN
biolink: issn
go: ISSN
miriam: issn
n2t: issn
name: International Standard Serial Number
pattern: ^\d{4}-\d{3}[\dX]$
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/$1
itis:
description: Information system with taxonomic data on plants, animals, fungi, and
microbes of North America and the world.
example: '589462'
homepage: https://www.itis.gov/
mappings:
fairsharing: FAIRsharing.t19hpa
wikidata: P815
name: Integrated Taxonomic Information System
pattern: ^\d+$
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$1
iuphar.family:
description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
properties of identified mammalian sodium, calcium and potassium channels, as
well as the related cyclic nucleotide-modulated ion channels and the recently
described transient receptor potential channels. It includes information on nomenclature
systems, and on inter and intra-species molecular structure variation. This collection
references families of receptors or subunits.
example: '78'
homepage: http://www.guidetopharmacology.org/
mappings:
biocontext: IUPHAR.FAMILY
miriam: iuphar.family
n2t: iuphar.family
prefixcommons: iuphar.family
name: IUPHAR family
pattern: ^\d+$
preferred_prefix: iuphar.family
synonyms:
- IUPHARfam
uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1
iuphar.ligand:
description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
properties of identified mammalian sodium, calcium and potassium channels, as
well as the related cyclic nucleotide-modulated ion channels and the recently
described transient receptor potential channels. It includes information on nomenclature
systems, and on inter and intra-species molecular structure variation. This collection
references ligands.
example: '1755'
homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all
mappings:
biocontext: IUPHAR.LIGAND
biolink: GTOPDB
miriam: iuphar.ligand
n2t: iuphar.ligand
wikidata: P595
name: Guide to Pharmacology Ligand
pattern: ^\d+$
preferred_prefix: iuphar.ligand
synonyms:
- IUPHAR_LIGAND
- IUPHAR_LIGAND_ID
uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1
iuphar.receptor:
description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
properties of identified mammalian sodium, calcium and potassium channels, as
well as the related cyclic nucleotide-modulated ion channels and transient receptor
potential channels. It includes information on nomenclature systems, and on inter
and intra-species molecular structure variation. This collection references individual
receptors or subunits.
example: '101'
homepage: http://www.guidetopharmacology.org/targets.jsp
mappings:
biocontext: IUPHAR.RECEPTOR
go: IUPHAR_RECEPTOR
miriam: iuphar.receptor
n2t: iuphar.receptor
wikidata: P5458
name: Guide to Pharmacology Target
pattern: ^\d+$
preferred_prefix: iuphar.receptor
synonyms:
- IUPHAR_GPCR
- IUPHARobj
uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1
jax:
description: Information about the C57BL/6J. Includes genetic background and disease
data.
example: '004435'
homepage: https://www.jax.org/strain
mappings:
biocontext: JAX
fairsharing: FAIRsharing.5701h1
name: Jackson Laboratories Strain
pattern: ^\d{6}$
preferred_prefix: jax
uri_format: https://www.jax.org/strain/$1
jaxmice:
description: JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory.
example: '005012'
homepage: http://jaxmice.jax.org/
mappings:
biocontext: JAXMICE
miriam: jaxmice
n2t: jaxmice
name: JAX Mice
pattern: ^\d+$
preferred_prefix: jaxmice
uri_format: http://jaxmice.jax.org/strain/$1.html
jcggdb:
description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase)
is a database that aims to integrate all glycan-related data held in various repositories
in Japan. This includes databases for large-quantity synthesis of glycogenes and
glycans, analysis and detection of glycan structure and glycoprotein, glycan-related
differentiation markers, glycan functions, glycan-related diseases and transgenic
and knockout animals, etc.
example: JCGG-STR008690
homepage: http://jcggdb.jp/index_en.html
mappings:
biocontext: JCGGDB
miriam: jcggdb
n2t: jcggdb
name: Japan Consortium for Glycobiology and Glycotechnology Database
pattern: ^JCGG-STR\d{6}$
preferred_prefix: jcggdb
uri_format: http://jcggdb.jp/idb/jcggdb/$1
jcm:
description: The Japan Collection of Microorganisms (JCM) collects, catalogues,
and distributes cultured microbial strains, restricted to those classified in
Risk Group 1 or 2.
example: '17254'
homepage: http://www.jcm.riken.go.jp/
mappings:
biocontext: JCM
fairsharing: FAIRsharing.h2wrt2
miriam: jcm
n2t: jcm
ncbi: JCM
prefixcommons: jcm
name: Japan Collection of Microorganisms
pattern: ^\d+$
preferred_prefix: jcm
uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1
jcrb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell line collections
example: JCRB1355
homepage: https://cellbank.nibiohn.go.jp
mappings:
cellosaurus: JCRB
name: JRBC Cell Bank
preferred_prefix: jcrb
uri_format: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1
jcsd:
description: The Japan Chemical Substance Dictionary is an organic compound dictionary
database prepared by the Japan Science and Technology Agency (JST).
example: J55.713G
homepage: http://jglobal.jst.go.jp/en/
mappings:
biocontext: JCSD
miriam: jcsd
n2t: jcsd
prefixcommons: jcsd
name: Japan Chemical Substance Dictionary
pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$
preferred_prefix: jcsd
uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1
jstor:
description: JSTOR (Journal Storage) is a digital library containing digital versions
of historical academic journals, as well as books, pamphlets and current issues
of journals. Some public domain content is free to access, while other articles
require registration.
example: '3075966'
homepage: http://www.jstor.org/
mappings:
biocontext: JSTOR
go: JSTOR
miriam: jstor
n2t: jstor
name: Digital archive of scholarly articles
pattern: ^\d+$
preferred_prefix: jstor
uri_format: http://www.jstor.org/stable/$1
jws:
description: JWS Online is a repository of curated biochemical pathway models, and
additionally provides the ability to run simulations of these models in a web
browser.
example: achcar11
homepage: http://jjj.biochem.sun.ac.za/models/
mappings:
biocontext: JWS
miriam: jws
n2t: jws
prefixcommons: jws
name: JWS Online
pattern: ^\w+$
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
kclb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell line collections
example: '10020.2'
homepage: https://cellbank.snu.ac.kr/english
mappings:
cellosaurus: KCLB
name: Korean Cell Line Bank
preferred_prefix: kclb
uri_format: https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1
kegg:
comment: KEGG prefix has been split into several others
deprecated: true
description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource
for understanding high-level functions and utilities of the biological system,
such as the cell, the organism and the ecosystem, from molecular-level information,
especially large-scale molecular datasets generated by genome sequencing and other
high-throughput experimental technologies.
example: hsa00190
homepage: http://www.kegg.jp/
mappings:
biocontext: KEGG
cheminf: 000409
go: KEGG
miriam: kegg
n2t: kegg
uniprot: KEGG
name: Kyoto Encyclopedia of Genes and Genomes
pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$
preferred_prefix: kegg
synonyms:
- KEGG
uri_format: http://www.kegg.jp/entry/$1
kegg.compound:
description: KEGG compound contains our knowledge on the universe of chemical substances
that are relevant to life.
example: C12345
homepage: https://www.genome.jp/kegg/ligand.html
mappings:
biocontext: KEGG.COMPOUND
miriam: kegg.compound
n2t: kegg.compound
prefixcommons: kegg.compound
wikidata: P665
name: KEGG Compound
part_of: kegg
pattern: ^C\d+$
preferred_prefix: kegg.compound
synonyms:
- KEGG COMPOUND
- KEGG.COMPOUND
uri_format: https://www.kegg.jp/entry/$1
kegg.dgroup:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: " KEGG DGROUP contains structurally and functionally related groups\
\ of D number entries in KEGG DRUG. There are five types of drug groups.\n\n \
\ Chemical - grouped as identical chemical structures with minor variations\
\ of salts, hydration states, etc.\n Structure - grouped as similar chemical\
\ structures having the same skeleton, etc.\n Target - grouped by drug targets\n\
\ Class - drug classes often representing similar mechanisms of action\n \
\ Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing\
\ enzymes and transporters\n\nChemical groups are often used for identifying essentially\
\ the same active ingredients of drugs in different countries."
example: DG00301
homepage: http://www.genome.jp/kegg/reaction/
mappings:
biolink: KEGG.DGROUP
name: KEGG Drug Group
part_of: kegg
pattern: ^DG\d+$
preferred_prefix: kegg.dgroup
references:
- https://github.com/prefixcommons/prefixes/pull/4
synonyms:
- KEGG_DGROUP
- KEGG_DRUG_GROUP
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:
biocontext: KEGG.DISEASE
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/$1
kegg.drug:
description: KEGG DRUG contains chemical structures of drugs and additional information
such as therapeutic categories and target molecules.
example: D00123
homepage: https://www.genome.jp/kegg/drug/
mappings:
biocontext: KEGG.DRUG
miriam: kegg.drug
n2t: kegg.drug
prefixcommons: kegg.drug
wikidata: P665
name: KEGG Drug
part_of: kegg
pattern: ^D\d+$
preferred_prefix: kegg.drug
synonyms:
- KEGG DRUG
- KEGG.DRUG
uri_format: https://www.kegg.jp/entry/$1
kegg.environ:
description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential
oils, and other health-promoting substances, which are mostly natural products
of plants. It will contain environmental substances and other health-damagine
substances as well. Each KEGG ENVIRON entry is identified by the E number and
is associated with the chemical component, efficacy information, and source species
information whenever applicable.
example: ev:E00032
homepage: http://www.genome.jp/kegg/drug/environ.html
mappings:
biocontext: KEGG.ENVIRON
miriam: kegg.environ
n2t: kegg.environ
name: KEGG Environ
part_of: kegg
pattern: ^(ev\:)?E\d+$
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:$1
kegg.genes:
description: KEGG GENES is a collection of gene catalogs for all complete genomes
and some partial genomes, generated from publicly available resources.
example: bsu:BSU01340
homepage: http://www.genome.jp/kegg/genes.html
mappings:
biocontext: KEGG.GENES
biolink: KEGG.GENE
miriam: kegg.genes
n2t: kegg.genes
wikidata: P665
name: KEGG Genes
part_of: kegg
pattern: ^\w+:[\w\d\.-]*$
preferred_prefix: kegg.genes
uri_format: http://www.kegg.jp/entry/$1
kegg.genome:
description: KEGG Genome is a collection of organisms whose genomes have been completely
sequenced.
example: T06648
homepage: http://www.genome.jp/kegg/catalog/org_list.html
mappings:
biocontext: KEGG.GENOME
miriam: kegg.genome
n2t: kegg.genome
prefixcommons: kegg.genome
wikidata: P665
name: KEGG Genome
part_of: kegg
pattern: ^(T0\d+|\w{3,5})$
preferred_prefix: kegg.genome
synonyms:
- kegg_genome
- kegg_genomes
uri_format: http://www.kegg.jp/entry/$1
kegg.glycan:
description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of
experimentally determined glycan structures. It contains all unique structures
taken from CarbBank, structures entered from recent publications, and structures
present in KEGG pathways.
example: G00123
homepage: https://www.genome.jp/kegg/glycan/
mappings:
biocontext: KEGG.GLYCAN
miriam: kegg.glycan
n2t: kegg.glycan
prefixcommons: kegg.glycan
name: KEGG Glycan
part_of: kegg
pattern: ^G\d+$
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:$1
kegg.metagenome:
description: The KEGG Metagenome Database collection information on environmental
samples (ecosystems) of genome sequences for multiple species.
example: T30002
homepage: http://www.genome.jp/kegg/catalog/org_list3.html
mappings:
biocontext: KEGG.METAGENOME
miriam: kegg.metagenome
n2t: kegg.metagenome
prefixcommons: kegg.metagenome
name: KEGG Metagenome
part_of: kegg
pattern: ^T3\d+$
preferred_prefix: kegg.metagenome
uri_format: http://www.kegg.jp/entry/$1
kegg.module:
description: KEGG Modules are manually defined functional units used in the annotation
and biological interpretation of sequenced genomes. Each module corresponds to
a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway,
structural, functional or signature modules.
example: M00002
homepage: http://www.kegg.jp/kegg/module.html
mappings:
biocontext: KEGG.MODULE
miriam: kegg.module
n2t: kegg.module
name: KEGG Module
part_of: kegg
pattern: ^([a-z]{3,5}_)?M\d{5}$
preferred_prefix: kegg.module
uri_format: http://www.kegg.jp/entry/$1
kegg.orthology:
description: KEGG Orthology (KO) consists of manually defined, generalised ortholog
groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all
organisms.
example: K00001
homepage: http://www.genome.jp/kegg/ko.html
mappings:
biocontext: KEGG.ORTHOLOGY
miriam: kegg.orthology
n2t: kegg.orthology
prefixcommons: kegg.orthology
name: KEGG Orthology
part_of: kegg
pattern: ^K\d+$
preferred_prefix: kegg.orthology
uri_format: http://www.kegg.jp/entry/$1
kegg.pathway:
description: KEGG PATHWAY is a collection of manually drawn pathway maps representing
our knowledge on the molecular interaction and reaction networks.
example: rsk00410
homepage: https://www.genome.jp/kegg/pathway.html
mappings:
biocontext: KEGG-path
biolink: KEGG.PATHWAY
go: KEGG_PATHWAY
miriam: kegg.pathway
n2t: kegg.pathway
prefixcommons: kegg.pathway
wikidata: P665
name: KEGG Pathways Database
part_of: kegg
pattern: ^\w{2,4}\d{5}$
preferred_prefix: kegg.pathway
synonyms:
- KEGG-path
- KEGG_PATHWAY
uri_format: https://www.kegg.jp/entry/$1
kegg.rclass:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: KEGG RCLASS contains classification of reactions based on the chemical
structure transformation patterns of substrate-product pairs (reactant pairs),
which are represented by the so-called RDM patterns.
example: RC00001
homepage: http://www.genome.jp/kegg/reaction/
mappings:
biolink: KEGG.RCLASS
name: KEGG Reaction Class
part_of: kegg
pattern: ^RC\d+$
preferred_prefix: kegg.rclass
references:
- https://github.com/prefixcommons/prefixes/pull/2
synonyms:
- KEGG_RCLASS
- KEGG_REACTION_CLASS
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:
biocontext: KEGG.REACTION
go: KEGG_REACTION
miriam: kegg.reaction
n2t: kegg.reaction
prefixcommons: kegg.reaction
wikidata: P665
name: KEGG Reaction
part_of: kegg
pattern: ^R\d+$
preferred_prefix: kegg.reaction
synonyms:
- KEGG_REACTION
uri_format: https://www.kegg.jp/entry/$1
kerafast:
description: Cell line collections
example: EJH014
homepage: https://www.kerafast.com/
mappings:
cellosaurus: Kerafast
name: Kerafast cell lines
preferred_prefix: kerafast
uri_format: https://www.kerafast.com/Search?SearchTerm="$1"
knapsack:
description: 'KNApSAcK provides information on metabolites and the
taxonomic class with which they are associated.'
example: C00000001
homepage: http://www.knapsackfamily.com/KNApSAcK/
mappings:
biocontext: KNAPSACK
miriam: knapsack
n2t: knapsack
wikidata: P2064
name: KNApSAcK
pattern: ^C\d{8}$
preferred_prefix: knapsack
uri_format: http://www.knapsackfamily.com/knapsack_core/information.php?word=$1
kupo:
appears_in:
- cl
comment: Website is down, now it redirects to something else that is not related
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
example: 0001009
homepage: http://www.kupkb.org/
name: Kidney and Urinary Pathway Ontology
pattern: ^\d{7}$
preferred_prefix: kupo
references:
- https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7
kyinno:
description: Cell line collections
example: KC-0979
homepage: https://www.kyinno.com/
mappings:
cellosaurus: KYinno
name: KYinno cell lines
preferred_prefix: kyinno
uri_format: https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf
labo:
banana: LABO
contact:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
depends_on:
- iao
- obi
- ogms
- omiabis
- omrse
- opmi
description: LABO is an ontology of informational entities formalizing clinical
laboratory tests prescriptions and reporting documents.
download_owl: http://purl.obolibrary.org/obo/labo.owl
example: '0000124'
homepage: https://github.com/OpenLHS/LABO
license: CC BY 4.0
mappings:
bioportal: LABO
obofoundry: LABO
ols: labo
ontobee: LABO
name: clinical LABoratory Ontology
pattern: ^\d{7}$
preferred_prefix: LABO
repository: https://github.com/OpenLHS/LABO
uri_format: http://purl.obolibrary.org/obo/LABO_$1
version: '2021-06-08'
lbo:
contact:
email: caripark@iastate.edu
github: caripark
name: Carissa Park
orcid: 0000-0002-2346-5201
description: A vocabulary for cattle, chicken, horse, pig, and sheep breeds.
download_obo: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo
download_owl: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl
example: 0000487
homepage: http://bioportal.bioontology.org/ontologies/LBO
mappings:
bioportal: LBO
fairsharing: FAIRsharing.309v57
ols: lbo
name: Livestock Breed Ontology
pattern: ^\d{7}$
preferred_prefix: lbo
repository: https://github.com/AnimalGenome/livestock-breed-ontology
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/$1
lepao:
banana: LEPAO
contact:
email: lagonzalezmo@unal.edu.co
github: luis-gonzalez-m
name: Luis A. Gonzalez-Montana
orcid: 0000-0002-9136-9932
depends_on:
- aism
- bfo
- bspo
- caro
- pato
- ro
- uberon
description: The Lepidoptera Anatomy Ontology contains terms used for describing
the anatomy and phenotype of moths and butterflies in biodiversity research.
download_obo: http://purl.obolibrary.org/obo/lepao.obo
download_owl: http://purl.obolibrary.org/obo/lepao.owl
example: '0000005'
homepage: https://github.com/insect-morphology/lepao
license: CC BY 4.0
mappings:
bioportal: LEPAO
obofoundry: LEPAO
ols: lepao
name: Lepidoptera Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: LEPAO
repository: https://github.com/insect-morphology/lepao
uri_format: http://purl.obolibrary.org/obo/LEPAO_$1
version: '2021-11-20'
lgai.cede:
description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset
with molecular instance level annotations (i.e. atom-bond level position annotations
within an image) for molecular structure images. This dataset was designed to
encourage research on detection-based pipelines for Optical Chemical Structure
Recognition (OCSR).
example: LGCEDe-S-000002244
homepage: https://www.lgresearch.ai
mappings:
miriam: lgai.cede
name: LG Chemical Entity Detection Dataset (LGCEDe)
pattern: ^LGCEDe-S-\d{9}$
preferred_prefix: lgai.cede
uri_format: https://s3.us-east-2.amazonaws.com/lg.cede/$1
lgic:
comment: Website is gone
deprecated: true
description: The Ligand-Gated Ion Channel database provides nucleic and proteic
sequences of the subunits of ligand-gated ion channels. These transmembrane proteins
can exist under different conformations, at least one of which forms a pore through
the membrane connecting two neighbouring compartments. The database can be used
to generate multiple sequence alignments from selected subunits, and gives the
atomic coordinates of subunits, or portion of subunits, where available.
example: 5HT3Arano
homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
mappings:
biocontext: LGIC
miriam: lgic
n2t: lgic
name: Ligand-Gated Ion Channel database
pattern: ^\w+$
preferred_prefix: lgic
uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php
licebase:
description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major
pathogens of salmon, significantly impacting upon the global salmon farming industry.
Lice control is primarily accomplished through chemotherapeutants, though emerging
resistance necessitates the development of new treatment methods (biological agents,
prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing
genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome
browser, and access to related high-thoughput genomics data. LiceBase also mines
and stores data from related genome sequencing and functional genomics projects.
example: EMLSAT00000003403
homepage: https://licebase.org
mappings:
biocontext: LICEBASE
fairsharing: FAIRsharing.c7w81a
miriam: licebase
n2t: licebase
name: LiceBase
pattern: ^[A-Za-z0-9\-\/]+$
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/$1
ligandbox:
description: LigandBox is a database of 3D compound structures. Compound information
is collected from the catalogues of various commercial suppliers, with approved
drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical
compound in the database has several 3D conformers with hydrogen atoms and atomic
charges, which are ready to be docked into receptors using docking programs. Various
physical properties, such as aqueous solubility (LogS) and carcinogenicity have
also been calculated to characterize the ADME-Tox properties of the compounds.
example: D00001
homepage: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en
mappings:
biocontext: LIGANDBOX
miriam: ligandbox
n2t: ligandbox
name: LigandBox
pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$
preferred_prefix: ligandbox
uri_format: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1
ligandexpo:
description: Ligand Expo is a data resource for finding information about small
molecules bound to proteins and nucleic acids.
example: ABC
homepage: http://ligand-depot.rutgers.edu/index.html
mappings:
biocontext: LIGANDEXPO
fairsharing: FAIRsharing.2ma4gq
miriam: ligandexpo
n2t: ligandexpo
prefixcommons: ligandexpo
name: Ligand Expo
pattern: ^(\w){3}$
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
ligea:
comment: This might just be a provider for CCLE
description: Polymorphism and mutation databases
example: CCLE_867
homepage: http://hpc-bioinformatics.cineca.it/fusion/main
mappings:
cellosaurus: LiGeA
name: Cancer cell LInes GEne fusions portAl
preferred_prefix: ligea
uri_format: http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1
limore:
description: Cell line databases/resources
example: Li7
homepage: https://www.picb.ac.cn/limore/home
mappings:
cellosaurus: LIMORE
name: Liver Cancer Model Repository
preferred_prefix: limore
uri_format: https://www.picb.ac.cn/limore/cellLines/single?para=$1
lincs.cell:
description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims
to create a network-based understanding of biology by cataloging changes in gene
expression and other cellular processes that occur when cells are exposed to a
variety of perturbing agents. The LINCS cell model system can have the following
cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated
cells, and embryonic stem cells. The metadata contains information provided by
each LINCS Data and Signature Generation Center (DSGC) and the association with
a tissue or organ from which the cells were derived, in many cases are also associated
to a disease.'
example: LCL-2085
homepage: http://lincsportal.ccs.miami.edu/cells/
mappings:
biocontext: LINCS.CELL
cellosaurus: LINCS_LDP
miriam: lincs.cell
n2t: lincs.cell
name: LINCS Cell
pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$
preferred_prefix: lincs.cell
synonyms:
- LINCS_LDP
uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1
lincs.data:
description: The Library of Network-Based Cellular Signatures (LINCS) Program aims
to create a network-based understanding of biology by cataloguing changes in gene
expression and other cellular processes that occur when cells are exposed to perturbing
agents. The data is organized and available as datasets, each including experimental
data, metadata and a description of the dataset and assay. The dataset group comprises
datasets for the same experiment but with different data level results (data processed
to a different level).
example: LDS-1110
homepage: http://lincsportal.ccs.miami.edu/datasets/
mappings:
biocontext: LINCS.DATA
miriam: lincs.data
n2t: lincs.data
name: LINCS Data
pattern: ^[EL]D[SG]-\d+$
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/$1
lincs.protein:
description: The HMS LINCS Database currently contains information on experimental
reagents (small molecule perturbagens, cells, and proteins). It aims to collect
and disseminate information relating to the fundamental principles of cellular
response in humans to perturbation. This collection references proteins.
example: '200282'
homepage: http://lincs.hms.harvard.edu/db/proteins/
mappings:
biocontext: LINCS.PROTEIN
miriam: lincs.protein
n2t: lincs.protein
name: LINCS Protein
pattern: ^\d+$
preferred_prefix: lincs.protein
uri_format: https://lincs.hms.harvard.edu/db/proteins/$1
lincs.smallmolecule:
description: The Library of Network-Based Cellular Signatures (LINCS) Program aims
to create a network-based understanding of biology by cataloging changes in gene
expression and other cellular processes that occur when cells are exposed to a
variety of perturbing agents. The LINCS small molecule collection is used as perturbagens
in LINCS experiments. The small molecule metadata includes substance-specific
batch information provided by each LINCS Data and Signature Generation Center
(DSGC).
example: LSM-6306
homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/
mappings:
biocontext: LINCS.SMALLMOLECULE
miriam: lincs.smallmolecule
n2t: lincs.smallmolecule
name: LINCS Small Molecule
pattern: ^LSM-\d+$
preferred_prefix: lincs.smallmolecule
synonyms:
- lincs
uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1
linguist:
description: Registry of programming languages for the Linguist program for detecting
and highlighting programming languages.
example: Python
homepage: https://github.com/github/linguist
mappings:
miriam: linguist
name: Linguist
pattern: ^[a-zA-Z0-9 +#'*]+$
preferred_prefix: linguist
repository: https://github.com/github/linguist
uri_format: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1
lipidbank:
description: LipidBank is an open, publicly free database of natural lipids including
fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
example: BBA0001
homepage: http://lipidbank.jp/index.html
mappings:
biocontext: LIPIDBANK
fairsharing: FAIRsharing.bdn9br
miriam: lipidbank
n2t: lipidbank
prefixcommons: lipidbank
name: LipidBank
pattern: ^\w+\d+$
preferred_prefix: lipidbank
uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1
lipidmaps:
description: The LIPID MAPS Lipid Classification System is comprised of eight lipid
categories, each with its own subclassification hierarchy. All lipids in the LIPID
MAPS Structure Database (LMSD) have been classified using this system and have
been assigned LIPID MAPS ID's which reflects their position in the classification
hierarchy.
example: LMPR0102010012
homepage: http://www.lipidmaps.org
mappings:
biocontext: LIPIDMAPS
cheminf: '000564'
fairsharing: FAIRsharing.cpneh8
miriam: lipidmaps
n2t: lipidmaps
prefixcommons: lipidmaps
scholia: lipidmaps
wikidata: P2063
name: LIPID MAPS
pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$
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:
biocontext: LIPRO
bioportal: LIPRO
obofoundry: LIPRO
name: Lipid Ontology
preferred_prefix: LIPRO
uri_format: http://purl.obolibrary.org/obo/LIPRO_$1
lncipedia:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
mappings:
fairsharing: FAIRsharing.84c1a7
name: LNCipedia
preferred_prefix: lncipedia
loggerhead:
banana: LOGGERHEAD
contact:
email: peteremidford@yahoo.com
github: null
name: Peter Midford
orcid: 0000-0001-6512-3296
deprecated: true
homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html
mappings:
biocontext: LOGGERHEAD
obofoundry: 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
fairsharing: FAIRsharing.2mk2zb
name: Logical Observation Identifiers Names and Codes
preferred_prefix: loinc
synonyms:
- LNC
uri_format: https://loinc.org/$1
lonza:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Contains information about cells and data sheets related to transfection.
example: '968'
homepage: https://knowledge.lonza.com
mappings:
cellosaurus: Lonza
name: Lonza
pattern: ^\d+$
preferred_prefix: lonza
uri_format: https://knowledge.lonza.com/cell?id=$1
lotus:
comment: IDs are actually leading to the structural part of LOTUS only, which might
change in the future. Will adapt the regexp in case.
contact:
email: adriano.rutz@ik.me
github: adafede
name: Adriano Rutz
orcid: 0000-0003-0443-9902
contributor:
email: null
github: adafede
name: Adriano Rutz
orcid: 0000-0003-0443-9902
description: LOTUS, actually, represents the most exhaustive resource of documented
structure-organism pairs. Within the frame of current computational approaches
in Natural Produts’s research and related fields, these documented structure-organism
pairs should allow a more complete understanding of organisms and their chemistry.
example: LTS0004651
homepage: https://lotus.naturalproducts.net
name: LOTUS Initiative for Open Natural Products Research
pattern: ^LTS\d{7}$
preferred_prefix: lotus
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://lotus.naturalproducts.net/compound/lotus_id/$1
lpt:
contact:
email: caripark@iastate.edu
github: caripark
name: Carissa Park
orcid: 0000-0002-2346-5201
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary
for the description of traits (measurable or observable characteristics) pertaining
to products produced by or obtained from the body of an agricultural animal or
bird maintained for use and profit.
download_obo: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo
download_owl: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl
example: '0000001'
homepage: https://github.com/AnimalGenome/livestock-product-trait-ontology
mappings:
biocontext: LPT
bioportal: LPT
fairsharing: FAIRsharing.g78mbm
name: Livestock Product Trait Ontology
pattern: ^\d+$
preferred_prefix: lpt
repository: https://github.com/AnimalGenome/livestock-product-trait-ontology
uri_format: http://purl.obolibrary.org/obo/LPT_$1
lrg:
description: A Locus Reference Genomic (LRG) is a manually curated record that contains
stable genomic, transcript and protein reference sequences for reporting clinically
relevant sequence variants. All LRGs are generated and maintained by the NCBI
and EMBL-EBI.
example: LRG_1
homepage: http://www.lrg-sequence.org/
mappings:
biocontext: LRG
miriam: lrg
n2t: lrg
name: Locus Reference Genomic
pattern: ^LRG_\d+$
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/$1.xml
lspci:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Internal identifiers form the LSP for ChEBML compound classes (e.g.,
combining various salts and ions)
example: '1'
homepage: https://labsyspharm.github.io/lspci/
name: Laboratory of Systems Pharmacology Compound
pattern: ^\d+$
preferred_prefix: lspci
uri_format: https://labsyspharm.github.io/lspci/$1
lter:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Ecological terms
example: '182'
homepage: https://vocab.lternet.edu/vocab/vocab/index.php
name: Long Term Ecological Research Controlled Vocabulary
pattern: ^\d+$
preferred_prefix: lter
uri_format: https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1
ma:
banana: MA
contact:
email: Terry.Hayamizu@jax.org
github: tfhayamizu
name: Terry Hayamizu
orcid: 0000-0002-0956-8634
description: A structured controlled vocabulary of the adult anatomy of the mouse
(Mus)
download_obo: http://purl.obolibrary.org/obo/ma.obo
download_owl: http://purl.obolibrary.org/obo/ma.owl
example: '0002502'
homepage: https://github.com/obophenotype/mouse-anatomy-ontology
license: CC BY 4.0
mappings:
biocontext: MA
bioportal: MA
fairsharing: FAIRsharing.pdwqcr
go: MA
miriam: ma
n2t: ma
obofoundry: MA
ols: ma
ontobee: MA
prefixcommons: ma
name: Mouse adult gross anatomy
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: MA
repository: https://github.com/obophenotype/mouse-anatomy-ontology
uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1
version: '2017-02-07'
macie:
description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database
of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction
describing the chemical compounds involved, as well as the species name in which
the reaction occurs. The individual reaction stages for each overall reaction
are listed with mechanisms, alternative mechanisms, and amino acids involved.
example: M0001
homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html
mappings:
biocontext: MACIE
fairsharing: FAIRsharing.7xkx69
miriam: macie
n2t: macie
prefixcommons: macie
name: Mechanism, Annotation and Classification in Enzymes
pattern: ^M\d{4}$
preferred_prefix: macie
uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1
maizegdb.locus:
description: MaizeGDB is the maize research community's central repository for genetics
and genomics information.
example: '25011'
homepage: http://www.maizegdb.org/
mappings:
biocontext: MAIZEGDB.LOCUS
fairsharing: FAIRsharing.aq280w
go: MaizeGDB_Locus
miriam: maizegdb.locus
n2t: maizegdb.locus
ncbi: MaizeGDB
prefixcommons: maizegdb
uniprot: MaizeGDB
name: MaizeGDB Locus
pattern: ^\d+$
preferred_prefix: maizegdb.locus
synonyms:
- MaizeGDB
uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1
mamo:
banana: MAMO
contact:
email: nicolas@ascistance.co.uk
github: gambardella
name: Nicolas Gambardella
orcid: 0000-0002-6309-7327
description: The Mathematical Modelling Ontology (MAMO) is a classification of the
types of mathematical models used mostly in the life sciences, their variables,
relationships and other relevant features.
download_owl: http://purl.obolibrary.org/obo/mamo.owl
example: '0000026'
homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/
license: Artistic License 2.0
mappings:
biocontext: MAMO
bioportal: MAMO
fairsharing: FAIRsharing.kbz5jh
miriam: mamo
n2t: mamo
obofoundry: MAMO
ols: mamo
ontobee: MAMO
name: Mathematical modeling ontology
pattern: ^\d{7}$
preferred_prefix: MAMO
repository: http://sourceforge.net/p/mamo-ontology
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:
biocontext: MAO
obofoundry: MAO
prefixcommons: mao
name: Multiple alignment
preferred_prefix: MAO
uri_format: http://purl.obolibrary.org/obo/MAO_$1
massbank:
description: MassBank is a federated database of reference spectra from different
instruments, including high-resolution mass spectra of small metabolites (<3000
Da).
example: PB000166
homepage: http://www.massbank.jp
mappings:
biocontext: MASSBANK
fairsharing: FAIRsharing.dk451a
miriam: massbank
n2t: massbank
wikidata: P6689
name: MassBank
pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$
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=$1
massive:
description: MassIVE is a community resource developed by the NIH-funded Center
for Computational Mass Spectrometry to promote the global, free exchange of mass
spectrometry data.
example: MSV000082131
homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
mappings:
biocontext: MASSIVE
fairsharing: FAIRsharing.LYsiMd
miriam: massive
n2t: massive
uniprot: MassIVE
name: MassIVE
pattern: ^MSV\d+$
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=$1
mat:
banana: MAT
contact:
email: j.bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
deprecated: true
example: '0000000'
mappings:
biocontext: MAT
bioportal: MAT
obofoundry: MAT
name: Minimal Anatomical Terminology
pattern: ^\d{7}$
preferred_prefix: MAT
uri_format: http://purl.obolibrary.org/obo/MAT_$1
matrixdb:
appears_in:
- complexportal
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/
mappings:
fairsharing: FAIRsharing.91yrz6
prefixcommons: matrixdb
name: MatrixDB
preferred_prefix: matrixdb
uri_format: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1
matrixdb.association:
description: MatrixDB stores experimentally determined interactions involving at
least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan
interactions, as well as interactions with lipids and cations.
example: P00747__P07355
homepage: http://matrixdb.univ-lyon1.fr/
mappings:
biocontext: MATRIXDB.ASSOCIATION
miriam: matrixdb.association
n2t: matrixdb.association
name: MatrixDB Association
pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$
preferred_prefix: matrixdb.association
uri_format: http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association
maxo:
appears_in:
- ecto
banana: MAXO
contact:
email: Leigh.Carmody@jax.org
github: LCCarmody
name: Leigh Carmody
orcid: 0000-0001-7941-2961
depends_on:
- chebi
- foodon
- go
- iao
- ro
- uberon
description: An ontology to represent medically relevant actions, procedures, therapies,
interventions, and recommendations.
download_json: http://purl.obolibrary.org/obo/maxo.json
download_obo: http://purl.obolibrary.org/obo/maxo.obo
download_owl: http://purl.obolibrary.org/obo/maxo.owl
example: 0000008
homepage: https://github.com/monarch-initiative/MAxO
license: CC BY 3.0
mappings:
biolink: MAXO
bioportal: MAXO
obofoundry: MAXO
ols: maxo
ontobee: MAXO
name: Medical Action Ontology
pattern: ^\d{7}$
preferred_prefix: MAXO
repository: https://github.com/monarch-initiative/MAxO
uri_format: http://purl.obolibrary.org/obo/MAXO_$1
version: '2022-04-11'
mba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
mouse brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo
example: '688'
homepage: https://mouse.brain-map.org
name: Mouse Brain Atlas
pattern: ^\d+$
preferred_prefix: MBA
mcc:
deprecated: true
mappings:
bioportal: MCCL
name: Cell Line Ontology [derivative]
preferred_prefix: mcc
mco:
banana: MCO
contact:
email: citlalli.mejiaalmonte@gmail.com
github: citmejia
name: Citlalli Mejía-Almonte
orcid: 0000-0002-0142-5591
depends_on:
- bfo
- chebi
- cl
- clo
- micro
- ncbitaxon
- ncit
- obi
- omit
- omp
- pato
- peco
- uberon
- zeco
description: Microbial Conditions Ontology is an ontology...
download_obo: http://purl.obolibrary.org/obo/mco.obo
download_owl: http://purl.obolibrary.org/obo/mco.owl
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
repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
uri_format: http://purl.obolibrary.org/obo/MCO_$1
version: '2019-05-15'
mdm:
description: The MDM (Medical Data Models) Portal is a meta-data registry for creating,
analysing, sharing and reusing medical forms. Electronic forms are central in
numerous processes involving data, including the collection of data through electronic
health records (EHRs), Electronic Data Capture (EDC), and as case report forms
(CRFs) for clinical trials. The MDM Portal provides medical forms in numerous
export formats, facilitating the sharing and reuse of medical data models and
exchange between information systems.
example: '4776'
homepage: https://medical-data-models.org/
mappings:
biocontext: MDM
bioportal: MDM
fairsharing: FAIRsharing.wnk2eq
miriam: mdm
n2t: mdm
name: Medical Data Models
pattern: ^\d+$
preferred_prefix: mdm
uri_format: https://medical-data-models.org/forms/$1
meddra:
description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed
by the International Council for Harmonisation of Technical Requirements for Registration
of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology
to facilitate sharing of regulatory information internationally for medical products
used by humans. It is used within regulatory processes, safety monitoring, as
well as for marketing activities. Products covered by the scope of MedDRA include
pharmaceuticals, biologics, vaccines and drug-device combination products. The
MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level
Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into
Lowest Level Terms (LLT).
example: '10015919'
homepage: http://bioportal.bioontology.org/ontologies/MEDDRA
mappings:
biocontext: MEDDRA
bioportal: MEDDRA
fairsharing: FAIRsharing.ad3137
miriam: meddra
n2t: meddra
wikidata: P3201
name: Medical Dictionary for Regulatory Activities Terminology
pattern: ^\d+$
preferred_prefix: meddra
synonyms:
- MEDRA
- MeDRA
- MedDRA
- Medical Dictionary for Regulatory Activities
uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1
medgen:
description: MedGen is a portal for information about conditions and phenotypes
related to Medical Genetics. Terms from multiple sources are aggregated into concepts,
each of which is assigned a unique identifier and a preferred name and symbol.
The core content of the record may include names, identifiers used by other databases,
mode of inheritance, clinical features, and map location of the loci affecting
the disorder.
example: '760050'
homepage: https://www.ncbi.nlm.nih.gov/medgen/
mappings:
biocontext: MedGen
biolink: medgen
miriam: medgen
n2t: medgen
ncbi: MedGen
name: Human Medical Genetics
pattern: ^[CN]*\d{4,7}$
preferred_prefix: medgen
uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1
medlineplus:
description: MedlinePlus is the National Institutes of Health's Web site for patients
and their families and friends. Produced by the National Library of Medicine,
it provides information about diseases, conditions, and wellness issues using
non-technical terms and language.
example: 002804
homepage: http://www.nlm.nih.gov/medlineplus/
mappings:
biocontext: MEDLINEPLUS
bioportal: MEDLINEPLUS
fairsharing: FAIRsharing.bf8dsb
miriam: medlineplus
n2t: medlineplus
name: MedlinePlus Health Topics
pattern: ^\d+$
preferred_prefix: medlineplus
uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm
merops:
description: The MEROPS database is an information resource for peptidases (also
termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
them.
example: S01.001
homepage: http://merops.sanger.ac.uk/index.htm
mappings:
biocontext: MEROPS
fairsharing: FAIRsharing.2s4n8r
go: MEROPS
miriam: merops
n2t: merops
prefixcommons: merops
uniprot: MEROPS
name: MEROPS peptidase database
pattern: ^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$
preferred_prefix: merops
uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$1
merops.family:
description: The MEROPS database is an information resource for peptidases (also
termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
them. These are hierarchically classified and assigned to a Family on the basis
of statistically significant similarities in amino acid sequence. Families thought
to be homologous are grouped together in a Clan. This collection references peptidase
families.
example: S1
homepage: http://merops.sanger.ac.uk/index.htm
mappings:
biocontext: MEROPS.FAMILY
miriam: merops.family
n2t: merops.family
name: MEROPS Family
pattern: ^[SCTAGMNU]\d+$
preferred_prefix: merops.family
uri_format: http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1
merops.inhibitor:
description: The MEROPS database is an information resource for peptidases (also
termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
them. This collections references inhibitors.
example: I31.952
homepage: http://merops.sanger.ac.uk/index.htm
mappings:
biocontext: MEROPS.INHIBITOR
miriam: merops.inhibitor
n2t: merops.inhibitor
name: MEROPS Inhibitor
pattern: ^I\d{2}\.\d{3}$
preferred_prefix: merops.inhibitor
uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1
mesh:
description: MeSH (Medical Subject Headings) is the National Library of Medicine's
controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
in a hierarchical structure that permits searching at various levels of specificity.
This thesaurus is used by NLM for indexing articles from biomedical journals,
cataloguing of books, documents, etc.
example: C063233
example_extras:
- D000001
homepage: http://id.nlm.nih.gov/mesh/
mappings:
biocontext: MESH
biolink: MESH
bioportal: MESH
cellosaurus: MeSH
fairsharing: FAIRsharing.qnkw45
go: MeSH
miriam: mesh
n2t: mesh
prefixcommons: mesh
scholia: mesh
wikidata: P486
name: Medical Subject Headings
pattern: ^(C|D)\d{6,9}$
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=$1
mesh.2012:
description: MeSH (Medical Subject Headings) is the National Library of Medicine's
controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
in a hierarchical structure that permits searching at various levels of specificity.
This thesaurus is used by NLM for indexing articles from biomedical journals,
cataloging of books, documents, etc. This collection references MeSH terms published
in 2012.
example: '17186'
homepage: http://www.nlm.nih.gov/mesh/
mappings:
biocontext: MESH.2012
miriam: mesh.2012
n2t: mesh.2012
name: MeSH 2012
pattern: ^[A-Za-z0-9]+$
preferred_prefix: mesh.2012
uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded
mesh.2013:
description: MeSH (Medical Subject Headings) is the National Library of Medicine's
controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
in a hierarchical structure that permits searching at various levels of specificity.
This thesaurus is used by NLM for indexing articles from biomedical journals,
cataloging of books, documents, etc. This collection references MeSH terms published
in 2013.
example: '17165'
homepage: http://www.nlm.nih.gov/mesh/
mappings:
biocontext: MESH.2013
miriam: mesh.2013
n2t: mesh.2013
name: MeSH 2013
pattern: ^[A-Za-z0-9]+$
preferred_prefix: mesh.2013
uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded
metabolights:
description: MetaboLights is a database for Metabolomics experiments and derived
information. The database is cross-species, cross-technique and covers metabolite
structures and their reference spectra as well as their biological roles, locations
and concentrations, and experimental data from metabolic experiments. This collection
references individual metabolomics studies.
example: MTBLS1
homepage: https://www.ebi.ac.uk/metabolights/
mappings:
biocontext: METABOLIGHTS
cellosaurus: MetaboLights
miriam: metabolights
n2t: metabolights
wikidata: P3890
name: MetaboLights Compound
pattern: ^MTBLS\d+$
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/$1
metacyc.compound:
description: MetaCyc is a curated database of experimentally elucidated metabolic
pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different
organisms. MetaCyc contains pathways involved in both primary and secondary metabolism,
as well as associated metabolites, reactions, enzymes, and genes. The goal of
MetaCyc is to catalog the universe of metabolism by storing a representative sample
of each experimentally elucidated pathway.
example: CPD-10330
homepage: https://metacyc.org
mappings:
biocontext: METACYC.COMPOUND
biolink: MetaCyc
fairsharing: FAIRsharing.yytevr
go: MetaCyc
miriam: metacyc.compound
n2t: metacyc.compound
name: Metabolic Encyclopedia of metabolic and other pathways
pattern: ^[A-Za-z0-9+_.%-:]+$
preferred_prefix: metacyc.compound
synonyms:
- MetaCyc
uri_format: https://metacyc.org/compound?orgid=META&id=$1
metacyc.reaction:
description: MetaCyc is a curated database of experimentally elucidated metabolic
pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different
organisms. MetaCyc contains pathways involved in both primary and secondary metabolism,
as well as associated metabolites, reactions, enzymes, and genes. The goal of
MetaCyc is to catalog the universe of metabolism by storing a representative sample
of each experimentally elucidated pathway.
example: RXN-14904
homepage: https://metacyc.org
mappings:
biocontext: METACYC.REACTION
biolink: metacyc.reaction
miriam: metacyc.reaction
n2t: metacyc.reaction
name: MetaCyc Reaction
pattern: ^[A-Za-z0-9+_.%-:]+$
preferred_prefix: metacyc.reaction
uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1
metanetx.chemical:
description: MetaNetX/MNXref integrates various information from genome-scale metabolic
network reconstructions such as information on reactions, metabolites and compartments.
This information undergoes a reconciliation process to minimise for discrepancies
between different data sources, and makes the data accessible under a common namespace.
