3dmet:
description: 3DMET is a database collecting three-dimensional structures of natural
metabolites.
example: B00162
homepage: http://www.3dmet.dna.affrc.go.jp/
keywords:
- chemical
- life science
- metabolite
- metabolomics
- structure
mappings:
biocontext: 3DMET
edam: '2635'
fairsharing: FAIRsharing.5ab0n7
miriam: 3dmet
n2t: 3dmet
prefixcommons: 3dmet
wikidata: P2796
name: 3D Metabolites
pattern: ^B\d{5}$
preferred_prefix: 3dmet
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/3dmet:$1
publications:
- doi: 10.2142/biophysico.15.0_87
pmc: PMC5992871
pubmed: '29892514'
title: 'Chemical curation to improve data accuracy: recent development of the
3DMET database.'
year: 2018
- doi: 10.1021/ci300309k
pmc: null
pubmed: '23293959'
title: 'Three-dimensional structure database of natural metabolites (3DMET): a
novel database of curated 3D structures.'
year: 2013
uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1
4dn.biosource:
description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network
and other reference nucleomics data sets. The 4D Nucleome Network aims to understand
the principles underlying nuclear organization in space and time, the role nuclear
organization plays in gene expression and cellular function, and how changes in
nuclear organization affect normal development as well as various diseases.
example: 4DNSR73BT2A2
homepage: https://data.4dnucleome.org/biosources
keywords:
- dna
- life science
- protein
mappings:
cellosaurus: 4DN
fairsharing: FAIRsharing.CugtbQ
miriam: 4dn
prefixcommons: 4dn
name: 4D Nucleome Data Portal Biosource
pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$
preferred_prefix: 4dn.biosource
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/4dn:$1
publications:
- doi: 10.1038/nature23884
pmc: PMC5617335
pubmed: '28905911'
title: The 4D nucleome project.
year: 2017
synonyms:
- 4DN
twitter: 4dn_dcic
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
contributor_extras:
- email: laylamichan@ciencias.unam.mx
github: lmichan
name: Layla Michán Aguirre
orcid: 0000-0002-5798-662X
- email: mineromero2901@ciencias.unam.mx
github: MinRo60
name: Minerva María Romero Pérez
orcid: 0000-0002-6240-9325
- email: victorinolavida@ciencias.unam.mx
github: Victorinolavida
name: José Victorino Ruiz Lavida
orcid: 0000-0001-5130-7705
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
aaindex:
description: Identifier of an entry from the AAindex database.
example: BUNA790102
homepage: http://www.genome.ad.jp/aaindex/
keywords:
- protein
mappings:
edam: '1128'
prefixcommons: aaindex
name: AAindex
preferred_prefix: aaindex
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/aaindex:$1
publications:
- doi: 10.1093/nar/gkm998
pmc: PMC2238890
pubmed: '17998252'
title: 'AAindex: amino acid index database, progress report 2008.'
year: 2007
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.genome.jp/dbget-bin/www_bget?aaindex:$1
aao:
contact:
email: david.c.blackburn@gmail.com
github: null
name: David Blackburn
orcid: 0000-0002-1810-9886
deprecated: true
description: A structured controlled vocabulary of the anatomy of Amphibians. Note
that AAO is currently being integrated into Uberon.
example: 0000138
homepage: http://github.com/seger/aao
keywords:
- anatomy
- obo
- ontology
mappings:
biocontext: AAO
fairsharing: FAIRsharing.mxx5rp
obofoundry: aao
prefixcommons: aao
name: Amphibian gross anatomy
pattern: ^\d{7}$
preferred_prefix: AAO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/aao:$1
publications:
- doi: 10.1186/2041-1480-5-21
pmc: PMC4089931
pubmed: '25009735'
title: Unification of multi-species vertebrate anatomy ontologies for comparative
biology in Uberon.
year: 2014
- doi: 10.1142/9789812772435_0035
pmc: null
pubmed: '17992749'
title: An anatomical ontology for amphibians.
year: 2007
rdf_uri_format: http://purl.obolibrary.org/obo/AAO_$1
uri_format: http://purl.obolibrary.org/obo/AAO_$1
abcd:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The ABCD (AntiBodies Chemically Defined) database is a manually curated
depository of sequenced antibodies
example: AD834
homepage: https://web.expasy.org/abcd/
keywords:
- immunology
- molecular biology
mappings:
cellosaurus: ABCD
fairsharing: FAIRsharing.Z8OKi5
uniprot: DB-0236
name: AntiBodies Chemically Defined database
preferred_prefix: abcd
publications:
- doi: 10.1093/nar/gkz714
pmc: PMC6943046
pubmed: '31410491'
title: 'The ABCD database: a repository for chemically defined antibodies.'