This collection references chemical or metabolic components.
example: MNXM1723
homepage: https://www.metanetx.org/
mappings:
biocontext: METANETX.CHEMICAL
miriam: metanetx.chemical
n2t: metanetx.chemical
name: MetaNetX chemical
pattern: ^(MNXM\d+|BIOMASS|WATER)$
preferred_prefix: metanetx.chemical
uri_format: https://www.metanetx.org/chem_info/$1
metanetx.compartment:
description: MetaNetX/MNXref integrates various information from genome-scale metabolic
network reconstructions such as information on reactions, metabolites and compartments.
This information undergoes a reconciliation process to minimise for discrepancies
between different data sources, and makes the data accessible under a common namespace.
This collection references cellular compartments.
example: MNXC15
homepage: https://www.metanetx.org/
mappings:
biocontext: METANETX.COMPARTMENT
miriam: metanetx.compartment
n2t: metanetx.compartment
name: MetaNetX compartment
pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$
preferred_prefix: metanetx.compartment
uri_format: https://www.metanetx.org/comp_info/$1
metanetx.reaction:
description: MetaNetX/MNXref integrates various information from genome-scale metabolic
network reconstructions such as information on reactions, metabolites and compartments.
This information undergoes a reconciliation process to minimise for discrepancies
between different data sources, and makes the data accessible under a common namespace.
This collection references reactions.
example: MNXR101574
homepage: https://www.metanetx.org/
mappings:
biocontext: METANETX.REACTION
biolink: METANETX.REACTION
miriam: metanetx.reaction
n2t: metanetx.reaction
name: MetaNetX reaction
pattern: ^(MNXR\d+|EMPTY)$
preferred_prefix: metanetx.reaction
uri_format: https://www.metanetx.org/equa_info/$1
metlin:
description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a
repository of metabolite information as well as tandem mass spectrometry data,
providing public access to its comprehensive MS and MS/MS metabolite data. An
annotated list of known metabolites and their mass, chemical formula, and structure
are available, with each metabolite linked to external resources for further reference
and inquiry.
example: '1455'
homepage: http://masspec.scripps.edu/
mappings:
biocontext: METLIN
miriam: metlin
n2t: metlin
name: Metabolite and Tandem Mass Spectrometry Database
pattern: ^\d{4}$
preferred_prefix: metlin
uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1
mex:
description: A public place to process, interpret and share GC/MS metabolomics datasets.
example: '36'
homepage: https://www.metabolome-express.org/
mappings:
biocontext: MEX
miriam: mex
n2t: mex
name: Metabolome Express
pattern: ^\d+$
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=$1
mf:
banana: MF
contact:
email: janna.hastings@gmail.com
github: jannahastings
name: Janna Hastings
orcid: 0000-0002-3469-4923
description: The Mental Functioning Ontology is an overarching ontology for all
aspects of mental functioning.
download_owl: http://purl.obolibrary.org/obo/mf.owl
example: 0000091
homepage: https://github.com/jannahastings/mental-functioning-ontology
license: CC BY 3.0
mappings:
biocontext: MF
bioportal: MF
fairsharing: FAIRsharing.4gm9gt
obofoundry: MF
ols: mf
ontobee: MF
name: Mental Functioning Ontology
pattern: ^\d{7}$
preferred_prefix: MF
repository: https://github.com/jannahastings/mental-functioning-ontology
uri_format: http://purl.obolibrary.org/obo/MF_$1
version: '2021-11-17'
mfmo:
banana: MFMO
contact:
email: druzinsk@uic.edu
github: RDruzinsky
name: Robert Druzinsky
orcid: 0000-0002-1572-1316
depends_on:
- uberon
description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the
muscles of the head and neck that participate in feeding, swallowing, and other
oral-pharyngeal behaviors.
download_owl: http://purl.obolibrary.org/obo/mfmo.owl
example: 0000208
homepage: https://github.com/rdruzinsky/feedontology
license: CC BY 3.0
mappings:
biocontext: MFMO
bioportal: MFMO
fairsharing: FAIRsharing.669cnk
obofoundry: MFMO
ols: mfmo
ontobee: MFMO
name: Mammalian Feeding Muscle Ontology
pattern: ^\d{7}$
preferred_prefix: MFMO
repository: https://github.com/RDruzinsky/feedontology
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, Oryzias latipes.
download_owl: http://purl.obolibrary.org/obo/mfo.owl
mappings:
biocontext: MFO
bioportal: MFO
obofoundry: MFO
prefixcommons: mfo
name: Medaka fish anatomy and development
preferred_prefix: MFO
uri_format: http://purl.obolibrary.org/obo/MFO_$1
mfoem:
banana: MFOEM
contact:
email: janna.hastings@gmail.com
github: jannahastings
name: Janna Hastings
orcid: 0000-0002-3469-4923
description: An ontology of affective phenomena such as emotions, moods, appraisals
and subjective feelings.
download_owl: http://purl.obolibrary.org/obo/mfoem.owl
example: '000204'
homepage: https://github.com/jannahastings/emotion-ontology
license: CC BY 3.0
mappings:
biocontext: MFOEM
bioportal: MFOEM
fairsharing: FAIRsharing.dx30m8
obofoundry: MFOEM
ols: mfoem
ontobee: MFOEM
name: Emotion Ontology
pattern: ^\d{6}$
preferred_prefix: MFOEM
repository: https://github.com/jannahastings/emotion-ontology
uri_format: http://purl.obolibrary.org/obo/MFOEM_$1
version: '2021-11-17'
mfomd:
banana: MFOMD
contact:
email: janna.hastings@gmail.com
github: jannahastings
name: Janna Hastings
orcid: 0000-0002-3469-4923
description: The Mental Disease Ontology is developed to facilitate representation
for all aspects of mental disease. It is an extension of the Ontology for General
Medical Science (OGMS) and Mental Functioning Ontology (MF).
download_owl: http://purl.obolibrary.org/obo/mfomd.owl
example: '0000046'
homepage: https://github.com/jannahastings/mental-functioning-ontology
license: CC BY 3.0
mappings:
biocontext: MFOMD
bioportal: MFOMD
fairsharing: FAIRsharing.q053vb
obofoundry: MFOMD
ols: mfomd
ontobee: MFOMD
name: Mental Disease Ontology
pattern: ^\d{7}$
preferred_prefix: MFOMD
repository: https://github.com/jannahastings/mental-functioning-ontology
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:$1
mgi:
banana: MGI
description: The Mouse Genome Database (MGD) project includes data on gene characterization,
nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes,
allelic variants and mutants, and strain data.
example: '6017782'
homepage: http://www.informatics.jax.org/
mappings:
biocontext: MGI
cellosaurus: MGI
fairsharing: FAIRsharing.fcwyhz
go: MGI
miriam: mgi
n2t: mgi
ncbi: MGI
prefixcommons: mgi
uniprot: MGI
wikidata: P671
name: Mouse Genome Informatics
namespace_in_lui: true
pattern: ^\d+$
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:$1
mgnify.analysis:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Analyses of microbiome data within MGnify
example: MGYA00002270
homepage: https://www.ebi.ac.uk/metagenomics/
name: MGnify Analysis
pattern: ^MGYA\d+$
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/$1
mi:
banana: MI
contact:
email: pporras@ebi.ac.uk
github: pporrasebi
name: Pablo Porras Millán
orcid: 0000-0002-8429-8793
description: The Molecular Interactions (MI) ontology forms a structured controlled
vocabulary for the annotation of experiments concerned with protein-protein interactions.
MI is developed by the HUPO Proteomics Standards Initiative.
download_obo: http://purl.obolibrary.org/obo/mi.obo
download_owl: http://purl.obolibrary.org/obo/mi.owl
example: 0058
homepage: https://github.com/HUPO-PSI/psi-mi-CV
license: CC BY 4.0
mappings:
biocontext: MI
biolink: MI
bioportal: MI
go: PSI-MI
miriam: mi
n2t: psimi
obofoundry: MI
ols: mi
ontobee: MI
prefixcommons: psi.mi
name: Molecular Interactions Controlled Vocabulary
namespace_in_lui: true
pattern: ^\d{4}$
preferred_prefix: MI
repository: https://github.com/HUPO-PSI/psi-mi-CV
synonyms:
- PSI-MI
uri_format: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1
miaa:
comment: same as MAT
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
name: Minimal Information About Anatomy ontology
preferred_prefix: miaa
references:
- https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf
miapa:
banana: MIAPA
contact:
email: hilmar.lapp@duke.edu
github: hlapp
name: Hilmar Lapp
orcid: 0000-0001-9107-0714
description: 'The MIAPA ontology is intended to be an application ontology for the
purpose of semantic annotation of phylogenetic data according to the requirements
and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA)
metadata reporting standard. The ontology leverages (imports) primarily from the
CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and
SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds
some assertions of its own, as well as some classes and individuals that may eventually
get pushed down into one of the respective source ontologies.
This ontology is maintained at http://github.com/miapa/miapa, and requests for
changes or additions should be filed at the issue tracker there. The discussion
list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be
found at the project''s main page at http://evoio.org/wiki/MIAPA.'
download_owl: http://purl.obolibrary.org/obo/miapa.owl
example: '0000010'
homepage: http://www.evoio.org/wiki/MIAPA
license: CC0 1.0
mappings:
biocontext: MIAPA
bioportal: MIAPA
fairsharing: FAIRsharing.ca48xs
obofoundry: MIAPA
ols: miapa
ontobee: MIAPA
name: Minimum Anformation About a Phylogenetic Analysis Ontology
pattern: ^\d{7}$
preferred_prefix: MIAPA
repository: https://github.com/evoinfo/miapa
uri_format: http://purl.obolibrary.org/obo/MIAPA_$1
version: '2017-05-09'
micro:
appears_in:
- mco
banana: MICRO
contact:
email: carrine.blank@umontana.edu
github: carrineblank
name: Carrine Blank
orcid: 0000-0002-2100-6351
description: An ontology of prokaryotic phenotypic and metabolic characters
download_owl: http://purl.obolibrary.org/obo/micro.owl
example: 0002999
homepage: https://github.com/carrineblank/MicrO
license: CC BY 2.0
mappings:
biocontext: MICRO
fairsharing: FAIRsharing.brhpb0
obofoundry: MICRO
ols: micro
ontobee: MicrO
name: Ontology of Prokaryotic Phenotypic and Metabolic Characters
pattern: ^\d{7}$
preferred_prefix: MICRO
repository: https://github.com/carrineblank/MicrO
uri_format: http://purl.obolibrary.org/obo/MICRO_$1
version: 1.5.1
microscope:
description: MicroScope is an integrative resource that supports systematic and
efficient revision of microbial genome annotation, data management and comparative
analysis.
example: '5601141'
homepage: http://www.genoscope.cns.fr/agc/microscope
mappings:
biocontext: MICROSCOPE
fairsharing: FAIRsharing.3t5qc3
miriam: microscope
n2t: microscope
name: MicroScope
pattern: ^\d+$
preferred_prefix: microscope
uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1
microsporidia:
description: MicrosporidiaDB is one of the databases that can be accessed through
the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic
pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium,
Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported
by a taxon-specific database built upon the same infrastructure, the EuPathDB
portal offers an entry point to all these resources, and the opportunity to leverage
orthology for searches across genera.
example: ECU03_0820i
homepage: http://microsporidiadb.org/micro/
mappings:
biocontext: MICROSPORIDIA
miriam: microsporidia
n2t: microsporidia
prefixcommons: microsporidia
name: MicrosporidiaDB
pattern: ^\w+$
preferred_prefix: microsporidia
uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
millipore:
description: Cell line collections
example: SCC111
homepage: https://www.merckmillipore.com/
mappings:
cellosaurus: Millipore
name: Merck Millipore (EMD Millipore)
preferred_prefix: millipore
uri_format: https://www.merckmillipore.com/catalogue/item/$1
mimodb:
description: MimoDB is a database collecting peptides that have been selected from
random peptide libraries based on their ability to bind small compounds, nucleic
acids, proteins, cells, tissues and organs. It also stores other information such
as the corresponding target, template, library, and structures. As of March 2016,
this database was renamed Biopanning Data Bank.
example: '1'
homepage: http://immunet.cn/bdb/
mappings:
biocontext: MIMODB
fairsharing: FAIRsharing.bv0zjz
miriam: mimodb
n2t: mimodb
prefixcommons: mimodb
name: MimoDB
pattern: ^\d+$
preferred_prefix: mimodb
uri_format: http://immunet.cn/bdb/index.php/mimoset/$1
minid:
description: Minid are identifiers used to provide robust reference to intermediate
data generated during the course of a research investigation.
example: b97957
homepage: https://fair-research.org
mappings:
biocontext: MINID
miriam: minid
n2t: minid
name: Minimal Viable Identifier
pattern: ^[A-Za-z0-9]+$
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/$1
mint:
description: The Molecular INTeraction database (MINT) stores, in a structured format,
information about molecular interactions by extracting experimental details from
work published in peer-reviewed journals.
example: MINT-10000
homepage: http://mint.bio.uniroma2.it/mint/
mappings:
biocontext: MINT
fairsharing: FAIRsharing.2bdvmk
miriam: mint
n2t: mint
prefixcommons: mint
uniprot: MINT
name: Molecular Interaction Database
pattern: ^MINT\-\d{1,7}$
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=$1
mipmod:
description: MIPModDb is a database of comparative protein structure models of MIP
(Major Intrinsic Protein) family of proteins, identified from complete genome
sequence. It provides key information of MIPs based on their sequence and structures.
example: HOSAPI0399
homepage: http://bioinfo.iitk.ac.in/MIPModDB
mappings:
biocontext: MIPMOD
miriam: mipmod
n2t: mipmod
prefixcommons: mipmod
name: MIPModDB
pattern: ^\w+$
preferred_prefix: mipmod
uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1
mir:
banana: MIR
description: The Identifiers.org registry contains registered namespace and provider
prefixes with associated access URIs for a large number of high quality data collections.
These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION”
or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other
data resources.
example: '00100037'
homepage: https://registry.identifiers.org/registry
mappings:
biocontext: MIR
miriam: mir
n2t: mir
name: Identifiers.org Registry
namespace_in_lui: true
pattern: ^\d{8}$
preferred_prefix: mir
uri_format: https://registry.identifiers.org/registry?query="MIR:$1"
mirbase:
description: The miRBase Sequence Database is a searchable database of published
miRNA sequences and annotation. The data were previously provided by the miRNA
Registry. Each entry in the miRBase Sequence database represents a predicted hairpin
portion of a miRNA transcript (termed mir in the database), with information on
the location and sequence of the mature miRNA sequence (termed miR).
example: MI0026471
homepage: http://www.mirbase.org/
mappings:
biocontext: MIRBASE
biolink: mirbase
fairsharing: FAIRsharing.hmgte8
miriam: mirbase
n2t: mirbase
ncbi: miRBase
prefixcommons: mirbase
wikidata: P2870
name: miRBase pre-miRNA
pattern: ^MI\d{7}$
preferred_prefix: mirbase
uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1
mirbase.family:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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=$1
mirbase.mature:
description: The miRBase Sequence Database is a searchable database of published
miRNA sequences and annotation. This collection refers specifically to the mature
miRNA sequence.
example: MIMAT0046872
homepage: http://www.mirbase.org/
mappings:
biocontext: MIRBASE.MATURE
miriam: mirbase.mature
n2t: mirbase.mature
prefixcommons: mirbase.mature
wikidata: P2871
name: miRBase mature miRNA
pattern: ^MIMAT\d{7}$
preferred_prefix: mirbase.mature
synonyms:
- MIRBASEM
uri_format: http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1
mirex:
description: mirEX is a comprehensive platform for comparative analysis of primary
microRNA expression data, storing RT–qPCR-based gene expression profile over seven
development stages of Arabidopsis. It also provides RNA structural models, publicly
available deep sequencing results and experimental procedure details. This collection
provides profile information for a single microRNA over all development stages.
example: 165a
homepage: http://comgen.pl/mirex/?page=home
mappings:
biocontext: MIREX
fairsharing: FAIRsharing.q3b39v
miriam: mirex
n2t: mirex
name: mirEX
pattern: ^\d+(\w+)?$
preferred_prefix: mirex
uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes
miriam:
description: Identifiers.org is an established resolving system that enables the
referencing of data for the scientific community, with a current focus on the
Life Sciences domain.
example: pubmed
homepage: https://www.ebi.ac.uk
mappings:
fairsharing: FAIRsharing.ap169a
miriam: identifiers.namespace
name: Identifiers.org namespace
pattern: ^[a-z_\.]+$
preferred_prefix: miriam
synonyms:
- identifiers.namespace
uri_format: https://registry.identifiers.org/registry/$1
miriam.collection:
deprecated: true
description: MIRIAM Registry is an online resource created to catalogue collections
(Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources
(physical locations) providing access to those data collections. The Registry
provides unique and perennial URIs for each entity of those data collections.
example: MIR:00000008
homepage: https://www.ebi.ac.uk/miriam/
mappings:
biocontext: MIRIAM.COLLECTION
miriam: miriam.collection
n2t: miriam.collection
name: MIRIAM Registry collection
pattern: ^MIR:000\d{5}$
preferred_prefix: miriam.collection
uri_format: https://www.ebi.ac.uk/miriam/main/$1
miriam.resource:
comment: yo dawg i heard you like registries...
description: MIRIAM Registry is an online resource created to catalogue data types
(Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding
resources (or physical locations), whether these are controlled vocabularies or
databases.
example: MIR:00100005
homepage: https://www.ebi.ac.uk/miriam/
mappings:
biocontext: MIRIAM.RESOURCE
miriam: miriam.resource
n2t: miriam.resource
prefixcommons: miriam.resource
name: MIRIAM Registry resource
pattern: ^MIR:001\d{5}$
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.
download_owl: http://purl.obolibrary.org/obo/mirnao.owl
homepage: http://code.google.com/p/mirna-ontology/
license: CC0 1.0
mappings:
biocontext: MIRNAO
bioportal: MIRNAO
obofoundry: MIRNAO
ontobee: miRNAO
name: microRNA Ontology
preferred_prefix: MIRNAO
uri_format: http://purl.obolibrary.org/obo/MIRNAO_$1
mirnest:
description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA
predictions conducted on Expressed Sequence Tags of animal and plant species.
example: MNEST029358
homepage: http://rhesus.amu.edu.pl/mirnest/copy/
mappings:
biocontext: MIRNEST
fairsharing: FAIRsharing.5pfx4r
miriam: mirnest
n2t: mirnest
prefixcommons: mirnest
name: miRNEST
pattern: ^MNEST\d+$
preferred_prefix: mirnest
uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1
miro:
banana: MIRO
contact:
email: louis@imbb.forth.gr
github: null
name: Christos (Kitsos) Louis
orcid: null
description: Application ontology for entities related to insecticide resistance
in mosquitos
download_obo: http://purl.obolibrary.org/obo/miro.obo
download_owl: http://purl.obolibrary.org/obo/miro.owl
example: '40000617'
homepage: https://github.com/VEuPathDB-ontology/MIRO
mappings:
biocontext: MIRO
bioportal: MIRO
fairsharing: FAIRsharing.sjf113
obofoundry: MIRO
ols: miro
ontobee: MIRO
name: Mosquito insecticide resistance
pattern: ^\d{8}$
preferred_prefix: MIRO
repository: https://github.com/VEuPathDB-ontology/MIRO
uri_format: http://purl.obolibrary.org/obo/MIRO_$1
version: '2014-05-14'
mirtarbase:
description: miRTarBase is a database of miRNA-target interactions (MTIs), collected
manually from relevant literature, following Natural Language Processing of the
text to identify research articles related to functional studies of miRNAs. Generally,
the collected MTIs are validated experimentally by reporter assay, western blot,
microarray and next-generation sequencing experiments.
example: MIRT000002
homepage: http://mirtarbase.mbc.nctu.edu.tw/
mappings:
biocontext: MIRTARBASE
fairsharing: FAIRsharing.f0bxfg
miriam: mirtarbase
n2t: mirtarbase
name: miRTarBase
pattern: ^MIRT\d{6}$
preferred_prefix: mirtarbase
uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1
mirte:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: This website provides access to our 2003 and 2005 miRNA-Target predictions
for Drosophila miRNAs
example: miR-1
homepage: http://www.russelllab.org/miRNAs/
name: miRNA Target Prediction at EMBL
preferred_prefix: mirte
mlc:
description: MLCommons Association artifacts, including benchmark results, datasets,
and saved models.
example: 0.7-123
homepage: https://mlcommons.org/en/
mappings:
miriam: mlc
name: MLCommons Association
pattern: ^[0-9a-zA-Z\.\-\_]+$
preferred_prefix: mlc
uri_format: https://www.mlcommons.org/mlc-id/$1
mmdb:
description: The Molecular Modeling Database (MMDB) is a database of experimentally
determined structures obtained from the Protein Data Bank (PDB). Since structures
are known for a large fraction of all protein families, structure homologs may
facilitate inference of biological function, or the identification of binding
or catalytic sites.
example: '50885'
homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure
mappings:
biocontext: MMDB
miriam: mmdb
n2t: mmdb
prefixcommons: mmdb
name: Molecular Modeling Database
pattern: ^\d{1,5}$
preferred_prefix: mmdb
uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1
mmmp.biomaps:
description: A collection of molecular interaction maps and pathways involved in
cancer development and progression with a focus on melanoma.
example: '37'
homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp
mappings:
biocontext: MMMP:BIOMAPS
biolink: mmmp.biomaps
miriam: mmmp:biomaps
n2t: biomaps
name: Melanoma Molecular Map Project Biomaps
pattern: ^\d+$
preferred_prefix: mmmp.biomaps
synonyms:
- mmmp:biomaps
uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1
mmo:
banana: MMO
contact:
email: jrsmith@mcw.edu
github: jrsjrs
name: Jennifer Smith
orcid: 0000-0002-6443-9376
description: 'A representation of the variety of methods used to make clinical and
phenotype measurements. '
download_obo: http://purl.obolibrary.org/obo/mmo.obo
download_owl: http://purl.obolibrary.org/obo/mmo.owl
example: '0000574'
homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000
license: CC0 1.0
mappings:
biocontext: MMO
bioportal: MMO
fairsharing: FAIRsharing.bgkyd7
obofoundry: MMO
ols: mmo
ontobee: MMO
name: Measurement method ontology
pattern: ^\d{7}$
preferred_prefix: MMO
repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology
uri_format: http://purl.obolibrary.org/obo/MMO_$1
version: '2019-03-27'
mmp.cat:
description: MarCat is a gene (protein) catalogue of uncultivable and cultivable
marine genes and proteins derived from metagenomics samples.
example: MMP743597.11
homepage: https://mmp.sfb.uit.no/databases/marcat/
mappings:
biocontext: MMP.CAT
miriam: mmp.cat
n2t: mmp.cat
name: MarCat
pattern: ^MMP\d+.\d+$
preferred_prefix: mmp.cat
uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1
mmp.db:
description: MarDB includes all sequenced marine microbial genomes regardless of
level of completeness.
example: MMP02954345.1
homepage: https://mmp.sfb.uit.no/databases/mardb/
mappings:
biocontext: MMP.DB
miriam: mmp.db
n2t: mmp.db
name: MarDB
pattern: ^MMP\d+.\d+$
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/$1
mmp.ref:
description: MarRef is a manually curated marine microbial reference genome database
that contains completely sequenced genomes.
example: MMP3312982.2
homepage: https://mmp.sfb.uit.no/databases/marref/
mappings:
biocontext: MMP.REF
miriam: mmp.ref
n2t: mmp.ref
name: MarRef
pattern: ^MMP\d+.\d+$
preferred_prefix: mmp.ref
uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1
mmrrc:
description: The MMRRC database is a repository of available mouse stocks and embryonic
stem cell line collections.
example: '70'
homepage: https://www.mmrrc.org
mappings:
biocontext: MMRRC
cellosaurus: MMRRC
fairsharing: FAIRsharing.9dpd18
miriam: mmrrc
n2t: mmrrc
name: Mutant Mouse Resource and Research Centers
pattern: ^\d+$
preferred_prefix: mmrrc
uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1
mmsl:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Lexicon is a foundational database with comprehensive drug product
and disease nomenclature information. It includes drug names, drug product information,
disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names
and common abbreviations. A comprehensive list of standard or customized disease
names and ICD-9 codes is also included.
example: '3355'
homepage: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html
name: Multum MediSource Lexicon
pattern: ^\d+$
preferred_prefix: mmsl
synonyms:
- MMSL_CODE
mmusdv:
banana: MmusDv
contact:
email: frederic.bastian@unil.ch
github: fbastian
name: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: Life cycle stages for Mus Musculus
download_obo: http://purl.obolibrary.org/obo/mmusdv.obo
download_owl: http://purl.obolibrary.org/obo/mmusdv.owl
example: '0000066'
homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv
license: CC BY 3.0
mappings:
biocontext: MMUSDV
biolink: MmusDv
bioportal: MMUSDV
fairsharing: FAIRsharing.zchb68
obofoundry: MmusDv
ols: mmusdv
ontobee: MMUSDV
name: Mouse Developmental Stages
pattern: ^\d{7}$
preferred_prefix: MmusDv
repository: https://github.com/obophenotype/developmental-stage-ontologies
synonyms:
- MmusDv
uri_format: http://purl.obolibrary.org/obo/MMUSDV_$1
version: '2020-03-10'
mo:
banana: MO
contact:
email: stoeckrt@pcbi.upenn.edu
github: null
name: Chris Stoeckert
orcid: 0000-0002-5714-991X
deprecated: true
description: The MGED Ontology (MO) provides terms for annotating all aspects of
a microarray experiment from the design of the experiment and array layout, through
to the preparation of the biological sample and the protocols used to hybridize
the RNA and analyze the data.
download_owl: http://purl.obolibrary.org/obo/mo.owl
example: ArrayGroup
homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php
mappings:
biocontext: MO
bioportal: MO
miriam: mo
n2t: mo
obofoundry: MO
name: Microarray experimental conditions
pattern: ^\w+$
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_$1
mobidb:
description: MobiDB is a database of protein disorder and mobility annotations.
example: P10636
homepage: http://mobidb.bio.unipd.it
mappings:
biocontext: MOBIDB
fairsharing: FAIRsharing.jwra3e
miriam: mobidb
n2t: mobidb
uniprot: MobiDB
name: MobiDB
pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$
preferred_prefix: mobidb
provides: uniprot
uri_format: https://mobidb.org/$1
mod:
banana: MOD
contact:
email: pierre-alain.binz@chuv.ch
github: pabinz
name: Pierre-Alain Binz
orcid: 0000-0002-0045-7698
description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims
to define a concensus nomenclature and ontology reconciling, in a hierarchical
representation, the complementary descriptions of residue modifications.
download_obo: http://purl.obolibrary.org/obo/mod.obo
download_owl: http://purl.obolibrary.org/obo/mod.owl
example: '01467'
homepage: http://www.psidev.info/MOD
license: CC BY 4.0
mappings:
biocontext: MOD
bioportal: PSIMOD
fairsharing: FAIRsharing.2m4ms9
go: PSI-MOD
miriam: mod
n2t: mod
obofoundry: MOD
ols: mod
ontobee: MOD
prefixcommons: psi.mod
name: Protein modification
namespace_in_lui: true
pattern: ^\d{5}$
preferred_prefix: MOD
repository: https://github.com/HUPO-PSI/psi-mod-CV
synonyms:
- PSI-MOD
uri_format: https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1
modeldb:
description: ModelDB is a curated, searchable database of published models in the
computational neuroscience domain. It accommodates models expressed in textual
form, including procedural or declarative languages (e.g. C++, XML dialects) and
source code written for any simulation environment.
example: '45539'
homepage: http://senselab.med.yale.edu/ModelDB/
mappings:
biocontext: MODELDB
fairsharing: FAIRsharing.5rb3fk
miriam: modeldb
n2t: modeldb
prefixcommons: modeldb
name: ModelDB
pattern: ^\d+$
preferred_prefix: modeldb
uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1
molbase:
description: Molbase provides compound data information for researchers as well
as listing suppliers and price information. It can be searched by keyword or CAS
indetifier.
example: 128796-39-4
homepage: http://www.molbase.com/
mappings:
biocontext: MOLBASE
miriam: molbase
n2t: molbase
name: Molbase
pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$
preferred_prefix: molbase
uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1
molbase.sheffield:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: An online database of inorganic compounds, MolBase was constructed
by Dr Mark Winter of the University of Sheffield with input from undergraduate
students.
example: '1868'
homepage: https://winter.group.shef.ac.uk/molbase/
name: MolBase
pattern: ^\d+$
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:
fairsharing: FAIRsharing.CWzk3C
miriam: molmedb
name: MolMeDB
pattern: ^[m,M]{2}[0-9]{5}[0-9]*$
preferred_prefix: molmedb
uri_format: https://molmedb.upol.cz/mol/$1
mondo:
banana: MONDO
contact:
email: nicole@tislab.org
github: nicolevasilevsky
name: Nicole Vasilevsky
orcid: 0000-0001-5208-3432
description: A semi-automatically constructed ontology that merges in multiple disease
resources to yield a coherent merged ontology.
download_json: http://purl.obolibrary.org/obo/mondo.json
download_obo: http://purl.obolibrary.org/obo/mondo.obo
download_owl: http://purl.obolibrary.org/obo/mondo.owl
example: '0000001'
homepage: https://monarch-initiative.github.io/mondo
license: CC BY 4.0
mappings:
biocontext: MONDO
bioportal: MONDO
fairsharing: FAIRsharing.b2979t
obofoundry: MONDO
ols: mondo
ontobee: MONDO
wikidata: P5270
name: Monarch Disease Ontology
pattern: ^\d{7}$
preferred_prefix: MONDO
repository: https://github.com/monarch-initiative/mondo
uri_format: http://purl.obolibrary.org/obo/MONDO_$1
version: '2022-05-02'
mop:
banana: MOP
contact:
email: batchelorc@rsc.org
github: batchelorc
name: Colin Batchelor
orcid: 0000-0001-5985-7429
description: MOP is the molecular process ontology. It contains the molecular processes
that underlie the name reaction ontology RXNO, for example cyclization, methylation
and demethylation.
download_obo: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo
download_owl: http://purl.obolibrary.org/obo/mop.owl
example: 0000079
homepage: https://github.com/rsc-ontologies/rxno
license: CC BY 4.0
mappings:
biocontext: MOP
bioportal: MOP
fairsharing: FAIRsharing.mct09a
obofoundry: MOP
ols: mop
ontobee: MOP
name: Molecular Process Ontology
pattern: ^\d{7}$
preferred_prefix: MOP
repository: https://github.com/rsc-ontologies/rxno
uri_format: http://purl.obolibrary.org/obo/MOP_$1
version: '2022-02-01'
morpheus:
description: 'The Morpheus model repository is an open-access data resource to store,
search and retrieve unpublished and published computational models of spatio-temporal
and multicellular biological systems, encoded in the MorpheusML language and readily
executable with the Morpheus software.
'
example: M0001
homepage: https://morpheus.gitlab.io/
mappings:
miriam: morpheus
name: Morpheus model repository
pattern: ^M[0-9]{4,}$
preferred_prefix: morpheus
uri_format: https://morpheus.gitlab.io/models/$1
mp:
appears_in:
- chiro
- scdo
banana: MP
contact:
email: drsbello@gmail.com
github: sbello
name: Sue Bello
orcid: 0000-0003-4606-0597
description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic
information related to the mouse and other mammalian species. This ontology has
been applied to mouse phenotype descriptions in various databases allowing comparisons
of data from diverse mammalian sources. It can facilitate in the identification
of appropriate experimental disease models, and aid in the discovery of candidate
disease genes and molecular signaling pathways.
download_json: http://purl.obolibrary.org/obo/mp.json
download_obo: http://purl.obolibrary.org/obo/mp.obo
download_owl: http://purl.obolibrary.org/obo/mp.owl
example: '0005452'
homepage: http://www.informatics.jax.org/searches/MP_form.shtml
license: CC BY 4.0
mappings:
biocontext: MP
bioportal: MP
fairsharing: FAIRsharing.kg1x4z
miriam: mp
n2t: mp
obofoundry: MP
ols: mp
ontobee: MP
prefixcommons: mp
name: Mammalian Phenotype Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: MP
repository: https://github.com/mgijax/mammalian-phenotype-ontology
uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1
mpath:
banana: MPATH
contact:
email: pns12@hermes.cam.ac.uk
github: PaulNSchofield
name: Paul Schofield
orcid: 0000-0002-5111-7263
description: A structured controlled vocabulary of mutant and transgenic mouse pathology
phenotypes
download_obo: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo
download_owl: http://purl.obolibrary.org/obo/mpath.owl
example: '728'
homepage: http://www.pathbase.net
license: CC BY 3.0
mappings:
biocontext: MPATH
bioportal: MPATH
fairsharing: FAIRsharing.3wbgm0
obofoundry: MPATH
ols: mpath
ontobee: MPATH
prefixcommons: mpath
name: Mouse pathology ontology
pattern: ^\d+$
preferred_prefix: MPATH
repository: https://github.com/PaulNSchofield/mpath
synonyms:
- MPATH
uri_format: http://purl.obolibrary.org/obo/MPATH_$1
version: '2020-05-19'
mpid:
description: The microbial protein interaction database (MPIDB) provides physical
microbial interaction data. The interactions are manually curated from the literature
or imported from other databases, and are linked to supporting experimental evidence,
as well as evidences based on interaction conservation, protein complex membership,
and 3D domain contacts.
example: '172'
homepage: http://www.jcvi.org/mpidb/about.php
mappings:
biocontext: MPID
fairsharing: FAIRsharing.eyjkws
miriam: mpid
n2t: mpid
name: Microbial Protein Interaction Database
pattern: ^\d+$
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
synonyms:
- mpidb
uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1
mpio:
banana: MPIO
contact:
email: mbrochhausen@uams.edu
github: mbrochhausen
name: Mathias Brochhausen
orcid: 0000-0003-1834-3856
description: An ontology of minimum information regarding potential drug-drug interaction
information.
download_owl: http://purl.obolibrary.org/obo/mpio.owl
example: '0000004'
homepage: https://github.com/MPIO-Developers/MPIO
license: CC BY 4.0
mappings:
biocontext: MPIO
bioportal: MPIO
obofoundry: MPIO
ols: mpio
ontobee: MPIO
name: Minimum PDDI Information Ontology
pattern: ^\d{7}$
preferred_prefix: MPIO
repository: https://github.com/MPIO-Developers/MPIO
uri_format: http://purl.obolibrary.org/obo/MPIO_$1
version: '2019-01-30'
mro:
banana: MRO
contact:
email: bpeters@lji.org
github: bpeters42
name: Bjoern Peters
orcid: 0000-0002-8457-6693
description: The MHC Restriction Ontology is an application ontology capturing how
Major Histocompatibility Complex (MHC) restriction is defined in experiments,
spanning exact protein complexes, individual protein chains, serotypes, haplotypes
and mutant molecules, as well as evidence for MHC restrictions.
download_owl: http://purl.obolibrary.org/obo/mro.owl
example: '0000634'
homepage: https://github.com/IEDB/MRO
license: CC BY 3.0
mappings:
biocontext: MRO
bioportal: MRO
fairsharing: FAIRsharing.k893xa
obofoundry: MRO
ols: mro
ontobee: MRO
name: MHC Restriction Ontology
pattern: ^\d{7}$
preferred_prefix: MRO
repository: https://github.com/IEDB/MRO
uri_format: http://purl.obolibrary.org/obo/MRO_$1
version: '2022-03-14'
ms:
banana: MS
contact:
email: gerhard.mayer@rub.de
github: germa
name: Gerhard Mayer
orcid: 0000-0002-1767-2343
depends_on:
- pato
- uo
description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the
PSI MS-related data standards. The CV contains a logical hierarchical structure
to ensure ease of maintenance and the development of software that makes use of
complex semantics. The CV contains terms required for a complete description of
an MS analysis pipeline used in proteomics, including sample labeling, digestion
enzymes, instrumentation parts and parameters, software used for identification
and quantification of peptides/proteins and the parameters and scores used to
determine their significance.
download_obo: http://purl.obolibrary.org/obo/ms.obo
download_owl: http://purl.obolibrary.org/obo/ms.owl
example: '1000560'
homepage: http://www.psidev.info/groups/controlled-vocabularies
license: CC BY 3.0
mappings:
biocontext: MS
bioportal: MS
miriam: ms
n2t: ms
obofoundry: MS
ols: ms
ontobee: MS
name: Mass spectrometry ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: MS
repository: https://github.com/HUPO-PSI/psi-ms-CV
uri_format: https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1
msigdb:
description: The Molecular Signatures Database (MSigDB) is a collection of annotated
gene sets for use with GSEA software. From this web site, you can
example: NADELLA_PRKAR1A_TARGETS_DN
homepage: https://www.gsea-msigdb.org
mappings:
biolink: MSigDB
name: Molecular Signatures Database
preferred_prefix: msigdb
synonyms:
- msig
msio:
description: an application ontology for supporting description and annotation of
mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics
studies.
download_owl: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl
example: '0000111'
homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO
mappings:
ols: msio
name: Metabolomics Standards Initiative Ontology
pattern: ^\d{7}$
preferred_prefix: msio
repository: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO
version: 1.0.1
multicellds:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
mappings:
fairsharing: FAIRsharing.pqzyd5
name: MultiCellDS
preferred_prefix: multicellds
uri_format: http://multicellds.org/MultiCellDB/$1
multicellds.cell_line:
description: MultiCellDS is data standard for multicellular simulation, experimental,
and clinical data. A digital cell line is a hierarchical organization of quantitative
phenotype data for a single biological cell line, including the microenvironmental
context of the measurements and essential metadata.
example: MCDS_L_0000000001
homepage: http://multicellds.org/MultiCellDB.php
mappings:
biocontext: MULTICELLDS.CELL_LINE
miriam: multicellds.cell_line
n2t: multicellds.cell_line
name: MultiCellDS Digital Cell Line
part_of: multicellds
pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$
preferred_prefix: multicellds.cell_line
uri_format: http://multicellds.org/MultiCellDB/$1
multicellds.collection:
description: MultiCellDS is data standard for multicellular simulation, experimental,
and clinical data. A collection groups one or more individual uniquely identified
cell lines, snapshots, or collections. Primary uses are times series (collections
of snapshots), patient cohorts (collections of cell lines), and studies (collections
of time series collections).
example: MCDS_C_0000000001
homepage: http://multicellds.org/MultiCellDB.php
mappings:
biocontext: MULTICELLDS.COLLECTION
miriam: multicellds.collection
n2t: multicellds.collection
name: MultiCellDS collection
part_of: multicellds
pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$
preferred_prefix: multicellds.collection
uri_format: http://multicellds.org/MultiCellDB/$1
multicellds.snapshot:
description: MultiCellDS is data standard for multicellular simulation, experimental,
and clinical data. A digital snapshot is a single-time output of the microenvironment
(including basement membranes and the vascular network), any cells contained within,
and essential metadata. Cells may include phenotypic data.
example: MCDS_S_0000000001
homepage: http://multicellds.org/MultiCellDB.php
mappings:
biocontext: MULTICELLDS.SNAPSHOT
miriam: multicellds.snapshot
n2t: multicellds.snapshot
name: MultiCellDS Digital snapshot
part_of: multicellds
pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$
preferred_prefix: multicellds.snapshot
uri_format: http://multicellds.org/MultiCellDB/$1
mw.project:
description: Metabolomics Workbench stores metabolomics data for small and large
studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository
and Coordinating Center (DRCC).
example: PR000001
homepage: http://www.metabolomicsworkbench.org/
mappings:
biocontext: MW.PROJECT
miriam: mw.project
n2t: mw.project
name: Metabolomics Workbench Project
pattern: ^PR[0-9]{6}$
preferred_prefix: mw.project
uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1
mw.study:
description: Metabolomics Workbench stores metabolomics data for small and large
studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository
and Coordinating Center (DRCC).
example: ST000900
homepage: http://www.metabolomicsworkbench.org/
mappings:
biocontext: MW.STUDY
miriam: mw.study
n2t: mw.study
name: Metabolomics Workbench Study
pattern: ^ST[0-9]{6}$
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=$1
myco.lepra:
description: Mycobrowser is a resource that provides both in silico generated and
manually reviewed information within databases dedicated to the complete genomes
of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
Mycobacterium smegmatis. This collection references Mycobacteria leprae information.
example: ML0224
homepage: http://mycobrowser.epfl.ch/leprosy.html
mappings:
biocontext: MYCO.LEPRA
miriam: myco.lepra
n2t: myco.lepra
prefixcommons: myco.lepra
name: MycoBrowser leprae
pattern: ^ML\w+$
preferred_prefix: myco.lepra
uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1
myco.marinum:
description: Mycobrowser is a resource that provides both in silico generated and
manually reviewed information within databases dedicated to the complete genomes
of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
Mycobacterium smegmatis. This collection references Mycobacteria marinum information.
example: MMAR_2462
homepage: http://mycobrowser.epfl.ch/marinolist.html
mappings:
biocontext: MYCO.MARINUM
miriam: myco.marinum
n2t: myco.marinum
prefixcommons: myco.marinum
name: MycoBrowser marinum
pattern: ^MMAR\_\d+$
preferred_prefix: myco.marinum
uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1
myco.smeg:
description: Mycobrowser is a resource that provides both in silico generated and
manually reviewed information within databases dedicated to the complete genomes
of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.
example: MSMEG_3769
homepage: http://mycobrowser.epfl.ch/smegmalist.html
mappings:
biocontext: MYCO.SMEG
miriam: myco.smeg
n2t: myco.smeg
prefixcommons: myco.smeg
name: MycoBrowser smegmatis
pattern: ^MSMEG\w+$
preferred_prefix: myco.smeg
uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1
myco.tuber:
description: Mycobrowser is a resource that provides both in silico generated and
manually reviewed information within databases dedicated to the complete genomes
of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and
Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis
information.
example: Rv1908c
homepage: http://tuberculist.epfl.ch/
mappings:
biocontext: MYCO.TUBER
miriam: myco.tuber
n2t: myco.tuber
ncbi: TubercuList
prefixcommons: tuberculist
uniprot: TubercuList
name: TubercuList knowledge base
pattern: ^Rv\d{4}(A|B|c)?$
preferred_prefix: myco.tuber
synonyms:
- TubercuList
uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1
mycobank:
description: MycoBank is an online database, documenting new mycological names and
combinations, eventually combined with descriptions and illustrations.
example: '349124'
homepage: http://www.mycobank.org/
mappings:
biocontext: MYCOBANK
fairsharing: FAIRsharing.v8se8r
miriam: mycobank
n2t: mycobank
ncbi: MycoBank
prefixcommons: mycobank
name: Fungal Nomenclature and Species Bank
pattern: ^\d+$
preferred_prefix: mycobank
uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1
mzspec:
banana: mzspec
description: The Universal Spectrum Identifier (USI) is a compound identifier that
provides an abstract path to refer to a single spectrum generated by a mass spectrometer,
and potentially the ion that is thought to have produced it.
example: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2
homepage: http://proteomecentral.proteomexchange.org/
mappings:
biocontext: MZSPEC
miriam: mzspec
n2t: mzspec
name: Universal Spectrum Identifier
namespace_in_lui: true
pattern: ^.+$
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
n2t:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ARK resolver as well as resolver built with common prefixes as in
Identifiers.org
example: chebi
homepage: https://n2t.net
name: Name-to-Thing
preferred_prefix: n2t
uri_format: 'https://n2t.net/$1:'
namerxn:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The nomenclature used for named reactions in text mining software from
NextMove. While it's proprietary, there are a few publications listing parts.