year: 2020
uri_format: https://web.expasy.org/abcd/ABCD_$1
abm:
contributor_extras:
- email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
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/search?query=$1
abs:
contact:
email: enrique.blanco@crg.eu
github: null
name: Enrique Blanco
orcid: 0000-0001-6261-7370
description: The database of Annotated regulatory Binding Sites (from orthologous
promoters), ABS, is a public database of known binding sites identified in promoters
of orthologous vertebrate genes that have been manually curated from bibliography.
example: A0014
homepage: http://genome.crg.es/datasets/abs2005/
keywords:
- biology
- gene
- interaction
- regulation
mappings:
biocontext: ABS
edam: '2741'
fairsharing: FAIRsharing.7mnebr
miriam: abs
n2t: abs
prefixcommons: abs
name: Annotated Regulatory Binding Sites
pattern: ^A\d+$
preferred_prefix: abs
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/abs:$1
publications:
- doi: 10.1093/nar/gkj116
pmc: PMC1347478
pubmed: '16381947'
title: 'ABS: a database of Annotated regulatory Binding Sites from orthologous
promoters.'
year: 2006
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
keywords:
- semantic web
- social media
name: Activity Streams
preferred_prefix: ac
uri_format: http://www.w3.org/ns/activitystreams#$1
aceview.worm:
description: AceView provides a curated sequence representation of all public mRNA
sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST
and Trace). These are aligned on the genome and clustered into a minimal number
of alternative transcript variants and grouped into genes. In addition, alternative
features such as promoters, and expression in tissues is recorded. This collection
references C. elegans genes and expression.
example: aap-1
homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm
keywords:
- dna
- gene
- rna
mappings:
biocontext: ACEVIEW.WORM
miriam: aceview.worm
n2t: aceview.worm
prefixcommons: aceview.worm
name: Aceview Worm
pattern: ^[a-z0-9-]+$
preferred_prefix: aceview.worm
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/aceview.worm:$1
publications:
- doi: 10.1186/gb-2006-7-s1-s12
pmc: PMC1810549
pubmed: '16925834'
title: 'AceView: a comprehensive cDNA-supported gene and transcripts annotation.'
year: 2006
uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1
adcad:
contact:
email: brycemecum@gmail.com
github: amoeba
name: Bryce Mecum
orcid: 0000-0002-0381-3766
contributor:
email: j.harry.caufield@gmail.com
github: caufieldjh
name: Harry Caufield
orcid: 0000-0001-5705-7831
description: An ontology to support disciplinary annotation of Arctic Data Center
datasets.
download_rdf: https://github.com/NCEAS/adc-disciplines/raw/main/ADCAD.ttl
example: '00000'
github_request_issue: 827
homepage: https://arcticdata.io/
keywords:
- ontology
license: CC-BY-4.0
mappings:
bioportal: ADCAD
name: Arctic Data Center Academic Disciplines Ontology
pattern: ^\d{5}$
preferred_prefix: adcad
repository: https://github.com/NCEAS/adc-disciplines
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://purl.dataone.org/odo/ADCAD_$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=$1
addgene:
description: Addgene is a non-profit plasmid repository. Addgene facilitates the
exchange of genetic material between laboratories by offering plasmids and their
associated cloning data to not-for-profit laboratories around the world.
example: '50943'
homepage: http://addgene.org/
keywords:
- life science
- plasmid
mappings:
fairsharing: FAIRsharing.8hcczk
miriam: addgene
n2t: addgene
prefixcommons: addgene
re3data: r3d100010741
name: Addgene Plasmid Repository
pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$
preferred_prefix: addgene
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/addgene:$1
publications:
- doi: 10.1093/nar/gku893
pmc: PMC4384007
pubmed: '25392412'
title: 'The Addgene repository: an international nonprofit plasmid and data resource.'
year: 2014
- doi: 10.1038/505272a
pmc: null
pubmed: '24429608'
title: Repositories share key research tools.
year: 2014
- doi: 10.1038/nbt.2177
pmc: null
pubmed: '22491276'
title: Addgene provides an open forum for plasmid sharing.
year: 2012
twitter: Addgene
uri_format: http://addgene.org/$1
adms:
contact:
email: bert.van.nuffelen@tenforce.com
github: bertvannuffelen
name: Bert Van Nuffelen
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A vocabulary for describing semantic assets, defined as highly reusable
metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code
lists, taxonomies, dictionaries, vocabularies).
example: Asset
homepage: http://www.w3.org/ns/adms
license: CC-BY-4.0
name: Asset Description Metadata Schema Vocabulary
preferred_prefix: adms
repository: https://github.com/SEMICeu/ADMS/
uri_format: http://www.w3.org/ns/adms#$1
ado:
contact:
email: alpha.tom.kodamullil@scai.fraunhofer.de
github: akodamullil
name: Alpha Tom Kodamullil
orcid: 0000-0001-9896-3531
depends_on:
- bfo
description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses
varieties of concepts related to Alzheimer'S Disease, foundamentally structured
by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational
entities that demonstrate the nextwork of the understanding on Alzheimer's disease
and can be readily applied for text mining.
download_owl: http://purl.obolibrary.org/obo/ado.owl
example: '0000001'
homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
keywords:
- health science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: ADO
bioportal: ADO
fairsharing: FAIRsharing.ckd4rf
obofoundry: ado
ols: ado
ontobee: ADO
name: Alzheimer's Disease Ontology
pattern: ^\d{7}$
preferred_prefix: ADO
publications:
- doi: 10.1016/j.jalz.2013.02.009
pmc: null
pubmed: '23830913'
title: 'ADO: a disease ontology representing the domain knowledge specific to
Alzheimer''s disease.'
year: 2013
rdf_uri_format: http://purl.obolibrary.org/obo/ADO_$1
repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
uri_format: http://purl.obolibrary.org/obo/ADO_$1
version: '2022-06-11'
adw:
contact:
email: adw_geeks@umich.edu
github: null
name: Animal Diversity Web technical staff
orcid: null
deprecated: true
description: Animal Diversity Web (ADW) is an online database of animal natural
history, distribution, classification, and conservation biology.
download_owl: http://aber-owl.net/media/ontologies/ADW/2/adw.owl
example: Lycalopex_vetulus
homepage: http://www.animaldiversity.org
keywords:
- anatomy
- life science
- obo
- ontology
mappings:
aberowl: ADW
biocontext: ADW
bioportal: ADW
fairsharing: FAIRsharing.t9fvdn
miriam: adw
n2t: adw
obofoundry: adw
name: Animal natural history and life history
pattern: ^[A-Z_a-z]+$
preferred_prefix: ADW
rdf_uri_format: http://purl.obolibrary.org/obo/ADW_$1
uri_format: https://animaldiversity.org/accounts/$1
aeo:
appears_in:
- ehdaa2
contact:
email: J.Bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
deprecated: true
description: AEO is an ontology of anatomical structures that expands CARO, the
Common Anatomy Reference Ontology
download_obo: http://purl.obolibrary.org/obo/aeo.obo
download_owl: http://purl.obolibrary.org/obo/aeo.owl
example: '0001017'
homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
keywords:
- anatomy
- life science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: AEO
bartoc: '181'
biocontext: AEO
bioportal: AEO
fairsharing: FAIRsharing.93ee19
obofoundry: aeo
ols: aeo
ontobee: AEO
name: Anatomical Entity Ontology
pattern: ^\d{7}$
preferred_prefix: AEO
publications:
- doi: 10.3389/fgene.2012.00018
pmc: PMC3278863
pubmed: '22347883'
title: The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues
and Organs.
year: 2012
rdf_uri_format: http://purl.obolibrary.org/obo/AEO_$1
repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
synonyms:
- AEO_RETIRED
uri_format: http://purl.obolibrary.org/obo/AEO_$1
version: '2014-12-05'
aeon:
contact:
email: Philip.Stroemert@tib.eu
github: StroemPhi
name: Philip Strömert
orcid: 0000-0002-1595-3213
contributor:
email: Philip.Stroemert@tib.eu
github: StroemPhi
name: Philip Strömert
orcid: 0000-0002-1595-3213
description: The academic event ontology, currently still in development and thus
unstable, is an OBO compliant reference ontology for describing academic events
such as conferences, workshops or seminars and their series. It is being developed
as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow
RDF representations of the academic events and series stored and curated in the
[ConfIDent platform](https://www.confident-conference.org/index.php/main_page).