487/1,855 have mappings to the Reaction Ontology (RXNO).
example: 4.2.78
homepage: https://www.nextmovesoftware.com/namerxn.html
name: NameRXN
preferred_prefix: namerxn
proprietary: true
references:
- https://www.nextmovesoftware.com/products/HazELNutPoster.pdf
- https://twitter.com/cthoyt/status/1443929184745758723
- https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.6b00153
- https://www.nature.com/articles/s42256-020-00284-w
napdi:
description: The Natural Product-Drug Interaction Research Data Repository, a publicly
accessible database where researchers can access scientific results, raw data,
and recommended approaches to optimally assess the clinical significance of pharmacokinetic
natural product-drug interactions (PK-NPDIs).
example: '28'
homepage: https://repo.napdi.org/
mappings:
biocontext: NAPDI
fairsharing: FAIRsharing.y9x8wk
miriam: napdi
n2t: napdi
name: Natural Product-Drug Interaction Research Data Repository
pattern: ^[0-9]+$
preferred_prefix: napdi
uri_format: https://repo.napdi.org/study/$1
napp:
description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based
on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic
regions from a reference genome are compared with other genomes to identify RNA
rich clusters.
example: '351'
homepage: http://napp.u-psud.fr/
mappings:
biocontext: NAPP
fairsharing: FAIRsharing.vr52p3
miriam: napp
n2t: napp
prefixcommons: napp
name: Nucleic Acids Phylogenetic Profiling
pattern: ^\d+$
preferred_prefix: napp
uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1
narcis:
description: NARCIS provides access to scientific information, including (open access)
publications from the repositories of all the Dutch universities, KNAW, NWO and
a number of research institutes, which is not referenced in other citation databases.
example: oai:cwi.nl:4725
homepage: http://www.narcis.nl
mappings:
biocontext: NARCIS
fairsharing: FAIRsharing.f63h4k
miriam: narcis
n2t: narcis
name: National Academic Research and Collaborations Information System
pattern: ^oai\:cwi\.nl\:\d+$
preferred_prefix: narcis
uri_format: http://www.narcis.nl/publication/RecordID/$1
nasc:
description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information
resources to the International Arabidopsis Genome Programme and the wider research
community.
example: N1899
homepage: http://arabidopsis.info/
mappings:
biocontext: NASC
fairsharing: FAIRsharing.2sqcxs
miriam: nasc
n2t: nasc
prefixcommons: nasc
name: NASC code
pattern: ^(\w+)?\d+$
preferred_prefix: nasc
uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1
nbn:
description: The National Bibliography Number (NBN), is a URN-based publication
identifier system employed by a variety of national libraries such as those of
Germany, the Netherlands and Switzerland. They are used to identify documents
archived in national libraries, in their native format or language, and are typically
used for documents which do not have a publisher-assigned identifier.
example: urn:nbn:fi:tkk-004781
homepage: http://nbn-resolving.org/resolve_urn.htm
mappings:
biocontext: NBN
miriam: nbn
n2t: nbn
name: National Bibliography Number
pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$
preferred_prefix: nbn
uri_format: http://nbn-resolving.org/resolver?identifier=$1&verb=redirect
nbo:
appears_in:
- ecto
- pcl
- scdo
banana: NBO
contact:
email: g.gkoutos@bham.ac.uk
github: gkoutos
name: George Gkoutos
orcid: 0000-0002-2061-091X
description: An ontology of human and animal behaviours and behavioural phenotypes
download_obo: https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo
download_owl: http://purl.obolibrary.org/obo/nbo.owl
example: '0000564'
homepage: https://github.com/obo-behavior/behavior-ontology/
license: CC BY 3.0
mappings:
biocontext: NBO
bioportal: NBO
fairsharing: FAIRsharing.pktgc6
obofoundry: NBO
ols: nbo
ontobee: NBO
name: Neuro Behavior Ontology
pattern: ^\d{7}$
preferred_prefix: NBO
repository: https://github.com/obo-behavior/behavior-ontology
uri_format: http://purl.obolibrary.org/obo/NBO_$1
version: '2021-02-15'
nbrc:
description: NITE Biological Research Center (NBRC) provides a collection of microbial
resources, performing taxonomic characterization of individual microorganisms
such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages
and DNA resources for academic research and industrial applications. A catalogue
is maintained which states strain nomenclature, synonyms, and culture and sequence
information.
example: '00001234'
homepage: http://www.nbrc.nite.go.jp/e/index.html
mappings:
biocontext: NBRC
fairsharing: FAIRsharing.ftamrc
miriam: nbrc
n2t: nbrc
ncbi: NBRC
prefixcommons: nbrc
name: NITE Biological Resource Center
pattern: ^\d+$
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: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The [National Center for Advancing Translational Sciences (NCATS)](https://ncats.nih.gov/)
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'
example_extras:
- 1IJV77EI07
homepage: https://drugs.ncats.io/
name: NCATS Drugs
preferred_prefix: ncats.drug
synonyms:
- inxight
- inxight-drugs
uri_format: https://drugs.ncats.io/drug/$1
ncbi.assembly:
description: A database providing information on the structure of assembled genomes,
assembly names and other meta-data, statistical reports, and links to genomic
sequence data.
example: GCF_000005845.2
homepage: https://www.ncbi.nlm.nih.gov/
mappings:
biocontext: NCBIAssembly
miriam: assembly
name: Assembly
pattern: ^[a-zA-Z0-9_\.]+$
preferred_prefix: ncbi.assembly
uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1
ncbi.genome:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: This resource organizes information on genomes including sequences,
maps, chromosomes, assemblies, and annotations.
example: '51'
homepage: https://www.ncbi.nlm.nih.gov/genome
mappings:
biocontext: NCBIGenome
name: NCBI Genome
pattern: ^\d+$
preferred_prefix: ncbi.genome
uri_format: https://www.ncbi.nlm.nih.gov/genome/$1
ncbi.resource:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A database-specific registry supporting curation in the NCBI GenBank
and related NCBI resources
example: ECOCYC
homepage: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/
name: NCBI Registry
preferred_prefix: ncbi.resource
uri_format: https://bioregistry.io/metaregistry/ncbi/$1
ncbibook:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The NCBI Bookshelf provides free online access to books and documents
in life science and healthcare. Search, read, and discover. '
example: NBK331
homepage: https://www.ncbi.nlm.nih.gov/books
name: NCBI Bookshelf
pattern: ^NBK\d+$
preferred_prefix: ncbibook
uri_format: https://www.ncbi.nlm.nih.gov/books/$1
ncbigene:
description: Entrez Gene is the NCBI's database for gene-specific information, focusing
on completely sequenced genomes, those with an active research community to contribute
gene-specific information, or those that are scheduled for intense sequence analysis.
example: '100010'
homepage: https://www.ncbi.nlm.nih.gov/gene
mappings:
biocontext: NCBIGene
biolink: NCBIGene
fairsharing: FAIRsharing.5h3maw
go: NCBIGene
miriam: ncbigene
n2t: ncbigene
ncbi: GeneID
prefixcommons: ncbigene
scholia: ncbi-gene
wikidata: P351
name: Entrez Gene
pattern: ^\d+$
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
- EntrezGene
- NCBIGene
- entrez
- entrez gene/locuslink
uri_format: https://www.ncbi.nlm.nih.gov/gene/$1
ncbiprotein:
description: The Protein database is a collection of sequences from several sources,
including translations from annotated coding regions in GenBank, RefSeq and TPA,
as well as records from SwissProt, PIR, PRF, and PDB.
example: CAA71118.1
homepage: https://www.ncbi.nlm.nih.gov/protein
mappings:
biocontext: NCBIProtein
go: NCBI_NP
miriam: ncbiprotein
n2t: ncbiprotein
prefixcommons: ncbi.protein
name: NCBI Protein
pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$
preferred_prefix: NCBIProtein
uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
ncbitaxon:
appears_in:
- agro
- chiro
- cl
- clo
- ecto
- envo
- foodon
- genepio
- go
- hso
- mco
- ons
- pcl
- pco
contact:
email: frederic.bastian@unil.ch
github: fbastian
name: Frederic Bastian
orcid: 0000-0002-9415-5104
description: The taxonomy contains the relationships between all living forms for
which nucleic acid or protein sequence have been determined.
download_json: http://purl.obolibrary.org/obo/ncbitaxon.json
download_obo: http://purl.obolibrary.org/obo/ncbitaxon.obo
download_owl: http://purl.obolibrary.org/obo/ncbitaxon.owl
example: '2170610'
homepage: https://github.com/obophenotype/ncbitaxon
license: CC0 1.0
mappings:
biocontext: NCBITaxon
bioportal: NCBITAXON
cellosaurus: NCBI_TaxID
fairsharing: FAIRsharing.fj07xj
go: taxon
miriam: taxonomy
n2t: taxonomy
ncbi: taxon
obofoundry: NCBITaxon
ols: ncbitaxon
ontobee: NCBITaxon
prefixcommons: taxonomy
scholia: ncbi-taxon
wikidata: P685
name: NCBI Taxonomy
pattern: ^\d+$
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
repository: https://github.com/obophenotype/ncbitaxon
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=$1
version: '2021-12-14'
ncim:
description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database
that covers most terminologies used by NCI for clinical care, translational and
basic research, and public information and administrative activities. It integrates
terms and definitions from different terminologies, including NCI Thesaurus, however
the representation is not identical.
example: C0026339
homepage: http://ncim.nci.nih.gov/
mappings:
biocontext: NCIM
miriam: ncim
n2t: ncim
name: NCI Metathesaurus
pattern: ^C\d+$
preferred_prefix: ncim
uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1
ncit:
appears_in:
- ecto
- mco
- ontoavida
- scdo
contact:
email: haendel@ohsu.edu
github: mellybelly
name: Melissa Haendel
orcid: 0000-0001-9114-8737
description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary
for clinical care, translational and basic research, and public information and
administrative activities, providing a stable and unique identification code.
download_obo: http://purl.obolibrary.org/obo/ncit.obo
download_owl: http://purl.obolibrary.org/obo/ncit.owl
example: C138986
homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
license: CC BY 4.0
mappings:
biocontext: NCIT
bioportal: NCIT
cellosaurus: NCIt
fairsharing: FAIRsharing.4cvwxa
miriam: ncit
n2t: ncit
obofoundry: NCIT
ols: ncit
ontobee: NCIT
prefixcommons: ncit
wikidata: P1748
name: NCI Thesaurus
pattern: ^C\d+$
preferred_prefix: NCIT
repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition
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=$1
version: 22.03d
ncro:
banana: NCRO
contact:
email: huang@southalabama.edu
github: Huang-OMIT
name: Jingshan Huang
orcid: 0000-0003-2408-2883
description: An ontology for non-coding RNA, both of biological origin, and engineered.
download_obo: https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo
download_owl: http://purl.obolibrary.org/obo/ncro.owl
example: 0002927
homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology
license: CC BY 4.0
mappings:
biocontext: NCRO
bioportal: NCRO
fairsharing: FAIRsharing.vppyga
obofoundry: NCRO
ols: ncro
ontobee: NCRO
name: Non-Coding RNA Ontology
pattern: ^\d{7}$
preferred_prefix: NCRO
repository: https://github.com/OmniSearch/ncro
uri_format: http://purl.obolibrary.org/obo/NCRO_$1
version: '2015-12-10'
ndc:
description: The National Drug Code (NDC) is a unique, three-segment number used
by the Food and Drug Administration (FDA) to identify drug products for commercial
use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates
the listed NDC numbers daily.
example: 0002-1975-61
homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/
mappings:
biocontext: NDC
miriam: ndc
n2t: ndc
name: National Drug Code
pattern: ^\d+\-\d+\-\d+$
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/$1
nddf:
description: FDB MedKnowledge encompasses medications approved by the U.S. Food
and Drug Administration, and information on commonly-used over-the-counter and
alternative therapy agents such as herbals, nutraceuticals and dietary supplements.
example: 002678
homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF
mappings:
biolink: NDDF
bioportal: NDDF
fairsharing: FAIRsharing.8qcbs0
name: National Drug Data File
pattern: ^\d{6}$
preferred_prefix: nddf
ndex:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
mappings:
fairsharing: FAIRsharing.8nq9t6
name: Network Data Exchange
preferred_prefix: ndex
uri_format: https://www.ndexbio.org/viewer/networks/$1
ndfrt:
description: 'NDF-RT combines the NDF hierarchical drug classification with a multi-category
reference model. The categories are: Cellular or Molecular Interactions [MoA];
Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases,
Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form];
Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories
[TC]; and VA Drug Interactions [VA Drug Interaction].'
example: N0000001662
homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT
mappings:
bioportal: NDFRT
fairsharing: FAIRsharing.901nkj
ontobee: NDF-RT
prefixcommons: ndfrt
wikidata: P2115
name: National Drug File - Reference Terminology
preferred_prefix: ndfrt
synonyms:
- NUI
- ndf-rt
nemo:
description: This namespace is about Neuroscience Multi-Omic data, specially focused
on that data generated from the BRAIN Initiative and related brain research projects.
example: smp-m3w9hbe
homepage: https://www.nemoarchive.org
mappings:
bioportal: NEMO
fairsharing: FAIRsharing.n66krd
miriam: nemo
name: Neural ElectroMagnetic Ontology
pattern: ^[a-z]{3}-[a-km-z0-9]{7}$
preferred_prefix: nemo
uri_format: https://assets.nemoarchive.org/$1
neurolex:
description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It
is supported by the Neuroscience Information Framework project and incorporates
information from the NIF standardised ontology (NIFSTD), and its predecessor,
the Biomedical Informatics Research Network Lexicon (BIRNLex).
example: Birnlex_721
homepage: http://www.neurolex.org/wiki/Main_Page
mappings:
biocontext: NEUROLEX
miriam: neurolex
n2t: neurolex
prefixcommons: neurolex
name: NeuroLex
pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$
preferred_prefix: neurolex
uri_format: http://www.neurolex.org/wiki/$1
neuromorpho:
description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed
neurons.
example: Rosa2
homepage: http://neuromorpho.org/index.jsp
mappings:
biocontext: NEUROMORPHO
miriam: neuromorpho
n2t: neuromorpho
prefixcommons: neuromorpho
name: NeuroMorpho
pattern: ^\w+$
preferred_prefix: neuromorpho
uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1
neuronames:
description: BrainInfo is designed to help you identify structures in the brain.
If you provide the name of a structure, BrainInfo will show it and tell you about
it.
example: '268'
homepage: http://braininfo.rprc.washington.edu/
mappings:
wikidata: P4394
name: NeuroNames
pattern: ^\d+$
preferred_prefix: neuronames
references:
- https://en.wikipedia.org/wiki/NeuroNames
synonyms:
- neuroname
uri_format: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1
neurondb:
description: 'NeuronDB provides a dynamically searchable database of three types
of neuronal properties: voltage gated conductances, neurotransmitter receptors,
and neurotransmitter substances. It contains tools that provide for integration
of these properties in a given type of neuron and compartment, and for comparison
of properties across different types of neurons and compartments.'
example: '265'
homepage: http://senselab.med.yale.edu/NeuronDB/
mappings:
biocontext: NEURONDB
fairsharing: FAIRsharing.45a10e
miriam: neurondb
n2t: neurondb
prefixcommons: neurondb
name: NeuronDB
pattern: ^\d+$
preferred_prefix: neurondb
uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1
neurovault.collection:
description: Neurovault is an online repository for statistical maps, parcellations
and atlases of the brain. This collection references sets (collections) of images.
example: '3304'
homepage: http://neurovault.org
mappings:
biocontext: NEUROVAULT.COLLECTION
miriam: neurovault.collection
n2t: neurovault.collection
name: NeuroVault Collection
pattern: ^[1-9][0-9]*$
preferred_prefix: neurovault.collection
uri_format: https://neurovault.org/collections/$1
neurovault.image:
description: Neurovault is an online repository for statistical maps, parcellations
and atlases of the brain. This collection references individual images.
example: '58788'
homepage: http://neurovault.org
mappings:
biocontext: NEUROVAULT.IMAGE
miriam: neurovault.image
n2t: neurovault.image
name: NeuroVault Image
pattern: ^[1-9][0-9]*$
preferred_prefix: neurovault.image
uri_format: https://neurovault.org/images/$1
nextdb:
description: NextDb is a database that provides information on the expression pattern
map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done
through EST analysis and systematic whole mount in situ hybridization. Information
available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237
cDNA clones.
example: 6b1
homepage: http://nematode.lab.nig.ac.jp/
mappings:
biocontext: NEXTDB
fairsharing: FAIRsharing.xz5m1a
miriam: nextdb
n2t: nextdb
ncbi: NextDB
prefixcommons: nextdb
name: Nematode Expression Pattern DataBase
pattern: ^[A-Za-z0-9]+$
preferred_prefix: nextdb
uri_format: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1
nextprot:
description: neXtProt is a resource on human proteins, and includes information
such as proteins’ function, subcellular location, expression, interactions and
role in diseases.
example: NX_O00165
homepage: https://www.nextprot.org/
mappings:
biocontext: NEXTPROT
fairsharing: FAIRsharing.62evqh
miriam: nextprot
n2t: nextprot
uniprot: neXtProt
name: nextProt
pattern: ^NX_\w+$
preferred_prefix: nextprot
synonyms:
- NXP
uri_format: https://www.nextprot.org/db/entry/$1
nextprot.family:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: "NeXtProt is a comprehensive human-centric discovery platform, offering\
\ its users a seamless integration of and navigation through protein-related data.\
\ \n(Developed by the SIB Swiss Institute of Bioinformatics)"
example: '01406'
homepage: https://www.nextprot.org/
name: neXtProt family
pattern: ^\d+$
preferred_prefix: nextprot.family
synonyms:
- NXPFA
uri_format: https://www.nextprot.org/term/FA-$1
ngl:
description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression,
and metabolic profiles, interfaces with existing databases for expanded research,
will offer tools to conduct data analysis, and is in the process of creating a
place online where scientists, researchers, teachers and students can connect
with their peers, share their results, and communicate with NASA.
example: GLDS-141
homepage: https://genelab-data.ndc.nasa.gov/genelab/
mappings:
biocontext: NGL
miriam: ngl
n2t: ngl
name: NASA GeneLab
pattern: ^GLDS-\d+$
preferred_prefix: ngl
uri_format: https://genelab-data.ndc.nasa.gov/genelab/accession/$1
nhcdr:
description: Cell line collections
example: ND50028
homepage: https://stemcells.nindsgenetics.org
mappings:
cellosaurus: NHCDR
name: NINDS Human Cell and Data Repository
preferred_prefix: nhcdr
uri_format: https://stemcells.nindsgenetics.org?line=$1
niaest:
description: A catalog of mouse genes expressed in early embryos, embryonic and
adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute
on Aging) assembled.This collection represents the name and sequence from individual
cDNA clones.
example: J0705A10
homepage: http://lgsun.grc.nia.nih.gov/cDNA/
mappings:
biocontext: NIAEST
fairsharing: FAIRsharing.xwqg9h
miriam: niaest
n2t: niaest
ncbi: niaEST
prefixcommons: niaest
name: NIA Mouse cDNA Project
pattern: ^\w\d{4}\w\d{2}(\-[35])?$
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:
biocontext: NIF_CELL
bioportal: NIFCELL
obofoundry: 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:
biocontext: NIF_DYSFUNCTION
obofoundry: 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:
biocontext: NIF_GROSSANATOMY
obofoundry: NIF_GROSSANATOMY
name: NIF Gross Anatomy
preferred_prefix: NIF_GROSSANATOMY
uri_format: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1
nist:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The NIST Chemistry WebBook provides users with easy access to chemical
and physical property data for chemical species through the internet. The data
provided in the site are from collections maintained by the NIST Standard Reference
Data Program and outside contributors. Data in the WebBook system are organized
by chemical species.
homepage: https://webbook.nist.gov/chemistry/
name: NIST Chemistry WebBook
no_own_terms: true
preferred_prefix: nist
synonyms:
- NIST
- NIST Chemistry WebBook
nlm:
description: Bibliographic data for all the journals, books, audiovisuals, computer
software, electronic resources and other materials that are in the library's holdings.
example: '101775319'
homepage: https://www.ncbi.nlm.nih.gov/nlmcatalog
mappings:
biolink: NLMID
name: National Library of Medicine Catalog
pattern: ^\d+$
preferred_prefix: nlm
uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1
nlxanat:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The InterLex project - a core component of SciCrunch and supported
by projects such as the Neuroscience Information Framework project (NIF), the
NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury
- is a dynamic lexicon of biomedical terms.
example: 090201
homepage: https://scicrunch.org/scicrunch/interlex/dashboard
name: NeuroLex Anatomy
part_of: neurolex
pattern: ^\d{6}$
preferred_prefix: nlxanat
uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1
nlxdys:
appears_in:
- mondo
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The InterLex project - a core component of SciCrunch and supported
by projects such as the Neuroscience Information Framework project (NIF), the
NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury
- is a dynamic lexicon of biomedical terms.
example: '20090303'
homepage: https://scicrunch.org/scicrunch/interlex/dashboard
name: NeuroLex Dysfunction
part_of: neurolex
pattern: ^\d+$
preferred_prefix: nlxdys
uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1
nmdc:
contact:
email: donny@polyneme.xyz
github: dwinston
name: Donny Winston
orcid: 0000-0002-8424-0604
contributor:
email: donny@polyneme.xyz
github: dwinston
name: Donny Winston
orcid: 0000-0002-8424-0604
description: An initiative to empower the research community to harness microbiome
data exploration and discovery through a collaborative integrative data science
ecosystem.
example: y3ax-8bq3-60
homepage: https://microbiomedata.org/
mappings:
miriam: nmdc
name: National Microbiome Data Collaborative
pattern: ^[\w\-.]{3,}$
preferred_prefix: nmdc
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://drs.microbiomedata.org/objects/$1
nmr:
banana: NMR
contact:
email: schober@imbi.uni-freiburg.de
github: null
name: Schober Daniel
orcid: null
deprecated: true
description: nmrCV is a controlled vocabulary to deliver standardized descriptors
for the open mark-up language for NMR raw and spectrum data, sanctioned by the
metabolomics standards initiative msi.
download_owl: https://nmrml.org/cv/stable/nmrCV.owl
example: '1000003'
homepage: http://msi-ontology.sourceforge.net/
mappings:
biocontext: NMR
bioportal: NMR
miriam: nmr
n2t: nmr
obofoundry: NMR
ols: nmrcv
prefixcommons: nmr
name: NMR-instrument specific component of metabolomics investigations
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: NMR
synonyms:
- nmrcv
uri_format: https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1
version: 1.1.0
nmrshiftdb2:
description: NMR database for organic structures and their nuclear magnetic resonance
(nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as
well as for searching spectra, structures and other properties.
example: '234'
homepage: https://nmrshiftdb.nmr.uni-koeln.de
mappings:
fairsharing: FAIRsharing.nYaZ1N
miriam: nmrshiftdb2
name: NMR Shift Database
pattern: ^[0-9]+$
preferred_prefix: nmrshiftdb2
uri_format: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1
nomen:
banana: NOMEN
contact:
email: diapriid@gmail.com
github: mjy
name: Matt Yoder
orcid: 0000-0002-5640-5491
description: NOMEN is a nomenclatural ontology for biological names (not concepts). It
encodes the goverened rules of nomenclature.
download_owl: http://purl.obolibrary.org/obo/nomen.owl
example: 0000295
homepage: https://github.com/SpeciesFileGroup/nomen
license: CC0 1.0
mappings:
bioportal: NOMEN
obofoundry: NOMEN
ols: nomen
ontobee: NOMEN
name: A nomenclatural ontology for biological names
pattern: ^\d{7}$
preferred_prefix: NOMEN
repository: https://github.com/SpeciesFileGroup/nomen
uri_format: http://purl.obolibrary.org/obo/NOMEN_$1
version: '2019-04-17'
noncodev3:
description: NONCODE is a database of expression and functional lncRNA (long noncoding
RNA) data obtained from microarray studies. LncRNAs have been shown to play key
roles in various biological processes such as imprinting control, circuitry controlling
pluripotency and differentiation, immune responses and chromosome dynamics. The
collection references NONCODE version 3. This was replaced in 2013 by version
4.
example: '377550'
homepage: http://www.noncode.org/
mappings:
biocontext: NONCODEV3
miriam: noncodev3
n2t: noncodev3
name: NONCODE v3
pattern: ^\d+$
preferred_prefix: noncodev3
uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1
noncodev4.gene:
description: NONCODE is a database of expression and functional lncRNA (long noncoding
RNA) data obtained from microarray studies. LncRNAs have been shown to play key
roles in various biological processes such as imprinting control, circuitry controlling
pluripotency and differentiation, immune responses and chromosome dynamics. The
collection references NONCODE version 4 and relates to gene regions.
example: NONHSAG00001
homepage: http://www.bioinfo.org/NONCODEv4/
mappings:
biocontext: NONCODEV4.GENE
miriam: noncodev4.gene
n2t: noncodev4.gene
name: NONCODE v4 Gene
pattern: ^NONHSAG\d{5}$
preferred_prefix: noncodev4.gene
uri_format: http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1
noncodev4.rna:
description: NONCODE is a database of expression and functional lncRNA (long noncoding
RNA) data obtained from microarray studies. LncRNAs have been shown to play key
roles in various biological processes such as imprinting control, circuitry controlling
pluripotency and differentiation, immune responses and chromosome dynamics. The
collection references NONCODE version 4 and relates to individual transcripts.
example: NONHSAT000001
homepage: http://www.bioinfo.org/NONCODEv4/
mappings:
biocontext: NONCODEV4.RNA
miriam: noncodev4.rna
n2t: noncodev4.rna
name: NONCODE v4 Transcript
pattern: ^NONHSAT\d{6}$
preferred_prefix: noncodev4.rna
uri_format: http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1
norine:
description: Norine is a database dedicated to nonribosomal peptides (NRPs). In
bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis,
an alternative ribosome-independent pathway called NRP synthesis allows peptide
production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic
amino acids whose primary structure is not always linear, often being more complex
and containing cycles and branchings.
example: NOR00681
homepage: http://bioinfo.lifl.fr/norine/
mappings:
biocontext: NORINE
fairsharing: FAIRsharing.gf8yhy
miriam: norine
n2t: norine
prefixcommons: norine
name: Nonribosomal Peptides Database
pattern: ^NOR\d+$
preferred_prefix: norine
uri_format: http://bioinfo.lifl.fr/norine/result.jsp?ID=$1
novus:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/$1
npass:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'Database for integrating species source of natural products & connecting
natural products to biological targets via experimental-derived quantitative
activity data.
'
example: NPC139585
homepage: http://bidd.group/NPASS/
name: Natural Product Activity and Species Source Database
pattern: ^NPC\d+$
preferred_prefix: npass
npo:
contact:
email: nathan.baker@pnl.gov
github: null
name: Nathan Baker
orcid: null
description: An ontology that represents the basic knowledge of physical, chemical
and functional characteristics of nanotechnology as used in cancer diagnosis and
therapy.
example: '1731'
homepage: https://bioportal.bioontology.org/ontologies/NPO
mappings:
bioportal: NPO
fairsharing: FAIRsharing.vy0p71
name: NanoParticle Ontology
pattern: ^\d+$
preferred_prefix: npo
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:
biocontext: NUCLEARBD
miriam: nuclearbd
n2t: 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:
biocontext: oa
bioportal: OA
name: Web Annotation Ontology
preferred_prefix: oa
uri_format: http://www.w3.org/ns/oa#$1
oae:
banana: OAE
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqunh He
orcid: 0000-0001-9189-9661
description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the
domain of adverse events. OAE aims to standardize adverse event annotation, integrate
various adverse event data, and support computer-assisted reasoning. OAE is a
community-based ontology. Its development follows the OBO Foundry principles.
Vaccine adverse events have been used as an initial testing use case. OAE also
studies adverse events associated with the administration of drug and nutritional
products, the operation of surgeries, and the usage of medical devices, etc.
download_owl: http://purl.obolibrary.org/obo/oae.owl
example: 0002959
homepage: https://github.com/OAE-ontology/OAE/
license: CC BY 3.0
mappings:
biocontext: OAE
bioportal: OAE
fairsharing: FAIRsharing.tw4q8x
obofoundry: OAE
ols: oae
ontobee: OAE
name: Ontology of Adverse Events
pattern: ^\d{7}$
preferred_prefix: OAE
repository: https://github.com/OAE-ontology/OAE
uri_format: http://purl.obolibrary.org/obo/OAE_$1
version: 1.2.44
oarcs:
banana: OARCS
contact:
email: mjyoder@illinois.edu
github: mjy
name: Matt Yoder
orcid: 0000-0002-5640-5491
description: OArCS is an ontology describing the Arthropod ciruclatory system.
download_owl: http://purl.obolibrary.org/obo/oarcs.owl
example: 0000029
homepage: https://github.com/aszool/oarcs
license: CC BY 3.0
mappings:
biocontext: OARCS
bioportal: OARCS
fairsharing: FAIRsharing.yqn857
obofoundry: OARCS
ols: oarcs
ontobee: OARCS
name: Ontology of Arthropod Circulatory Systems
pattern: ^\d{7}$
preferred_prefix: OARCS
repository: https://github.com/aszool/oarcs
uri_format: http://purl.obolibrary.org/obo/OARCS_$1
version: '2019-04-18'
oba:
appears_in:
- fovt
banana: OBA
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: A collection of biological attributes (traits) covering all kingdoms
of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait
ontology). Extends PATO.
download_obo: http://purl.obolibrary.org/obo/oba.obo
download_owl: http://purl.obolibrary.org/obo/oba.owl
example: '0000001'
homepage: https://github.com/obophenotype/bio-attribute-ontology
license: CC0 1.0
mappings:
biocontext: OBA
bioportal: OBA
fairsharing: FAIRsharing.mp0rwf
obofoundry: OBA
ols: oba
ontobee: OBA
name: Ontology of Biological Attributes
pattern: ^\d{7}$
preferred_prefix: OBA
repository: https://github.com/obophenotype/bio-attribute-ontology
uri_format: http://purl.obolibrary.org/obo/OBA_$1
version: '2021-12-03'
obcs:
banana: OBCS
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
description: 'OBCS stands for the Ontology of Biological and Clinical Statistics.
OBCS is an ontology in the domain of biological and clinical statistics. It is
aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations
(OBI). OBCS imports all possible biostatistics terms in OBI and includes many
additional biostatistics terms, some of which were proposed and discussed in the
OBI face-to-face workshop in Ann Arbor in 2012. '
download_owl: http://purl.obolibrary.org/obo/obcs.owl
example: '0000121'
homepage: https://github.com/obcs/obcs
license: CC BY 3.0
mappings:
biocontext: OBCS
bioportal: OBCS
fairsharing: FAIRsharing.5p12xh
obofoundry: OBCS
ols: obcs
ontobee: OBCS
name: Ontology of Biological and Clinical Statistics
pattern: ^\d{7}$
preferred_prefix: OBCS
repository: https://github.com/obcs/obcs
uri_format: http://purl.obolibrary.org/obo/OBCS_$1
version: '101'
obi:
appears_in:
- agro
- foodon
- hso
- labo
- mco
- one
- ons
- rbo
- scdo
banana: OBI
contact:
email: bpeters@lji.org
github: bpeters42
name: Bjoern Peters
orcid: 0000-0002-8457-6693
description: The Ontology for Biomedical Investigations (OBI) project is developing
an integrated ontology for the description of biological and clinical investigations.
The ontology will represent the design of an investigation, the protocols and
instrumentation used, the material used, the data generated and the type analysis
performed on it. Currently OBI is being built under the Basic Formal Ontology
(BFO).
download_obo: https://github.com/obi-ontology/obi/raw/master/views/obi.obo
download_owl: http://purl.obolibrary.org/obo/obi.owl
example: 0400109
homepage: http://obi-ontology.org
license: CC BY 4.0
mappings:
biocontext: OBI
bioportal: OBI
fairsharing: FAIRsharing.284e1z
go: OBI
miriam: obi
n2t: obi
obofoundry: OBI
ols: obi
ontobee: OBI
prefixcommons: obi
name: Ontology for Biomedical Investigations
pattern: ^\d{7}$
preferred_prefix: OBI
repository: https://github.com/obi-ontology/obi
uri_format: http://purl.obolibrary.org/obo/OBI_$1
version: '2022-01-03'
obib:
banana: OBIB
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
description: The Ontology for Biobanking (OBIB) is an ontology for the annotation
and modeling of the activities, contents, and administration of a biobank. Biobanks
are facilities that store specimens, such as bodily fluids and tissues, typically
along with specimen annotation and clinical data. OBIB is based on a subset of
the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology
(BFO) as its upper ontology, and is developed following OBO Foundry principles.
The first version of OBIB resulted from the merging of two existing biobank-related
ontologies, OMIABIS and biobank ontology.
download_owl: http://purl.obolibrary.org/obo/obib.owl
example: 0000389
homepage: https://github.com/biobanking/biobanking
license: CC BY 4.0
mappings:
biocontext: OBIB
bioportal: OBIB
fairsharing: FAIRsharing.bxc508
obofoundry: OBIB
ols: obib
ontobee: OBIB
name: Ontology for Biobanking
pattern: ^\d{7}$
preferred_prefix: OBIB
repository: https://github.com/biobanking/biobanking
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:
biocontext: OBO
fairsharing: FAIRsharing.847069
name: Internal OBO and PyOBO Relations
preferred_prefix: obo
uri_format: http://purl.obolibrary.org/obo/$1
oboformat:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Related to the OBO in OWL meta-model
example: alt_id
homepage: https://github.com/geneontology/go-ontology/tree/master/contrib
mappings:
biolink: oboformat
fairsharing: FAIRsharing.aa0eat
name: OBO Format
preferred_prefix: oboFormat
repository: https://github.com/geneontology/go-ontology
oboinowl:
description: This meta-ontology is self-describing. OBO metamodel properties are
described using OBO metamodel properties
download_obo: https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo
example: hasDbXref
homepage: https://github.com/geneontology/go-ontology/tree/master/contrib
mappings:
biocontext: OIO
name: OBO in OWL
preferred_prefix: oboInOwl
repository: https://github.com/geneontology/go-ontology
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/$1
oci:
description: "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number,\
\ where “oci:” is the identifier prefix, and is used to identify a citation as\
\ a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/\
\ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations\
\ Corpus are constructed by combining the OpenCitations Corpus local identifiers\
\ for the citing and cited bibliographic resources, separating them with a dash.\
\ For example, oci:2544384-7295288 is a valid OCI for the citation between two\
\ papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created\
\ for bibliographic resources described in an external bibliographic database,\
\ if they are similarly identified there by identifiers having a unique numerical\
\ part. For example, the OCI for the citation that exists between Wikidata resources\
\ Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also\
\ be created for bibliographic resources described in external bibliographic database\
\ such as Crossref or DataCite where they are identified by alphanumeric Digital\
\ Object Identifiers (DOIs), rather than purely numerical strings."
example: 1-18
homepage: http://opencitations.net
mappings:
biocontext: OCI
miriam: oci
n2t: oci
name: Open Citation Identifier
pattern: ^[0-9]+-[0-9]+$
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=$1
oclc:
description: The global library cooperative OCLC maintains WorldCat. WorldCat is
the world's largest network of library content and services. WorldCat libraries
are dedicated to providing access to their resources on the Web, where most people
start their search for information.
example: '634515043'
homepage: https://www.oclc.org/en/about.html
mappings:
biocontext: OCLC
miriam: oclc
n2t: oclc
name: Online Computer Library Center WorldCat
pattern: ^[0-9]+$
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/$1/datapackage?links=1
odc.sci:
description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven
repository to store, share, and publish spinal cord injury research data.
example: '602'
homepage: https://odc-sci.org
mappings:
fairsharing: FAIRsharing.M6Ruz3
miriam: odc.sci
name: Open Data Commons for Spinal Cord Injury
pattern: ^[0-9]*$
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/$1
odor:
description: OdorDB stores information related to odorous compounds, specifically
identifying those that have been shown to interact with olfactory receptors
example: '74'
homepage: http://senselab.med.yale.edu/OdorDB
mappings:
biocontext: ODOR
miriam: odor
n2t: odor
name: Odor Molecules DataBase
pattern: ^\d+$
preferred_prefix: odor
uri_format: http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5
ogg:
banana: OGG
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: 'OGG is a biological ontology in the area of genes and genomes. OGG
uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document
contains the genes and genomes of a list of selected organisms, including human,
two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M,
E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa
strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish,
fruit fly, yeast, etc.) may be found in other OGG subsets. '
download_owl: http://purl.obolibrary.org/obo/ogg.owl
example: '3000887619'
homepage: https://bitbucket.org/hegroup/ogg
license: CC BY 3.0
mappings:
biocontext: OGG
bioportal: OGG
fairsharing: FAIRsharing.zmx7nn
obofoundry: OGG
ols: ogg
ontobee: OGG
name: The Ontology of Genes and Genomes
pattern: ^\d+$
preferred_prefix: OGG
repository: https://bitbucket.org/hegroup/ogg
uri_format: http://purl.obolibrary.org/obo/OGG_$1
version: 1.0.59
ogi:
banana: OGI
deprecated: true
description: "OGI formalized the genomic element by defining an upper class 'genetic\
\ interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous\
\ physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.)\
\ between and including two points (Nucleic Acid Base Residue) on a chromosome\
\ or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated\
\ paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology”\
\ Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary\
\ Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\n\
Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI)\
\ to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding\
\ of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam,\
\ Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons\
\ (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology\
\ Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th-\
\ Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"
download_owl: http://purl.obolibrary.org/obo/ogi.owl
example: 0000019
homepage: https://code.google.com/archive/p/ontology-for-genetic-interval/
mappings:
biocontext: OGI
bioportal: OGI
obofoundry: OGI
ols: ogi
ontobee: OGI
name: Ontology for genetic interval
pattern: ^\d{7}$
preferred_prefix: OGI
synonyms:
- OGI.owl
uri_format: http://purl.obolibrary.org/obo/OGI_$1
version: '2.0'
ogms:
appears_in:
- labo
- scdo
banana: OGMS
contact:
email: baeverma@jcvi.org
github: BAevermann
name: Brian Aevermann
orcid: 0000-0003-1346-1327
description: 'The Ontology for General Medical Science (OGMS) is an ontology of
entities involved in a clinical encounter. OGMS includes very general terms that
are used across medical disciplines, including: ''disease'', ''disorder'', ''disease
course'', ''diagnosis'', ''patient'', and ''healthcare provider''. OGMS uses the
Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted
to humans, but many terms can be applied to a variety of organisms. OGMS provides
a formal theory of disease that can be further elaborated by specific disease
ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology
relations and is available in OWL and OBO formats.
OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis
and On Carcinomas and Other Pathological Entities. The ontology attempts to address
some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX)
and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly
called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal
Ontology.'
download_owl: http://purl.obolibrary.org/obo/ogms.owl
example: '0000031'
homepage: https://github.com/OGMS/ogms
license: CC BY 4.0
mappings:
biocontext: OGMS
bioportal: OGMS
fairsharing: FAIRsharing.rvz0m9
obofoundry: OGMS
ols: ogms
ontobee: OGMS
name: Ontology for General Medical Science
pattern: ^\d{7}$
preferred_prefix: OGMS
repository: https://github.com/OGMS/ogms
synonyms:
- ogms/OMRE
uri_format: http://purl.obolibrary.org/obo/OGMS_$1
version: '2021-08-19'
ogsf:
banana: OGSF
contact:
email: linikujp@gmail.com
github: linikujp
name: Asiyah Yu Lin
orcid: 0000-0002-5379-5359
description: An application ontology to represent genetic susceptibility to a specific
disease, adverse event, or a pathological process.
download_owl: http://purl.obolibrary.org/obo/ogsf.owl
example: '0000025'
homepage: https://github.com/linikujp/OGSF
license: CC BY 3.0
mappings:
biocontext: OGSF
bioportal: OGSF
fairsharing: FAIRsharing.egv2cz
obofoundry: OGSF
ols: ogsf
ontobee: OGSF
name: Ontology of Genetic Susceptibility Factor
pattern: ^\d{7}$
preferred_prefix: OGSF
repository: https://github.com/linikujp/OGSF
uri_format: http://purl.obolibrary.org/obo/OGSF_$1
version: '2.0'
ohd:
banana: OHD
contact:
email: wdduncan@gmail.com
github: wdduncan
name: Bill Duncan
orcid: 0000-0001-9625-1899
description: The Oral Health and Disease Ontology was created, initially, to represent
the content of dental practice health records.
download_owl: http://purl.obolibrary.org/obo/ohd.owl
example: '0000006'
homepage: https://purl.obolibrary.org/obo/ohd/home
license: CC BY 4.0
mappings:
biocontext: OHD
bioportal: OHD
fairsharing: FAIRsharing.bg7bb6
obofoundry: OHD
ols: ohd
ontobee: OHD
name: Oral Health and Disease Ontology
pattern: ^\d{7}$
preferred_prefix: OHD
repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology
uri_format: http://purl.obolibrary.org/obo/OHD_$1
version: '2016-06-27'
ohmi:
banana: OHMI
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: OHMI is a biomedical ontology that represents the entities and relations
in the domain of host-microbiome interactions.
download_owl: http://purl.obolibrary.org/obo/ohmi.owl
example: '0000460'
homepage: https://github.com/ohmi-ontology/ohmi
license: CC BY 4.0
mappings:
biocontext: OHMI
bioportal: OHMI
fairsharing: FAIRsharing.cz9cnp
obofoundry: OHMI
ols: ohmi
ontobee: OHMI
name: Ontology of Host-Microbiome Interactions
pattern: ^\d{7}$
preferred_prefix: OHMI
repository: https://github.com/ohmi-ontology/ohmi
uri_format: http://purl.obolibrary.org/obo/OHMI_$1
version: '2019-09-17'
ohpi:
banana: OHPI
contact:
email: edong@umich.edu
github: e4ong1031
name: Edison Ong
orcid: 0000-0002-5159-414X
description: OHPI is a biomedical ontology in the area of host-pathogen interactions.
OHPI is developed by following the OBO Foundry Principles (e.g., openness and
collaboration).
download_owl: http://purl.obolibrary.org/obo/ohpi.owl
example: '9001411'
homepage: https://github.com/OHPI/ohpi
license: CC BY 4.0
mappings:
bioportal: OHPI
fairsharing: FAIRsharing.vxpUJ6
obofoundry: OHPI
ols: ohpi
ontobee: OHPI
name: Ontology of Host Pathogen Interactions
pattern: ^\d+$
preferred_prefix: OHPI
repository: https://github.com/OHPI/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=$1&submit=Display&action=display
olatdv:
banana: OlatDv
contact:
email: frederic.bastian@unil.ch
github: fbastian
name: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: Life cycle stages for Medaka
download_obo: http://purl.obolibrary.org/obo/olatdv.obo
download_owl: http://purl.obolibrary.org/obo/olatdv.owl
example: '0000210'
homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv
license: CC BY 3.0
mappings:
biocontext: OLATDV
bioportal: OLATDV
fairsharing: FAIRsharing.c86z66
obofoundry: OlatDv
ols: olatdv
ontobee: OLATDV
name: Medaka Developmental Stages
pattern: ^\d{7}$
preferred_prefix: OlatDv
repository: https://github.com/obophenotype/developmental-stage-ontologies
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'
download_owl: https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf
example: Dimension
homepage: https://github.com/HajoRijgersberg/OM
mappings:
bioportal: OM
ols: om
name: Ontology of units of Measure
preferred_prefix: om
repository: https://github.com/HajoRijgersberg/OM
version: 2.0.35
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:
biocontext: OMA.GRP
miriam: oma.grp
n2t: 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:$1
oma.protein:
description: OMA (Orthologous MAtrix) is a database that identifies orthologs among
publicly available, complete genome sequences. It identifies orthologous relationships
which can be accessed either group-wise, where all group members are orthologous
to all other group members, or on a sequence-centric basis, where for a given
protein all its orthologs in all other species are displayed. This collection
references individual protein records.
example: HUMAN16963
homepage: https://omabrowser.org/cgi-bin/gateway.pl
mappings:
biocontext: OMA.PROTEIN
miriam: oma.protein
n2t: oma.protein
name: OMA Protein
pattern: ^[A-Z0-9]{5}\d+$
preferred_prefix: oma.protein
uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1
omia:
comment: website is down as of 2021-10-04
deprecated: true
description: Online Mendelian Inheritance in Animals is a a database of genes, inherited
disorders and traits in animal species (other than human and mouse).
example: '1000'
homepage: http://omia.angis.org.au/
mappings:
biocontext: OMIA
miriam: omia
n2t: omia
prefixcommons: omia
name: Online Mendelian Inheritance in Animals
pattern: ^\d+$
preferred_prefix: omia
uri_format: http://omia.angis.org.au/$1/
omiabis:
appears_in:
- labo
banana: OMIABIS
contact:
email: mbrochhausen@gmail.com
github: null
name: Mathias Brochhausen
orcid: 0000-0003-1834-3856
deprecated: true
description: An ontological version of MIABIS (Minimum Information About BIobank
data Sharing)
download_owl: http://purl.obolibrary.org/obo/omiabis.owl
example: 0001079
homepage: https://github.com/OMIABIS/omiabis-dev
license: CC BY 3.0
mappings:
biocontext: OMIABIS
bioportal: OMIABIS
obofoundry: OMIABIS
ols: omiabis
ontobee: OMIABIS
name: Ontologized MIABIS
pattern: ^\d{7}$
preferred_prefix: OMIABIS
repository: https://github.com/OMIABIS/omiabis-dev
uri_format: http://purl.obolibrary.org/obo/OMIABIS_$1
version: '2014-05-28'
omim:
contact:
email: ahamosh@jhmi.edu
github: ahamosh
name: Ada Hamosh
orcid: 0000-0002-1780-5230
description: Online Mendelian Inheritance in Man is a catalog of human genes and
genetic disorders.
example: '603903'
homepage: https://omim.org/
mappings:
biocontext: OMIM
bioportal: OMIM
fairsharing: FAIRsharing.azq2t6
go: OMIM
miriam: mim
n2t: mim
ncbi: MIM
prefixcommons: omim
uniprot: MIM
wikidata: P492
name: Online Mendelian Inheritance in Man
pattern: ^\d+$
preferred_prefix: omim
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
- mim
uri_format: https://omim.org/entry/$1
omim.ps:
contact:
email: ahamosh@jhmi.edu
github: ahamosh
name: Ada Hamosh
orcid: 0000-0002-1780-5230
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar
phenotypes across the genome.
example: PS214100
homepage: https://www.omim.org/phenotypicSeriesTitles/all
mappings:
biolink: OMIM.PS
name: OMIM Phenotypic Series
part_of: mim
pattern: ^PS\d+$
preferred_prefix: omim.ps
synonyms:
- MIMPS
- OMIMPS
- PS
- mim.ps
uri_format: https://omim.org/phenotypicSeries/$1
omit:
appears_in:
- mco
banana: OMIT
contact:
email: huang@southalabama.edu
github: Huang-OMIT
name: Jingshan Huang
orcid: 0000-0003-2408-2883
description: The purpose of the OMIT ontology is to establish data exchange standards
and common data elements in the microRNA (miR) domain. Biologists (cell biologists
in particular) and bioinformaticians can make use of OMIT to leverage emerging
semantic technologies in knowledge acquisition and discovery for more effective
identification of important roles performed by miRs in humans' various diseases
and biological processes (usually through miRs' respective target genes).
download_obo: https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo
download_owl: http://purl.obolibrary.org/obo/omit.owl
example: 0000069
homepage: http://omit.cis.usouthal.edu/
license: CC BY 3.0
mappings:
biocontext: OMIT
bioportal: OMIT
fairsharing: FAIRsharing.mf91p5
miriam: omit
n2t: omit
obofoundry: OMIT
ols: omit
ontobee: OMIT
name: Ontology for MicroRNA Target
pattern: ^\d{7}$
preferred_prefix: OMIT
repository: https://github.com/OmniSearch/omit
synonyms:
- OMIT
uri_format: https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1
version: '2019-06-07'
omo:
appears_in:
- pcl
banana: OMO
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
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).
download_owl: http://purl.obolibrary.org/obo/omo.owl
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
repository: https://github.com/information-artifact-ontology/ontology-metadata
uri_format: http://purl.obolibrary.org/obo/OMO_$1
version: '2022-04-27'
omop:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The OMOP Common Data Model allows for the systematic analysis of disparate
observational databases. The concept behind this approach is to transform data
contained within those databases into a common format (data model) as well as
a common representation (terminologies, vocabularies, coding schemes), and then
perform systematic analyses using a library of standard analytic routines that
have been written based on the common format.
homepage: https://www.ohdsi.org/data-standardization/the-common-data-model/
name: Observational Medical Outcomes Partnership
no_own_terms: true
preferred_prefix: omop
references:
- https://github.com/callahantiff/OMOP2OBO
omp:
appears_in:
- mco
banana: OMP
contact:
email: jimhu@tamu.edu
github: jimhu-tamu
name: James C. Hu
orcid: 0000-0001-9016-2684
description: An ontology of phenotypes covering microbes
download_obo: http://purl.obolibrary.org/obo/omp.obo
download_owl: http://purl.obolibrary.org/obo/omp.owl
example: '0005067'
homepage: http://microbialphenotypes.org
license: CC BY 3.0
mappings:
biocontext: OMP
bioportal: OMP
fairsharing: FAIRsharing.cc3f2x
obofoundry: OMP
ols: omp
ontobee: OMP
name: Ontology of Microbial Phenotypes
pattern: ^\d{7}$
preferred_prefix: OMP
repository: https://github.com/microbialphenotypes/OMP-ontology
uri_format: http://purl.obolibrary.org/obo/OMP_$1
version: '2022-04-11'
omrse:
appears_in:
- labo
banana: OMRSE
contact:
email: hoganwr@gmail.com
github: hoganwr
name: Bill Hogan
orcid: 0000-0002-9881-1017
description: This ontology covers the domain of social entities that are related
to health care, such as demographic information and the roles of various individuals
and organizations.
download_obo: https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo
download_owl: http://purl.obolibrary.org/obo/omrse.owl
example: '00000022'
homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview
license: CC BY 4.0
mappings:
biocontext: OMRSE
bioportal: OMRSE
fairsharing: FAIRsharing.z0p37e
obofoundry: OMRSE
ols: omrse
ontobee: OMRSE
name: Ontology of Medically Related Social Entities
pattern: ^\d{8}$
preferred_prefix: OMRSE
repository: https://github.com/ufbmi/OMRSE
uri_format: http://purl.obolibrary.org/obo/OMRSE_$1
version: '2022-04-06'
oncotree:
appears_in:
- efo
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/$1
one:
banana: ONE
contact:
email: chenyangnutrition@gmail.com
github: cyang0128
name: Chen Yang
orcid: 0000-0001-9202-5309
depends_on:
- foodon
- obi
- ons
description: An ontology to standardize research output of nutritional epidemiologic
studies.
download_owl: http://purl.obolibrary.org/obo/one.owl
example: '0001021'
homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies
license: CC BY 4.0
mappings:
bioportal: ONE
fairsharing: FAIRsharing.USxx0K
obofoundry: ONE
ols: one
ontobee: ONE
name: Ontology for Nutritional Epidemiology
pattern: ^\d{7}$
preferred_prefix: ONE
repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies
uri_format: http://purl.obolibrary.org/obo/ONE_$1
ons:
appears_in:
- one
banana: ONS
contact:
email: francesco.vitali@ibba.cnr.it
github: FrancescoVit
name: Francesco Vitali
orcid: 0000-0001-9125-4337
depends_on:
- bfo
- chebi
- envo
- foodon
- ncbitaxon
- obi
- ro
- uberon
description: The Ontology for Nutritional Studies (ONS) has been developed as part
of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define
a common language and building ontologies for nutritional studies.
download_owl: http://purl.obolibrary.org/obo/ons.owl
example: '0000060'
homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
license: CC BY 4.0
mappings:
bioportal: ONS
fairsharing: FAIRsharing.rfec93
obofoundry: ONS
ols: ons
ontobee: ONS
name: Ontology for Nutritional Studies
pattern: ^\d{7}$
preferred_prefix: ONS
repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies
uri_format: http://purl.obolibrary.org/obo/ONS_$1
version: June 2021 release
ontoavida:
banana: ONTOAVIDA
contact:
email: fortuna@ebd.csic.es
github: miguelfortuna
name: Miguel A. Fortuna
orcid: 0000-0002-8374-1941
depends_on:
- fbcv
- gsso
- ncit
- ro
- stato
description: 'The Ontology for Avida (OntoAvida) project aims to develop an integrated
vocabulary for the description of the most widely used computational approach
for performing experimental evolution using digital organisms (i.e., self-replicating
computer programs that evolve within a user-defined computational environment).
The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace
the field of digital evolution. This unique ontology has the potential to change
this picture overnight.
OntoAvida was initially developed by https://fortunalab.org, the computational
biology lab at the Doñana Biological Station (a research institute of the Spanish
National Research Council based at Seville, Spain). Contributors to OntoAvida
are expected to include members of the Digital Evolution Laboratory (https://devolab.org/)
at Michigan State University (USA).
More information can be found at https://obofoundry.org/ontology/ontoavida.html'
download_obo: http://purl.obolibrary.org/obo/ontoavida.obo
download_owl: http://purl.obolibrary.org/obo/ontoavida.owl
example: '00000001'
homepage: https://gitlab.com/fortunalab/ontoavida
license: CC BY 4.0
mappings:
bioportal: ONTOAVIDA
obofoundry: ONTOAVIDA
ols: ontoavida
ontobee: ONTOAVIDA
name: Ontology for Avida digital evolution platform
pattern: ^\d{8}$
preferred_prefix: ONTOAVIDA
repository: https://gitlab.com/fortunalab/ontoavida
uri_format: http://purl.obolibrary.org/obo/ONTOAVIDA_$1
version: '2022-03-15'
ontoneo:
banana: ONTONEO
contact:
email: fernanda.farinelli@gmail.com
github: FernandaFarinelli
name: Fernanda Farinelli
orcid: 0000-0003-2338-8872
description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary
to provide a representation of the data from electronic health records (EHRs)
involved in the care of the pregnant woman, and of her baby.
download_owl: http://purl.obolibrary.org/obo/ontoneo.owl
example: 00000098
homepage: http://ontoneo.com
license: CC BY 3.0
mappings:
biocontext: ONTONEO
bioportal: ONTONEO
fairsharing: FAIRsharing.5a4y1y
obofoundry: ONTONEO
ols: ontoneo
ontobee: ONTONEO
name: Obstetric and Neonatal Ontology
pattern: ^\d{8}$
preferred_prefix: ONTONEO
repository: https://github.com/ontoneo-project/Ontoneo
uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1
version: v1.6
oostt:
banana: OOSTT
contact:
email: mbrochhausen@gmail.com
github: mbrochhausen
name: Mathias Brochhausen
orcid: 0000-0003-1834-3856
description: An ontology built for representating the organizational components
of trauma centers and trauma systems.
download_owl: http://purl.obolibrary.org/obo/oostt.owl
example: 00000099
homepage: https://github.com/OOSTT/OOSTT
license: CC BY 4.0
mappings:
biocontext: OOSTT
bioportal: OOSTT
fairsharing: FAIRsharing.b4sa0w
obofoundry: OOSTT
ols: oostt
ontobee: OOSTT
name: Ontology of Organizational Structures of Trauma centers and Trauma systems
pattern: ^\d{8}$
preferred_prefix: OOSTT
repository: https://github.com/OOSTT/OOSTT
uri_format: http://purl.obolibrary.org/obo/OOSTT_$1
version: '2021-01-11'
opb:
description: The OPB is a reference ontology of classical physics as applied to
the dynamics of biological systems. It is designed to encompass the multiple structural
scales (multiscale atoms to organisms) and multiple physical domains (multidomain
fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered
in the study and analysis of biological organisms.
example: '00573'
homepage: http://bioportal.bioontology.org/ontologies/OPB
mappings:
biocontext: OPB
bioportal: OPB
fairsharing: FAIRsharing.qcceez
miriam: opb
n2t: opb
prefixcommons: opb
name: Ontology of Physics for Biology
pattern: ^\d+$
preferred_prefix: opb
uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1
openalex:
contact:
email: hpiwowar@gmail.com
github: hpiwowar
name: Heather Piwowar
orcid: 0000-0003-1613-5981
contributor:
email: null
github: dhimmel
name: Daniel Himmelstein
orcid: 0000-0002-3012-7446
description: OpenAlex is a fully open catalog of the global research system that
describes scholarly entities and how those entities are connected to each other.
example: W2741809807
homepage: https://openalex.org/
name: OpenAlex
pattern: ^[WAICV]\d{2,}$
preferred_prefix: openalex
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://openalex.org/$1
opl:
banana: OPL
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage
details of various parasites, including Trypanosoma sp., Leishmania major, and
Plasmodium sp., etc. In addition to life cycle stages, the ontology also models
necessary contextual details, such as host information, vector information, and
anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows
the rules set by the OBO Foundry consortium.
download_owl: http://purl.obolibrary.org/obo/opl.owl
example: 0000319
homepage: https://github.com/OPL-ontology/OPL
license: CC BY 4.0
mappings:
biocontext: OPL
bioportal: OPL
fairsharing: FAIRsharing.ez2nhb
obofoundry: OPL
ols: opl
ontobee: OPL
name: Ontology for Parasite LifeCycle
pattern: ^\d{7}$
preferred_prefix: OPL
repository: https://github.com/OPL-ontology/OPL
uri_format: http://purl.obolibrary.org/obo/OPL_$1
version: '2021-01-28'
opm:
description: The Orientations of Proteins in Membranes (OPM) database provides spatial
positions of membrane-bound peptides and proteins of known three-dimensional structure
in the lipid bilayer, together with their structural classification, topology
and intracellular localization.
example: 1h68
homepage: http://opm.phar.umich.edu/
mappings:
biocontext: OPM
fairsharing: FAIRsharing.7c683b
miriam: opm
n2t: opm
name: Orientations of Proteins in Membranes Database
pattern: ^[0-9][A-Za-z0-9]{3}$
preferred_prefix: opm
uri_format: http://opm.phar.umich.edu/protein.php?pdbid=$1
opmi:
appears_in:
- labo
- scdo
banana: OPMI
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: OPMI is a biomedical ontology in the area of precision medicine and
its related investigations. It is community-driven and developed by following
the OBO Foundry ontology development principles.
download_owl: http://purl.obolibrary.org/obo/opmi.owl
example: '0000101'
homepage: https://github.com/OPMI/opmi
license: CC BY 4.0
mappings:
bioportal: OPMI
obofoundry: OPMI
ols: opmi
ontobee: OPMI
name: Ontology of Precision Medicine and Investigation
pattern: ^\d{7}$
preferred_prefix: OPMI
repository: https://github.com/OPMI/opmi
uri_format: http://purl.obolibrary.org/obo/OPMI_$1
version: 1.0.152
orcid:
description: ORCID (Open Researcher and Contributor ID) is an open, non-profit,
community-based effort to create and maintain a registry of unique identifiers
for individual researchers. ORCID records hold non-sensitive information such
as name, email, organization name, and research activities.
example: 0000-0002-5355-2576
homepage: https://orcid.org
mappings:
biocontext: ORCID
biolink: ORCID
miriam: orcid
n2t: orcid
scholia: orcid
wikidata: P496
name: Open Researcher and Contributor
pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$
preferred_prefix: orcid
synonyms:
- ORCID
- ORCiD
uri_format: https://orcid.org/$1
ordb:
description: The Olfactory Receptor Database (ORDB) is a repository of genomics
and proteomics information of olfactory receptors (ORs). It includes a broad range
of chemosensory genes and proteins, that includes in addition to ORs the taste
papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory
receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal
pheromone receptors (FPRs).
example: '8497'
homepage: http://senselab.med.yale.edu/OrDB/
mappings:
biocontext: ORDB
fairsharing: FAIRsharing.6375zh
miriam: ordb
n2t: ordb
prefixcommons: ordb
name: Olfactory Receptor Database
pattern: ^\d+$
preferred_prefix: ordb
uri_format: http://senselab.med.yale.edu/ORDB/Data/$1
oridb.sacch:
description: OriDB is a database of collated genome-wide mapping studies of confirmed
and predicted replication origin sites in Saccharomyces cerevisiae and the fission
yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae.
example: '1'
homepage: http://cerevisiae.oridb.org/index.php
mappings:
biocontext: ORIDB.SACCH
miriam: oridb.sacch
n2t: oridb.sacch
name: OriDB Saccharomyces
pattern: ^\d+$
preferred_prefix: oridb.sacch
uri_format: http://cerevisiae.oridb.org/details.php?id=$1
oridb.schizo:
description: OriDB is a database of collated genome-wide mapping studies of confirmed
and predicted replication origin sites in Saccharomyces cerevisiae and the fission
yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces
pombe.
example: '1'
homepage: http://pombe.oridb.org/index.php
mappings:
biocontext: ORIDB.SCHIZO
miriam: oridb.schizo
n2t: oridb.schizo
name: OriDB Schizosaccharomyces
pattern: ^\d+$
preferred_prefix: oridb.schizo
uri_format: http://pombe.oridb.org/details.php?id=$1
ornaseq:
banana: ORNASEQ
contact:
email: safisher@upenn.edu
github: safisher
name: Stephen Fisher
orcid: 0000-0001-8034-7685
description: An application ontology designed to annotate next-generation sequencing
experiments performed on RNA.
download_owl: http://purl.obolibrary.org/obo/ornaseq.owl
example: '0000010'
homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml
license: CC BY 4.0
mappings:
bioportal: ORNASEQ
obofoundry: ORNASEQ
ols: ornaseq
ontobee: ORNASEQ
name: Ontology of RNA Sequencing
pattern: ^\d{7}$
preferred_prefix: ORNASEQ
repository: https://github.com/safisher/ornaseq
uri_format: http://purl.obolibrary.org/obo/ORNASEQ_$1
version: '2019-07-08'
orphanet:
description: Orphanet is a reference portal for information on rare diseases and
orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of
patients with rare diseases.
example: '85163'
homepage: http://www.orpha.net/consor/
mappings:
biocontext: Orphanet
fairsharing: FAIRsharing.6bd5k6
miriam: orphanet
n2t: orphanet
prefixcommons: orphanet
uniprot: Orphanet
wikidata: P1550
name: Orphanet
pattern: ^\d+$
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
synonyms:
- ORPHA
uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1
orphanet.ordo:
description: "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary\
\ for rare diseases, capturing relationships between diseases, genes and other\
\ relevant features which will form a useful resource for the computational analysis\
\ of rare diseases.\r\nIt integrates a nosology (classification of rare diseases),\
\ relationships (gene-disease relations, epiemological data) and connections with\
\ other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC,\
\ ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."
download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl
example: C023
example_extras:
- '478'
homepage: https://www.ebi.ac.uk/ols/ontologies/ordo
mappings:
biocontext: ORPHANET.ORDO
biolink: ORPHA
bioportal: ORDO
cellosaurus: ORDO
fairsharing: FAIRsharing.pbbnwa
miriam: orphanet.ordo
n2t: orphanet.ordo
ols: ordo
name: Orphanet Rare Disease Ontology
pattern: ^C?\d+$
preferred_prefix: orphanet.ordo
synonyms:
- ordo
uri_format: http://www.orpha.net/ORDO/Orphanet_$1
version: '4.0'
orth:
contact:
email: jfernand@um.es
github: jesualdotomasfernandezbreis
name: Jesualdo Tomás Fernández-Breis
orcid: 0000-0002-7558-2880
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.'
download_owl: https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl
example: HomologyRelation
homepage: https://github.com/qfo/OrthologyOntology
mappings:
bioportal: ORTH
fairsharing: FAIRsharing.4877h0
ols: orth
name: Orthology Ontology
preferred_prefix: orth
repository: https://github.com/qfo/OrthologyOntology
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: https://www.orthodb.org
mappings:
biocontext: ORTHODB
fairsharing: FAIRsharing.x989d5
miriam: orthodb
n2t: orthodb
prefixcommons: orthodb
uniprot: OrthoDB
name: OrthoDB
pattern: ^\w+$
preferred_prefix: orthodb
provides: uniprot
uri_format: http://cegg.unige.ch/orthodb/results?searchtext=$1
oryzabase.gene:
description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
plant by integrating biological data with molecular genomic information. It contains
information about rice development and anatomy, rice mutants, and genetic resources,
especially for wild varieties of rice. Developmental and anatomical descriptions
include in situ gene expression data serving as stage and tissue markers. This
collection references gene information.
example: '117'
homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
mappings:
biocontext: ORYZABASE.GENE
miriam: oryzabase.gene
n2t: oryzabase.gene
name: Oryzabase Gene
pattern: ^\d+$
preferred_prefix: oryzabase.gene
uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1
oryzabase.mutant:
description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
plant by integrating biological data with molecular genomic information. It contains
information about rice development and anatomy, rice mutants, and genetic resources,
especially for wild varieties of rice. Developmental and anatomical descriptions
include in situ gene expression data serving as stage and tissue markers. This
collection references mutant strain information.
example: '21393'
homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
mappings:
biocontext: ORYZABASE.MUTANT
miriam: oryzabase.mutant
n2t: oryzabase.mutant
name: Oryzabase Mutant
pattern: ^\d+$
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/$1
oryzabase.stage:
description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
plant by integrating biological data with molecular genomic information. It contains
information about rice development and anatomy, rice mutants, and genetic resources,
especially for wild varieties of rice. Developmental and anatomical descriptions
include in situ gene expression data serving as stage and tissue markers. This
collection references development stage information.
example: '34'
homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
mappings:
biocontext: ORYZABASE.STAGE
miriam: oryzabase.stage
n2t: oryzabase.stage
name: Oryzabase Stage
pattern: ^\d+$
preferred_prefix: oryzabase.stage
uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1
oryzabase.strain:
description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot
plant by integrating biological data with molecular genomic information. It contains
information about rice development and anatomy, rice mutants, and genetic resources,
especially for wild varieties of rice. Developmental and anatomical descriptions
include in situ gene expression data serving as stage and tissue markers. This
collection references wild strain information.
example: '1'
homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
mappings:
biocontext: ORYZABASE.STRAIN
miriam: oryzabase.strain
n2t: oryzabase.strain
name: Oryzabase Strain
pattern: ^\d+$
preferred_prefix: oryzabase.strain
uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1
otl:
description: Oryza Tag Line is a database that was developed to collect information
generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion
lines resulting in potential gene disruptions. It collates morpho-physiological
alterations observed during field evaluation, with each insertion line documented
through a generic passport data including production records, seed stocks and
FST information.
example: AADB12
homepage: http://oryzatagline.cirad.fr/
mappings:
biocontext: OTL
fairsharing: FAIRsharing.61c2x6
miriam: otl
n2t: otl
prefixcommons: otl
name: Oryza Tag Line
pattern: ^A[A-Z]+\d+$
preferred_prefix: otl
uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1
ovae:
banana: OVAE
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqunh He
orcid: 0000-0001-9189-9661
description: 'OVAE is a biomedical ontology in the area of vaccine adverse events.
OVAE is an extension of the community-based Ontology of Adverse Events (OAE). '
download_owl: http://purl.obolibrary.org/obo/ovae.owl
example: 0000609
homepage: http://www.violinet.org/ovae/
license: CC BY 3.0
mappings:
biocontext: OVAE
bioportal: OVAE
fairsharing: FAIRsharing.w4x6n4
obofoundry: OVAE
ols: ovae
ontobee: OVAE
name: Ontology of Vaccine Adverse Events
pattern: ^\d{7}$
preferred_prefix: OVAE
repository: https://github.com/OVAE-Ontology/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:
biocontext: owl
fairsharing: FAIRsharing.atygwy
name: Web Ontology Language
preferred_prefix: owl
uri_format: http://www.w3.org/2002/07/owl#$1
p3db.protein:
description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides
information on experimentally determined phosphorylation sites in the proteins
of various plant species. This collection references plant proteins that contain
phosphorylation sites.
example: '70'
homepage: http://www.p3db.org/
mappings:
biocontext: P3DB.PROTEIN
miriam: p3db.protein
n2t: p3db.protein
name: P3DB Protein
pattern: ^\d+$
preferred_prefix: p3db.protein
uri_format: http://www.p3db.org/protein.php?id=$1&ref=0
p3db.site:
description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides
information on experimentally determined phosphorylation sites in the proteins
of various plant species. This collection references phosphorylation sites in
proteins.
example: '65'
homepage: http://www.p3db.org/
mappings:
biocontext: P3DB.SITE
miriam: p3db.site
n2t: p3db.site
name: P3DB Site
pattern: ^\d+$
preferred_prefix: p3db.site
uri_format: http://www.p3db.org/phosphosite.php?id=$1&ref=0
paleodb:
description: The Paleobiology Database seeks to provide researchers and the public
with information about the entire fossil record. It stores global, collection-based
occurrence and taxonomic data for marine and terrestrial animals and plants of
any geological age, as well as web-based software for statistical analysis of
the data.
example: '83088'
homepage: http://paleodb.org/
mappings:
biocontext: PALEODB
miriam: paleodb
n2t: paleodb
prefixcommons: paleodb
name: Paleobiology Database
pattern: ^\d+$
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/$1.url
panther.family:
description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification
System is a resource that classifies genes by their functions, using published
scientific experimental evidence and evolutionary relationships to predict function
even in the absence of direct experimental evidence. This collection references
groups of genes that have been organised as families.
example: PTHR12345
homepage: http://www.pantherdb.org/
mappings:
biocontext: PANTHER.FAMILY
biolink: PANTHER.FAMILY
go: PANTHER
miriam: panther.family
n2t: panther.family
name: Protein ANalysis THrough Evolutionary Relationships Classification System
part_of: panther
pattern: ^PTHR\d{5}(\:SF\d{1,3})?$
preferred_prefix: panther.family
uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1
panther.node:
description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification
System is a resource that classifies genes by their functions, using published
scientific experimental evidence and evolutionary relationships to predict function
even in the absence of direct experimental evidence. PANTHER tree is a key element
of the PANTHER System to represent ‘all’ of the evolutionary events in the gene
family. PANTHER nodes represent the evolutionary events, either speciation or
duplication, within the tree. PANTHER is maintaining stable identifier for these
nodes.
example: PTN000000026
homepage: http://pantree.org/
mappings:
biocontext: PANTHER.NODE
miriam: panther.node
n2t: panther.node
name: PANTHER Node
part_of: panther
pattern: ^PTN\d{9}$
preferred_prefix: panther.node
uri_format: http://www.pantree.org/node/annotationNode.jsp?id=$1
panther.pathway:
description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification
System is a resource that classifies genes by their functions, using published
scientific experimental evidence and evolutionary relationships to predict function
even in the absence of direct experimental evidence. The PANTHER Pathway collection
references pathway information, primarily for signaling pathways, each with subfamilies
and protein sequences mapped to individual pathway components.
example: P00024
homepage: http://www.pantherdb.org/
mappings:
biocontext: PANTHER.PATHWAY
miriam: panther.pathway
n2t: panther.pathway
name: PANTHER Pathway
part_of: panther
pattern: ^P\d{5}$
preferred_prefix: panther.pathway
uri_format: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1
panther.pthcmp:
description: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships)\
\ Classification System is a resource that classifies genes by their functions,\
\ using published scientific experimental evidence and evolutionary relationships\
\ to predict function even in the absence of direct experimental evidence. The\
\ PANTHER Pathway Component collection references specific classes of molecules\
\ that play the same mechanistic role within a pathway, across species. Pathway\r\
\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified\
\ component is a protein, DNA, or transcribed RNA, it is associated with protein\
\ sequences in the PANTHER protein family trees through manual curation."
example: P00266
homepage: http://www.pantherdb.org/
mappings:
biocontext: PANTHER.PTHCMP
miriam: panther.pthcmp
n2t: panther.pthcmp
name: PANTHER Pathway Component
part_of: panther
pattern: ^(G|P|U|C|S)\d{5}$
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: jaiswalp
name: Pankaj Jaiswal
orcid: 0000-0002-1005-8383
deprecated: true
homepage: http://www.plantontology.org
mappings:
biocontext: PAO
obofoundry: PAO
name: Plant Anatomy Ontology
preferred_prefix: PAO
uri_format: http://purl.obolibrary.org/obo/PAO_$1
pass2:
deprecated: true
description: The PASS2 database provides alignments of proteins related at the superfamily
level and are characterized by low sequence identity.
example: '46977'
homepage: http://caps.ncbs.res.in/pass2
mappings:
biocontext: PASS2
miriam: pass2
n2t: pass2
prefixcommons: pass2
name: Protein Alignment organised as Structural Superfamily
pattern: ^\d+$
preferred_prefix: pass2
uri_format: http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1
pathbank:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: PathBank is an interactive, visual database containing more than 100
000 machine-readable pathways found in model organisms such as humans, mice, E.
coli, yeast, and Arabidopsis thaliana.
example: SMP0000219
homepage: https://pathbank.org
mappings:
fairsharing: FAIRsharing.3xwMon
name: PathBank
pattern: ^(SMP|PW)\d+$
preferred_prefix: pathbank
uri_format: https://pathbank.org/view/$1
pathwaycommons:
description: Pathway Commons is a convenient point of access to biological pathway
information collected from public pathway databases, which you can browse or search.
It is a collection of publicly available pathways from multiple organisms that
provides researchers with convenient access to a comprehensive collection of pathways
from multiple sources represented in a common language.
example: '485991'
homepage: http://www.pathwaycommons.org/pc/
mappings:
biocontext: PATHWAYCOMMONS
miriam: pathwaycommons
n2t: pathwaycommons
prefixcommons: pathwaycommons
uniprot: PathwayCommons
name: Pathway Commons
pattern: ^\d+$
preferred_prefix: pathwaycommons
uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1
pato:
appears_in:
- agro
- aism
- cdno
- cl
- colao
- ecocore
- ecto
- fovt
- lepao
- mco
- ms
- pcl
- pco
- phipo
- planp
- rbo
- xpo
- zp
banana: PATO
contact:
email: g.gkoutos@gmail.com
github: gkoutos
name: George Gkoutos
orcid: 0000-0002-2061-091X
description: PATO is an ontology of phenotypic qualities, intended for use in a
number of applications, primarily defining composite phenotypes and phenotype annotation.
download_json: http://purl.obolibrary.org/obo/pato.json
download_obo: http://purl.obolibrary.org/obo/pato.obo
download_owl: http://purl.obolibrary.org/obo/pato.owl
example: 0001998
homepage: https://github.com/pato-ontology/pato/
license: CC BY 3.0
mappings:
biocontext: PATO
bioportal: PATO
fairsharing: FAIRsharing.ezwdhz
go: PATO
miriam: pato
n2t: pato
obofoundry: PATO
ols: pato
ontobee: PATO
prefixcommons: pato
name: Phenotype And Trait Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: PATO
repository: https://github.com/pato-ontology/pato
uri_format: https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1
version: '2022-02-20'
pav:
contributor:
email: null
github: matentzn
name: Nico Matentzoglu
orcid: 0000-0002-7356-1779
description: PAV is a lightweight ontology for tracking provenance, authorship,
and versioning. It specializes the W3C provenance ontology PROV-O in order to
describe authorship, curation and digital creation of online resources.
example: authoredBy
homepage: https://pav-ontology.github.io/pav/
mappings:
biocontext: pav
biolink: pav
bioportal: PAV
fairsharing: FAIRsharing.nbfwwv
name: Provenance, Authoring, and Versioning Vocabulary
pattern: ^[a-z][a-zA-Z]+$
preferred_prefix: pav
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://purl.org/pav/$1
paxdb.organism:
description: PaxDb is a resource dedicated to integrating information on absolute
protein abundance levels across different organisms. Publicly available experimental
data are mapped onto a common namespace and, in the case of tandem mass spectrometry
data, re-processed using a standardized spectral counting pipeline. Data sets
are scored and ranked to assess consistency against externally provided protein-network
information. PaxDb provides whole-organism data as well as tissue-resolved data,
for numerous proteins. This collection references protein abundance information
by species.
example: '9606'
homepage: http://pax-db.org/
mappings:
biocontext: PAXDB.ORGANISM
miriam: paxdb.organism
n2t: paxdb.organism
name: PaxDb Organism
pattern: ^\d+$
preferred_prefix: paxdb.organism
uri_format: http://pax-db.org/#!species/$1
paxdb.protein:
description: PaxDb is a resource dedicated to integrating information on absolute
protein abundance levels across different organisms. Publicly available experimental
data are mapped onto a common namespace and, in the case of tandem mass spectrometry
data, re-processed using a standardized spectral counting pipeline. Data sets
are scored and ranked to assess consistency against externally provided protein-network
information. PaxDb provides whole-organism data as well as tissue-resolved data,
for numerous proteins. This collection references individual protein abundance
levels.
example: '977869'
homepage: http://pax-db.org/
mappings:
biocontext: PAXDB.PROTEIN
miriam: paxdb.protein
n2t: paxdb.protein
name: PaxDb Protein
pattern: ^\d+$
preferred_prefix: paxdb.protein
uri_format: http://pax-db.org/#!protein/$1
pazar:
description: The PAZAR database unites independently created and maintained data
collections of transcription factor and regulatory sequence annotation. It provides
information on the sequence and target of individual transcription factors.
example: TF0001053
homepage: http://www.pazar.info/
mappings:
biocontext: PAZAR
fairsharing: FAIRsharing.33yggg
miriam: pazar
n2t: pazar
prefixcommons: pazar
name: Pazar Transcription Factor
pattern: ^TF\w+$
preferred_prefix: pazar
uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1
pba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
primate brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo
example: '128011350'
homepage: https://www.blueprintnhpatlas.org/
name: Primate Brain Atlas
pattern: ^\d+$
preferred_prefix: PBA
pcl:
banana: PCL
contact:
email: davidos@ebi.ac.uk
github: dosumis
name: David Osumi-Sutherland
orcid: 0000-0002-7073-9172
depends_on:
- bfo
- chebi
- cl
- go
- nbo
- ncbitaxon
- omo
- pato
- pr
- ro
- so
- uberon
description: Cell types that are provisionally defined by experimental techniques
such as single cell transcriptomics rather than a straightforward & coherent set
of properties.
download_json: http://purl.obolibrary.org/obo/pcl.json
download_obo: http://purl.obolibrary.org/obo/pcl.obo
download_owl: http://purl.obolibrary.org/obo/pcl.owl
example: '0011124'
homepage: https://github.com/obophenotype/provisional_cell_ontology
license: CC BY 4.0
mappings:
bioportal: PCL
obofoundry: PCL
ols: pcl
name: Provisional Cell Ontology
pattern: ^\d{7}$
preferred_prefix: PCL
repository: https://github.com/obophenotype/provisional_cell_ontology
uri_format: http://purl.obolibrary.org/obo/PCL_$1
version: '2022-04-27'
pco:
appears_in:
- ecocore
- envo
banana: PCO
contact:
email: rlwalls2008@gmail.com
github: ramonawalls
name: Ramona Walls
orcid: 0000-0001-8815-0078
depends_on:
- bfo
- caro
- envo
- go
- iao
- ncbitaxon
- pato
- ro
description: The Population and Community Ontology (PCO) describes material entities,
qualities, and processes related to collections of interacting organisms such
as populations and communities. It is taxon neutral, and can be used for any species,
including humans. The classes in the PCO are useful for describing evolutionary
processes, organismal interactions, and ecological experiments. Practical applications
of the PCO include community health care, plant pathology, behavioral studies,
sociology, and ecology.
download_owl: http://purl.obolibrary.org/obo/pco.owl
example: '0000021'
homepage: https://github.com/PopulationAndCommunityOntology/pco
license: CC0 1.0
mappings:
biocontext: PCO
bioportal: PCO
fairsharing: FAIRsharing.vq28qp
obofoundry: PCO
ols: pco
ontobee: PCO
name: Population and Community Ontology
pattern: ^\d{7}$
preferred_prefix: PCO
repository: https://github.com/PopulationAndCommunityOntology/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:
biocontext: PD_ST
obofoundry: PD_ST
name: Platynereis stage ontology
preferred_prefix: PD_ST
uri_format: http://purl.obolibrary.org/obo/PD_ST_$1
pdb:
description: The Protein Data Bank is the single worldwide archive of structural
data of biological macromolecules.
example: 2gc4
homepage: https://www.wwpdb.org/
mappings:
biocontext: PDB
fairsharing: FAIRsharing.mckkb4
go: PDB
miriam: pdb
n2t: pdb
ncbi: PDB
prefixcommons: pdbj
uniprot: RCSB-PDB
wikidata: P638
name: PDB Structure
pattern: ^[0-9][A-Za-z0-9]{3}$
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
- code: rcsb
description: RCSB PDB
homepage: https://www.rcsb.org/
name: RCSB PDB
uri_format: https://www.rcsb.org/structure/$1
- code: pdbj
description: Protein Data Bank Japan (PDBj)
homepage: http://www.pdbj.org/
name: Protein Data Bank Japan (PDBj)
uri_format: https://pdbj.org/mine/summary/$1
- code: pdbe
description: Protein Databank in Europe (PDBe)
homepage: http://www.pdbe.org/
name: Protein Databank in Europe (PDBe)
uri_format: https://www.ebi.ac.uk/pdbe/entry/pdb/$1
synonyms:
- RCSB_PDB
- pdbe
- pdbj
- wwpdb
uri_format: https://www.wwpdb.org/pdb?id=$1
pdb-ccd:
comment: might be same as pdb.ligand, not sure though
description: The Chemical Component Dictionary is as an external reference file
describing all residue and small molecule components found in Protein Data Bank
entries. It contains detailed chemical descriptions for standard and modified
amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical
definition includes descriptions of chemical properties such as stereochemical
assignments, aromatic bond assignments, idealized coordinates, chemical descriptors
(SMILES & InChI), and systematic chemical names.
example: AB0
example_extras:
- A
- PI
has_canonical: pdb.ligand
homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/
mappings:
biocontext: PDB-CCD
miriam: pdb-ccd
n2t: pdb-ccd
name: Chemical Component Dictionary
pattern: ^\w{1,3}$
preferred_prefix: pdb-ccd
synonyms:
- pdbechem
uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1
pdb.ligand:
description: The Protein Data Bank is the single worldwide archive of structural
data of biological macromolecules. This collection references ligands.
example: TRQ
homepage: http://www.pdb.org/
mappings:
biocontext: PDB.LIGAND
miriam: pdb.ligand
n2t: pdb.ligand
prefixcommons: pdbligand
wikidata: P3636
name: Protein Data Bank Ligand
pattern: ^[A-Za-z0-9]+$
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=$1
pdro:
banana: PDRO
contact:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
description: An ontology to describe entities related to prescription of drugs
download_owl: http://purl.obolibrary.org/obo/pdro.owl
example: 0010039
homepage: https://github.com/OpenLHS/PDRO
license: CC BY 4.0
mappings:
biocontext: PDRO
bioportal: PDRO
fairsharing: FAIRsharing.9te3ev
obofoundry: PDRO
ols: pdro
ontobee: PDRO
name: The Prescription of Drugs Ontology
pattern: ^\d{7}$
preferred_prefix: PDRO
repository: https://github.com/OpenLHS/PDRO
uri_format: http://purl.obolibrary.org/obo/PDRO_$1
version: '2021-06-08'
pdumdv:
banana: PdumDv
contact:
email: frederic.bastian@unil.ch
github: fbastian
name: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: Life cycle stages for Platynereis dumerilii
download_obo: http://purl.obolibrary.org/obo/pdumdv.obo
download_owl: http://purl.obolibrary.org/obo/pdumdv.owl
example: '0001410'
homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv
license: CC BY 3.0
mappings:
biocontext: PDUMDV
bioportal: PDUMDV
fairsharing: FAIRsharing.493qns
obofoundry: PdumDv
ols: pdumdv
ontobee: PDUMDV
name: Platynereis Developmental Stages
pattern: ^\d{7}$
preferred_prefix: PdumDv
repository: https://github.com/obophenotype/developmental-stage-ontologies
synonyms:
- PdumDv
uri_format: http://purl.obolibrary.org/obo/PDUMDV_$1
version: '2020-03-10'
peco:
appears_in:
- agro
- mco
banana: PECO
contact:
email: jaiswalp@science.oregonstate.edu
github: jaiswalp
name: Pankaj Jaiswal
orcid: 0000-0002-1005-8383
description: A structured, controlled vocabulary which describes the treatments,
growing conditions, and/or study types used in plant biology experiments.
download_obo: https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo
download_owl: http://purl.obolibrary.org/obo/peco.owl
example: '0007114'
homepage: http://planteome.org/
license: CC BY 4.0
mappings:
biocontext: PECO
bioportal: PECO
fairsharing: FAIRsharing.6yNXYK
obofoundry: PECO
ols: peco
ontobee: PECO
name: Plant Experimental Conditions Ontology
pattern: ^\d{7}$
preferred_prefix: PECO
repository: https://github.com/Planteome/plant-experimental-conditions-ontology
uri_format: http://purl.obolibrary.org/obo/PECO_$1
version: '2020-08-21'
ped:
description: The Protein Ensemble Database is an open access database for the deposition
of structural ensembles, including intrinsically disordered proteins.
example: PED00037
homepage: https://proteinensemble.org/
mappings:
fairsharing: FAIRsharing.31385c
miriam: ped
name: Protein Ensemble Database
pattern: ^PED\d{5}$
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/$1
peff:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
download_obo: https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo
example: '0001011'
homepage: https://www.psidev.info/peff
name: PSI Extended File Format
pattern: ^\d{7}$
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:
biocontext: PEPTIDEATLAS
fairsharing: FAIRsharing.dvyrsz
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
perkinelmer:
description: Cell line collections
example: SCC111
homepage: https://www.perkinelmer.com/
mappings:
cellosaurus: PerkinElmer
name: PerkinElmer cell line collection
preferred_prefix: perkinelmer
uri_format: https://www.perkinelmer.com/searchresult?searchName=$1
peroxibase:
description: Peroxibase provides access to peroxidase sequences from all kingdoms
of life, and provides a series of bioinformatics tools and facilities suitable
for analysing these sequences.
example: '5282'
homepage: http://peroxibase.toulouse.inra.fr/
mappings:
biocontext: PEROXIBASE
fairsharing: FAIRsharing.z1czxj
miriam: peroxibase
n2t: peroxibase
prefixcommons: peroxibase
uniprot: PeroxiBase
name: Peroxibase
pattern: ^\d+$
preferred_prefix: peroxibase
uri_format: http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1
pesticides:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Alan Wood’s 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/$1.html
pfam:
description: The Pfam database contains information about protein domains and families.