download_owl: https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl
example: '0000001'
github_request_issue: 617
homepage: https://tibonto.github.io/aeon/
keywords:
- ontology
license: CC-BY-4.0
name: Academic Event Ontology
pattern: ^\d{7}$
preferred_prefix: aeon
repository: https://github.com/tibonto/aeon
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://purl.obolibrary.org/obo/AEON_$1
aero:
contact:
email: mcourtot@gmail.com
github: null
name: Melanie Courtot
orcid: 0000-0002-9551-6370
deprecated: true
description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at
supporting clinicians at the time of data entry, increasing quality and accuracy
of reported adverse events
download_owl: http://purl.obolibrary.org/obo/aero.owl
example: '0000125'
homepage: http://purl.obolibrary.org/obo/aero
keywords:
- biomedical science
- health science
- medicine
- obo
- ontology
- preclinical studies
license: CC-BY-3.0
mappings:
aberowl: AERO
biocontext: AERO
bioportal: AERO
fairsharing: FAIRsharing.rycy2x
obofoundry: aero
ols: aero
name: Adverse Event Reporting Ontology
pattern: ^\d{7}$
preferred_prefix: AERO
rdf_uri_format: http://purl.obolibrary.org/obo/AERO_$1
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=$1
afo:
contact:
email: more.info@allotrope.org
github: null
name: Allotrope Foundation
orcid: null
description: Allotrope Merged Ontology Suite
download_owl: http://purl.allotrope.org/voc/afo/merged/REC/2023/03/merged-without-qudt-and-inferred
homepage: https://www.allotrope.org/
keywords:
- agricultural engineering
- agriculture
- biology
- environmental science
- food chemistry
- forest management
- ontology
- veterinary medicine
mappings:
aberowl: AFO
bioportal: AFO
fairsharing: FAIRsharing.595710
ols: afo
ontobee: AFO
name: Allotrope Merged Ontology Suite
no_own_terms: true
preferred_prefix: afo
version: 2023/03
aftol.taxonomy:
contributor_extras:
- email: laylamichan@ciencias.unam.mx
github: lmichan
name: Layla Michán Aguirre
orcid: 0000-0002-5798-662X
description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated
to significantly enhancing our understanding of the evolution of the Kingdom Fungi,
which represents one of the major clades of life. There are roughly 80,000 described
species of Fungi, but the actual diversity in the group has been estimated to
be about 1.5 million species.
example: '959'
homepage: https://aftol.umn.edu
mappings:
biocontext: AFTOL.TAXONOMY
miriam: aftol.taxonomy
n2t: aftol.taxonomy
name: Assembling the Fungal Tree of Life - Taxonomy
pattern: ^\d+$
preferred_prefix: aftol.taxonomy
uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1
agilent.probe:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent
design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows
x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows
x 192 cols). Version 2 of this array contains long intergenic non-coding RNA
(lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute,
along with an update of mRNA content when compared to version 1. Probes were designed
using GRCh37 assembly of the human genome. Annotation of probes came from the
following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank
(April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute
TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.'
example: A_24_P98555
homepage: https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt
keywords:
- transcriptomics
name: Agilent Probe
pattern: ^A_\d+_.+$
preferred_prefix: agilent.probe
references:
- http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt
agricola:
contributor_extras:
- email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
- email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
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
uniprot: DB-0266
name: Agricultural Online Access
pattern: ^\d+$
preferred_prefix: agricola
publications:
- doi: 10.1093/nar/gkz813
pmc: PMC6943066
pubmed: '31552413'
title: 'Alliance of Genome Resources Portal: unified model organism research platform.'
year: 2020
synonyms:
- AGR
- AGRICOLA_ID
uri_format: https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1
agrkb:
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
contributor:
email: null
github: sierra-moxon
name: Sierra Moxon
orcid: 0000-0002-8719-7760
description: 'The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us)
creates identifiers for several biological entity types including genes, other
sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles,
genotypes, strains, environments and experiments, phenotype annotations, expression
annotations, disease annotations, interactions, and variant annotations.
The Alliance of Genome Resources was founded by the following Model Organism databases
and the Gene Ontology Consortium and distributes high-quality, curated knowledge
about several model organisms in a single, unified location:
- [ZFIN](https://zfin.org) - Zebrafish Information Network
- [WormBase](https://wormbase.org)
- [MGI](https://www.mgi.org) - Mouse Genome Informatics
- [RGD](https://rgd.mcw.edu) - Rat Genome Database
- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database
- [FlyBase](https://flybase.org)
- [Xenbase](https://www.xenbase.org)'
example: '100000000000001'
github_request_issue: 359
homepage: https://www.alliancegenome.org
keywords:
- model organism database
mappings:
biolink: AGRKB
name: Alliance of Genome Resources Knowledge Base
pattern: ^[1-9][0-9]{14}$
preferred_prefix: agrkb
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://www.alliancegenome.org/accession/$1
agro:
contact:
email: m.a.laporte@cgiar.org
github: marieALaporte
name: Marie-Angélique Laporte
orcid: 0000-0002-8461-9745
depends_on:
- bfo
- envo
- foodon
- go
- iao
- ncbitaxon
- obi
- pato
- peco
- po
- ro
- to
- uo
- xco
description: AgrO is an ontlogy for representing agronomic practices, techniques,
variables and related entities
download_obo: https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo
download_owl: http://purl.obolibrary.org/obo/agro.owl
example: '00020007'
homepage: https://github.com/AgriculturalSemantics/agro
keywords:
- agriculture
- agronomy
- farming systems research
- obo
- ontology
- plant breeding
license: CC-BY-4.0
mappings:
aberowl: AGRO
agroportal: AGRO
biocontext: AGRO
bioportal: AGRO
fairsharing: FAIRsharing.m40bhw
obofoundry: agro
ols: agro
ontobee: AGRO
name: Agronomy Ontology
pattern: ^\d{8}$
preferred_prefix: AGRO
rdf_uri_format: http://purl.obolibrary.org/obo/AGRO_$1
repository: https://github.com/AgriculturalSemantics/agro
uri_format: http://purl.obolibrary.org/obo/AGRO_$1
version: '2022-11-02'
agrovoc:
banana: c_
contact:
email: agrovoc@fao.org
github: null
name: AGROVOC Team
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: AGROVOC is a multilingual and controlled vocabulary designed to cover
concepts and terminology under FAO's areas of interest. It is the largest Linked
Open Data set about agriculture available for public use and its greatest impact
is through providing the access and visibility of data across domains and languages.
example: '2842'
homepage: https://data.apps.fao.org/catalog/organization/agrovoc
keywords:
- agriculture
- botany
- data management
- environmental science
- fisheries science
- forest management
- nutritional science
mappings:
agroportal: AGROVOC
bartoc: '305'
ecoportal: AGROVOC
fairsharing: FAIRsharing.anpj91
wikidata: P8061
name: Agronomy Vocabulary
pattern: ^[a-z0-9]+$
preferred_prefix: agrovoc
publications:
- doi: 10.4060/cb2838en
pmc: null
pubmed: null
title: AGROVOC
year: 2021
- doi: 10.3390/engproc2021009017
pmc: null
pubmed: null
title: 'How Agricultural Digital Innovation Can Benefit from Semantics: The Case
of the AGROVOC Multilingual Thesaurus'
year: 2021
- doi: 10.1016/j.compag.2020.105965
pmc: null
pubmed: null
title: 'AGROVOC: The linked data concept hub for food and agriculture'
year: 2022
rdf_uri_format: http://aims.fao.org/aos/agrovoc/$1
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
twitter: FAOAIMS
uri_format: http://aims.fao.org/aos/agrovoc/c_$1
agsd:
description: A comprehensive catalogue of animal genome size data where haploid
DNA contents (C-values, in picograms) are currently available for 4972 species
(3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published
sources.
example: '4779'
homepage: http://www.genomesize.com
keywords:
- dna
- genome
- life science
mappings:
fairsharing: FAIRsharing.efp5v2
prefixcommons: agsd
re3data: r3d100012517
name: Animal Genome Size Database
preferred_prefix: agsd
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/agsd:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.genomesize.com/result_species.php?id=$1
aism:
appears_in:
- colao
- lepao
contact:
email: entiminae@gmail.com
github: JCGiron
name: Jennifer C. Girón
orcid: 0000-0002-0851-6883
depends_on:
- bfo
- bspo
- caro
- pato
- ro
- uberon
description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
contains terms used to describe the cuticle - as a single anatomical structure
- and the skeletal muscle system, to be used in insect biodiversity research.