For each entry a protein sequence alignment and a Hidden Markov Model is stored.
example: PF11779
homepage: https://pfam.xfam.org/
mappings:
biocontext: PFAM
fairsharing: FAIRsharing.y3scf6
go: Pfam
miriam: pfam
n2t: pfam
ncbi: PFAM
prefixcommons: pfam
uniprot: Pfam
wikidata: P3519
name: Pfam
pattern: ^PF\d{5}$
preferred_prefix: pfam
synonyms:
- PF
uri_format: https://pfam.xfam.org/family/$1
pfam.clan:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Higher order grouping of Pfam families
example: CL0192
homepage: https://pfam.xfam.org
name: Pfam Clans
pattern: ^CL\d+$
preferred_prefix: pfam.clan
uri_format: https://pfam.xfam.org/clan/$1
pfr:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Database that provides a central location for scientists to browse
uniquely observed proteoforms and to contribute their own datasets.
example: '1001'
homepage: http://repository.topdownproteomics.org/proteoforms
mappings:
fairsharing: FAIRsharing.wqsxtg
name: Proteoform Atlas
pattern: ^\d+$
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:
biocontext: PGDSO
obofoundry: 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/$1
pgx:
description: The Progenetix database provides an overview of mutation data in cancer,
with a focus on copy number abnormalities (CNV / CNA), for all types of human
malignancies. The resource contains genome profiles of more than 130'000 individual
samples and represents about 700 cancer types, according to the NCIt "neoplasm"
classification. Additionally to this genome profiles and associated metadata,
the website present information about thousands of publications referring to cancer
genome profiling experiments, and services for mapping cancer classifications
and accessing supplementary data through its APIs.
example: pgxbs-kftva5zv
homepage: https://progenetix.org/
mappings:
biocontext: PGX
cellosaurus: Progenetix
fairsharing: FAIRsharing.65tdnz
miriam: pgx
n2t: pgx
name: Progenetix
pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$
preferred_prefix: pgx
synonyms:
- Progenetix
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/$1
pharmacodb.dataset:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Web-application assembling the largest in vitro drug screens in a single
database, and allowing users to easily query the union of studies released to
date. Query by dataset.
example: '1'
homepage: https://pharmacodb.ca/datasets
name: PharmacoDB Datasets
pattern: ^\d+$
preferred_prefix: pharmacodb.dataset
uri_format: https://pharmacodb.ca/datasets/$1
pharmacodb.tissue:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Web-application assembling the largest in vitro drug screens in a single
database, and allowing users to easily query the union of studies released to
date. Query by tissue.
example: '13'
homepage: https://pharmacodb.ca/tissues
name: PharmacoDB Tissues
pattern: ^\d+$
preferred_prefix: pharmacodb.tissue
uri_format: https://pharmacodb.ca/tissues/$1
pharmgkb.disease:
description: The PharmGKB database is a central repository for genetic, genomic,
molecular and cellular phenotype data and clinical information about people who
have participated in pharmacogenomics research studies. The data includes, but
is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research
in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
domains.
example: PA447218
homepage: http://www.pharmgkb.org/
mappings:
biocontext: PHARMGKB.DISEASE
miriam: pharmgkb.disease
n2t: pharmgkb.disease
prefixcommons: pharmgkb.disease
wikidata: P7001
name: PharmGKB Disease
pattern: ^PA\d+$
preferred_prefix: pharmgkb.disease
uri_format: http://www.pharmgkb.org/disease/$1
pharmgkb.drug:
description: The PharmGKB database is a central repository for genetic, genomic,
molecular and cellular phenotype data and clinical information about people who
have participated in pharmacogenomics research studies. The data includes, but
is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research
in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
domains.
example: PA448710
homepage: http://www.pharmgkb.org/
mappings:
biocontext: PHARMGKB.DRUG
miriam: pharmgkb.drug
n2t: pharmgkb.drug
prefixcommons: pharmgkb.drug
wikidata: P7001
name: PharmGKB Drug
pattern: ^PA\d+$
preferred_prefix: pharmgkb.drug
uri_format: http://www.pharmgkb.org/drug/$1
pharmgkb.gene:
description: The PharmGKB database is a central repository for genetic, genomic,
molecular and cellular phenotype data and clinical information about people who
have participated in pharmacogenomics research studies. The data includes, but
is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research
in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter
domains.
example: PA131
homepage: http://www.pharmgkb.org/
mappings:
biocontext: PHARMGKB.GENE
bioportal: PHARMGKB
go: PharmGKB
miriam: pharmgkb.gene
n2t: pharmgkb.gene
prefixcommons: pharmgkb.gene
wikidata: P7001
name: Pharmacogenetics and Pharmacogenomics Knowledge Base
pattern: ^PA\w+$
preferred_prefix: pharmgkb.gene
uri_format: http://www.pharmgkb.org/gene/$1
pharmgkb.pathways:
description: "The PharmGKB database is a central repository for genetic, genomic,\
\ molecular and cellular phenotype data and clinical information about people\
\ who have participated in pharmacogenomics research studies. The data includes,\
\ but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic\
\ research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter\
\ domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways\
\ which focus on candidate genes and gene groups and associated genotype and phenotype\
\ data of relevance for pharmacogenetic and pharmacogenomic studies."
example: PA146123006
homepage: http://www.pharmgkb.org/
mappings:
biocontext: PHARMGKB.PATHWAYS
miriam: pharmgkb.pathways
n2t: pharmgkb.pathways
prefixcommons: pharmgkb.pathways
wikidata: P7001
name: PharmGKB Pathways
pattern: ^PA\d+$
preferred_prefix: pharmgkb.pathways
uri_format: http://www.pharmgkb.org/pathway/$1
phenolexplorer:
description: Phenol-Explorer is an electronic database on polyphenol content in
foods. Polyphenols form a wide group of natural antioxidants present in a large
number of foods and beverages. They contribute to food characteristics such as
taste, colour or shelf-life. They also participate in the prevention of several
major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative
diseases or osteoporosis.
example: '75'
homepage: http://www.phenol-explorer.eu/foods/
mappings:
biocontext: PHENOLEXPLORER
miriam: phenolexplorer
n2t: phenolexplorer
name: Phenol-Explorer
pattern: ^\d+$
preferred_prefix: phenolexplorer
uri_format: http://phenol-explorer.eu/foods/$1
phenx:
description: A Web-based catalog of recommended measurement protocols
example: '130502'
homepage: https://www.phenxtoolkit.org/
mappings:
bioportal: PHENX
fairsharing: FAIRsharing.y5jcwa
name: PhenX Toolkit
pattern: ^\d+$
preferred_prefix: phenx
uri_format: https://www.phenxtoolkit.org/protocols/view/$1
phipo:
banana: PHIPO
contact:
email: alayne.cuzick@rothamsted.ac.uk
github: CuzickA
name: Alayne Cuzick
orcid: 0000-0001-8941-3984
depends_on:
- pato
description: Ontology of species-neutral phenotypes observed in pathogen-host interactions.
download_obo: http://purl.obolibrary.org/obo/phipo.obo
download_owl: http://purl.obolibrary.org/obo/phipo.owl
example: '0000001'
homepage: https://github.com/PHI-base/phipo
license: CC BY 3.0
mappings:
bioportal: PHIPO
obofoundry: PHIPO
ols: phipo
ontobee: PHIPO
name: Pathogen Host Interaction Phenotype Ontology
pattern: ^\d{7}$
preferred_prefix: PHIPO
repository: https://github.com/PHI-base/phipo
uri_format: http://purl.obolibrary.org/obo/PHIPO_$1
version: '2021-07-14'
phosphopoint.kinase:
description: PhosphoPOINT is a database of the human kinase and phospho-protein
interactome. It describes the interactions among kinases, their potential substrates
and their interacting (phospho)-proteins. It also incorporates gene expression
and uses gene ontology (GO) terms to annotate interactions. This collection references
kinase information.
example: AURKA
homepage: http://kinase.bioinformatics.tw/
mappings:
biocontext: PHOSPHOPOINT.KINASE
miriam: phosphopoint.kinase
n2t: phosphopoint.kinase
name: PhosphoPoint Kinase
pattern: ^\w+$
preferred_prefix: phosphopoint.kinase
uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1
phosphopoint.protein:
description: PhosphoPOINT is a database of the human kinase and phospho-protein
interactome. It describes the interactions among kinases, their potential substrates
and their interacting (phospho)-proteins. It also incorporates gene expression
and uses gene ontology (GO) terms to annotate interactions. This collection references
phosphoprotein information.
example: AURKA
homepage: http://kinase.bioinformatics.tw/
mappings:
biocontext: PHOSPHOPOINT.PROTEIN
miriam: phosphopoint.protein
n2t: phosphopoint.protein
name: PhosphoPoint Phosphoprotein
pattern: ^\w+$
preferred_prefix: phosphopoint.protein
uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0
phosphosite.protein:
description: PhosphoSite is a mammalian protein database that provides information
about in vivo phosphorylation sites. This datatype refers to protein-level information,
providing a list of phosphorylation sites for each protein in the database.
example: '12300'
homepage: http://www.phosphosite.org/homeAction.do
mappings:
biocontext: PHOSPHOSITE.PROTEIN
miriam: phosphosite.protein
n2t: phosphosite.protein
name: PhosphoSite Protein
pattern: ^\d{5}$
preferred_prefix: phosphosite.protein
uri_format: http://www.phosphosite.org/proteinAction.do?id=$1
phosphosite.residue:
description: PhosphoSite is a mammalian protein database that provides information
about in vivo phosphorylation sites. This datatype refers to residue-level information,
providing a information about a single modification position in a specific protein
sequence.
example: '2842'
homepage: http://www.phosphosite.org/homeAction.do
mappings:
biocontext: PHOSPHOSITE.RESIDUE
miriam: phosphosite.residue
n2t: phosphosite.residue
name: PhosphoSite Residue
pattern: ^\d+$
preferred_prefix: phosphosite.residue
uri_format: http://www.phosphosite.org/siteAction.do?id=$1
phylomedb:
description: PhylomeDB is a database of complete phylomes derived for different
genomes within a specific taxonomic range. It provides alignments, phylogentic
trees and tree-based orthology predictions for all encoded proteins.
example: Phy000CLXM_RAT
homepage: http://phylomedb.org/
mappings:
biocontext: PHYLOMEDB
fairsharing: FAIRsharing.7hxxc4
miriam: phylomedb
n2t: phylomedb
prefixcommons: phylomedb
uniprot: PhylomeDB
name: PhylomeDB
pattern: ^\w+$
preferred_prefix: phylomedb
uri_format: http://phylomedb.org/?seqid=$1
phytozome.locus:
description: Phytozome is a project to facilitate comparative genomic studies amongst
green plants. Famlies of orthologous and paralogous genes that represent the modern
descendents of ancestral gene sets are constructed at key phylogenetic nodes.
These families allow easy access to clade specific orthology/paralogy relationships
as well as clade specific genes and gene expansions. This collection references
locus information.
example: Glyma0021s00410
homepage: http://www.phytozome.net/
mappings:
biocontext: PHYTOZOME.LOCUS
miriam: phytozome.locus
n2t: phytozome.locus
ncbi: Phytozome
name: Plant Genome Network
pattern: ^[A-Za-z0-9]+$
preferred_prefix: phytozome.locus
synonyms:
- JGI Phytozome
uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1
pictar:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
example: hsa-let-7a
homepage: https://pictar.mdc-berlin.de/
name: PicTar
preferred_prefix: pictar
synonyms:
- pictar-vert
pid.pathway:
description: The Pathway Interaction Database is a highly-structured, curated collection
of information about known human biomolecular interactions and key cellular processes
assembled into signaling pathways. This datatype provides access to pathway information.
example: eff796f3-6195-11e5-8ac5-06603eb7f303
homepage: http://pid.nci.nih.gov/
mappings:
biocontext: PID.PATHWAY
fairsharing: FAIRsharing.ncgh1j
miriam: pid.pathway
n2t: pid.pathway
prefixcommons: pid
name: 'NCI Pathway Interaction Database: Pathway'
pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$
preferred_prefix: pid.pathway
synonyms:
- pid
uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1
pigqtldb:
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
designed to house publicly all available QTL and single-nucleotide polymorphism/gene
association data on livestock animal species. This collection references pig QTLs.
example: '14'
homepage: https://www.animalgenome.org/QTLdb
mappings:
biocontext: PIGQTLDB
miriam: pigqtldb
n2t: pigqtldb
prefixcommons: pigqtldb
name: Animal Genome Pig QTL
part_of: qtldb
pattern: ^\d+$
preferred_prefix: pigqtldb
uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
pina:
description: Protein Interaction Network Analysis (PINA) platform is an integrated
platform for protein interaction network construction, filtering, analysis, visualization
and management. It integrates protein-protein interaction data from six public
curated databases and builds a complete, non-redundant protein interaction dataset
for six model organisms.
example: Q13485
homepage: http://cbg.garvan.unsw.edu.au/pina/
mappings:
biocontext: PINA
fairsharing: FAIRsharing.7q4gsz
miriam: pina
n2t: pina
name: Protein Interaction Network Analysis
pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9])$
preferred_prefix: pina
provides: uniprot
uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1
piroplasma:
description: PiroplasmaDB is one of the databases that can be accessed through the
EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: TA14985
homepage: http://piroplasmadb.org/
mappings:
biocontext: PIROPLASMA
miriam: piroplasma
n2t: piroplasma
name: PiroplasmaDB
pattern: ^TA\d+$
preferred_prefix: piroplasma
uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
pirsf:
description: The PIR SuperFamily concept is being used as a guiding principle to
provide comprehensive and non-overlapping clustering of UniProtKB sequences into
a hierarchical order to reflect their evolutionary relationships.
example: PIRSF000100
homepage: https://pir.georgetown.edu/
mappings:
biocontext: PIRSF
fairsharing: FAIRsharing.vssch2
go: PIRSF
miriam: pirsf
n2t: pirsf
prefixcommons: pirsf
uniprot: PIRSF
name: PIR Superfamily Classification System
pattern: ^PIRSF\d{6}$
preferred_prefix: pirsf
uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1
pkdb:
description: 'PK-DB an open database for pharmacokinetics information from clinical
trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality
pharmacokinetics data enriched with the required meta-information for computational
modeling and data integration. '
example: PKDB00198
homepage: https://www.hu-berlin.de/?set_language=en&cl=en
mappings:
fairsharing: FAIRsharing.AYegqK
miriam: pkdb
name: PK-DB
pattern: ^PKDB[0-9]{5}$
preferred_prefix: pkdb
uri_format: https://pk-db.com/data/$1
plana:
appears_in:
- planp
banana: PLANA
contact:
email: smr@stowers.org
github: srobb1
name: Sofia Robb
orcid: 0000-0002-3528-5267
depends_on:
- ro
- uberon
description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental
stages and adult biotypes of Schmidtea mediterranea.
download_obo: http://purl.obolibrary.org/obo/plana.obo
download_owl: http://purl.obolibrary.org/obo/plana.owl
example: '0000001'
homepage: https://github.com/obophenotype/planaria-ontology
license: CC BY 3.0
mappings:
biocontext: PLANA
bioportal: PLANA
fairsharing: FAIRsharing.g1qrqs
obofoundry: PLANA
ols: plana
ontobee: PLANA
name: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology
pattern: ^\d{7}$
preferred_prefix: PLANA
repository: https://github.com/obophenotype/planaria-ontology
uri_format: http://purl.obolibrary.org/obo/PLANA_$1
version: '2022-03-02'
planp:
banana: PLANP
contact:
email: smr@stowers.org
github: srobb1
name: Sofia Robb
orcid: 0000-0002-3528-5267
depends_on:
- go
- pato
- plana
- ro
description: Planarian Phenotype Ontology is an ontology of phenotypes observed
in the planarian Schmidtea mediterranea.
download_obo: http://purl.obolibrary.org/obo/planp.obo
download_owl: http://purl.obolibrary.org/obo/planp.owl
example: '0000001'
homepage: https://github.com/obophenotype/planarian-phenotype-ontology
license: CC BY 3.0
mappings:
bioportal: PLANP
obofoundry: PLANP
ols: planp
ontobee: PLANP
name: Planarian Phenotype Ontology
pattern: ^\d+$
preferred_prefix: PLANP
repository: https://github.com/obophenotype/planarian-phenotype-ontology
uri_format: http://purl.obolibrary.org/obo/PLANP_$1
version: '2020-03-28'
planttfdb:
description: The Plant TF database (PlantTFDB) systematically identifies transcription
factors for plant species. It includes annotation for identified TFs, including
information on expression, regulation, interaction, conserved elements, phenotype
information. It also provides curated descriptions and cross-references to other
life science databases, as well as identifying evolutionary relationship among
identified factors.
example: Ath_AT1G01030.1
homepage: http://planttfdb.cbi.pku.edu.cn
mappings:
biocontext: PLANTTFDB
fairsharing: FAIRsharing.ex3fqk
miriam: planttfdb
n2t: planttfdb
prefixcommons: planttfdb
name: Plant Transcription Factor Database
pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$
preferred_prefix: planttfdb
uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1
plasmodb:
description: AmoebaDB is one of the databases that can be accessed through the EuPathDB
(http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: PF11_0344
homepage: http://plasmodb.org/plasmo/
mappings:
biocontext: PLASMODB
fairsharing: FAIRsharing.g4n8sw
go: PlasmoDB
miriam: plasmodb
n2t: plasmodb
ncbi: ApiDB_PlasmoDB
prefixcommons: plasmodb
name: PlasmoDB
pattern: ^\w+$
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:
biocontext: PLO
obofoundry: PLO
name: Plasmodium Life Cycle
preferred_prefix: PLO
uri_format: http://purl.obolibrary.org/obo/PLO_$1
pmap.cutdb:
description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
PMAP is comprised of five databases, linked together in one environment. CutDB
is a database of individual proteolytic events (cleavage sites).
example: '25782'
homepage: http://cutdb.burnham.org
mappings:
biocontext: PMAP.CUTDB
miriam: pmap.cutdb
n2t: pmap.cutdb
prefixcommons: pmap.cutdb
name: CutDB
pattern: ^\d+$
preferred_prefix: pmap.cutdb
uri_format: http://cutdb.burnham.org/relation/show/$1
pmap.substratedb:
description: The Proteolysis MAP is a resource for proteolytic networks and pathways.
PMAP is comprised of five databases, linked together in one environment. SubstrateDB
contains molecular information on documented protease substrates.
example: '1915'
homepage: http://substrate.burnham.org/
mappings:
biocontext: PMAP.SUBSTRATEDB
miriam: pmap.substratedb
n2t: pmap.substratedb
prefixcommons: pmap.substratedb
name: SubstrateDB
pattern: ^\d+$
preferred_prefix: pmap.substratedb
uri_format: http://substrate.burnham.org/protein/annotation/$1/html
pmc:
description: PMC International (PMCI) is a free full-text archive of biomedical
and life sciences journal literature. PMCI is a collaborative effort between the
U.S. National Institutes of Health and the National Library of Medicine, the publishers
whose journal content makes up the PMC archive, and organizations in other countries
that share NIH's and NLM's interest in archiving life sciences literature.
example: PMC3084216
homepage: http://europepmc.org/
mappings:
biocontext: PMCID
fairsharing: FAIRsharing.wpt5mp
go: PMCID
miriam: pmc
n2t: pmc
prefixcommons: pmc
wikidata: P932
name: Pubmed Central
pattern: ^PMC\d+$
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/$1
pmdb:
description: The Protein Model DataBase (PMDB), is a database that collects manually
built three dimensional protein models, obtained by different structure prediction
techniques.
example: PM0012345
homepage: https://bioinformatics.cineca.it/PMDB/
mappings:
biocontext: PMDB
fairsharing: FAIRsharing.wkaakq
miriam: pmdb
n2t: pmdb
prefixcommons: pmdb
name: Protein Model Database
pattern: ^PM\d{7}$
preferred_prefix: pmdb
uri_format: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1
pmp:
description: The number of known protein sequences exceeds those of experimentally
solved protein structures. Homology (or comparative) modeling methods make use
of experimental protein structures to build models for evolutionary related proteins.
The Protein Model Portal (PMP) provides a single portal to access these models,
which are accessed through their UniProt identifiers.
example: Q0VCA6
homepage: http://www.proteinmodelportal.org/
mappings:
biocontext: PMP
miriam: pmp
n2t: pmp
prefixcommons: pmp
name: Protein Model Portal
pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9])$
preferred_prefix: pmp
provides: uniprot
uri_format: http://www.proteinmodelportal.org/query/uniprot/$1
pmr:
description: Resource for the community to store, retrieve, search, reference, and
reuse CellML models.
example: ebf69ca24298b28b2361e7d43eb52d6c
homepage: https://www.auckland.ac.nz/en.html
mappings:
bioportal: PMR
fairsharing: FAIRsharing.bcjrnq
miriam: pmr
name: Physical Medicine and Rehabilitation
pattern: ^[a-z0-9]{32,32}$
preferred_prefix: pmr
uri_format: https://models.physiomeproject.org/exposure/$1
po:
appears_in:
- agro
- ecocore
- envo
- genepio
banana: PO
contact:
email: jaiswalp@science.oregonstate.edu
github: jaiswalp
name: Pankaj Jaiswal
orcid: 0000-0002-1005-8383
description: The Plant Ontology is a structured vocabulary and database resource
that links plant anatomy, morphology and growth and development to plant genomics
data.
download_obo: http://purl.obolibrary.org/obo/po.obo
download_owl: http://purl.obolibrary.org/obo/po.owl
example: 0009089
homepage: http://browser.planteome.org/amigo
license: CC BY 4.0
mappings:
biocontext: PO
bioportal: PO
fairsharing: FAIRsharing.3ngg40
go: PO
miriam: po
n2t: po
obofoundry: PO
ols: po
ontobee: PO
prefixcommons: po
name: Plant Ontology
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: PO
repository: https://github.com/Planteome/plant-ontology
uri_format: http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1
version: '2021-08-13'
pocketome:
description: Pocketome is an encyclopedia of conformational ensembles of all druggable
binding sites that can be identified experimentally from co-crystal structures
in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule
binding site in a protein which has been co-crystallized in complex with at least
one drug-like small molecule, and is represented in at least two PDB entries.
example: 1433C_TOBAC_1_252
homepage: http://www.pocketome.org/sfSearch.cgi?act=browseall
mappings:
biocontext: POCKETOME
fairsharing: FAIRsharing.tc6df8
miriam: pocketome
n2t: pocketome
name: Pocketome
pattern: ^[A-Za-z_0-9]+$
preferred_prefix: pocketome
uri_format: http://www.pocketome.org/files/$1.html
polbase:
description: Polbase is a database of DNA polymerases providing information on polymerase
protein sequence, target DNA sequence, enzyme structure, sequence mutations and
details on polymerase activity.
example: 19-T4
homepage: http://polbase.neb.com/
mappings:
biocontext: POLBASE
fairsharing: FAIRsharing.s9ztmd
miriam: polbase
n2t: polbase
name: PolBase
pattern: ^[A-Za-z-0-9]+$
preferred_prefix: polbase
uri_format: https://polbase.neb.com/polymerases/$1#sequences
pombase:
description: PomBase is a model organism database established to provide access
to molecular data and biological information for the fission yeast Schizosaccharomyces
pombe. It encompasses annotation of genomic sequence and features, comprehensive
manual literature curation and genome-wide data sets.
example: SPCC13B11.01
homepage: http://www.pombase.org/
mappings:
biocontext: PomBase
biolink: PomBase
fairsharing: FAIRsharing.8jsya3
go: PomBase
miriam: pombase
n2t: pombase
ncbi: PomBase
prefixcommons: pombase
uniprot: PomBase
wikidata: P6245
name: PomBase
pattern: ^S\w+(\.)?\w+(\.)?$
preferred_prefix: pombase
synonyms:
- PomBase
uri_format: http://www.pombase.org/spombe/result/$1
poro:
banana: PORO
contact:
email: robert.thacker@stonybrook.edu
github: bobthacker
name: Bob Thacker
orcid: 0000-0002-9654-0073
depends_on:
- ro
- uberon
description: An ontology describing the anatomical structures and characteristics
of Porifera (sponges)
download_obo: http://purl.obolibrary.org/obo/poro.obo
download_owl: http://purl.obolibrary.org/obo/poro.owl
example: '0000550'
homepage: https://github.com/obophenotype/porifera-ontology
license: CC BY 3.0
mappings:
biocontext: PORO
bioportal: PORO
fairsharing: FAIRsharing.93g1th
obofoundry: PORO
ols: poro
ontobee: PORO
name: Porifera Ontology
pattern: ^\d{7}$
preferred_prefix: PORO
repository: https://github.com/obophenotype/porifera-ontology
uri_format: http://purl.obolibrary.org/obo/PORO_$1
version: '2016-10-06'
ppdb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'PPDB is a comprehensive source of data on pesticide chemical, physical
and biological properties. '
example: '1484'
homepage: https://sitem.herts.ac.uk/aeru/ppdb/
mappings:
fairsharing: FAIRsharing.7k8zh0
name: Pesticide Properties DataBase
pattern: ^\d+$
preferred_prefix: ppdb
uri_format: https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm
ppo:
banana: PPO
contact:
email: rlwalls2008@gmail.com
github: ramonawalls
name: Ramona Walls
orcid: 0000-0001-8815-0078
description: An ontology for describing the phenology of individual plants and populations
of plants, and for integrating plant phenological data across sources and scales.
download_owl: http://purl.obolibrary.org/obo/ppo.owl
example: 0002058
homepage: https://github.com/PlantPhenoOntology/PPO
license: CC BY 3.0
mappings:
biocontext: PPO
bioportal: PPO
fairsharing: FAIRsharing.hakg7c
obofoundry: PPO
ols: ppo
ontobee: PPO
name: Plant Phenology Ontology
pattern: ^\d{7}$
preferred_prefix: PPO
repository: https://github.com/PlantPhenoOntology/PPO
uri_format: http://purl.obolibrary.org/obo/PPO_$1
version: '2018-10-26'
ppr:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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/$1
pr:
appears_in:
- chiro
- cl
- pcl
- scdo
- uberon
banana: PR
contact:
email: dan5@georgetown.edu
github: nataled
name: Darren Natale
orcid: 0000-0001-5809-9523
description: The PRotein Ontology (PRO) has been designed to describe the relationships
of proteins and protein evolutionary classes, to delineate the multiple protein
forms of a gene locus (ontology for protein forms), and to interconnect existing
ontologies.
download_obo: http://purl.obolibrary.org/obo/pr.obo
download_owl: http://purl.obolibrary.org/obo/pr.owl
example: '000000024'
homepage: http://proconsortium.org
license: CC BY 4.0
mappings:
biocontext: PR
bioportal: PR
fairsharing: FAIRsharing.4ndncv
go: PR
miriam: pr
n2t: pr
obofoundry: PR
ols: pr
ontobee: PR
prefixcommons: pr
uniprot: PRO
wikidata: P4926
name: Protein Ontology
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: PR
repository: https://github.com/PROconsortium/PRoteinOntology
synonyms:
- PR
- PRO
uri_format: https://proconsortium.org/app/entry/PR:$1
version: '65.0'
prefixcommons:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A registry of life science prefxes
example: ChEBI
homepage: https://prefixcommons.org
name: Prefix Commons
preferred_prefix: prefixcommons
uri_format: https://bioregistry.io/metaregistry/prefixcommons/$1
pride:
description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
compliant, public data repository that provides protein and peptide identifications
together with supporting evidence. This collection references experiments and
assays.
download_owl: https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo
example: '1'
homepage: https://github.com/PRIDE-Utilities/pride-ontology
mappings:
biocontext: PRIDE
cellosaurus: PRIDE
fairsharing: FAIRsharing.e1byny
miriam: pride
n2t: pride
ols: pride
prefixcommons: pride
uniprot: PRIDE
name: PRIDE Controlled Vocabulary
pattern: ^\d+$
preferred_prefix: pride
repository: https://github.com/PRIDE-Utilities/pride-ontology
uri_format: https://www.ebi.ac.uk/pride/archive/assays/$1
pride.project:
description: The PRIDE PRoteomics IDEntifications database is a centralized, standards
compliant, public data repository that provides protein and peptide identifications
together with supporting evidence. This collection references projects.
example: PXD000440
homepage: https://www.ebi.ac.uk/pride/
mappings:
biocontext: PRIDE.PROJECT
miriam: pride.project
n2t: pride.project
name: PRIDE Project
pattern: ^P(X|R)D\d{6}$
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/$1
prints:
description: PRINTS is a compendium of protein fingerprints. A fingerprint is a
group of conserved motifs used to characterise a protein family; its diagnostic
power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually
the motifs do not overlap, but are separated along a sequence, though they may
be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities
more flexibly and powerfully than can single motifs, full diagnostic potency deriving
from the mutual context provided by motif neighbours.
example: PR00001
homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/
mappings:
biocontext: PRINTS
fairsharing: FAIRsharing.h8r843
go: PRINTS
miriam: prints
n2t: prints
uniprot: PRINTS
name: PRINTS compendium of protein fingerprints
pattern: ^PR\d{5}$
preferred_prefix: prints
uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off
probonto:
description: ProbOnto, is an ontology-based knowledge base of probability distributions,
featuring uni- and multivariate distributions with their defining functions, characteristics,
relationships and reparameterisation formulae. It can be used for annotation
of models, facilitating the encoding of distribution-based models, related functions
and quantities.
download_owl: https://raw.githubusercontent.com/probonto/ontology/master/probonto4ols.owl
example: PROB_c0000005
homepage: http://probonto.org
mappings:
biocontext: PROBONTO
fairsharing: FAIRsharing.8zqzm9
miriam: probonto
n2t: probonto
ols: probonto
name: Probability Distribution Ontology
pattern: ^PROB_c\d+$
preferred_prefix: probonto
uri_format: https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1
version: 2.5.0
prodom:
description: ProDom is a database of protein domain families generated from the
global comparison of all available protein sequences.
example: PD10000
homepage: http://prodom.prabi.fr/prodom/current/html/home.php
mappings:
biocontext: PRODOM
fairsharing: FAIRsharing.a8z6gz
miriam: prodom
n2t: prodom
prefixcommons: prodom
name: ProDom
pattern: ^PD\d+$
preferred_prefix: prodom
uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1
proglyc:
description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial
and archaeal glycoproteins with at least one experimentally validated glycosite
(glycosylated residue). Each entry in the database is fully cross-referenced and
enriched with available published information about source organism, coding gene,
protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl
transferases (OSTs/GTs), supporting references, and applicable additional information.
example: AC119
homepage: http://www.proglycprot.org/
mappings:
biocontext: PROGLYC
miriam: proglyc
n2t: proglyc
name: ProGlycProt
pattern: ^[A-Z]C\d{1,3}$
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:
biocontext: PROPREO
bioportal: PROPREO
obofoundry: PROPREO
prefixcommons: propreo
name: Proteomics data and process provenance
preferred_prefix: PROPREO
uri_format: http://purl.obolibrary.org/obo/PROPREO_$1
prosite:
description: PROSITE consists of documentation entries describing protein domains,
families and functional sites as well as associated patterns and profiles to identify
them.
example: PS00001
homepage: https://www.expasy.org/prosite/
mappings:
biocontext: PROSITE
fairsharing: FAIRsharing.vwc6bd
go: Prosite
miriam: prosite
n2t: prosite
prefixcommons: prosite
uniprot: PROSITE
wikidata: P4355
name: PROSITE
pattern: ^PS\d{5}$
preferred_prefix: prosite
uri_format: https://prosite.expasy.org/$1
protclustdb:
description: ProtClustDB is a collection of related protein sequences (clusters)
consisting of Reference Sequence proteins encoded by complete genomes. This database
contains both curated and non-curated clusters.
example: O80725
homepage: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters
mappings:
biocontext: PROTCLUSTDB
fairsharing: FAIRsharing.da493y
miriam: protclustdb
n2t: protclustdb
prefixcommons: protclustdb
name: ProtClustDB
pattern: ^\w+$
preferred_prefix: protclustdb
uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1
proteomicsdb.peptide:
comment: The fact that this has .peptide as a subspace is a bit of a misnomer. Its
original registration with MIRIAM uses a subview over the protein to point to
peptides, but the identifiers in this semantic space seem to be about proteins.
description: ProteomicsDB is an effort dedicated to expedite the identification
of the human proteome and its use across the scientific community. This human
proteome data is assembled primarily using information from liquid chromatography
tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell
lines and body fluids. Information is accessible for individual proteins, or on
the basis of protein coverage on the encoding chromosome, and for peptide components
of a protein. This collection provides access to the peptides identified for a
given protein.
example: '53504'
homepage: https://www.proteomicsdb.org/#peptideSearch
mappings:
biocontext: PROTEOMICSDB.PEPTIDE
miriam: proteomicsdb.peptide
n2t: proteomicsdb.peptide
name: ProteomicsDB Peptide
pattern: ^\d+$
preferred_prefix: proteomicsdb.peptide
uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1
proteomicsdb.protein:
description: ProteomicsDB is an effort dedicated to expedite the identification
of the human proteome and its use across the scientific community. This human
proteome data is assembled primarily using information from liquid chromatography
tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell
lines and body fluids. Information is accessible for individual proteins, or on
the basis of protein coverage on the encoding chromosome, and for peptide components
of a protein. This collection provides access to individual proteins.
example: '53504'
homepage: https://www.proteomicsdb.org/#human
mappings:
biocontext: PROTEOMICSDB.PROTEIN
miriam: proteomicsdb.protein
n2t: proteomicsdb.protein
name: ProteomicsDB Protein
pattern: ^\d+$
preferred_prefix: proteomicsdb.protein
uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary
protonet.cluster:
description: ProtoNet provides automatic hierarchical classification of protein
sequences in the UniProt database, partitioning the protein space into clusters
of similar proteins. This collection references cluster information.
example: '4349895'
homepage: http://www.protonet.cs.huji.ac.il/
mappings:
biocontext: PROTONET.CLUSTER
miriam: protonet.cluster
n2t: protonet.cluster
prefixcommons: protonet.cluster
name: ProtoNet Cluster
pattern: ^\d+$
preferred_prefix: protonet.cluster
uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1
protonet.proteincard:
description: ProtoNet provides automatic hierarchical classification of protein
sequences in the UniProt database, partitioning the protein space into clusters
of similar proteins. This collection references protein information.
example: '16941567'
homepage: http://www.protonet.cs.huji.ac.il/
mappings:
biocontext: PROTONET.PROTEINCARD
miriam: protonet.proteincard
n2t: protonet.proteincard
prefixcommons: protonet.proteincard
name: ProtoNet ProteinCard
pattern: ^\d+$
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.
download_owl: http://www.w3.org/ns/prov-o-20130430
example: Activity
homepage: https://www.w3.org/ns/prov
mappings:
biocontext: prov
biolink: prov
ols: prov
name: PROV Namespace
preferred_prefix: prov
uri_format: http://www.w3.org/ns/prov#$1
version: '2013-04-30'
pscdb:
description: The PSCDB (Protein Structural Change DataBase) collects information
on the relationship between protein structural change upon ligand binding. Each
entry page provides detailed information about this structural motion.
example: '051'
homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html
mappings:
biocontext: PSCDB
fairsharing: FAIRsharing.3d4jx0
miriam: pscdb
n2t: pscdb
name: Protein Structural Change Database
pattern: ^\d+$
preferred_prefix: pscdb
uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html
psdo:
banana: PSDO
contact:
email: zachll@umich.edu
github: zachll
name: Zach Landis-Lewis
orcid: 0000-0002-9117-9338
depends_on:
- bfo
- iao
- ro
- stato
description: Performance Summary Display Ontology (PSDO) (pronounced "pseudo" or
"sudo") is an application ontology about charts, tables, and graphs that are used
to communicate performance information to employees and teams in organizations.
PSDO's domain focus is on healthcare organizations that use performance summary
displays in clinical dashboards and feedback interventions for healthcare professionals
and teams. The displays commonly show information about the quality of care and
health outcomes that has been derived from clinical data using performance measures
(aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal
Ontology as its upper level ontology. This work is not peer-reviewed.
download_owl: http://purl.obolibrary.org/obo/psdo.owl
example: '0000055'
homepage: https://github.com/Display-Lab/psdo
license: CC BY 3.0
mappings:
bioportal: PSDO
obofoundry: PSDO
ols: psdo
ontobee: PSDO
name: Performance Summary Display Ontology
pattern: ^\d{7}$
preferred_prefix: PSDO
repository: https://github.com/Display-Lab/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
prefixcommons: pseudogene
name: PseudoGene
preferred_prefix: pseudogene
synonyms:
- pseudogene.org
uri_format: http://tables.pseudogene.org/[?species_name]/$1
pseudomonas:
description: The Pseudomonas Genome Database is a resource for peer-reviewed, continually
updated annotation for all Pseudomonas species. It includes gene and protein sequence
information, as well as regulation and predicted function and annotation.
example: PSEEN0001
homepage: http://www.pseudomonas.com/
mappings:
biocontext: PSEUDOMONAS
miriam: pseudomonas
n2t: pseudomonas
name: Pseudomonas Genome Database
pattern: ^P\w+$
preferred_prefix: pseudomonas
uri_format: http://www.pseudomonas.com/feature/show/?locus_tag=$1
psipar:
description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled
vocabulary for the annotation of experiments concerned with interactions, and
interactor production methods. PAR is developed by the HUPO Proteomics Standards
Initiative and contains the majority of the terms from the PSI-MI controlled vocabular,
as well as additional terms.
example: PAR:0116
homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR
mappings:
biocontext: PSIPAR
miriam: psipar
n2t: psipar
name: Protein Affinity Reagents
pattern: ^PAR:\d+$
preferred_prefix: psipar
uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=$1
pso:
banana: PSO
contact:
email: cooperl@oregonstate.edu
github: cooperl09
name: Laurel Cooper
orcid: 0000-0002-6379-8932
depends_on:
- ro
description: The Plant Stress Ontology describes biotic and abiotic stresses that
a plant may encounter.
download_obo: http://purl.obolibrary.org/obo/pso.obo
download_owl: http://purl.obolibrary.org/obo/pso.owl
example: '0000013'
homepage: https://github.com/Planteome/plant-stress-ontology
license: CC BY 3.0
mappings:
bioportal: PSO
fairsharing: FAIRsharing.dyj433
obofoundry: PSO
ols: pso
ontobee: PSO
name: Plant Stress Ontology
pattern: ^\d{7}$
preferred_prefix: PSO
repository: https://github.com/Planteome/plant-stress-ontology
uri_format: http://purl.obolibrary.org/obo/PSO_$1
version: '2020-05-19'
pspub:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Documentation of the Phenoscape Curation Workflow
homepage: https://wiki.phenoscape.org/wiki/Curation_workflow
name: Phenoscape Publication
preferred_prefix: pspub
pubchem.bioassay:
description: PubChem provides information on the biological activities of small
molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
PubChem bioassay archives active compounds and bioassay results.
example: '1018'
homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay
mappings:
biocontext: PUBCHEM.BIOASSAY
go: PubChem_BioAssay
miriam: pubchem.bioassay
n2t: pubchem.bioassay
prefixcommons: pubchem.bioassay
name: NCBI PubChem database of bioassay records
pattern: ^\d+$
preferred_prefix: pubchem.bioassay
uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1
pubchem.compound:
description: PubChem provides information on the biological activities of small
molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
PubChem Compound archives chemical structures and records.
example: '100101'
homepage: https://pubchem.ncbi.nlm.nih.gov/
mappings:
biocontext: CID
biolink: CID
cellosaurus: PubChem
cheminf: '000140'
fairsharing: FAIRsharing.g63c77
go: PubChem_Compound
miriam: pubchem.compound
n2t: pubchem.compound
prefixcommons: pubchem.compound
scholia: pubchem
wikidata: P662
name: PubChem CID
pattern: ^\d+$
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/$1
pubchem.element:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: PubChem Element gives information on chemical elements like Hydrogen,
with the local identifier corresponding to the atomic number.
example: '1'
homepage: https://pubchem.ncbi.nlm.nih.gov/periodic-table
name: PubChem Element
pattern: ^\d+$
preferred_prefix: pubchem.element
uri_format: https://pubchem.ncbi.nlm.nih.gov/element/$1
pubchem.substance:
description: PubChem provides information on the biological activities of small
molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.
PubChem Substance archives chemical substance records.
example: '100101'
homepage: https://pubchem.ncbi.nlm.nih.gov/
mappings:
biocontext: PUBCHEM.SUBSTANCE
cheminf: '000141'
go: PubChem_Substance
miriam: pubchem.substance
n2t: pubchem.substance
prefixcommons: pubchem.substance
wikidata: P2153
name: PubChem Substance ID (SID)
pattern: ^\d+$
preferred_prefix: pubchem.substance
synonyms:
- DSSTox_Generic_SID
uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1
publons.researcher:
description: Database of researchers to track publications, citation metrics, peer
reviews, and journal editing work.
example: '1981638'
homepage: https://publons.com/researcher
mappings:
biolink: ResearchID
name: Publons Researcher
pattern: ^\d+$
preferred_prefix: publons.researcher
uri_format: https://publons.com/researcher/$1
pubmed:
description: PubMed is a service of the U.S. National Library of Medicine that includes
citations from MEDLINE and other life science journals for biomedical articles
back to the 1950s.
example: '16333295'
homepage: https://www.ncbi.nlm.nih.gov/PubMed/
mappings:
biocontext: PMID
cellosaurus: PubMed
cheminf: '000302'
fairsharing: FAIRsharing.a5sv8m
go: PMID
miriam: pubmed
n2t: pubmed
prefixcommons: pubmed
scholia: pubmed
wikidata: P698
name: PubMed
pattern: ^\d+$
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/$1
pw:
banana: PW
contact:
email: gthayman@mcw.edu
github: gthayman
name: G. Thomas Hayman
orcid: 0000-0002-9553-7227
description: 'The Pathway Ontology captures information on biological networks,
the relationships between netweorks and the alterations or malfunctioning of such
networks within a hierarchical structure. The five main branches of the ontology
are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor
complex human conditions.'
download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo
download_owl: http://purl.obolibrary.org/obo/pw.owl
example: '0000423'
homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
license: CC BY 4.0
mappings:
biocontext: PW
bioportal: PW
fairsharing: FAIRsharing.f73xhd
miriam: pw
n2t: pw
obofoundry: PW
ols: pw
ontobee: PW
prefixcommons: pw
wikidata: P7333
name: Pathway ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: PW
repository: https://github.com/rat-genome-database/PW-Pathway-Ontology
uri_format: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1
version: '2019-10-23'
px:
description: The ProteomeXchange provides a single point of submission of Mass Spectrometry
(MS) proteomics data for the main existing proteomics repositories, and encourages
the data exchange between them for optimal data dissemination.
example: PXD000500
homepage: http://www.proteomexchange.org/
mappings:
biocontext: PX
miriam: px
n2t: px
name: ProteomeXchange
pattern: ^(R)?PXD\d{6}$
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
fairsharing: FAIRsharing.d3pqw7
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
synonyms:
- irgsp
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=$1
rbk:
description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects
working to optimize approaches for the isolation, expansion, and differentiation
of appropriate kidney cell types and their integration into complex structures
that replicate human kidney function.
example: Q-2958
homepage: https://www.rebuildingakidney.org/
mappings:
biocontext: RBK
fairsharing: FAIRsharing.78d3ad
miriam: rbk
n2t: rbk
name: Rebuilding a Kidney
pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
preferred_prefix: rbk
uri_format: https://www.rebuildingakidney.org/id/$1
rbo:
banana: RBO
contact:
email: daniel.c.berrios@nasa.gov
github: DanBerrios
name: Daniel C. Berrios
orcid: 0000-0003-4312-9552
depends_on:
- bfo
- chmo
- envo
- obi
- pato
- ro
- uo
description: RBO is an ontology for the effects of radiation on biota in terrestrial
and space environments.
download_json: http://purl.obolibrary.org/obo/rbo.json
download_obo: http://purl.obolibrary.org/obo/rbo.obo
download_owl: http://purl.obolibrary.org/obo/rbo.owl
example: '00000105'
homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO
license: CC BY 3.0
mappings:
bioportal: RBO
obofoundry: RBO
ols: rbo
ontobee: RBO
name: Radiation Biology Ontology
pattern: ^\d{8}$
preferred_prefix: RBO
repository: https://github.com/Radiobiology-Informatics-Consortium/RBO
uri_format: http://purl.obolibrary.org/obo/RBO_$1
version: '2022-04-16'
rcb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Collection of many cell lines derived from human and other various
animals, preserved by the RIKEN BioResource Research Center.
example: RCB0002
homepage: https://cell.brc.riken.jp/en/rcb
mappings:
cellosaurus: RCB
name: RIKEN Bioresource Center Cell Bank
pattern: ^RCB\d+$
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:
biocontext: rdf
fairsharing: FAIRsharing.p77ph9
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:
biocontext: rdfs
bioportal: RDFS
fairsharing: FAIRsharing.v9n3gk
name: RDF Schema
preferred_prefix: rdfs
uri_format: http://www.w3.org/2000/01/rdf-schema#$1
rdo:
description: Ontologies of diseases that integrates many types of data for Rattus
Norvegicus, Homo Sapiens, Mus Musculus and other organisms.
download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo
download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl
example: '9002859'
homepage: https://ratmine.mcw.edu/ontology/disease/
mappings:
bioportal: RDO
name: RGD Disease_Ontology
pattern: ^\d{7}$
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/$1
reactome:
description: The Reactome project is a collaboration to develop a curated resource
of core pathways and reactions in human biology.
example: R-BTA-418592
homepage: https://www.reactome.org/
mappings:
biocontext: REACT
cheminf: '000411'
go: Reactome
miriam: reactome
n2t: reactome
prefixcommons: reactome
uniprot: Reactome
wikidata: P3937
name: Reactome
pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$
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/$1
reaxys:
description: Reaxys is a web-based tool for the retrieval of chemistry information
and data from published literature, including journals and patents. The information
includes chemical compounds, chemical reactions, chemical properties, related
bibliographic data, substance data with synthesis planning information, as well
as experimental procedures from selected journals and patents. It is licensed
by Elsevier.
example: '1257009'
homepage: https://www.reaxys.com
mappings:
wikidata: P1579
name: Reaxys
pattern: ^\d+$
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:
biocontext: REBASE
fairsharing: FAIRsharing.9sb9qh
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: cthoyt
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=$1
refseq:
description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive,
integrated, non-redundant set of sequences, including genomic DNA, transcript
(RNA), and protein products.
example: NP_012345
has_canonical: ncbiprotein
homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/
mappings:
biocontext: RefSeq
fairsharing: FAIRsharing.4jg0qw
go: RefSeq
miriam: refseq
n2t: refseq
prefixcommons: refseq
uniprot: RefSeq
name: Reference Sequence Collection
pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$
preferred_prefix: refseq
synonyms:
- REFSEQ_PROT
uri_format: https://www.ncbi.nlm.nih.gov/protein/$1
reo:
comment: 'From James O.: It was an ontology for "reagents" developed by @Matthew
Brush. Since OBI was interested in reagents, Matt developed it in coordination
with OBI and had plans to submit it to OBO. I believe that REO was once included
in Ontobee, and OBI even started using some REO terms. But REO was never submitted
to OBO. I believe it was abandoned.'
contact:
email: matt@tislab.org
github: mbrush
name: Matthew Brush
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org)
to model the domain of biomedical research reagents, considered broadly to include
materials applied “chemically” in scientific techniques to facilitate generation
of data and research materials. ReO is a modular ontology that re-uses existing
ontologies to facilitate cross-domain interoperability. It consists of reagents
and their properties, linking diverse biological and experimental entities to
which they are related. ReO supports community use cases by providing a flexible,
extensible, and deeply integrated framework that can be adapted and extended with
more specific modeling to meet application needs.
download_owl: https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl
example: 0000079
homepage: https://github.com/tis-lab/reagent-ontology
mappings:
ontobee: REO
name: Reagent Ontology
pattern: ^\d{7}$
preferred_prefix: reo
references:
- https://github.com/obi-ontology/obi/issues/1015
- https://code.google.com/archive/p/reagent-ontology/
- https://github.com/obi-ontology/obi/issues/1135
repository: https://github.com/tis-lab/reagent-ontology
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
provides: uniprot
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/$1
reproduceme:
description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan
ontology to describe a complete path of a scientific experiment. It expresses
the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides
a set of classes and properties to represent a scientific experiment including
its computational and non-computational steps to track the provenance of results.
It describes a complete path of a scientific experiment considering the use-case
of biological imaging and microscopy experiments, computational experiments, including
Jupyter notebooks and scripts. It describes an experiment and its data, agents,
activities, plans, steps, variables, instruments, materials, and settings required
for its reproducibility.
download_owl: https://sheeba-samuel.github.io/REPRODUCE-ME/doc/reproduce-me.xml
example: MicrobeamManipulation
homepage: https://w3id.org/reproduceme/research
mappings:
bioportal: REPRODUCE-ME
ols: reproduceme
name: REPRODUCE-ME Ontology
preferred_prefix: reproduceme
version: '1.1'
resid:
banana: RESID
contact:
email: john.garavelli@ebi.ac.uk
github: null
name: John Garavelli
orcid: null
deprecated: true
description: The RESID Database of Protein Modifications is a comprehensive collection
of annotations and structures for protein modifications including amino-terminal,
carboxyl-terminal and peptide chain cross-link post-translational modifications.
example: AA0001
homepage: http://www.ebi.ac.uk/RESID/
mappings:
biocontext: RESID
go: RESID
miriam: resid
n2t: resid
obofoundry: RESID
prefixcommons: resid
name: Protein covalent bond
pattern: ^AA\d{4}$
preferred_prefix: RESID
uri_format: http://pir0.georgetown.edu/cgi-bin/resid?id=$1
reto:
description: Regulation of Transcription
download_obo: https://www.bio.ntnu.no/ontology/ReTO/reto.obo
download_owl: https://www.bio.ntnu.no/ontology/ReTO/reto.owl
homepage: http://www.semantic-systems-biology.org/apo
mappings:
bioportal: RETO
fairsharing: FAIRsharing.4qyf0f
ols: reto
name: Regulation of Transcription Ontology
no_own_terms: true
preferred_prefix: reto
version: '2019-09-17'
rex:
banana: REX
description: An ontology of physico-chemical processes, i.e. physico-chemical changes
occurring in course of time.
download_owl: http://purl.obolibrary.org/obo/rex.owl
example: '0000512'
homepage: https://www.ebi.ac.uk/chebi/
mappings:
biocontext: REX
bioportal: REX
fairsharing: FAIRsharing.g0a7s0
obofoundry: REX
ols: rex
ontobee: REX
prefixcommons: rex
name: Physico-chemical process
part_of: chebi
pattern: ^\d{7}$
preferred_prefix: REX
uri_format: http://purl.obolibrary.org/obo/REX_$1
version: '2017-11-19'
rexo:
description: Regulation of Gene Expression
download_obo: https://www.bio.ntnu.no/ontology/ReXO/rexo.obo
download_owl: https://www.bio.ntnu.no/ontology/ReXO/rexo.owl
homepage: http://www.semantic-systems-biology.org/apo
mappings:
bioportal: REXO
fairsharing: FAIRsharing.recas1
ols: rexo
name: Regulation of Gene Expression Ontology
no_own_terms: true
preferred_prefix: rexo
version: '2019-04-11'
rfam:
description: 'The Rfam database is a collection of RNA families, each represented
by multiple sequence alignments, consensus secondary structures and covariance
models (CMs). The families in Rfam break down into three broad functional classes:
non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs.
Typically these functional RNAs often have a conserved secondary structure which
may be better preserved than the RNA sequence. The CMs used to describe each family
are a slightly more complicated relative of the profile hidden Markov models (HMMs)
used by Pfam. CMs can simultaneously model RNA sequence and the structure in an
elegant and accurate fashion.'
example: RF00230
homepage: https://rfam.xfam.org/
mappings:
biocontext: RFAM
fairsharing: FAIRsharing.fex4c8
go: Rfam
miriam: rfam
n2t: rfam
ncbi: RFAM
name: Rfam database of RNA families
pattern: ^RF\d{5}$
preferred_prefix: rfam
uri_format: https://rfam.xfam.org/family/$1
rgd:
description: Rat Genome Database seeks to collect, consolidate, and integrate rat
genomic and genetic data with curated functional and physiological data and make
these data widely available to the scientific community. This collection references
genes.
example: '7499841'
homepage: http://rgd.mcw.edu/
mappings:
biocontext: RGD
bioportal: RGD
cellosaurus: RGD
fairsharing: FAIRsharing.pfg82t
go: RGD
miriam: rgd
n2t: rgd
ncbi: RGD
prefixcommons: rgd
uniprot: RGD
wikidata: P3853
name: Rat Genome Database
pattern: ^\d{4,}$
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=$1
rgd.qtl:
description: Rat Genome Database seeks to collect, consolidate, and integrate rat
genomic and genetic data with curated functional and physiological data and make
these data widely available to the scientific community. This collection references
quantitative trait loci (qTLs), providing phenotype and disease descriptions,
mapping, and strain information as well as links to markers and candidate genes.
example: '1354581'
homepage: http://rgd.mcw.edu/
mappings:
biocontext: RGD.QTL
miriam: rgd.qtl
n2t: rgd.qtl
name: Rat Genome Database qTL
pattern: ^\d+$
preferred_prefix: rgd.qtl
uri_format: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1
rgd.strain:
description: Rat Genome Database seeks to collect, consolidate, and integrate rat
genomic and genetic data with curated functional and physiological data and make
these data widely available to the scientific community. This collection references
strain reports, which include a description of strain origin, disease, phenotype,
genetics and immunology.
example: '5688061'
homepage: http://rgd.mcw.edu/
mappings:
biocontext: RGD.STRAIN
miriam: rgd.strain
n2t: rgd.strain
name: Rat Genome Database strain
pattern: ^\d+$
preferred_prefix: rgd.strain
uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1
rhea:
description: ' Rhea is an expert-curated knowledgebase of chemical and transport
reactions of biological interest. Enzyme-catalyzed and spontaneously occurring
reactions are curated from peer-reviewed literature and represented in a computationally
tractable manner by using the ChEBI (Chemical Entities of Biological Interest)
ontology to describe reaction participants.
Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as
many additional reactions and can be used for enzyme annotation, genome-scale
metabolic modeling and omics-related analyses. Rhea is the standard for enzyme
and transporter annotation in UniProtKB.'
example: '12345'
homepage: https://www.rhea-db.org/
mappings:
biocontext: RHEA
fairsharing: FAIRsharing.pn1sr5
go: RHEA
miriam: rhea
n2t: rhea
prefixcommons: rhea
name: Rhea, the Annotated Reactions Database
pattern: ^\d{5}$
preferred_prefix: rhea
synonyms:
- RHEA
uri_format: https://www.rhea-db.org/rhea/$1
ricegap:
description: The objective of this project is to provide high quality annotation
for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated
with functional annotation including expression data, gene ontologies, and tagged
lines.
example: LOC_Os02g13300
homepage: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml
mappings:
biocontext: RICEGAP
miriam: ricegap
n2t: ricegap
name: Rice Genome Annotation Project
pattern: ^LOC\_Os\d{1,2}g\d{5}$
preferred_prefix: ricegap
uri_format: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1
ricenetdb.compound:
description: 'RiceNetDB is currently the most comprehensive regulatory database
on Oryza Sativa based on genome annotation. It was displayed in three levels:
GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
mapping.'
example: OSC1416
homepage: http://bis.zju.edu.cn/ricenetdb
mappings:
biocontext: RICENETDB.COMPOUND
miriam: ricenetdb.compound
n2t: ricenetdb.compound
name: RiceNetDB Compound
pattern: ^OSC\d{4}$
preferred_prefix: ricenetdb.compound
uri_format: http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1
ricenetdb.gene:
description: 'RiceNetDB is currently the most comprehensive regulatory database
on Oryza Sativa based on genome annotation. It was displayed in three levels:
GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
mapping.'
example: LOC_Os01g49190.1
homepage: http://bis.zju.edu.cn/ricenetdb/
mappings:
biocontext: RICENETDB.GENE
miriam: ricenetdb.gene
n2t: ricenetdb.gene
name: RiceNetDB Gene
pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$
preferred_prefix: ricenetdb.gene
uri_format: http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1
ricenetdb.mirna:
description: 'RiceNetDB is currently the most comprehensive regulatory database
on Oryza Sativa based on genome annotation. It was displayed in three levels:
GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
mapping.'
example: osa-miR446
homepage: http://bis.zju.edu.cn/ricenetdb
mappings:
biocontext: RICENETDB.MIRNA
miriam: ricenetdb.mirna
n2t: ricenetdb.mirna
name: RiceNetDB miRNA
pattern: ^osa-miR\d{3,5}[a-z]{0,1}$
preferred_prefix: ricenetdb.mirna
uri_format: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1
ricenetdb.protein:
description: 'RiceNetDB is currently the most comprehensive regulatory database
on Oryza Sativa based on genome annotation. It was displayed in three levels:
GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
mapping.'
example: LOC_Os01g49190
homepage: http://bis.zju.edu.cn/ricenetdb/
mappings:
biocontext: RICENETDB.PROTEIN
miriam: ricenetdb.protein
n2t: ricenetdb.protein
name: RiceNetDB Protein
pattern: ^LOC\_Os\d{1,2}g\d{5}$
preferred_prefix: ricenetdb.protein
uri_format: http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1
ricenetdb.reaction:
description: 'RiceNetDB is currently the most comprehensive regulatory database
on Oryza Sativa based on genome annotation. It was displayed in three levels:
GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite
mapping.'
example: OSR0818
homepage: http://bis.zju.edu.cn/ricenetdb
mappings:
biocontext: RICENETDB.REACTION
miriam: ricenetdb.reaction
n2t: ricenetdb.reaction
name: RiceNetDB Reaction
pattern: ^OSR\d{4}$
preferred_prefix: ricenetdb.reaction
uri_format: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1
rnacentral:
description: RNAcentral is a public resource that offers integrated access to a
comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating
group of Expert Databases.
example: URS0000759CF4
homepage: https://rnacentral.org/
mappings:
biocontext: RNACENTRAL
fairsharing: FAIRsharing.KcCjL7
go: RNAcentral
miriam: rnacentral
n2t: rnacentral
ncbi: RNAcentral
name: RNAcentral
pattern: ^URS[0-9A-F]{10}(\_\d+)?$
preferred_prefix: rnacentral
synonyms:
- LNCRNADB
uri_format: https://rnacentral.org/rna/$1
rnamod:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A comprehensive listing of post-transcriptionally modified nucleosides
from RNA -
example: '051'
homepage: http://rna.rega.kuleuven.be/rnamods/
name: The RNA Modification Database
pattern: ^\d{3}$
preferred_prefix: rnamod
uri_format: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1
rnamods:
description: The RNA modification database provides a comprehensive listing of post-transcriptionally
modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides
of known structure, including those from established sequence positions, as well
as those detected or characterized from hydrolysates of RNA.
example: '101'
homepage: http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm
mappings:
biocontext: RNAMODS
go: RNAmods
miriam: rnamods
n2t: rnamods
prefixcommons: rnamods
name: RNA Modification Database
pattern: ^\d{3}$
preferred_prefix: rnamods
uri_format: http://mods.rna.albany.edu/mods/modifications/view/$1
rnao:
banana: RNAO
contact:
email: BatchelorC@rsc.org
github: null
name: Colin Batchelor
orcid: 0000-0001-5985-7429
description: Controlled vocabulary pertaining to RNA function and based on RNA sequences,
secondary and three-dimensional structures.
download_obo: http://purl.obolibrary.org/obo/rnao.obo
download_owl: http://purl.obolibrary.org/obo/rnao.owl
example: 0000128
homepage: https://github.com/bgsu-rna/rnao
license: CC0 1.0
mappings:
biocontext: RNAO
bioportal: RNAO
fairsharing: FAIRsharing.kqt2h2
obofoundry: RNAO
ols: rnao
ontobee: RNAO
prefixcommons: rnao
name: RNA ontology
pattern: ^\d{7}$
preferred_prefix: RNAO
repository: https://github.com/BGSU-RNA/rnao
uri_format: http://purl.obolibrary.org/obo/RNAO_$1
version: '2019-04-15'
ro:
appears_in:
- agro
- aism
- cdno
- cl
- clao
- clyh
- colao
- cteno
- ecao
- ecocore
- ecto
- envo
- foodon
- fovt
- genepio
- go
- hso
- lepao
- maxo
- ons
- ontoavida
- pcl
- pco
- plana
- planp
- poro
- psdo
- pso
- rbo
- upa
- xpo
- zp
banana: RO
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: The OBO Relation Ontology provides consistent and unambiguous formal
definitions of the relational expressions used in biomedical ontologies.
download_json: http://purl.obolibrary.org/obo/ro.json
download_obo: http://purl.obolibrary.org/obo/ro.obo
download_owl: http://purl.obolibrary.org/obo/ro.owl
example: '0002533'
homepage: https://oborel.github.io/
license: CC0 1.0
mappings:
biocontext: OBO_REL
biolink: RO
bioportal: OBOREL
fairsharing: FAIRsharing.1vrrdh
go: RO
miriam: ro
n2t: ro
obofoundry: RO
ols: ro
ontobee: RO
prefixcommons: ro
wikidata: P3590
name: Relation Ontology
pattern: ^\d{7}$
preferred_prefix: RO
repository: https://github.com/oborel/obo-relations
synonyms:
- RO_proposed_relation
- obo_rel
- oborel
uri_format: http://purl.obolibrary.org/obo/RO_$1
version: '2022-05-23'
rouge:
description: The Rouge protein database contains results from sequence analysis
of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.
example: mKIAA4200
homepage: http://www.kazusa.or.jp/rouge/
mappings:
biocontext: ROUGE
fairsharing: FAIRsharing.vdbagq
miriam: rouge
n2t: rouge
prefixcommons: rouge
uniprot: Rouge
name: Rodent Unidentified Gene-Encoded Large Proteins
pattern: ^m\w+$
preferred_prefix: rouge
uri_format: https://www.kazusa.or.jp/rouge/gfpage/$1
rrid:
banana: RRID
description: "The Research Resource Identification Initiative provides RRIDs to\
\ 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases\
\ / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\
\nThe initiative works with participating journals to intercept manuscripts in\
\ the publication process that use these resources, and allows publication authors\
\ to incorporate RRIDs within the methods sections. It also provides resolver\
\ services that access curated data from 10 data sources: the antibody registry\
\ (a curated catalog of antibodies), the SciCrunch registry (a curated catalog\
\ of software tools and databases), and model organism nomenclature authority\
\ databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These\
\ RRIDs are aggregated and can be searched through SciCrunch."
example: AB_262044
homepage: https://scicrunch.org/resolver
mappings:
biocontext: RRID
fairsharing: FAIRsharing.ATwSZG
miriam: rrid
n2t: rrid
name: Research Resource Identification
namespace_in_lui: true
pattern: ^[a-zA-Z]+.+$
preferred_prefix: rrid
uri_format: https://scicrunch.org/resolver/RRID:$1
rs:
banana: RS
contact:
email: sjwang@mcw.edu
github: shurjenw
name: Shur-Jen Wang
orcid: 0000-0001-5256-8683
description: Ontology of rat strains
download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo
download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl
example: 0001807
homepage: http://rgd.mcw.edu/rgdweb/search/strains.html
license: CC BY 4.0
mappings:
biocontext: RS
bioportal: RS
fairsharing: FAIRsharing.vajn3f
obofoundry: RS
ols: rs
ontobee: RS
prefixcommons: rs
name: Rat Strain Ontology
pattern: ^\d{7}$
preferred_prefix: RS
repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology
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/$1
rxno:
banana: RXNO
contact:
email: batchelorc@rsc.org
github: batchelorc
name: Colin Batchelor
orcid: 0000-0001-5985-7429
description: RXNO is the name reaction ontology. It contains more than 500 classes
representing organic reactions such as the Diels–Alder cyclization.
download_obo: https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo
download_owl: http://purl.obolibrary.org/obo/rxno.owl
example: '0000253'
homepage: https://github.com/rsc-ontologies/rxno
license: CC BY 4.0
mappings:
biocontext: RXNO
bioportal: RXNO
fairsharing: FAIRsharing.w4tncg
obofoundry: RXNO
ols: rxno
ontobee: RXNO
wikidata: P2106
name: Name Reaction Ontology
pattern: ^\d{7}$
preferred_prefix: RXNO
repository: https://github.com/rsc-ontologies/rxno
uri_format: http://purl.obolibrary.org/obo/RXNO_$1
version: '2021-12-16'
rxnorm:
description: RxNorm provides normalized names for clinical drugs and links its names
to many of the drug vocabularies commonly used in pharmacy management and drug
interaction software, including those of First Databank, Micromedex, and Gold
Standard Drug Database. By providing links between these vocabularies, RxNorm
can mediate messages between systems not using the same software and vocabulary.
example: '221058'
homepage: https://www.nlm.nih.gov/research/umls/rxnorm/
mappings:
biocontext: RXCUI
biolink: RXCUI
bioportal: RXNORM
fairsharing: FAIRsharing.36pf8q
wikidata: P3345
name: RxNorm
pattern: ^[0-9]{1,7}$
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=$1
sabiork.ec:
description: SABIO-RK is a relational database system that contains information
about biochemical reactions, their kinetic equations with their parameters, and
the experimental conditions under which these parameters were measured. The EC
record provides for a given enzyme classification (EC) the associated list of
enzyme-catalysed reactions and their corresponding kinetic data.
example: 2.7.1.1
homepage: http://sabiork.h-its.org/
mappings:
biocontext: SABIORK.EC
miriam: sabiork.ec
n2t: sabiork.ec
prefixcommons: sabiork.ec
name: SABIO-RK EC Record
pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$
preferred_prefix: sabiork.ec
provides: eccode
uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1
sabiork.kineticrecord:
description: SABIO-RK is a relational database system that contains information
about biochemical reactions, their kinetic equations with their parameters, and
the experimental conditions under which these parameters were measured. The kinetic
record data set provides information regarding the kinetic law, measurement conditions,
parameter details and other reference information.
example: '5046'
homepage: http://sabiork.h-its.org/
mappings:
biocontext: SABIORK.KINETICRECORD
go: SABIO-RK
miriam: sabiork.kineticrecord
n2t: sabiork.kineticrecord
name: SABIO Reaction Kinetics
pattern: ^\d+$
preferred_prefix: sabiork.kineticrecord
uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1
sabiork.reaction:
description: SABIO-RK is a relational database system that contains information
about biochemical reactions, their kinetic equations with their parameters, and
the experimental conditions under which these parameters were measured. The reaction
data set provides information regarding the organism in which a reaction is observed,
pathways in which it participates, and links to further information.
example: '75'
homepage: http://sabiork.h-its.org/
mappings:
biocontext: SABIORK.REACTION
fairsharing: FAIRsharing.cwx04e
miriam: sabiork.reaction
n2t: sabiork.reaction
prefixcommons: sabiork.reaction
uniprot: SABIO-RK
name: SABIO-RK Reaction
pattern: ^\d+$
preferred_prefix: sabiork.reaction
synonyms:
- SABIO-RK
uri_format: http://sabiork.h-its.org/reacdetails.jsp?reactid=$1
sael:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
name: Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List
preferred_prefix: sael
references:
- https://pubmed.ncbi.nlm.nih.gov/18629134/
salk:
appears_in:
- efo
comment: spider stuff!
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Scientific research institute for neuroscience, genetics, immunology,
plant biology and more.
example: '037727'
homepage: https://www.salk.edu/
name: Salk Institute for Biological Studies
pattern: ^\d{6}$
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:
biocontext: SAO
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_$1
sasbdb:
description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository
for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and
derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural
information on biological macromolecules in solution at a resolution of 1-2 nm.
SASBDB provides freely accessible and downloadable experimental data, which are
deposited together with the relevant experimental conditions, sample details,
derived models and their fits to the data.
example: SASDAX8
homepage: http://www.sasbdb.org/
mappings:
biocontext: SASBDB
fairsharing: FAIRsharing.i1F3Hb
miriam: sasbdb
n2t: sasbdb
uniprot: SASBDB
name: Small Angle Scattering Biological Data Bank
pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$
preferred_prefix: sasbdb
uri_format: http://www.sasbdb.org/data/$1
sbo:
appears_in:
- scdo
banana: SBO
contact:
email: sheriff@ebi.ac.uk
github: rsmsheriff
name: Rahuman Sheriff
orcid: 0000-0003-0705-9809
description: The goal of the Systems Biology Ontology is to develop controlled vocabularies
and ontologies tailored specifically for the kinds of problems being faced in
Systems Biology, especially in the context of computational modeling. SBO is a
project of the BioModels.net effort.
download_owl: http://purl.obolibrary.org/obo/sbo.owl
example: 0000485
homepage: http://www.ebi.ac.uk/sbo/
license: Artistic License 2.0
mappings:
biocontext: SBO
bioportal: SBO
fairsharing: FAIRsharing.s19src
miriam: sbo
n2t: sbo
obofoundry: SBO
ols: sbo
ontobee: SBO
prefixcommons: sbo
name: Systems Biology Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: SBO
repository: https://github.com/EBI-BioModels/SBO
uri_format: https://www.ebi.ac.uk/sbo/main/SBO:$1
version: '2021-08-28'
scdo:
banana: SCDO
contact:
email: giant.plankton@gmail.com
github: JadeHotchkiss
name: Jade Hotchkiss
orcid: 0000-0002-2193-0704
depends_on:
- apollosv
- aro
- chebi
- chmo
- cmo
- doid
- dron
- duo
- envo
- eupath
- exo
- gaz
- gsso
- hp
- hsapdv
- ico
- ido
- idomal
- mp
- nbo
- ncit
- obi
- ogms
- opmi
- pr
- sbo
- stato
- symp
- uo
- vo
- vt
description: An ontology for the standardization of terminology and integration
of knowledge about Sickle Cell Disease.
download_obo: http://purl.obolibrary.org/obo/scdo.obo
download_owl: http://purl.obolibrary.org/obo/scdo.owl
example: 0000728
homepage: https://scdontology.h3abionet.org/
license: GPL-3.0
mappings:
bioportal: SCDO
fairsharing: FAIRsharing.kkq6pw
obofoundry: SCDO
ols: scdo
ontobee: SCDO
name: Sickle Cell Disease Ontology
pattern: ^\d{7}$
preferred_prefix: SCDO
repository: https://github.com/scdodev/scdo-ontology
uri_format: http://purl.obolibrary.org/obo/SCDO_$1
version: '2021-04-15'
schem:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Selventa legacy chemical namespace used with the Biological Expression
Language
example: A0001
homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets
name: Selventa Chemicals
pattern: ^A\d{4}$
preferred_prefix: schem
scholia.resource:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A frontend to Wikidata
example: doi
homepage: https://scholia.toolforge.org/
name: Scholia Registry
preferred_prefix: scholia.resource
uri_format: https://bioregistry.io/metaregistry/scholia/$1
scomp:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Selventa legacy complex namespace used with the Biological Expression
Language
example: C0001
homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets
name: Selventa Complexes
pattern: ^C\d{4}$
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:
biocontext: SCOP
fairsharing: FAIRsharing.wjzty
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=$1
scopus:
description: "Scopus is the largest abstract and citation database of peer-reviewed\
\ literature: scientific journals, books and conference proceedings. \nDelivering\
\ a comprehensive overview of the world's research output in the fields of science,\
\ technology, medicine, social sciences, and arts \nand humanities, Scopus features\
\ smart tools to track, analyze and visualize research."
example: '56305849200'
homepage: https://www.scopus.com
mappings:
biolink: ScopusID
fairsharing: FAIRsharing.0a674c
name: Scopus Researcher
pattern: ^\d+$
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:
biocontext: SCRETF
miriam: scretf
n2t: scretf
name: ScerTF
pattern: ^\w+$
preferred_prefix: scretf
uri_format: http://stormo.wustl.edu/ScerTF/details/$1
sdbs:
description: The Spectral Database for Organic Compounds (SDBS) is an integrated
spectral database system for organic compounds. It provides access to 6 different
types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier
transform infrared spectrum (FT-IR), and NMR spectra.
example: '4544'
homepage: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi
mappings:
biocontext: SDBS
miriam: sdbs
n2t: sdbs
name: Spectral Database for Organic Compounds
pattern: ^\d+$
preferred_prefix: sdbs
uri_format: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1
sdgio:
description: An OBO-compliant ontology representing the entities referenced by the
SDGs, their targets, and indicators.
download_owl: https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl
example: '00020134'
homepage: https://github.com/SDG-InterfaceOntology/sdgio
mappings:
fairsharing: FAIRsharing.d5ff6e
ols: sdgio
ontobee: SDGIO
name: Sustainable Development Goals Interface Ontology
pattern: ^\d{8}$
preferred_prefix: sdgio
references:
- https://github.com/SDG-InterfaceOntology/sdgio/issues/233
repository: https://github.com/SDG-InterfaceOntology/sdgio
version: '2018-08-10'
sdis:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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 Diseases
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:$1
seed:
description: This cooperative effort, which includes Fellowship for Interpretation
of Genomes (FIG), Argonne National Laboratory, and the University of Chicago,
focuses on the development of the comparative genomics environment called the
SEED. It is a framework to support comparative analysis and annotation of genomes,
and the development of curated genomic data (annotation). Curation is performed
at the level of subsystems by an expert annotator, across many genomes, and not
on a gene by gene basis. This collection references subsystems.
example: Biotin_biosynthesis
homepage: http://seed-viewer.theseed.org/seedviewer.cgi
mappings:
biocontext: SEED
go: SEED
miriam: seed
n2t: seed
ncbi: SEED
name: The SEED;
pattern: ^\w+$
preferred_prefix: seed
uri_format: http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1
seed.compound:
description: This cooperative effort, which includes Fellowship for Interpretation
of Genomes (FIG), Argonne National Laboratory, and the University of Chicago,
focuses on the development of the comparative genomics environment called the
SEED. It is a framework to support comparative analysis and annotation of genomes,
and the development of curated genomic data (annotation). Curation is performed
at the level of subsystems by an expert annotator, across many genomes, and not
on a gene by gene basis. This collection references subsystems.
example: cpd15380
homepage: http://modelseed.org/
mappings:
biocontext: SEED.COMPOUND
miriam: seed.compound
n2t: seed.compound
name: SEED Compound
pattern: ^cpd\d+$
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/$1
sep:
banana: SEP
contact:
email: psidev-gps-dev@lists.sourceforge.net
github: null
name: SEP developers via the PSI and MSI mailing lists
orcid: null
deprecated: true
description: A structured controlled vocabulary for the annotation of sample processing
and separation techniques in scientific experiments.
download_obo: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo
download_owl: http://purl.obolibrary.org/obo/sep.owl
example: '00073'
homepage: https://psidev.info/sepcv
mappings:
biocontext: SEP
bioportal: SEP
obofoundry: SEP
ontobee: SEP
prefixcommons: sep
name: Sample processing and separation techniques
pattern: ^\d{5}$
preferred_prefix: SEP
uri_format: http://purl.obolibrary.org/obo/SEP_$1
sepio:
banana: SEPIO
contact:
email: mhb120@gmail.com
github: mbrush
name: Matthew Brush
orcid: 0000-0002-1048-5019
description: An ontology for representing the provenance of scientific claims and
the evidence that supports them.
download_owl: http://purl.obolibrary.org/obo/sepio.owl
example: 0000048
homepage: https://github.com/monarch-initiative/SEPIO-ontology
license: CC BY 3.0
mappings:
biocontext: SEPIO
bioportal: SEPIO
obofoundry: SEPIO
ols: sepio
ontobee: SEPIO
name: Scientific Evidence and Provenance Information Ontology
pattern: ^\d{7}$
preferred_prefix: SEPIO
repository: https://github.com/monarch-initiative/SEPIO-ontology
uri_format: http://purl.obolibrary.org/obo/SEPIO_$1
version: $Revision$
sfam:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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:
biocontext: SGD
fairsharing: FAIRsharing.pzvw40
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/$1
sgd.pathways:
description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces
genome database (SGD).
example: PWY3O-214
homepage: http://pathway.yeastgenome.org/
mappings:
biocontext: SGD.PATHWAYS
miriam: sgd.pathways
n2t: sgd.pathways
prefixcommons: sgd.pathways
name: Saccharomyces genome database pathways
pattern: ^PWY\w{2}\-\d{3}$
preferred_prefix: sgd.pathways
uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1
sgn:
description: The Sol Genomics Network (SGN) is a database and website dedicated
to the genomic information of the nightshade family, which includes species such
as tomato, potato, pepper, petunia and eggplant.
example: '0001'
homepage: http://solgenomics.net/
mappings:
biocontext: SGN
fairsharing: FAIRsharing.3zqvaf
go: SGN
miriam: sgn
n2t: sgn
ncbi: SGN
prefixcommons: sgn
name: Sol Genomics Network
pattern: ^\d+$
preferred_prefix: sgn
uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1
sheepqtldb:
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
designed to house publicly all available QTL and single-nucleotide polymorphism/gene
association data on livestock animal species. This collection references sheep
QTLs.
example: '19803'
homepage: https://www.animalgenome.org/QTLdb
mappings:
biocontext: SHEEPQTLDB
miriam: sheepqtldb
n2t: sheepqtldb
prefixcommons: sheepqtldb
name: Animal Genome Sheep QTL
part_of: qtldb
pattern: ^\d+$
preferred_prefix: sheepqtldb
uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
sibo:
banana: SIBO
contact:
email: cjmungall@lbl.gov
github: null
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: Social Behavior in insects
download_obo: http://purl.obolibrary.org/obo/sibo.obo
download_owl: http://purl.obolibrary.org/obo/sibo.owl
example: 0000509
homepage: https://github.com/obophenotype/sibo
license: CC BY 3.0
mappings:
biocontext: SIBO
bioportal: SIBO
fairsharing: FAIRsharing.q09hck
obofoundry: SIBO
ols: sibo
ontobee: SIBO
name: Social Insect Behavior Ontology
pattern: ^\d{7}$
preferred_prefix: SIBO
repository: https://github.com/obophenotype/sibo
uri_format: http://purl.obolibrary.org/obo/SIBO_$1
version: '2015-06-15'
sider.drug:
description: SIDER (Side Effect Resource) is a public, computer-readable side effect
resource that connects drugs to side effect terms. It aggregates dispersed public
information on side effects. This collection references drugs in SIDER.
example: '2244'
homepage: http://sideeffects.embl.de/
mappings:
biocontext: SIDER.DRUG
miriam: sider.drug
n2t: sider.drug
name: SIDER Drug
pattern: ^\d+$
preferred_prefix: sider.drug
uri_format: http://sideeffects.embl.de/drugs/$1
sider.effect:
description: SIDER (Side Effect Resource) is a public, computer-readable side effect
resource that connects drugs to side effect terms. It aggregates dispersed public
information on side effects. This collection references side effects of drugs
as referenced in SIDER.
example: C0017565
homepage: http://sideeffects.embl.de/
mappings:
biocontext: SIDER.EFFECT
miriam: sider.effect
n2t: sider.effect
name: SIDER Side Effect
pattern: ^C\d+$
preferred_prefix: sider.effect
provides: umls
uri_format: http://sideeffects.embl.de/se/$1
sigmaaldirch:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/$1
signaling-gateway:
description: The Signaling Gateway provides information on mammalian proteins
involved in cellular signaling.
example: A001094
homepage: http://www.signaling-gateway.org/molecule
mappings:
biocontext: SIGNALING-GATEWAY
miriam: signaling-gateway
n2t: signaling-gateway
prefixcommons: signaling-gateway
name: Signaling Gateway
pattern: ^A\d{6}$
preferred_prefix: signaling-gateway
uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1
signor:
description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in
a structured format signaling information published in the scientific literature.
example: SIGNOR-C41
homepage: https://signor.uniroma2.it/
mappings:
fairsharing: FAIRsharing.ss78t4
miriam: signor
uniprot: SIGNOR
name: Signaling Network Open Resource
pattern: ^SIGNOR\-[A-Z]+\d+$
preferred_prefix: signor
synonyms:
- SIGNOR
uri_format: https://signor.uniroma2.it/relation_result.php?id=$1
signor.relation:
comment: Currently, you can put a SIGNOR relation ID into the main page search box
and it will resolve, but there is not currently a way to resolve them via a URL
pattern
contributor:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
description: Identifiers for relationships between proteins and complexes, along
with their type and provenance
example: SIGNOR-252737
homepage: https://signor.uniroma2.it
name: SIGNOR Relation
part_of: signor
pattern: ^SIGNOR-\d+$
preferred_prefix: signor.relation
reviewer:
email: cthoyt@gmail.com
github: cthoyt
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.
download_owl: http://semanticscience.org/ontology/sio/v1.53/sio-release.owl
example: 000912
homepage: https://github.com/micheldumontier/semanticscience
mappings:
biocontext: SIO
biolink: SIO
bioportal: SIO
fairsharing: FAIRsharing.dpkb5f
miriam: sio
ols: sio
ontobee: SIO
name: Semanticscience Integrated Ontology
pattern: ^\d{6}$
preferred_prefix: sio
repository: https://github.com/micheldumontier/semanticscience
uri_format: https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1
version: '1.53'
sisu:
description: The Sequencing Initiative Suomi (SISu) project is an international
collaboration to harmonize and aggregate whole genome and exome sequence data
from Finnish samples, providing data for researchers and clinicians. The SISu
project allows for the search of variants to determine their attributes and occurrence
in Finnish cohorts, and provides summary data on single nucleotide variants and
indels from exomes, sequenced in disease-specific and population genetic studies.
example: 17:41223048
homepage: http://www.sisuproject.fi/
mappings:
biocontext: SISU
fairsharing: FAIRsharing.t1a232
miriam: sisu
n2t: sisu
name: Sequencing Initiative Suomi
pattern: ^[0-9]+:[0-9]+$
preferred_prefix: sisu
uri_format: http://search.sisuproject.fi/#/variant/$1
sitex:
description: SitEx is a database containing information on eukaryotic protein functional
sites. It stores the amino acid sequence positions in the functional site, in
relation to the exon structure of encoding gene This can be used to detect the
exons involved in shuffling in protein evolution, or to design protein-engineering
experiments.
example: '1000'
homepage: http://www-bionet.sscc.ru/sitex/
mappings:
biocontext: SITEX
fairsharing: FAIRsharing.5mr9c5
miriam: sitex
n2t: sitex
prefixcommons: sitex
name: SitEx
pattern: ^\d+$
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:
biocontext: skos
name: Simple Knowledge Organization System
preferred_prefix: skos
uri_format: http://www.w3.org/2004/02/skos/core#$1
slkbase:
description: Cell line databases/resources
example: '3618'
homepage: https://sumlineknowledgebase.com/
mappings:
cellosaurus: SLKBase
name: SUM Breast Cancer Cell Line Knowledge Base
pattern: ^\d+$
preferred_prefix: slkbase
uri_format: https://sumlineknowledgebase.com/?page_id=$1
smart:
description: The Simple Modular Architecture Research Tool (SMART) is an online
tool for the identification and annotation of protein domains, and the analysis
of domain architectures.
example: SM00015
homepage: http://smart.embl-heidelberg.de/
mappings:
biocontext: SMART
fairsharing: FAIRsharing.hsbpq3
go: SMART
miriam: smart
n2t: smart
prefixcommons: smart
uniprot: SMART
name: Simple Modular Architecture Research Tool
pattern: ^SM\d{5}$
preferred_prefix: smart
uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1
smid:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'SMIDs (Small Molecule Identifiers) represent gene-style identifiers
for small molecules newly identified in C. elegans and other nematodes. SMIDs
aim to make life easier for describing biogenic small molecules in metabolomic
and genomic applications. '
example: '137'
homepage: https://smid-db.org/
name: C. elegans Small Molecule Identifier Database
pattern: ^\d+$
preferred_prefix: smid
synonyms:
- SMID-DB
uri_format: https://smid-db.org/smid/$1
smiles:
description: Documentation of SMILES (Simplified Molecular Input Line Entry System),
a line notation (a typographical method using printable characters) for entering
and representing molecules and reactions.
example: COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1
homepage: https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
mappings:
fairsharing: FAIRsharing.qv4b3c
wikidata: P233
name: Simplified molecular-input line-entry system
preferred_prefix: smiles
smpdb:
description: The Small Molecule Pathway Database (SMPDB) contains small molecule
pathways found in humans, which are presented visually. All SMPDB pathways include
information on the relevant organs, subcellular compartments, protein cofactors,
protein locations, metabolite locations, chemical structures and protein quaternary
structures. Accompanying data includes detailed descriptions and references, providing
an overview of the pathway, condition or processes depicted in each diagram.
example: SMP0000219
homepage: https://smpdb.ca/
mappings:
biocontext: SMPDB
biolink: PathWhiz
fairsharing: FAIRsharing.y1zyaq
miriam: smpdb
n2t: smpdb
prefixcommons: smpdb
name: Small Molecule Pathway Database
pattern: ^SMP\d+$
preferred_prefix: smpdb
synonyms:
- SMP
uri_format: https://smpdb.ca/view/$1
snap:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
mappings:
prefixcommons: snap
name: Snapshot
preferred_prefix: snap
uri_format: http://snap.humgen.au.dk/views/geneview.cgi?gene=$1
snomedct:
description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms),
is a systematically organized computer processable collection of medical terminology
covering most areas of clinical information such as diseases, findings, procedures,
microorganisms, pharmaceuticals, etc.
download_owl: http://snomed.info/sct/900000000000207008/version/20200131
example: '284196006'
homepage: http://www.snomedbrowser.com/
mappings:
biocontext: SNOMED
biolink: SNOMEDCT
bioportal: SNOMEDCT
fairsharing: FAIRsharing.d88s6e
miriam: snomedct
n2t: snomedct
ols: snomed
prefixcommons: snomedct
wikidata: P5806
name: SNOMED CT (International Edition)
pattern: ^(\w+)?\d+$
preferred_prefix: snomedct
synonyms:
- SCTID
- SCTID_2010_1_31
- SNOMECT
- SNOMED
- SNOMEDCT
- SNOMEDCTCT
- SNOMEDCTCT_2018_03_01
- SNOMEDCTCT_2019_03_01
- SNOMEDCT_2005_07_31
- SNOMEDCT_2010_1_31
- SNOMEDCT_2020_03_01
- SNOMEDCT_US
- SNOMEDCT_US_2015_03_01
- SNOMEDCT_US_2016_03_01
- 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
- SNOMEDCT_US_2021_03_01
- SNOMEDCT_US_2021_07_31
- SNOMEDCT_US_2021_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/$1
version: '2020-01-31'
snornabase:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'A comprehensive database of
human H/ACA and C/D box snoRNAs.'
example: SR0000178
homepage: https://www-snorna.biotoul.fr/
name: snoRNABase
preferred_prefix: snornabase
snp2tfbs:
description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect
transcription factor binding (TFB) in the Human genome.
example: rs11603840
homepage: https://ccg.epfl.ch/snp2tfbs/
mappings:
miriam: snp2tfbs
name: SNP to Transcription Factor Binding Sites
pattern: ^rs[0-9]+$
preferred_prefix: snp2tfbs
provides: dbsnp
uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1
so:
appears_in:
- pcl
banana: SO
contact:
email: keilbeck@genetics.utah.edu
github: keilbeck
name: Karen Eilbeck
orcid: 0000-0002-0831-6427
description: The Sequence Ontology (SO) is a structured controlled vocabulary for
the parts of a genomic annotation. It provides a common set of terms and definitions
to facilitate the exchange, analysis and management of genomic data.
download_obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo
download_owl: http://purl.obolibrary.org/obo/so.owl
example: '0001157'
homepage: http://www.sequenceontology.org/
license: CC BY 4.0
mappings:
biocontext: SO
bioportal: SO
fairsharing: FAIRsharing.6bc7h9
go: SO
miriam: so
n2t: so
obofoundry: SO
ols: so
ontobee: SO
prefixcommons: so
name: Sequence types and features ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: SO
repository: https://github.com/The-Sequence-Ontology/SO-Ontologies
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:
biocontext: SOPHARM
bioportal: SOPHARM
obofoundry: SOPHARM
name: Suggested Ontology for Pharmacogenomics
preferred_prefix: SOPHARM
uri_format: http://purl.obolibrary.org/obo/SOPHARM_$1
soybase:
description: SoyBase is a repository for curated genetics, genomics and related
data resources for soybean.
example: BARC-013845-01256
homepage: http://soybase.org/
mappings:
biocontext: SOYBASE
fairsharing: FAIRsharing.z4agsr
miriam: soybase
n2t: soybase
ncbi: SoyBase
name: Glycine max Genome Database
pattern: ^\w+(\-)?\w+(\-)?\w+$
preferred_prefix: soybase
uri_format: http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1
span:
comment: see also snap. This ontology only exists in description in the paper and
does not have an associated web resource
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Theoretical explanation of to a purely spatiotemporal ontology of change
and process, as part of a modular ontology of the dynamic features of reality.
homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf
name: Span
preferred_prefix: span
spd:
banana: SPD
contact:
email: ramirez@macn.gov.ar
github: martinjramirez
name: Martin Ramirez
orcid: 0000-0002-0358-0130
description: An ontology for spider comparative biology including anatomical parts
(e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk,
web, borrow).
download_owl: http://purl.obolibrary.org/obo/spd.owl
example: '0000001'
homepage: http://research.amnh.org/atol/files/
license: CC BY 3.0
mappings:
biocontext: SPD
bioportal: SPD
fairsharing: FAIRsharing.yecp83
obofoundry: SPD
ols: spd
ontobee: SPD
prefixcommons: spd
wikidata: P4537
name: Spider Ontology
pattern: ^\d{7}$
preferred_prefix: SPD
repository: https://github.com/obophenotype/spider-ontology
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/$1
spike.map:
description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository
that can store, organise and allow retrieval of pathway information in a way that
will be useful for the research community. The database currently focuses primarily
on pathways describing DNA damage response, cell cycle, programmed cell death
and hearing related pathways. Pathways are regularly updated, and additional pathways
are gradually added. The complete database and the individual maps are freely
exportable in several formats. This collection references pathway maps.
example: spike00001
homepage: http://www.cs.tau.ac.il/~spike/
mappings:
biocontext: SPIKE.MAP
miriam: spike.map
n2t: spike.map
name: SPIKE Map
pattern: ^spike\d{5}$
preferred_prefix: spike.map
uri_format: http://www.cs.tau.ac.il/~spike/maps/$1.html
splash:
description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier
for spectra, and is independent of how the spectra were acquired or processed.
It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared
spectroscopy, ultraviolet and nuclear magnetic resonance.
example: splash10-0zq2000000-77302b0326a418630a84
homepage: http://mona.fiehnlab.ucdavis.edu/
mappings:
biocontext: SPLASH
miriam: splash
n2t: splash
name: Spectra Hash Code
pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$
preferred_prefix: splash
uri_format: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1
spp:
description: The Signaling Pathways Project is an integrated 'omics knowledgebase
based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets
involving genetic and small molecule manipulations of cellular receptors, enzymes
and transcription factors. Our goal is to create a resource where scientists can
routinely generate research hypotheses or validate bench data relevant to cellular
signaling pathways.
example: 10.1621/vwN2g2HaX3
homepage: https://www.signalingpathways.org/index.jsf
mappings:
fairsharing: FAIRsharing.WxI96O
miriam: spp
name: Signaling Pathways Project
pattern: ^10.\w{4}/\w{10}$
preferred_prefix: spp
uri_format: https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1
sprint:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database.
PRINTS-S is the relational cousin of the PRINTS data bank of protein family fingerprints.
example: PR00001
homepage: http://130.88.97.239/dbbrowser/sprint/
mappings:
prefixcommons: sprint
name: Search PRINTS-S
pattern: ^PR\d{5}$
preferred_prefix: sprint
uri_format: 130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1
srao:
description: The FAIRsharing Subject Ontology (SRAO) is an application ontology
for the categorization of research disciplines across all research domains, from
the humanities to the natural sciences. It utilizes multiple external vocabularies.
download_owl: https://raw.githubusercontent.com/FAIRsharing/subject-ontology/master/releases/SRAO.owl
example: '0000400'
homepage: https://github.com/FAIRsharing/subject-ontology
mappings:
fairsharing: FAIRsharing.b1xD9f
ols: srao
name: FAIRsharing Subject Ontology
pattern: ^\d{7}$
preferred_prefix: srao
repository: https://github.com/FAIRsharing/subject-ontology
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
pattern: ^\d+$
preferred_prefix: ssbd.dataset
uri_format: https://ssbd.riken.jp/database/dataset/$1
ssbd.project:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Systems Science of Biological Dynamics database (SSBD:database) is
an added-value database for biological dynamics. It provides a rich set of open
resources for analyzing quantitative data and microscopy images of biological
objects, such as single-molecule, cell, tissue, individual, etc., and software
tools for analysis. Quantitative biological data and microscopy images are collected
from a variety of species, sources, and methods. These include data obtained from
both experiments and computational simulations.
example: '1'
homepage: https://ssbd.riken.jp
name: System Science of Biological Dynamics project
pattern: ^\d+$
preferred_prefix: ssbd.project
uri_format: https://ssbd.riken.jp/database/project/$1
stap:
description: STAP (Statistical Torsional Angles Potentials) was developed since,
according to several studies, some nuclear magnetic resonance (NMR) structures
are of lower quality, are less reliable and less suitable for structural analysis
than high-resolution X-ray crystallographic structures. The refined NMR solution
structures (statistical torsion angle potentials; STAP) in the database are refined
from the Protein Data Bank (PDB).
example: 1a24
homepage: http://psb.kobic.re.kr/STAP/refinement/
mappings:
biocontext: STAP
fairsharing: FAIRsharing.ja9cdq
miriam: stap
n2t: stap
name: Statistical Torsional Angles Potentials
pattern: ^[0-9][A-Za-z0-9]{3}$
preferred_prefix: stap
uri_format: http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1
stato:
appears_in:
- ontoavida
- psdo
- scdo
banana: STATO
contact:
email: alejandra.gonzalez.beltran@gmail.com
github: agbeltran
name: Alejandra Gonzalez-Beltran
orcid: 0000-0003-3499-8262
description: STATO is the statistical methods ontology. It contains concepts and
properties related to statistical methods, probability distributions and other
concepts related to statistical analysis, including relationships to study designs
and plots.
download_owl: http://purl.obolibrary.org/obo/stato.owl
example: 0000288
homepage: http://stato-ontology.org/
license: CC BY 3.0
mappings:
biocontext: STATO
bioportal: STATO
fairsharing: FAIRsharing.na5xp
obofoundry: STATO
ols: stato
ontobee: STATO
name: The Statistical Methods Ontology
pattern: ^\d{7}$
preferred_prefix: STATO
repository: https://github.com/ISA-tools/stato
uri_format: http://purl.obolibrary.org/obo/STATO_$1
version: '1.4'
stitch:
description: STITCH is a resource to explore known and predicted interactions of
chemicals and proteins. Chemicals are linked to other chemicals and proteins by
evidence derived from experiments, databases and the literature.
example: BQJCRHHNABKAKU
homepage: http://stitch.embl.de/
mappings:
biocontext: STITCH
fairsharing: FAIRsharing.zhwa8x
miriam: stitch
n2t: stitch
prefixcommons: stitch
name: Search Tool for Interactions of Chemicals
pattern: ^\w{14}$
preferred_prefix: stitch
uri_format: http://stitch.embl.de/interactions/$1
storedb:
banana: STOREDB
description: STOREDB database is a repository for data used by the international
radiobiology community, archiving and sharing primary data outputs from research
on low dose radiation. It also provides a directory of bioresources and databases
for radiobiology projects containing information and materials that investigators
are willing to share. STORE supports the creation of a low dose radiation research
commons.
example: STUDY1040
homepage: https://www.storedb.org/
mappings:
biocontext: STOREDB
fairsharing: FAIRsharing.6h8d2r
miriam: storedb
n2t: storedb
name: Store DB
pattern: ^(STUDY|FILE|DATASET)\d+$
preferred_prefix: storedb
uri_format: https://www.storedb.org/?$1
string:
description: "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is\
\ a database of known and predicted protein interactions.\r\nThe interactions\
\ include direct (physical) and indirect (functional) associations; they are derived\
\ from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression,\
\ Previous Knowledge. STRING quantitatively integrates interaction data from these\
\ sources for a large number of organisms, and transfers information between these\
\ organisms where applicable."
example: P53350
homepage: http://string.embl.de/
mappings:
biocontext: STRING
fairsharing: FAIRsharing.9b7wvk
miriam: string
n2t: string
prefixcommons: string
uniprot: STRING
name: Search Tool for Retrieval of Interacting Genes/Proteins
pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$
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
provides: uniprot
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/$1
subtilist:
description: "SubtiList serves to collate and integrate various aspects of the genomic\
\ information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\
\nSubtiList provides a complete dataset of DNA and protein sequences derived from\
\ the paradigm strain B. subtilis 168, linked to the relevant annotations and\
\ functional assignments."
example: BG11523
homepage: http://genolist.pasteur.fr/SubtiList/
mappings:
biocontext: SUBTILIST
fairsharing: FAIRsharing.40j2vd
miriam: subtilist
n2t: subtilist
ncbi: SubtiList
prefixcommons: subtilist
name: Bacillus subtilis genome sequencing project
pattern: ^BG\d+$
preferred_prefix: subtilist
uri_format: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1
subtiwiki:
description: "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis.\
\ It provides comprehensive information on all genes and their proteins and RNA\
\ products, as well as information related to the current investigation of the\
\ gene/protein. \r\nNote: Currently, direct access to RNA products is restricted.\
\ This is expected to be rectified soon."
example: BSU29180
homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page
mappings:
biocontext: SUBTIWIKI
fairsharing: FAIRsharing.2ck3st
miriam: subtiwiki
n2t: subtiwiki
prefixcommons: subtiwiki
name: SubtiWiki
pattern: ^BSU\d{5}$
preferred_prefix: subtiwiki
uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1
sugarbind:
description: The SugarBind Database captures knowledge of glycan binding of human
pathogen lectins and adhesins, where each glycan-protein binding pair is associated
with at least one published reference. It provides information on the pathogen
agent, the lectin/adhesin involved, and the human glycan ligand. This collection
provides information on ligands.
example: lectins/172
homepage: http://sugarbind.expasy.org/
mappings:
biocontext: SUGARBIND
fairsharing: FAIRsharing.d064y6
miriam: sugarbind
n2t: sugarbind
name: SugarBind
pattern: ^[A-Za-z]+\/[0-9]+$
preferred_prefix: sugarbind
uri_format: http://sugarbind.expasy.org/$1
supfam:
description: SUPERFAMILY provides structural, functional and evolutionary information
for proteins from all completely sequenced genomes, and large sequence collections
such as UniProt.
example: SSF57615
homepage: http://supfam.org/SUPERFAMILY/
mappings:
biocontext: SUPFAM
miriam: supfam
n2t: supfam
uniprot: SUPFAM
name: SUPERFAMILY
pattern: ^\w+$
preferred_prefix: supfam
uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1
sweetrealm:
description: The Semantic Web for Earth and Environmental Terminology is a mature
foundational ontology that contains over 6000 concepts organized in 200 ontologies
represented in OWL. Top level concepts include Representation (math, space, science,
time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.),
Phenomena (macro-scale ecological and physical), Processes (micro-scale physical,
biological, chemical, and mathematical), Human Activities (Decision, Commerce,
Jurisdiction, Environmental, Research).
download_obo: https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo
example: ANOVA
homepage: https://bioportal.bioontology.org/ontologies/SWEET
mappings:
bioportal: SWEET
name: Semantic Web for Earth and Environment Technology Ontology
preferred_prefix: sweetrealm
swh:
banana: swh
description: Software Heritage is the universal archive of software source code.
example: 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d
homepage: https://archive.softwareheritage.org
mappings:
biocontext: SWH
miriam: swh
n2t: swh
name: Software Heritage
namespace_in_lui: true
pattern: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$
preferred_prefix: swh
uri_format: https://archive.softwareheritage.org/browse/swh:$1
swiss-model:
description: The SWISS-MODEL Repository is a database of 3D protein structure models
generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein
sequences.
example: P23298
homepage: https://swissmodel.expasy.org
mappings:
biocontext: SWISS-MODEL
fairsharing: FAIRsharing.vxz9pn
miriam: swiss-model
n2t: swiss-model
prefixcommons: swissmodel
name: SWISS-MODEL Repository
pattern: ^\w+$
preferred_prefix: swiss-model
provides: uniprot
uri_format: https://swissmodel.expasy.org/repository/uniprot/$1
swisslipid:
banana: SLM
description: SwissLipids is a curated resource that provides information about known
lipids, including lipid structure, metabolism, interactions, and subcellular and
tissue localization. Information is curated from peer-reviewed literature and
referenced using established ontologies, and provided with full provenance and
evidence codes for curated assertions.
example: '000000341'
homepage: http://www.swisslipids.org/#/
mappings:
biocontext: SWISSLIPID
fairsharing: FAIRsharing.pxr7x2
miriam: slm
n2t: swisslipid
uniprot: SwissLipids
wikidata: P8691
name: SwissLipid
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: swisslipid
synonyms:
- slm
- swisslipids
uri_format: https://www.swisslipids.org/#/entity/SLM:$1
swissregulon:
description: A database of genome-wide annotations of regulatory sites. It contains
annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers
an intuitive interface showing genomic information in a graphical form.
example: AHR
homepage: http://swissregulon.unibas.ch
mappings:
biocontext: SWISSREGULON
fairsharing: FAIRsharing.7fnx38
miriam: swissregulon
n2t: swissregulon
name: SwissRegulon
pattern: ^[A-Za-z0-9]+$
preferred_prefix: swissregulon
uri_format: http://swissregulon.unibas.ch/query/$1
swo:
banana: SWO
contact:
email: allyson.lister@oerc.ox.ac.uk
github: allysonlister
name: Allyson Lister
orcid: 0000-0002-7702-4495
description: The Software Ontology (SWO) is a resource for describing software tools,
their types, tasks, versions, provenance and associated data. It contains detailed
information on licensing and formats as well as software applications themselves,
mainly (but not limited) to the bioinformatics community.
download_owl: https://github.com/allysonlister/swo/raw/master/release/swo.owl
example: '0000144'
homepage: https://github.com/allysonlister/swo
license: CC BY 4.0
mappings:
biocontext: SWO
bioportal: SWO
fairsharing: FAIRsharing.sp3szt
obofoundry: SWO
ols: swo
ontobee: SWO
prefixcommons: swo
name: Software ontology
pattern: ^\d{7}$
preferred_prefix: SWO
repository: https://github.com/allysonlister/swo
uri_format: http://purl.obolibrary.org/obo/SWO_$1
version: '1.7'
symp:
appears_in:
- scdo
banana: SYMP
contact:
email: lynn.schriml@gmail.com
github: lschriml
name: Lynn Schriml
orcid: 0000-0001-8910-9851
description: The Symptom Ontology has been developed as a standardized ontology
for symptoms of human diseases.
download_obo: http://purl.obolibrary.org/obo/symp.obo
download_owl: http://purl.obolibrary.org/obo/symp.owl
example: 0019171
homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page
license: CC0 1.0
mappings:
biocontext: SYMP
bioportal: SYMP
fairsharing: FAIRsharing.ay74mj
obofoundry: SYMP
ols: symp
ontobee: SYMP
wikidata: P8656
name: Symptom Ontology
pattern: ^\d{7}$
preferred_prefix: SYMP
repository: https://github.com/DiseaseOntology/SymptomOntology
synonyms:
- SYMP
uri_format: http://purl.obolibrary.org/obo/SYMP_$1
version: '2022-04-05'
syoid:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
name: Gemina Symptom Ontology
preferred_prefix: syoid
references:
- https://github.com/DiseaseOntology/SymptomOntology/issues/7#event-4223716562
t3db:
description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource
that combines detailed toxin data with comprehensive toxin target information.
example: T3D0001
homepage: http://www.t3db.org/
mappings:
biocontext: T3DB
fairsharing: FAIRsharing.psn0h2
miriam: t3db
n2t: t3db
prefixcommons: t3db
name: Toxin and Toxin Target Database
pattern: ^T3D\d+$
preferred_prefix: t3db
uri_format: http://www.t3db.org/toxins/$1
tads:
banana: TADS
contact:
email: dsonensh@odu.edu
github: null
name: Daniel Sonenshine
orcid: null
description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae'
download_obo: http://purl.obolibrary.org/obo/tads.obo
download_owl: http://purl.obolibrary.org/obo/tads.owl
example: '0000547'
homepage: https://www.vectorbase.org/ontology-browser
license: CC BY 4.0
mappings:
biocontext: TADS
bioportal: TADS
fairsharing: FAIRsharing.8wm364
obofoundry: TADS
ols: tads
ontobee: TADS
name: Tick Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: TADS
repository: https://github.com/VEuPathDB-ontology/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:
biocontext: TAHE
obofoundry: 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:
biocontext: TAHH
obofoundry: TAHH
name: Terminology of Anatomy of Human Histology
preferred_prefix: TAHH
uri_format: http://purl.obolibrary.org/obo/TAHH_$1
tair.gene:
description: The Arabidopsis Information Resource (TAIR) maintains a database of
genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
This is the reference gene model for a given locus.
example: '2200934'
homepage: http://arabidopsis.org/index.jsp
mappings:
biocontext: TAIR.GENE
miriam: tair.gene
n2t: tair.gene
prefixcommons: tair.gene
name: TAIR Gene
pattern: ^\d{7}$
preferred_prefix: tair.gene
uri_format: http://arabidopsis.org/servlets/TairObject?accession=Gene:$1
tair.locus:
description: The Arabidopsis Information Resource (TAIR) maintains a database of
genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
The name of a Locus is unique and used by TAIR, TIGR, and MIPS.
example: '2200950'
homepage: http://arabidopsis.org/index.jsp
mappings:
biocontext: TAIR.LOCUS
go: TAIR
miriam: tair.locus
n2t: tair.locus
ncbi: TAIR
prefixcommons: tair.locus
name: The Arabidopsis Information Resource
pattern: ^\d+$
preferred_prefix: tair.locus
uri_format: http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1
tair.protein:
description: The Arabidopsis Information Resource (TAIR) maintains a database of
genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
This provides protein information for a given gene model and provides links to
other sources such as UniProtKB and GenPept
example: '1009107926'
homepage: http://arabidopsis.org/index.jsp
mappings:
biocontext: TAIR.PROTEIN
miriam: tair.protein
n2t: tair.protein
prefixcommons: tair.protein
name: TAIR Protein
pattern: ^\d{10}$
preferred_prefix: tair.protein
uri_format: http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1
tao:
banana: TAO
contact:
email: wasila.dahdul@usd.edu
github: null
name: Wasila Dahdul
orcid: 0000-0003-3162-7490
deprecated: true
description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but
intended to cover terms relevant to other taxa
download_owl: http://purl.obolibrary.org/obo/tao.owl
example: 0000086
homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology
license: CC0 1.0
mappings:
biocontext: TAO
bioportal: TAO
obofoundry: TAO
prefixcommons: tao
name: Teleost Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: TAO
synonyms:
- TAO_RETIRED
uri_format: http://purl.obolibrary.org/obo/TAO_$1
tarbase:
description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions,
as well as miRNA- and gene-related facts to information specific to the interaction
and the experimental validation methodologies used.
example: hsa-let-7a-2-3p
homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
mappings:
biocontext: TARBASE
fairsharing: FAIRsharing.a0k4cd
miriam: tarbase
n2t: tarbase
name: TarBase
pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)$
preferred_prefix: tarbase
uri_format: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1
taxrank:
banana: TAXRANK
contact:
email: balhoff@renci.org
github: balhoff
name: Jim Balhoff
orcid: 0000-0002-8688-6599
description: A vocabulary of taxonomic ranks (species, family, phylum, etc)
download_obo: http://purl.obolibrary.org/obo/taxrank.obo
download_owl: http://purl.obolibrary.org/obo/taxrank.owl
example: '0000001'
homepage: https://github.com/phenoscape/taxrank
license: CC0 1.0
mappings:
biocontext: TAXRANK
bioportal: TAXRANK
fairsharing: FAIRsharing.p1sejz
obofoundry: TAXRANK
ols: taxrank
ontobee: TAXRANK
prefixcommons: taxrank
name: Taxonomic rank vocabulary
pattern: ^\d{7}$
preferred_prefix: TAXRANK
repository: https://github.com/phenoscape/taxrank
uri_format: http://purl.obolibrary.org/obo/TAXRANK_$1
version: '2016-04-15'
tcb:
description: Cell line collections
example: '2966'
homepage: https://www.pirbright.ac.uk/tick-cell-lines-views-page
mappings:
cellosaurus: TCB
name: Tick Cell Biobank
pattern: ^\d+$
preferred_prefix: tcb
uri_format: https://www.pirbright.ac.uk/node/$1
tcdb:
description: The database details a comprehensive IUBMB approved classification
system for membrane transport proteins known as the Transporter Classification
(TC) system. The TC system is analogous to the Enzyme Commission (EC) system for
classification of enzymes, but incorporates phylogenetic information additionally.
example: 5.A.1.1.1
homepage: https://www.tcdb.org
mappings:
biocontext: TCDB
fairsharing: FAIRsharing.p3bzqb
go: TC
miriam: tcdb
n2t: tcdb
prefixcommons: tcdb
uniprot: TCDB
wikidata: P7260
name: Transporter Classification Database
pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$
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:
fairsharing: FAIRsharing.XykycZ
go: TFClass
name: Classification of Transcription Factors in Mammalia
preferred_prefix: tfclass
uri_format: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1
tgd:
description: The Tetrahymena Genome Database (TGD) Wiki is a database of information
about the Tetrahymena thermophila genome sequence. It provides information curated
from the literature about each published gene, including a standardized gene name,
a link to the genomic locus, gene product annotations utilizing the Gene Ontology,
and links to published literature.
example: TTHERM_00648910
homepage: http://ciliate.org/index.php/
mappings:
biocontext: TGD
go: TGD
miriam: tgd
n2t: tgd
prefixcommons: tgd
name: Tetrahymena Genome Database
pattern: ^TTHERM\_\d+$
preferred_prefix: tgd
uri_format: http://ciliate.org/index.php/feature/details/$1
tgma:
banana: TGMA
contact:
email: topalis@imbb.forth.gr
github: null
name: Pantelis Topalis
orcid: null
description: A structured controlled vocabulary of the anatomy of mosquitoes.
download_obo: http://purl.obolibrary.org/obo/tgma.obo
download_owl: http://purl.obolibrary.org/obo/tgma.owl
example: 0000984
homepage: https://www.vectorbase.org/ontology-browser
license: CC0 1.0
mappings:
biocontext: TGMA
bioportal: TGMA
fairsharing: FAIRsharing.dqnfkg
obofoundry: TGMA
ols: tgma
ontobee: TGMA
prefixcommons: tgma
name: Mosquito gross anatomy ontology
pattern: ^\d{7}$
preferred_prefix: TGMA
repository: https://github.com/VEuPathDB-ontology/TGMA
uri_format: http://purl.obolibrary.org/obo/TGMA_$1
version: '2013-06-03'
tgn:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
example: '1023371'
homepage: https://www.getty.edu/research/tools/vocabularies/tgn/
name: Getty Thesaurus of Geographic Names
pattern: ^\d+$
preferred_prefix: tgn
references:
- https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200
uri_format: http://vocab.getty.edu/page/tgn/$1
th:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/$1
tigrfam:
description: TIGRFAMs is a resource consisting of curated multiple sequence alignments,
Hidden Markov Models (HMMs) for protein sequence classification, and associated
information designed to support automated annotation of (mostly prokaryotic) proteins.
example: TIGR00010
homepage: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi
mappings:
biocontext: TIGRFAM
miriam: tigrfam
n2t: tigrfam
ncbi: TIGRFAM
name: TIGR protein families
pattern: ^TIGR\d+$
preferred_prefix: tigrfam
references:
- https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt
- https://github.com/biopragmatics/bioregistry/issues/366
uri_format: https://www.ncbi.nlm.nih.gov/cdd?term=$1
tkg:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Collection of cell lines by Tohoku University. This includes transplantable
animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series)
cell lines as well as human, murine cell lines and hybridoma cells.
example: '0221'
homepage: http://www2.idac.tohoku.ac.jp/dep/ccr/
mappings:
cellosaurus: TKG
name: Tohoku University cell line catalog
pattern: ^\d+$
preferred_prefix: tkg
uri_format: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html
tngb:
description: Cell line collections
example: '67035'
homepage: http://biobanknetwork.telethon.it/
mappings:
cellosaurus: TNGB
name: Telethon Network of Genetic Biobanks
pattern: ^\d+$
preferred_prefix: tngb
uri_format: http://biobanknetwork.telethon.it/Sample/View?sampleId=$1
to:
appears_in:
- agro
banana: TO
contact:
email: jaiswalp@science.oregonstate.edu
github: jaiswalp
name: Pankaj Jaiswal
orcid: 0000-0002-1005-8383
description: A controlled vocabulary to describe phenotypic traits in plants.
download_obo: http://purl.obolibrary.org/obo/to.obo
download_owl: http://purl.obolibrary.org/obo/to.owl
example: '0000630'
homepage: http://browser.planteome.org/amigo
license: CC BY 4.0
mappings:
biocontext: TO
bioportal: PTO
fairsharing: FAIRsharing.w69t6r
obofoundry: TO
ols: to
ontobee: TO
name: Plant Trait Ontology
pattern: ^\d{7}$
preferred_prefix: TO
repository: https://github.com/Planteome/plant-trait-ontology
uri_format: http://purl.obolibrary.org/obo/TO_$1
version: '2022-04-13'
tokue:
deprecated: true
description: Cell line databases/resources
homepage: http://cell-lines.toku-e.com
mappings:
cellosaurus: TOKU-E
name: TOKU-E Cell-culture Database
preferred_prefix: tokue
uri_format: http://cell-lines.toku-e.com/Cell-Lines_$1.html
tol:
description: "The Tree of Life Web Project (ToL) is a collaborative effort of biologists\
\ and nature enthusiasts from around the world. On more than 10,000 World Wide\
\ Web pages, the project provides information about biodiversity, the characteristics\
\ of different groups of organisms, and their evolutionary history (phylogeny).\
\ \r\n\r\nEach page contains information about a particular group, with pages\
\ linked one to another hierarchically, in the form of the evolutionary tree of\
\ life. Starting with the root of all Life on Earth and moving out along diverging\
\ branches to individual species, the structure of the ToL project thus illustrates\
\ the genetic connections between all living things."
example: '98034'
homepage: http://tolweb.org/tree/
mappings:
biocontext: TOL
miriam: tol
n2t: tol
name: Tree of Life
pattern: ^\d+$
preferred_prefix: tol
uri_format: http://tolweb.org/$1
topdb:
description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection
of transmembrane protein datasets containing experimentally derived topology information.
It contains information gathered from the literature and from public databases
availableon transmembrane proteins. Each record in TOPDB also contains information
on the given protein sequence, name, organism and cross references to various
other databases.
example: AP00378
homepage: http://topdb.enzim.hu/
mappings:
biocontext: TOPDB
miriam: topdb
n2t: topdb
prefixcommons: topdb
name: Topology Data Bank of Transmembrane Proteins
pattern: ^[A-Z0-9]+$
preferred_prefix: topdb
uri_format: http://topdb.enzim.hu/?m=show&id=$1
topfind:
description: 'TopFIND is a database of protein termini, terminus modifications and
their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis
thaliana, Saccharomyces cerevisiae and Escherichia coli.'
example: Q9UKQ2
homepage: https://topfind.clip.msl.ubc.ca
mappings:
biocontext: TOPFIND
fairsharing: FAIRsharing.rkpmhn
miriam: topfind
n2t: topfind
name: TopFind
pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9])$
preferred_prefix: topfind
provides: uniprot
uri_format: http://clipserve.clip.ubc.ca/topfind/proteins/$1
toxoplasma:
description: ToxoDB is one of the databases that can be accessed through the EuPathDB
(http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: TGME49_053730
homepage: http://toxodb.org/toxo/
mappings:
biocontext: TOXOPLASMA
miriam: toxoplasma
n2t: toxoplasma
name: ToxoDB
pattern: ^\w+$
preferred_prefix: toxoplasma
uri_format: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
trans:
banana: TRANS
contact:
email: lynn.schriml@gmail.com
github: lschriml
name: Lynn Schriml
orcid: 0000-0001-8910-9851
description: The Pathogen Transmission Ontology describes the tranmission methods
of human disease pathogens describing how a pathogen is transmitted from one host,
reservoir, or source to another host. The pathogen transmission may occur either
directly or indirectly and may involve animate vectors or inanimate vehicles.
download_obo: http://purl.obolibrary.org/obo/trans.obo
download_owl: http://purl.obolibrary.org/obo/trans.owl
example: '0000024'
homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology
license: CC0 1.0
mappings:
biocontext: TRANS
bioportal: TRANS
fairsharing: FAIRsharing.nygmp7
obofoundry: TRANS
ols: trans
ontobee: TRANS
name: Pathogen Transmission Ontology
pattern: ^\d{7}$
preferred_prefix: TRANS
repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology
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/$1
treebase:
description: TreeBASE is a relational database designed to manage and explore information
on phylogenetic relationships. It includes phylogenetic trees and data matrices,
together with information about the relevant publication, taxa, morphological
and sequence-based characters, and published analyses. Data in TreeBASE are exposed
to the public if they are used in a publication that is in press or published
in a peer-reviewed scientific journal, etc.
example: TB2:S1000
homepage: http://treebase.org/
mappings:
biocontext: TREEBASE
fairsharing: FAIRsharing.zcn4w4
miriam: treebase
n2t: treebase
prefixcommons: treebase
name: TreeBASE
pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$
preferred_prefix: treebase
uri_format: http://purl.org/phylo/treebase/phylows/study/$1?format=html
treefam:
description: TreeFam is a database of phylogenetic trees of gene families found
in animals. Automatically generated trees are curated, to create a curated resource
that presents the accurate evolutionary history of all animal gene families, as
well as reliable ortholog and paralog assignments.
example: TF101014
homepage: http://www.treefam.org/
mappings:
biocontext: TREEFAM
miriam: treefam
n2t: treefam
prefixcommons: treefam
uniprot: TreeFam
name: TreeFam
pattern: ^\w{1,2}\d+$
preferred_prefix: treefam
uri_format: http://www.treefam.org/family/$1
trichdb:
description: TrichDB is one of the databases that can be accessed through the EuPathDB
(http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: TVAG_386080
homepage: http://trichdb.org/trichdb/
mappings:
biocontext: TRICHDB
fairsharing: FAIRsharing.pv0ezt
miriam: trichdb
n2t: trichdb
name: TrichDB
pattern: ^\w+$
preferred_prefix: trichdb
uri_format: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
tritrypdb:
description: TriTrypDB is one of the databases that can be accessed through the
EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: Tb927.8.620
homepage: http://tritrypdb.org/tritrypdb/
mappings:
biocontext: TRITRYPDB
fairsharing: FAIRsharing.fs1z27
go: TriTrypDB
miriam: tritrypdb
n2t: tritrypdb
name: TriTrypDB
pattern: ^\w+(\.)?\w+(\.)?\w+$
preferred_prefix: tritrypdb
uri_format: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1
ttd.drug:
description: The Therapeutic Target Database (TTD) is designed to provide information
about the known therapeutic protein and nucleic acid targets described in the
literature, the targeted disease conditions, the pathway information and the corresponding
drugs/ligands directed at each of these targets. Cross-links to other databases
allow the access to information about the sequence, 3D structure, function, nomenclature,
drug/ligand binding properties, drug usage and effects, and related literature
for each target.
example: DAP000773
homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp
mappings:
biocontext: TTD.DRUG
miriam: ttd.drug
n2t: ttd.drug
name: TTD Drug
pattern: ^DAP\d+$
preferred_prefix: ttd.drug
uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1
ttd.target:
description: The Therapeutic Target Database (TTD) is designed to provide information
about the known therapeutic protein and nucleic acid targets described in the
literature, the targeted disease conditions, the pathway information and the corresponding
drugs/ligands directed at each of these targets. Cross-links to other databases
are also introduced to facilitate the access of information about the sequence,
3D structure, function, nomenclature, drug/ligand binding properties, drug usage
and effects, and related literature for each target.
example: TTDS00056
homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp
mappings:
biocontext: TTD.TARGET
miriam: ttd.target
n2t: ttd.target
name: TTD Target
pattern: ^TTDS\d+$
preferred_prefix: ttd.target
uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1
tto:
banana: TTO
contact:
email: balhoff@renci.org
github: balhoff
name: Jim Balhoff
orcid: 0000-0002-8688-6599
description: An ontology covering the taxonomy of teleosts (bony fish)
download_obo: http://purl.obolibrary.org/obo/tto.obo
download_owl: http://purl.obolibrary.org/obo/tto.owl
example: '1058367'
homepage: https://github.com/phenoscape/teleost-taxonomy-ontology
license: CC0 1.0
mappings:
biocontext: TTO
bioportal: TTO
fairsharing: FAIRsharing.1rj558
obofoundry: TTO
ols: tto
ontobee: TTO
prefixcommons: tto
name: Teleost taxonomy ontology
pattern: ^\d+$
preferred_prefix: TTO
repository: https://github.com/phenoscape/teleost-taxonomy-ontology
uri_format: http://purl.obolibrary.org/obo/TTO_$1
version: '2018-03-26'
txpo:
banana: TXPO
contact:
email: yuki.yamagata@riken.jp
github: yuki-yamagata
name: Yuki Yamagata
orcid: 0000-0002-9673-1283
description: 'Elucidating the mechanism of toxicity is crucial in drug safety evaluations.
TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity
courses and processes. The first version of TXPO focuses on liver toxicity.
The TXPO contains an is-a hierarchy that is organized into three layers: the top
layer contains general terms, mostly derived from the Basic Formal Ontology. The
intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell
Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID
and Relational ontology (RO). The lower layer contains toxicological terms.
In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe
knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which
facilitates capturing the comprehensive picture for understanding toxicity mechanisms.
A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp'
download_owl: http://purl.obolibrary.org/obo/txpo.owl
example: '0002066'
homepage: https://toxpilot.nibiohn.go.jp/
license: CC BY 3.0
mappings:
bioportal: TXPO
obofoundry: TXPO
ols: txpo
ontobee: TXPO
name: Toxic Process Ontology
pattern: ^\d{7}$
preferred_prefix: TXPO
repository: https://github.com/txpo-ontology/TXPO
uri_format: http://purl.obolibrary.org/obo/TXPO_$1
version: '2020-07-09'
uberon:
appears_in:
- aism
- amphx
- chiro
- cl
- clo
- clyh
- colao
- cteno
- ecao
- ecocore
- ecto
- envo
- foodon
- fovt
- genepio
- go
- hso
- lepao
- maxo
- mco
- mfmo
- ons
- pcl
- plana
- poro
- zp
banana: UBERON
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
depends_on:
- chebi
- cl
- go
- pr
description: Uberon is an integrated cross-species anatomy ontology representing
a variety of entities classified according to traditional anatomical criteria
such as structure, function and developmental lineage. The ontology includes comprehensive
relationships to taxon-specific anatomical ontologies, allowing integration of
functional, phenotype and expression data.
download_obo: http://purl.obolibrary.org/obo/uberon/basic.obo
download_owl: http://purl.obolibrary.org/obo/uberon.owl
example: '2005080'
homepage: http://uberon.org
license: CC BY 3.0
mappings:
biocontext: UBERON
bioportal: UBERON
cellosaurus: UBERON
fairsharing: FAIRsharing.4c0b6b
go: UBERON
miriam: uberon
n2t: uberon
obofoundry: UBERON
ols: uberon
ontobee: UBERON
wikidata: P1554
name: Uber Anatomy Ontology
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: UBERON
repository: https://github.com/obophenotype/uberon
synonyms:
- UBERON
- Uber-anatomy ontology
- Uberon
uri_format: http://purl.obolibrary.org/obo/UBERON_$1
version: '2022-04-18'
ubio.namebank:
description: NameBank is a "biological name server" focused on storing names and
objectively-derived nomenclatural attributes. NameBank is a repository for all
recorded names including scientific names, vernacular (or common names), misspelled
names, as well as ad-hoc nomenclatural labels that may have limited context.
example: '2555646'
homepage: http://www.ubio.org
mappings:
biocontext: UBIO.NAMEBANK
miriam: ubio.namebank
n2t: ubio.namebank
name: uBio NameBank
pattern: ^\d+$
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: cthoyt
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:
biocontext: UCSC
uniprot: UCSC
wikidata: P2576
name: UCSC Genome Browser
preferred_prefix: ucsc
uri_format: ftp://hgdownload.cse.ucsc.edu/goldenPath/$1
umbbd.compound:
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
contains information on microbial biocatalytic reactions and biodegradation pathways
for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide
information on microbial enzyme-catalyzed reactions that are important for biotechnology.
This collection refers to compound information.
example: c0001
homepage: http://umbbd.ethz.ch/
mappings:
biocontext: UMBBD.COMPOUND
miriam: umbbd.compound
n2t: umbbd.compound
wikidata: P8121
name: UM-BBD Compound
part_of: umbbd
pattern: ^c\d+$
preferred_prefix: umbbd.compound
synonyms:
- UM-BBD_compID
uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1
umbbd.enzyme:
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
contains information on microbial biocatalytic reactions and biodegradation pathways
for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide
information on microbial enzyme-catalyzed reactions that are important for biotechnology.
This collection refers to enzyme information.
example: e0333
homepage: http://umbbd.ethz.ch/
mappings:
biocontext: UMBBD.ENZYME
go: UM-BBD_enzymeID
miriam: umbbd.enzyme
n2t: umbbd.enzyme
name: EAWAG Biocatalysis/Biodegradation Database
part_of: umbbd
pattern: ^e\d+$
preferred_prefix: umbbd.enzyme
synonyms:
- UM-BBD_enzymeID
uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1
umbbd.pathway:
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
contains information on microbial biocatalytic reactions and biodegradation pathways
for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide
information on microbial enzyme-catalyzed reactions that are important for biotechnology.
This collection refers to pathway information.
example: ala
homepage: http://umbbd.ethz.ch/
mappings:
biocontext: UMBBD.PATHWAY
go: UM-BBD_pathwayID
miriam: umbbd.pathway
n2t: umbbd.pathway
name: EAWAG Biocatalysis/Biodegradation Database
part_of: umbbd
pattern: ^\w+$
preferred_prefix: umbbd.pathway
synonyms:
- UM-BBD_pathwayID
uri_format: http://eawag-bbd.ethz.ch/$1/$1_map.html
umbbd.reaction:
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
contains information on microbial biocatalytic reactions and biodegradation pathways
for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide
information on microbial enzyme-catalyzed reactions that are important for biotechnology.
This collection refers to reaction information.
example: r0001
homepage: http://umbbd.ethz.ch/
mappings:
biocontext: UMBBD.REACTION
go: UM-BBD_reactionID
miriam: umbbd.reaction
n2t: umbbd.reaction
name: EAWAG Biocatalysis/Biodegradation Database
part_of: umbbd
pattern: ^r\d+$
preferred_prefix: umbbd.reaction
synonyms:
- UM-BBD_reactionID
uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1
umbbd.rule:
description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)
contains information on microbial biocatalytic reactions and biodegradation pathways
for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System
(PPS) predicts microbial catabolic reactions using substructure searching, a rule-base,
and atom-to-atom mapping. The PPS recognizes organic functional groups found in
a compound and predicts transformations based on biotransformation rules. These
rules are based on reactions found in the UM-BBD database. This collection references
those rules.
example: bt0001
homepage: http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules
mappings:
biocontext: UMBBD.RULE
go: UM-BBD_ruleID
miriam: umbbd.rule
n2t: umbbd.rule
name: EAWAG Biocatalysis/Biodegradation Database
part_of: umbbd
pattern: ^bt\d+$
preferred_prefix: umbbd.rule
synonyms:
- UM-BBD_ruleID
uri_format: http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1
umls:
description: The Unified Medical Language System is a repository of biomedical vocabularies.
Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene
Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist
Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also
be linked to external resources such as GenBank.
example: C2584994
homepage: https://www.nlm.nih.gov/research/umls
mappings:
biocontext: UMLS
miriam: umls
n2t: umls
wikidata: P2892
name: Unified Medical Language System Concept Unique Identifier
pattern: ^C\d+$
preferred_prefix: umls
synonyms:
- UMLS
- UMLS CUI
- UMLS_CUI
- umls.cui
uri_format: http://linkedlifedata.com/resource/umls/id/$1
umls.aui:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An identifier for an atom; the smallest unit of naming in a source,
viz, a specific string with specific code values and identifiers from a specific
source. As such, they can be thought of as representing a single meaning with
a source Atoms are the units of terminology that come from sources and form the
building blocks of the concepts in the Metathesaurus.
example: A0118748
homepage: https://www.nlm.nih.gov/research/umls
name: Unified Medical Language System Atomic Unique Identifier
pattern: ^A\d+$
preferred_prefix: umls.aui
synonyms:
- UMLS_ICD9CM_2005_AUI
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:
biocontext: UNIGENE
fairsharing: FAIRsharing.ge1c3p
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=$1
unii:
description: The purpose of the joint FDA/USP Substance Registration System (SRS)
is to support health information technology initiatives by generating unique ingredient
identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The
UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric
identifier based on a substance’s molecular structure and/or descriptive information.
example: 3G6A5W338E
homepage: http://fdasis.nlm.nih.gov/srs/
mappings:
biocontext: UNII
cheminf: '000563'
miriam: unii
n2t: unii
wikidata: P652
name: Unique Ingredient Identifier
pattern: ^[A-Z0-9]+$
preferred_prefix: unii
uri_format: http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1
unimod:
description: Unimod is a public domain database created to provide a community supported,
comprehensive database of protein modifications for mass spectrometry applications.
That is, accurate and verifiable values, derived from elemental compositions,
for the mass differences introduced by all types of natural and artificial modifications.
Other important information includes any mass change, (neutral loss), that occurs
during MS/MS analysis, and site specificity, (which residues are susceptible to
modification and any constraints on the position of the modification within the
protein or peptide).
download_owl: http://www.unimod.org/obo/unimod.obo
example: '1200'
homepage: http://www.unimod.org/
mappings:
biocontext: UNIMOD
fairsharing: FAIRsharing.zZHCUQ
miriam: unimod
n2t: unimod
ols: unimod
name: Unimod protein modification database for mass spectrometry
pattern: ^\d+$
preferred_prefix: unimod
uri_format: http://www.unimod.org/modifications_view.php?editid1=$1
uniparc:
description: The UniProt Archive (UniParc) is a database containing non-redundant
protein sequence information from many sources. Each unique sequence is given
a stable and unique identifier (UPI) making it possible to identify the same protein
from different source databases.
example: UPI000000000A
homepage: https://www.ebi.ac.uk/uniparc/
mappings:
biocontext: UNIPARC
go: UniParc
miriam: uniparc
n2t: uniparc
prefixcommons: uniparc
name: UniProt Archive
pattern: ^UPI[A-F0-9]{10}$
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=$1
unipathway.compound:
description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous
chemical reactions. It provides a hierarchical representation of metabolic pathways
and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data
are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and
MetaCyc. This collection references compounds.
example: UPC04349
homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
mappings:
biocontext: UNIPATHWAY.COMPOUND
miriam: unipathway.compound
n2t: unipathway.compound
name: UniPathway Compound
pattern: ^UPC\d{5}$
preferred_prefix: unipathway.compound
uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1
unipathway.reaction:
description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous
chemical reactions. It provides a hierarchical representation of metabolic pathways
and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data
are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and
MetaCyc. This collection references individual reactions.
example: UCR00226
homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
mappings:
biocontext: UNIPATHWAY.REACTION
miriam: unipathway.reaction
n2t: unipathway.reaction
name: UniPathway Reaction
pattern: ^UCR\d{5}$
preferred_prefix: unipathway.reaction
uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1
uniprot:
description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for
protein sequence and functional information with extensive cross-references to
more than 120 external databases. Besides amino acid sequence and a description,
it also provides taxonomic data and citation information.
example: P0DP23
homepage: http://www.uniprot.org
mappings:
biocontext: UniProtKB
cellosaurus: UniProtKB
fairsharing: FAIRsharing.s1ne3g
go: UniProtKB
miriam: uniprot
n2t: uniprot
ncbi: UniProt
prefixcommons: uniprot
scholia: uniprot
wikidata: P352
name: UniProt Protein
pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z,
0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
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: indra
description: A large scale database of biomedical statements.
homepage: https://db.indra.bio
name: INDRA Database
uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@UP
- 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 ID
- uniprot/swiss-prot
uri_format: http://purl.uniprot.org/uniprot/$1
uniprot.chain:
description: This collection is a subset of UniProtKB that provides a means to reference
the proteolytic cleavage products of a precursor protein.
example: PRO_0000016681
homepage: https://www.uniprot.org
mappings:
miriam: uniprot.chain
name: UniProt Chain
part_of: uniprot
pattern: ^PRO_[0-9]{10}$
preferred_prefix: uniprot.chain
synonyms:
- UPPRO
uri_format: http://purl.uniprot.org/annotation/$1
uniprot.disease:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The human diseases in which proteins are involved are described in
UniProtKB entries with a controlled vocabulary.
download_obo: https://www.uniprot.org/diseases/?query=*&format=obo
example: '04240'
homepage: https://www.uniprot.org/diseases/
name: UniProt Diseases
part_of: uniprot
pattern: ^\d{5}$
preferred_prefix: uniprot.disease
synonyms:
- DI
- SP_DI
uri_format: https://www.uniprot.org/diseases/DI-$1
uniprot.isoform:
description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for
protein sequence and functional information with extensive cross-references to
more than 120 external databases. This collection is a subset of UniProtKB, and
provides a means to reference isoform information.
example: Q5BJF6-3
homepage: http://www.uniprot.org/
mappings:
biocontext: UNIPROT.ISOFORM
miriam: uniprot.isoform
n2t: uniprot.isoform
name: UniProt Isoform
part_of: uniprot
pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9])(\-\d+)$
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/$1
uniprot.keyword:
description: UniProtKB entries are tagged with keywords that can be used to retrieve
particular subsets of entries.
download_obo: https://www.uniprot.org/keywords/?format=obo
example: '1273'
homepage: http://www.uniprot.org/keywords/
mappings:
go: UniProtKB-KW
name: UniProt Keywords
part_of: uniprot
pattern: ^\d{4}$
preferred_prefix: uniprot.keyword
synonyms:
- SP_KW
- UniProtKB-KW
- uniprot.keyword
uri_format: https://www.uniprot.org/keywords/KW-$1
uniprot.location:
description: The subcellular locations in which a protein is found are described
in UniProtKB entries with a controlled vocabulary, which includes also membrane
topology and orientation terms.
download_obo: https://www.uniprot.org/locations/?query=*&format=obo
example: '0002'
homepage: https://www.uniprot.org/locations/
mappings:
go: UniProtKB-SubCell
name: UniProt Subcellular Locations
part_of: uniprot
pattern: ^\d+$
preferred_prefix: uniprot.location
synonyms:
- SP_SL
- UPLOC
- UniProtKB-SubCell
uri_format: https://www.uniprot.org/locations/SL-$1
uniprot.ptm:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The post-translational modifications used in the UniProt knowledgebase
(Swiss-Prot and TrEMBL). The definition of the post-translational modifications
usage as well as other information is provided in the following format
example: '0450'
homepage: https://www.uniprot.org/docs/ptmlist
name: UniProt Post-Translational Modification
part_of: uniprot
pattern: ^\d{4}$
preferred_prefix: uniprot.ptm
references:
- https://twitter.com/cthoyt/status/1510570256619778053
- https://www.uniprot.org/docs/ptmlist.txt
synonyms:
- PTM
uniprot.resource:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The cross-references section of UniProtKB entries displays explicit
and implicit links to databases such as nucleotide sequence databases, model organism
databases and genomics and proteomics resources.
example: '0174'
homepage: https://www.uniprot.org/database/
name: UniProt Resource
part_of: uniprot
pattern: ^\d{4}$
preferred_prefix: uniprot.resource
uri_format: https://www.uniprot.org/database/DB-$1
uniprot.tissue:
description: The UniProt Tissue List is a controlled vocabulary of terms used to
annotate biological tissues. It also contains cross-references to other ontologies
where tissue types are specified.
example: 0285
homepage: https://www.uniprot.org/docs/tisslist.txt
mappings:
biocontext: TISSUELIST
miriam: tissuelist
n2t: tissuelist
name: Tissue List
part_of: uniprot
pattern: ^\d{4}$
preferred_prefix: uniprot.tissue
uri_format: https://www.uniprot.org/tissues/TS-$1
uniprot.var:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The purpose of the UniProtKB/Swiss-Prot variant pages is: to display
the variant related information extracted from UniProtKB/Swiss-Prot, and to provide
useful additional information such as the conservation of the modified residues
across orthologous species.'
example: 068078
homepage: https://web.expasy.org/variant_pages
name: UniProt Variants
part_of: uniprot
pattern: ^\d+$
preferred_prefix: uniprot.var
synonyms:
- SP_VAR
- UPVAR
- UniProtKB_VAR
uri_format: https://web.expasy.org/variant_pages/VAR_$1.html
uniref:
description: The UniProt Reference Clusters (UniRef) provide clustered sets of sequences
from the UniProt Knowledgebase (including isoforms) and selected UniParc records
in order to obtain complete coverage of the sequence space at several resolutions
while hiding redundant sequences (but not their descriptions) from view.
example: UniRef90_P00750
homepage: https://www.uniprot.org/
mappings:
miriam: uniref
name: UniRef
pattern: ^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$
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/$1
unists:
description: UniSTS is a comprehensive database of sequence tagged sites (STSs)
derived from STS-based maps and other experiments. STSs are defined by PCR primer
pairs and are associated with additional information such as genomic position,
genes, and sequences.
example: '456789'
homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists
mappings:
biocontext: UNISTS
miriam: unists
n2t: unists
ncbi: UniSTS
prefixcommons: unists
name: Database of Sequence Tagged Sites
pattern: ^\d+$
preferred_prefix: unists
uri_format: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1
unite:
description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database.
It focuses on high-quality ITS sequences generated from fruiting bodies collected
and identified by experts and deposited in public herbaria. Entries may be supplemented
with metadata on describing locality, habitat, soil, climate, and interacting
taxa.
example: UDB000691
homepage: http://unite.ut.ee/
mappings:
biocontext: UNITE
fairsharing: FAIRsharing.cnwx8c
miriam: unite
n2t: unite
ncbi: UNITE
prefixcommons: unite
name: Molecular database for the identification of fungi
pattern: ^UDB\d{6}$
preferred_prefix: unite
uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1
unpd:
comment: The website is dead, there are no places to get the source information
except inside https://oolonek.github.io/ISDB/.
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
homepage: http://pkuxxj.pku.edu.cn/UNPD/
name: Universal Natural Products Database
preferred_prefix: unpd
references:
- http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database
- https://pharmacognosy.in/the-universal-natural-products-database-unpd/
- https://pubs.acs.org/doi/abs/10.1021/acs.jnatprod.6b01093
- https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062839
- https://oolonek.github.io/ISDB/
uo:
appears_in:
- agro
- ms
- rbo
- scdo
banana: UO
contact:
email: g.gkoutos@gmail.com
github: gkoutos
name: George Gkoutos
orcid: 0000-0002-2061-091X
description: Ontology of standardized units
download_obo: http://purl.obolibrary.org/obo/uo.obo
download_owl: http://purl.obolibrary.org/obo/uo.owl
example: 0000080
homepage: https://github.com/bio-ontology-research-group/unit-ontology
license: CC BY 3.0
mappings:
biocontext: UO
bioportal: UO
fairsharing: FAIRsharing.mjnypw
miriam: uo
n2t: uo
obofoundry: UO
ols: uo
ontobee: UO
prefixcommons: uo
name: Units of measurement ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: UO
repository: https://github.com/bio-ontology-research-group/unit-ontology
uri_format: https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1
version: '2020-03-10'
upa:
banana: UPA
contact:
email: Anne.Morgat@sib.swiss
github: amorgat
name: Anne Morgat
orcid: 0000-0002-1216-2969
depends_on:
- ro
deprecated: true
description: A manually curated resource for the representation and annotation of
metabolic pathways
download_obo: https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo
download_owl: http://purl.obolibrary.org/obo/upa.owl
example: UCR00513
homepage: https://github.com/geneontology/unipathway
license: CC BY 3.0
mappings:
biocontext: UNIPATHWAY
bioportal: UPA
go: UniPathway
obofoundry: UPA
ols: upa
ontobee: UPA
prefixcommons: unipathway
uniprot: UniPathway
name: Unipathway
pattern: ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$
preferred_prefix: UPA
repository: https://github.com/geneontology/unipathway
synonyms:
- UPa
- unipathway
- unipathway.pathway
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: 0000-0001-5208-3432
description: The uPheno ontology integrates multiple phenotype ontologies into a
unified cross-species phenotype ontology.
download_owl: https://github.com/obophenotype/upheno/blob/master/upheno.owl
homepage: https://github.com/obophenotype/upheno
license: CC0 1.0
mappings:
biocontext: UPHENO
bioportal: UPHENO
fairsharing: FAIRsharing.r41qhx
obofoundry: UPHENO
ols: upheno
ontobee: UPHENO
name: Unified Phenotype Ontology
no_own_terms: true
preferred_prefix: UPHENO
repository: https://github.com/obophenotype/upheno
uri_format: http://purl.obolibrary.org/obo/UPHENO_$1
version: '2017-10-31'
uspto:
description: The United States Patent and Trademark Office (USPTO) is the federal
agency for granting U.S. patents and registering trademarks. As a mechanism that
protects new ideas and investments in innovation and creativity, the USPTO is
at the cutting edge of the nation's technological progress and achievement.
example: '4145692'
homepage: http://patft.uspto.gov/netahtml/PTO/index.html
mappings:
biocontext: USPTO
miriam: uspto
n2t: uspto
name: United States Patent and Trademark Office
pattern: ^(D|PP|R|T|H|X|AI)?\d+$
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/$1
validatordb:
description: Database of validation results for ligands and non-standard residues
in the Protein Data Bank.
example: 2h6o
homepage: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/
mappings:
biocontext: VALIDATORDB
fairsharing: FAIRsharing.c9psgb
miriam: validatordb
n2t: validatordb
name: ValidatorDB
pattern: ^[A-Za-z0-9\/]+$
preferred_prefix: validatordb
provides: pdb
uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1
vandf:
description: 'The National Drug File (NDF) is produced by the U.S. Department of
Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained
electronic drug list used by the VHA hospitals and clinics. Facilities use the
NDF to check drug interactions, to manage orders, and to send outpatient prescriptions
to regional automated mail-out pharmacies. NDF includes information on clinical
drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. '
example: '4019477'
homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF
mappings:
biolink: VANDF
bioportal: VANDF
fairsharing: FAIRsharing.xn3pb3
name: Veterans Administration National Drug File
pattern: ^\d+$
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.
download_obo: http://purl.obolibrary.org/obo/vario.obo
download_owl: http://purl.obolibrary.org/obo/vario.owl
example: '0376'
homepage: http://variationontology.org
mappings:
biocontext: VARIO
bioportal: VARIO
fairsharing: FAIRsharing.65xkbs
miriam: vario
n2t: vario
obofoundry: VariO
ols: vario
ontobee: 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_$1
version: '2018-11-09'
vbase2:
description: The database VBASE2 provides germ-line sequences of human and mouse
immunoglobulin variable (V) genes.
example: humIGHV025
homepage: http://www.vbase2.org/vbase2.php
mappings:
biocontext: VBASE2
fairsharing: FAIRsharing.qvxhb1
miriam: vbase2
n2t: vbase2
ncbi: VBASE2
prefixcommons: vbase2
name: Integrative database of germ-line V genes from the immunoglobulin loci of
human and mouse
pattern: ^\w+$
preferred_prefix: vbase2
uri_format: http://www.vbase2.org/vgene.php?id=$1
vbrc:
description: The VBRC provides bioinformatics resources to support scientific research
directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae,
Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center
consists of a relational database and web application that support the data storage,
annotation, analysis, and information exchange goals of this work. Each data release
contains the complete genomic sequences for all viral pathogens and related strains
that are available for species in the above-named families. In addition to sequence
data, the VBRC provides a curation for each virus species, resulting in a searchable,
comprehensive mini-review of gene function relating genotype to biological phenotype,
with special emphasis on pathogenesis.
example: '35742'
homepage: http://vbrc.org/
mappings:
biocontext: VBRC
miriam: vbrc
n2t: vbrc
prefixcommons: vbrc
name: Viral Bioinformatics Resource Center
pattern: ^\d+$
preferred_prefix: vbrc
uri_format: http://vbrc.org/gene_detail.asp?gene_id=$1
vcell:
description: Models developed with the Virtual Cell (VCell) software prorgam.
example: '201022999'
homepage: https://health.uconn.edu/
mappings:
miriam: vcell
name: VCell Published Models
pattern: ^\d{5,}$
preferred_prefix: vcell
uri_format: https://vcell.org/biomodel-$1
vectorbase:
description: 'VectorBase is an NIAID-funded Bioinformatic Resource Center focused
on invertebrate vectors of human pathogens. VectorBase annotates and curates vector
genomes providing a web accessible integrated resource for the research community.
Currently, VectorBase contains genome information for three mosquito species:
Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus
humanus and a tick species Ixodes scapularis.'
example: ISCW007415
homepage: https://www.vectorbase.org/
mappings:
biocontext: VECTORBASE
fairsharing: FAIRsharing.3etvdn
miriam: vectorbase
n2t: vectorbase
ncbi: VectorBase
prefixcommons: vectorbase
name: Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
pattern: ^\D{4}\d{6}(\-\D{2})?$
preferred_prefix: vectorbase
uri_format: https://vectorbase.org/vectorbase/app/record/gene/$1
vega:
contributor:
email: cthoyt@gmail.com
github: cthoyt
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
mappings:
fairsharing: FAIRsharing.mr293q
prefixcommons: vega
name: Vertebrate Genome Annotation Database
preferred_prefix: vega
synonyms:
- VEGA
uri_format: http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1
vegbank:
description: 'VegBank is the vegetation plot database of the Ecological Society
of America''s Panel on Vegetation Classification. VegBank consists of three linked
databases that contain (1) vegetation plot records, (2) vegetation types recognized
in the U.S. National Vegetation Classification and other vegetation types submitted
by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other
plant taxa recorded in plot records. Vegetation records, community types and plant
taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated,
revised, interpreted, downloaded, and cited. '
example: VB.Ob.3736.GRSM125
homepage: http://vegbank.org/
mappings:
miriam: vegbank
name: VegBank
pattern: ^VB\.[A-Za-z][A-Za-z]\..*$
preferred_prefix: vegbank
uri_format: http://vegbank.org/cite/$1
vfb:
description: An interactive tool for neurobiologists to explore the detailed neuroanatomy,
neuron connectivity and gene expression of the Drosophila melanogaster.
example: '00000001'
homepage: https://VirtualFlyBrain.org
mappings:
fairsharing: FAIRsharing.nzaz6z
miriam: vfb
n2t: vfb
name: Virtual Fly Brain
pattern: ^[0-9a-zA-Z]{8}$
preferred_prefix: vfb
uri_format: http://virtualflybrain.org/reports/$1
vfdb.gene:
description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This
collection references VF genes.
example: VFG2154
homepage: http://www.mgc.ac.cn/VFs/
mappings:
biocontext: VFDB.GENE
miriam: vfdb.gene
n2t: vfdb.gene
name: VFDB Gene
pattern: ^\w+$
preferred_prefix: vfdb.gene
uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1
vfdb.genus:
description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This
collection references VF information by Genus.
example: Chlamydia
homepage: http://www.mgc.ac.cn/VFs/
mappings:
biocontext: VFDB.GENUS
miriam: vfdb.genus
n2t: vfdb.genus
name: VFDB Genus
pattern: ^\w+$
preferred_prefix: vfdb.genus
uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1
vgnc:
description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of
the established HGNC (HUGO Gene Nomenclature Committee) project that names human
genes. VGNC is responsible for assigning standardized names to genes in vertebrate
species that currently lack a nomenclature committee.
example: VGNC:3792
homepage: https://vertebrate.genenames.org
mappings:
cellosaurus: VGNC
fairsharing: FAIRsharing.5NhJFK
miriam: vgnc
ncbi: VGNC
uniprot: VGNC
name: Vertebrate Gene Nomenclature Committee
pattern: ^((VGNC|vgnc):)?\d{1,9}$
preferred_prefix: vgnc
uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1
vhog:
banana: VHOG
deprecated: true
download_obo: ftp://ftp.bgee.org/general/ontologies/vHOG.obo
download_owl: http://purl.obolibrary.org/obo/vhog.owl
example: '0000411'
mappings:
biocontext: VHOG
bioportal: VHOG
obofoundry: VHOG
prefixcommons: vhog
name: Vertebrate Homologous Organ Group Ontology
pattern: ^\d{7}$
preferred_prefix: VHOG
synonyms:
- VHOG_RETIRED
uri_format: http://purl.obolibrary.org/obo/VHOG_$1
viaf:
description: The VIAF® (Virtual International Authority File) combines multiple
name authority files into a single OCLC-hosted name authority service. The goal
of the service is to lower the cost and increase the utility of library authority
files by matching and linking widely-used authority files and making that information
available on the Web.
example: '75121530'
homepage: http://viaf.org
mappings:
miriam: viaf
n2t: viaf
scholia: viaf
name: Virtual International Authority File
pattern: ^\d+$
preferred_prefix: viaf
uri_format: http://viaf.org/viaf/$1
vido:
contact:
email: johnbeverley2021@u.northwestern.edu
github: johnbeve
name: John Beverly
orcid: 0000-0002-1118-1738
description: The Virus Infectious Disease Ontology (IDO Virus) is an extension of
the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines,
employs the Basic Formal Ontology as its starting point, and covers epidemiology,
classification, pathogenesis, and treatment of terms used by Virologists, i.e.
virus, prion, satellite, viroid, etc.
download_owl: http://purl.obolibrary.org/obo/2020-25-08/vido.owl
example: '0001114'
homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus
mappings:
bioportal: VIDO
ols: vido
ontobee: VIDO
name: The Virus Infectious Disease Ontology
pattern: ^\d{7}$
preferred_prefix: vido
repository: https://github.com/infectious-disease-ontology-extensions/ido-virus
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:
biocontext: VIPR
fairsharing: FAIRsharing.2qx8n8
miriam: vipr
n2t: vipr
ncbi: ViPR
name: Virus Pathogen Resource
pattern: ^[A-Za-z 0-9]+$
preferred_prefix: vipr
uri_format: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena
viralzone:
description: ViralZone is a resource bridging textbook knowledge with genomic and
proteomic sequences. It provides fact sheets on all known virus families/genera
with easy access to sequence data. A selection of reference strains (RefStrain)
provides annotated standards to circumvent the exponential increase of virus sequences.
Moreover ViralZone offers a complete set of detailed and accurate virion pictures.
example: '992'
homepage: http://www.expasy.org/viralzone/
mappings:
biocontext: VIRALZONE
fairsharing: FAIRsharing.tppk10
miriam: viralzone
n2t: viralzone
name: ViralZone
pattern: ^\d+$
preferred_prefix: viralzone
uri_format: http://viralzone.expasy.org/all_by_protein/$1.html
virsirna:
description: The VIRsiRNA database contains details of siRNA/shRNA which target
viral genome regions. It provides efficacy information where available, as well
as the siRNA sequence, viral target and subtype, as well as the target genomic
region.
example: virsi1909
homepage: http://crdd.osdd.net/servers/virsirnadb
mappings:
biocontext: VIRSIRNA
miriam: virsirna
n2t: virsirna
name: VIRsiRNA
pattern: ^virsi\d+$
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:
biocontext: VMHMETABOLITE
miriam: vmhmetabolite
n2t: 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:
biocontext: VMHREACTION
miriam: vmhreaction
n2t: vmhreaction
name: VMH reaction
pattern: ^[a-zA-Z0-9_\(\_\)\[\]]+$
preferred_prefix: vmhreaction
uri_format: https://www.vmh.life/#reaction/$1
vo:
appears_in:
- scdo
banana: VO
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqunh He
orcid: 0000-0001-9189-9661
description: The Vaccine Ontology (VO) is a biomedical ontology in the domain of
vaccine and vaccination. VO aims to standardize vaccine annotation, integrate
various vaccine data, and support computer-assisted reasoning. VO supports basic
vaccine R&D and clincal vaccine usage. VO is being developed as a community-based
ontology with support and collaborations from the vaccine and bio-ontology communities.
download_owl: http://purl.obolibrary.org/obo/vo.owl
example: 0000093
homepage: http://www.violinet.org/vaccineontology
license: CC BY 3.0
mappings:
biocontext: VO
bioportal: VO
fairsharing: FAIRsharing.zwtww5
obofoundry: VO
ols: vo
ontobee: VO
prefixcommons: vo
name: Vaccine Ontology
pattern: ^\d{7}$
preferred_prefix: VO
repository: https://github.com/vaccineontology/VO
uri_format: http://purl.obolibrary.org/obo/VO_$1
version: 1.1.193
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:
biocontext: 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: 0000-0003-3162-7490
deprecated: true
description: Vertebrate skeletal anatomy ontology.
download_owl: http://purl.obolibrary.org/obo/vsao.owl
homepage: https://www.nescent.org/phenoscape/Main_Page
mappings:
biocontext: VSAO
bioportal: VSAO
obofoundry: VSAO
name: Vertebrate Skeletal Anatomy Ontology
preferred_prefix: VSAO
synonyms:
- VSAO_RETIRED
uri_format: http://purl.obolibrary.org/obo/VSAO_$1
vsdb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Veterinary pharmaceuticals are biologically active and potentially
persistent substances which are recognised as a continuing threat to environmental
quality. Whilst the environmental risk of agricultural pesticides has had considerable
attention in recent decades, risks assessments for veterinary pharmaceuticals
have only relatively recently began to be addressed. Risk assessments and risk
modelling tend to be inherently data hungry processes and one of the main obstacles
to consistent, accurate and efficient assessments is the need for a reliable,
quality and comprehensive data source.
example: '1868'
homepage: https://sitem.herts.ac.uk/aeru/vsdb
name: Veterinary Substances DataBase
pattern: ^\d+$
preferred_prefix: vsdb
uri_format: https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm
vso:
description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for
General Medical Science (OGMS). VSO covers the four consensus human vital signs:
blood pressure, body temperature, respiration rate, pulse rate. VSO provides also
a controlled structured vocabulary for describing vital signs measurement data,
the various processes of measuring vital signs, and the various devices and anatomical
entities participating in such measurements. '
example: '0000041'
homepage: https://bioportal.bioontology.org/ontologies/VSO
mappings:
bioportal: VSO
fairsharing: FAIRsharing.jjb2p2
prefixcommons: vso
name: Vital Sign Ontology
pattern: ^\d{7}$
preferred_prefix: vso
uri_format: https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1
vt:
appears_in:
- scdo
banana: VT
contact:
email: caripark@iastate.edu
github: caripark
name: Carissa Park
orcid: 0000-0002-2346-5201
description: An ontology of traits covering vertebrates
download_obo: https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo
download_owl: http://purl.obolibrary.org/obo/vt.owl
example: 0000685
homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology
license: CC BY 4.0
mappings:
biocontext: VT
bioportal: VT
fairsharing: FAIRsharing.10gr18
obofoundry: VT
ols: vt
ontobee: VT
prefixcommons: vt
name: Vertebrate trait ontology
pattern: ^\d{7}$
preferred_prefix: VT
repository: https://github.com/AnimalGenome/vertebrate-trait-ontology
uri_format: http://purl.obolibrary.org/obo/VT_$1
vto:
banana: VTO
contact:
email: balhoff@renci.org
github: balhoff
name: Jim Balhoff
orcid: 0000-0002-8688-6599
description: Comprehensive hierarchy of extinct and extant vertebrate taxa.
download_obo: http://purl.obolibrary.org/obo/vto.obo
download_owl: http://purl.obolibrary.org/obo/vto.owl
example: '9008500'
homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology
license: CC0 1.0
mappings:
biocontext: VTO
bioportal: VTO
fairsharing: FAIRsharing.akmeb9
obofoundry: VTO
ols: vto
ontobee: VTO
name: Vertebrate Taxonomy Ontology
pattern: ^\d{7}$
preferred_prefix: VTO
repository: https://github.com/phenoscape/vertebrate-taxonomy-ontology
uri_format: http://purl.obolibrary.org/obo/VTO_$1
version: '2020-11-13'
vuid:
comment: The example corresponds to acetaminophen
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Veterans Health Administration is America’s largest integrated
health care system, providing care at 1,293 health care facilities, including
171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA
outpatient clinics), serving 9 million enrolled Veterans each year.
example: '4007166'
homepage: https://www.va.gov/health
name: Veterans Health Administration (VHA) unique identifier
pattern: ^\d+$
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
prefixcommons: vz
name: ViralZone
pattern: ^\d+$
preferred_prefix: vz
uri_format: https://viralzone.expasy.org/$1
wb.rnai:
description: WormBase is an online bioinformatics database of the biology and genome
of the model organism Caenorhabditis elegans and related nematodes. It is used
by the C. elegans research community both as an information resource and as a
mode to publish and distribute their results. This collection references RNAi
experiments, detailing target and phenotypes.
example: WBRNAi00086878
homepage: https://www.wormbase.org/
mappings:
biocontext: WB.RNAI
miriam: wb.rnai
n2t: wb.rnai
name: WormBase RNAi
pattern: ^WBRNAi\d{8}$
preferred_prefix: wb.rnai
uri_format: https://www.wormbase.org/species/c_elegans/rnai/$1
wbbt:
banana: WBbt
contact:
email: raymond@caltech.edu
github: raymond91125
name: Raymond Lee
orcid: 0000-0002-8151-7479
description: Ontology about the gross anatomy of the C. elegans
download_obo: http://purl.obolibrary.org/obo/wbbt.obo
download_owl: http://purl.obolibrary.org/obo/wbbt.owl
example: 0001290
homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
license: CC BY 4.0
mappings:
biocontext: WBBT
biolink: WBbt
bioportal: WB-BT
fairsharing: FAIRsharing.phk7dd
go: WBbt
obofoundry: WBbt
ols: wbbt
ontobee: WBbt
prefixcommons: wbbt
name: C. elegans Gross Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: WBbt
repository: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
synonyms:
- WBbt
uri_format: http://purl.obolibrary.org/obo/WBBT_$1
version: '2022-03-22'
wbls:
banana: WBls
contact:
email: cgrove@caltech.edu
github: chris-grove
name: Chris Grove
orcid: 0000-0001-9076-6015
description: Ontology about the development and life stages of the C. elegans
download_obo: http://purl.obolibrary.org/obo/wbls.obo
download_owl: http://purl.obolibrary.org/obo/wbls.owl
example: 0000690
homepage: https://github.com/obophenotype/c-elegans-development-ontology
license: CC BY 4.0
mappings:
biocontext: WBLS
biolink: WBls
bioportal: WB-LS
fairsharing: FAIRsharing.sm90nh
go: WBls
obofoundry: WBls
ols: wbls
ontobee: WBLS
prefixcommons: wbls
name: C. elegans development ontology
part_of: wormbase
pattern: ^\d{7}$
preferred_prefix: WBls
repository: https://github.com/obophenotype/c-elegans-development-ontology
synonyms:
- WBls
uri_format: http://www.wormbase.org/get?name=$1
version: '2022-03-22'
wbphenotype:
banana: WBPhenotype
contact:
email: cgrove@caltech.edu
github: chris-grove
name: Chris Grove
orcid: 0000-0001-9076-6015
description: Ontology about C. elegans and other nematode phenotypes
download_obo: http://purl.obolibrary.org/obo/wbphenotype.obo
download_owl: http://purl.obolibrary.org/obo/wbphenotype.owl
example: 0000983
homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology
license: CC BY 4.0
mappings:
biocontext: WBPhenotype
bioportal: WB-PHENOTYPE
fairsharing: FAIRsharing.agvc7y
go: WBPhenotype
obofoundry: WBPhenotype
ols: wbphenotype
ontobee: WBPhenotype
prefixcommons: wbphenotype
name: C. elegans phenotype
part_of: wormbase
pattern: ^\d{7}$
preferred_prefix: WBPhenotype
repository: https://github.com/obophenotype/c-elegans-phenotype-ontology
synonyms:
- WBPhenotype
uri_format: http://www.wormbase.org/get?name=$1
version: '2022-03-22'
webelements:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Browser for the periodic table of the elements
example: chromium
homepage: https://www.webelements.com/
name: Web Elements
pattern: ^\w+$
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
wicell:
description: Cell line collections
example: ai10e-kctd13b
homepage: https://www.wicell.org
mappings:
cellosaurus: WiCell
name: WiCell Research Institute Cell Collection
preferred_prefix: wicell
uri_format: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true
wikidata:
description: Wikidata is a collaboratively edited knowledge base operated by the
Wikimedia Foundation. It is intended to provide a common source of certain types
of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions
as a document-oriented database, centred on individual items. Items represent
topics, for which basic information is stored that identifies each topic.
example: Q2207226
homepage: https://www.wikidata.org/
mappings:
biocontext: WD_Entity
biolink: WIKIDATA
cellosaurus: Wikidata
cheminf: '000567'
fairsharing: FAIRsharing.6s749p
miriam: wikidata
n2t: wikidata
name: Wikidata
pattern: ^(Q|P)\d+$
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/$1
wikidata.property:
description: 'Wikidata is a free and open knowledge base that can be read and edited
by both humans and machines.
Wikidata acts as central storage for the structured data of its Wikimedia sister
projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. '
example: P4355
homepage: https://www.wikidata.org
mappings:
biocontext: WD_Prop
biolink: WIKIDATA_PROPERTY
name: Wikidata Property
pattern: ^P\d+$
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:$1
wikigenes:
description: WikiGenes is a collaborative knowledge resource for the life sciences,
which is based on the general wiki idea but employs specifically developed technology
to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide
a platform for the scientific community to collect, communicate and evaluate knowledge
about genes, chemicals, diseases and other biomedical concepts in a bottom-up
process.
example: '3771877'
homepage: http://www.wikigenes.org/
mappings:
biocontext: WIKIGENES
miriam: wikigenes
n2t: wikigenes
name: WikiGenes
pattern: ^\d+$
preferred_prefix: wikigenes
provides: ncbigene
uri_format: http://www.wikigenes.org/e/gene/e/$1.html
wikipathways:
description: "WikiPathways is a resource providing an open and public collection\
\ of pathway maps created and curated by the community in a Wiki like style.\r\
\nAll content is under the Creative Commons Attribution 3.0 Unported license."
example: WP732
homepage: http://www.wikipathways.org/
mappings:
biocontext: WIKIPATHWAYS
bioportal: WIKIPATHWAYS
fairsharing: FAIRsharing.g7b4rj
miriam: wikipathways
n2t: wikipathways
prefixcommons: wikipathways
scholia: wikipathways
wikidata: P2410
name: WikiPathways
pattern: ^WP\d{1,5}(\_r\d+)?$
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/$1
wikipedia.en:
description: Wikipedia is a multilingual, web-based, free-content encyclopedia project
based on an openly editable model. It is written collaboratively by largely anonymous
Internet volunteers who write without pay.
example: SM_UB-81
homepage: http://en.wikipedia.org/wiki/Main_Page
mappings:
biocontext: WIKIPEDIA.EN
go: Wikipedia
miriam: wikipedia.en
n2t: wikipedia.en
prefixcommons: wikipedia
name: Wikipedia
pattern: ^[A-Za-z-0-9_]+$
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/$1
worfdb:
description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete
set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis
elegans. This collection describes experimentally defined transcript structures
of unverified genes through RACE (Rapid Amplification of cDNA Ends).
example: T01B6.1
homepage: http://worfdb.dfci.harvard.edu/
mappings:
biocontext: WORFDB
miriam: worfdb
n2t: worfdb
ncbi: WorfDB
prefixcommons: worfdb
name: C. elegans ORFeome cloning project
pattern: ^\w+(\.\d+)$
preferred_prefix: worfdb
uri_format: http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1
wormbase:
description: WormBase is an online bioinformatics database of the biology and genome
of the model organism Caenorhabditis elegans and other nematodes. It is used by
the C. elegans research community both as an information resource and as a mode
to publish and distribute their results. This collection references WormBase-accessioned
entities.
example: WBGene00000001
homepage: https://www.wormbase.org/
mappings:
biocontext: WormBase
biolink: WBVocab
fairsharing: FAIRsharing.zx1td8
go: WB_REF
miriam: wb
n2t: wb
ncbi: WormBase
prefixcommons: wormbase
uniprot: WormBase
wikidata: P3860
name: WormBase database of nematode biology
pattern: ^WB[A-Z][a-z]+\d+$
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=$1
wormpep:
description: Wormpep contains the predicted proteins from the Caenorhabditis elegans
genome sequencing project.
example: CE28239
homepage: https://www.wormbase.org/db/seq/protein
mappings:
biocontext: WORMPEP
miriam: wormpep
n2t: wormpep
prefixcommons: wormpep
name: Wormpep
pattern: ^CE\d{5}$
preferred_prefix: wormpep
uri_format: https://www.wormbase.org/db/seq/protein?name=$1
worms:
description: The World Register of Marine Species (WoRMS) provides an authoritative
and comprehensive list of names of marine organisms. It includes synonyms for
valid taxonomic names allowing a more complete interpretation of taxonomic literature.
The content of WoRMS is administered by taxonomic experts.
example: '146421'
homepage: http://www.marinespecies.org/
mappings:
biocontext: WORMS
fairsharing: FAIRsharing.7g1bzj
miriam: worms
n2t: worms
name: World Register of Marine Species
pattern: ^\d+$
preferred_prefix: worms
uri_format: http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1
wwf.ecoregion:
comment: ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658
contributor:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: WWF ecoregions are large unit of land or water containing a geographically
distinct assemblage of species, natural communities, and environmental conditions.
example: AT1402
homepage: https://www.worldwildlife.org/biomes
mappings:
wikidata: P1294
name: World Wildlife Fund Ecoregion
pattern: ^AT\d+$
preferred_prefix: wwf.ecoregion
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
synonyms:
- WWF
uri_format: https://www.worldwildlife.org/ecoregions/$1
xao:
appears_in:
- xpo
banana: XAO
contact:
email: Erik.Segerdell@cchmc.org
github: seger
name: Erik Segerdell
orcid: 0000-0002-9611-1279
description: XAO represents the anatomy and development of the African frogs Xenopus
laevis and tropicalis.
download_obo: http://purl.obolibrary.org/obo/xao.obo
download_owl: http://purl.obolibrary.org/obo/xao.owl
example: 0004486
homepage: http://www.xenbase.org/anatomy/xao.do?method=display
license: CC BY 3.0
mappings:
biocontext: XAO
bioportal: XAO
fairsharing: FAIRsharing.17zapb
obofoundry: XAO
ols: xao
ontobee: XAO
wikidata: P4495
name: Xenopus Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: XAO
repository: https://github.com/xenopus-anatomy/xao
uri_format: http://purl.obolibrary.org/obo/XAO_$1
version: '2021-03-04'
xco:
appears_in:
- agro
- ecto
banana: XCO
contact:
email: jrsmith@mcw.edu
github: jrsjrs
name: Jennifer Smith
orcid: 0000-0002-6443-9376
description: Conditions under which physiological and morphological measurements
are made both in the clinic and in studies involving humans or model organisms.
download_obo: http://purl.obolibrary.org/obo/xco.obo
download_owl: http://purl.obolibrary.org/obo/xco.owl
example: 0000780
homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000
license: CC0 1.0
mappings:
biocontext: XCO
bioportal: XCO
fairsharing: FAIRsharing.x39h5y
obofoundry: XCO
ols: xco
ontobee: XCO
prefixcommons: xco
name: Experimental condition ontology
pattern: ^\d{7}$
preferred_prefix: XCO
repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology
uri_format: http://purl.obolibrary.org/obo/XCO_$1
version: '2019-12-18'
xenbase:
description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana)
tropicalis. It contains genomic, development data and community information for
Xenopus research. it includes gene expression patterns that incorporates image
data from the literature, large scale screens and community submissions.
example: XB-GENE-922462
homepage: https://www.xenbase.org/
mappings:
biocontext: Xenbase
biolink: Xenbase
fairsharing: FAIRsharing.jrv6wj
go: Xenbase
miriam: xenbase
n2t: xenbase
ncbi: Xenbase
prefixcommons: xenbase
uniprot: Xenbase
name: Xenbase
pattern: ^XB\-\w+\-\d+$
preferred_prefix: xenbase
uri_format: https://www.xenbase.org/common/xsearch.do?exactSearch=true&searchIn=7&searchValue=$1
ximbio:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell line collections
example: '151022'
homepage: https://ximbio.com
mappings:
cellosaurus: Ximbio
name: Ximbio
pattern: ^\d+$
preferred_prefix: ximbio
uri_format: https://ximbio.com/reagent/$1
xl:
deprecated: true
description: A structured controlled vocabulary for cross-linking reagents used
with proteomics mass spectrometry.
download_owl: http://purl.obolibrary.org/obo/xl.owl
homepage: http://www.psidev.info/groups/controlled-vocabularies
mappings:
biocontext: XL
ols: xl
ontobee: XL
name: Cross-linker reagents ontology
preferred_prefix: xl
uri_format: http://purl.obolibrary.org/obo/XL_$1
xlmod:
banana: XLMOD
contact:
email: lutz.fischer@tu-berlin.de
github: lutzfischer
name: Lutz Fischer
orcid: 0000-0003-4978-0864
description: A structured controlled vocabulary for cross-linking reagents used
with proteomics mass spectrometry.
download_obo: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo
download_owl: http://purl.obolibrary.org/obo/xlmod.owl
example: '00050'
homepage: http://www.psidev.info/groups/controlled-vocabularies
license: CC BY 3.0
mappings:
bioportal: XLMOD
obofoundry: XLMOD
ols: xlmod
ontobee: XLMOD
name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary
pattern: ^\d{5}$
preferred_prefix: XLMOD
repository: https://github.com/HUPO-PSI/xlmod-CV
uri_format: http://purl.obolibrary.org/obo/XLMOD_$1
version: '2019-10-28'
xmetdb:
banana: XMETDB
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: Metabolites in the Xenobiotics Metabolism Database.
example: '171'
homepage: https://xmetdb.org
name: Xenobiotics Metabolism Database
pattern: ^\d+$
preferred_prefix: xmetdb
uri_format: http://www.xmetdb.org/xmetdb/protocol/$1
xml:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Extensible Markup Language (XML) is a subset of SGML that is completely
described in this document. Its goal is to enable generic SGML to be served, received,
and processed on the Web in the way that is now possible with HTML. XML has been
designed for ease of implementation and for interoperability with both SGML and
HTML.
example: lang
homepage: https://www.w3.org/TR/xml/
mappings:
biocontext: xml
name: Extensible Markup Language
preferred_prefix: xml
uri_format: http://www.w3.org/XML/1998/namespace$1
xpo:
banana: XPO
contact:
email: Erik.Segerdell@cchmc.org
github: seger
name: Erik Segerdell
orcid: 0000-0002-9611-1279
depends_on:
- bfo
- chebi
- cl
- go
- iao
- pato
- ro
- xao
description: XPO represents anatomical, cellular, and gene function phenotypes occurring
throughout the development of the African frogs Xenopus laevis and tropicalis.
download_obo: http://purl.obolibrary.org/obo/xpo.obo
download_owl: http://purl.obolibrary.org/obo/xpo.owl
example: '0100002'
homepage: https://github.com/obophenotype/xenopus-phenotype-ontology
license: CC BY 3.0
mappings:
biolink: XPO
bioportal: XPO
obofoundry: XPO
ols: xpo
ontobee: XPO
name: Xenopus Phenotype Ontology
pattern: ^\d+$
preferred_prefix: XPO
repository: https://github.com/obophenotype/xenopus-phenotype-ontology
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:
biocontext: xsd
name: XML Schema Definition
preferred_prefix: xsd
uri_format: http://www.w3.org/2001/XMLSchema#$1
xuo:
appears_in:
- hsapdv
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
name: XUO
preferred_prefix: xuo
ydpm:
description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial
Proteomics Project. The project aims to increase the understanding of mitochondrial
function and biogenesis in the context of the cell. In the Deletion Project, strains
from the deletion collection were monitored under 9 different media conditions
selected for the study of mitochondrial function. The YDPM database contains both
the raw data and growth rates calculated for each strain in each media condition.
example: YAL001C
homepage: http://www-deletion.stanford.edu/YDPM/
mappings:
biocontext: YDPM
miriam: ydpm
n2t: ydpm
prefixcommons: ydpm
name: Yeast Deletion and the Mitochondrial Proteomics Project
pattern: ^Y[A-Z]{2}\d+[CW]$
preferred_prefix: ydpm
uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1
yeastintron:
description: The YEast Intron Database (version 4.3) contains information on the
spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression
data that relates to the efficiency of splicing relative to other processes in
strains of yeast lacking nonessential splicing factors. The data are displayed
on each intron page. This is an updated version of the previous dataset, which
can be accessed through [MIR:00000460].
example: SNR17A
homepage: http://intron.ucsc.edu/yeast4.3/
mappings:
biocontext: YEASTINTRON
miriam: yeastintron
n2t: yeastintron
name: Yeast Intron Database v4.3
pattern: ^[A-Z0-9]+$
preferred_prefix: yeastintron
uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1
yetfasco:
description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is
a database of transcription factor specificities for the yeast Saccharomyces cerevisiae
in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.
example: YOR172W_571.0
homepage: http://yetfasco.ccbr.utoronto.ca/
mappings:
biocontext: YETFASCO
miriam: yetfasco
n2t: yetfasco
name: YeTFasCo
pattern: ^\w+\_\d+(\.\d+)?$
preferred_prefix: yetfasco
uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1
yid:
description: The YEast Intron Database (version 3) contains information on the spliceosomal
introns of the yeast Saccharomyces cerevisiae. It includes expression data that
relates to the efficiency of splicing relative to other processes in strains of
yeast lacking nonessential splicing factors. The data are displayed on each intron
page. An updated version of the database is available through [MIR:00000521].
example: SNR17A
homepage: http://compbio.soe.ucsc.edu/yeast_introns.html
mappings:
biocontext: YID
miriam: yid
n2t: yid
name: Yeast Intron Database v3
pattern: ^[A-Z0-9]+$
preferred_prefix: yid
uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1
ymdb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Yeast Metabolome Database (YMDB) is a manually curated database
of small molecule metabolites found in or produced by Saccharomyces cerevisiae
(also known as Baker’s yeast and Brewer’s yeast).
example: YMDB00001
homepage: http://www.ymdb.ca
mappings:
fairsharing: FAIRsharing.tawpg2
name: Yeast Metabolome Database
pattern: ^YMDB\d+$
preferred_prefix: ymdb
uri_format: http://www.ymdb.ca/compounds/$1
ypo:
banana: YPO
contact:
email: cherry@genome.stanford.edu
github: null
name: Mike Cherry
orcid: 0000-0001-9163-5180
deprecated: true
homepage: http://www.yeastgenome.org/
mappings:
obofoundry: YPO
ols: ypo
name: Yeast phenotypes
preferred_prefix: YPO
uri_format: http://purl.obolibrary.org/obo/YPO_$1
yrcpdr:
description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as
a single point of access for the experimental data produced from many collaborations
typically studying Saccharomyces cerevisiae (baker's yeast). The experimental
data include large amounts of mass spectrometry results from protein co-purification
experiments, yeast two-hybrid interaction experiments, fluorescence microscopy
images and protein structure predictions.
example: '2673500'
homepage: http://www.yeastrc.org/pdr/
mappings:
biocontext: YRCPDR
fairsharing: FAIRsharing.karvzj
miriam: yrcpdr
n2t: yrcpdr
name: YRC PDR
pattern: ^\d+$
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: 0000-0002-9316-2919
deprecated: true
homepage: http://www.maizemap.org/
mappings:
biocontext: ZEA
bioportal: ZEA
obofoundry: ZEA
prefixcommons: zea
name: Maize gross anatomy
preferred_prefix: ZEA
uri_format: http://purl.obolibrary.org/obo/ZEA_$1
zeco:
appears_in:
- mco
banana: ZECO
contact:
email: ybradford@zfin.org
github: ybradford
name: Yvonne Bradford
orcid: 0000-0002-9900-7880
description: Ontology of Zebrafish Experimental Conditions
download_json: http://purl.obolibrary.org/obo/zeco.json
download_obo: http://purl.obolibrary.org/obo/zeco.obo
download_owl: http://purl.obolibrary.org/obo/zeco.owl
example: '0000171'
homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
license: CC BY 3.0
mappings:
biocontext: ZECO
bioportal: ZECO
fairsharing: FAIRsharing.np2wfz
obofoundry: ZECO
ols: zeco
ontobee: ZECO
name: Zebrafish Experimental Conditions Ontology
pattern: ^\d{7}$
preferred_prefix: ZECO
repository: https://github.com/ybradford/zebrafish-experimental-conditions-ontology
uri_format: http://purl.obolibrary.org/obo/ZECO_$1
version: '2022-02-14'
zfa:
appears_in:
- zp
banana: ZFA
contact:
email: van_slyke@zfin.org
github: cerivs
name: Ceri Van Slyke
orcid: 0000-0002-2244-7917
description: ZFA description.
download_obo: http://purl.obolibrary.org/obo/zfa.obo
download_owl: http://purl.obolibrary.org/obo/zfa.owl
example: 0005926
homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
license: CC BY 3.0
mappings:
biocontext: ZFA
bioportal: ZFA
fairsharing: FAIRsharing.s3r6sk
obofoundry: ZFA
ols: zfa
ontobee: ZFA
prefixcommons: zfa
name: Zebrafish anatomy and development ontology
pattern: ^\d{7}$
preferred_prefix: ZFA
repository: https://github.com/cerivs/zebrafish-anatomical-ontology
synonyms:
- ZFA_RETIRED
uri_format: http://purl.obolibrary.org/obo/ZFA_$1
version: '2022-03-15'
zfin:
description: ZFIN serves as the zebrafish model organism database. This collection
references all zebrafish biological entities in ZFIN.
example: ZDB-GENE-041118-11
homepage: http://zfin.org
mappings:
biocontext: ZFIN
fairsharing: FAIRsharing.ybxnhg
go: ZFIN
miriam: zfin
n2t: zfin
ncbi: ZFIN
prefixcommons: zfin
uniprot: ZFIN
wikidata: P3870
name: Zebrafish Information Network Gene
pattern: ^ZDB\-\w+\-\d+\-\d+$
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/$1
zfs:
banana: ZFS
contact:
email: van_slyke@zfin.org
github: cerivs
name: Ceri Van Slyke
orcid: 0000-0002-2244-7917
description: Developmental stages of the Zebrafish
download_obo: http://purl.obolibrary.org/obo/zfs.obo
download_owl: http://purl.obolibrary.org/obo/zfs.owl
example: '0000050'
homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources
license: CC BY 3.0
mappings:
biocontext: ZFS
bioportal: ZFS
fairsharing: FAIRsharing.bc8ayj
obofoundry: ZFS
ols: zfs
ontobee: ZFS
name: Zebrafish developmental stages ontology
pattern: ^\d{7}$
preferred_prefix: ZFS
repository: https://github.com/cerivs/zebrafish-anatomical-ontology
uri_format: http://purl.obolibrary.org/obo/ZFS_$1
version: '2020-03-10'
zinc:
description: ZINC is a free public resource for ligand discovery. The database contains
over twenty million commercially available molecules in biologically relevant
representations that may be downloaded in popular ready-to-dock formats and subsets.
The Web site enables searches by structure, biological activity, physical property,
vendor, catalog number, name, and CAS number.
example: ZINC1084
homepage: http://zinc15.docking.org/
mappings:
biocontext: ZINC
miriam: zinc
n2t: zinc
wikidata: P2084
name: ZINC is not Commercial
pattern: ^(ZINC)?\d+$
preferred_prefix: zinc
uri_format: http://zinc15.docking.org/substances/$1
zp:
banana: ZP
contact:
email: ybradford@zfin.org
github: ybradford
name: Yvonne Bradford
orcid: 0000-0002-9900-7880
depends_on:
- bfo
- bspo
- go
- pato
- ro
- uberon
- zfa
description: The Zebrafish Phenotype Ontology formally defines all phenotypes of
the Zebrafish model organism.
download_obo: http://purl.obolibrary.org/obo/zp.obo
download_owl: http://purl.obolibrary.org/obo/zp.owl
example: 0019030
homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology
license: CC BY 3.0
mappings:
biocontext: ZP
bioportal: ZP
obofoundry: ZP
ols: zp
ontobee: ZP
name: Zebrafish Phenotype Ontology
pattern: ^\d+$
preferred_prefix: ZP
repository: https://github.com/obophenotype/zebrafish-phenotype-ontology
uri_format: http://purl.obolibrary.org/obo/ZP_$1
version: '2021-12-12'