download_json: http://purl.obolibrary.org/obo/aism.json
download_obo: http://purl.obolibrary.org/obo/aism.obo
download_owl: http://purl.obolibrary.org/obo/aism.owl
example: '0000027'
homepage: https://github.com/insect-morphology/aism
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: AISM
bioportal: AISM
obofoundry: aism
ols: aism
ontobee: AISM
name: Ontology for the Anatomy of the Insect SkeletoMuscular system
pattern: ^\d{7}$
preferred_prefix: AISM
rdf_uri_format: http://purl.obolibrary.org/obo/AISM_$1
repository: https://github.com/insect-morphology/aism
uri_format: http://purl.obolibrary.org/obo/AISM_$1
version: '2023-04-14'
alfred:
comment: This resource doesn't exist on the web anymore
deprecated: true
description: ALFRED has been designed to make allele frequency data on anthropologically
defined human population samples readily available to the scientific community
and to link these polymorphism data to the molecular genetics-human genome databases.
example: LO362836C
homepage: http://alfred.med.yale.edu
keywords:
- classification
- genome
mappings:
prefixcommons: alfred
name: The ALlele FREquency Database
preferred_prefix: alfred
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/alfred:$1
publications:
- doi: 10.1093/nar/gkg043
pmc: PMC165490
pubmed: '12519999'
title: 'ALFRED: the ALelle FREquency Database. Update.'
year: 2003
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1
allergome:
description: Allergome is a repository of data related to all IgE-binding compounds.
Its purpose is to collect a list of allergenic sources and molecules by using
the widest selection criteria and sources.
example: '1948'
homepage: http://www.allergome.org/
keywords:
- allergen
- biomedical science
- health science
- life science
- medicine
mappings:
biocontext: ALLERGOME
fairsharing: FAIRsharing.w6cxgb
miriam: allergome
n2t: allergome
prefixcommons: allergome
uniprot: DB-0160
name: Allergome
pattern: ^\d+$
preferred_prefix: allergome
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/allergome:$1
publications:
- doi: 10.1007/s11882-009-0055-9
pmc: null
pubmed: '19671381'
title: 'Allergen databases: current status and perspectives.'
year: 2009
- doi: 10.1016/j.cellimm.2007.02.012
pmc: null
pubmed: '17434469'
title: 'Bioinformatics applied to allergy: allergen databases, from collecting
sequence information to data integration. The Allergome platform as a model.'
year: 2007
- doi: null
pmc: null
pubmed: '17393720'
title: 'Allergome: a unifying platform.'
year: 2006
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
keywords:
- alzheimer's disease
- genes
- variants
name: Alzforum Mutations
preferred_prefix: alzforum.mutation
synonyms:
- Alzforum_mut
uri_format: https://www.alzforum.org/mutations/$1
alzgene:
description: The AlzGene database provides a comprehensive, unbiased and regularly
updated field synopsis of genetic association studies performed in Alzheimer’s
disease. In addition, hundreds of up-to-date meta-analyses are available for all
eligible polymorphisms with sufficient data.
example: '88'
homepage: http://www.alzgene.org
keywords:
- gene
mappings:
prefixcommons: alzgene
name: Alzheimer Gene Database
preferred_prefix: alzgene
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/alzgene:$1
publications:
- doi: 10.1038/ng1934
pmc: null
pubmed: '17192785'
title: 'Systematic meta-analyses of Alzheimer disease genetic association studies:
the AlzGene database.'
year: 2007
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.alzgene.org/geneoverview.asp?geneid=$1
amoebadb:
description: AmoebaDB is one of the databases that can be accessed through the EuPathDB
(http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: EDI_244000
homepage: http://amoebadb.org/amoeba/
keywords:
- functional genomics
- genomics
- model organism
mappings:
biocontext: AMOEBADB
fairsharing: FAIRsharing.swbypy
miriam: amoebadb
n2t: amoebadb
prefixcommons: amoebadb
re3data: r3d100012457
name: AmoebaDB
pattern: ^EDI_\d+$
preferred_prefix: amoebadb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/amoebadb:$1
publications:
- doi: 10.1093/nar/gkp941
pmc: PMC2808945
pubmed: '19914931'
title: 'EuPathDB: a portal to eukaryotic pathogen databases.'
year: 2009
twitter: eupathdb
uri_format: https://amoebadb.org/amoeba/app/record/gene/$1
amphx:
contact:
email: hescriva@obs-banyuls.fr
github: hescriva
name: Hector Escriva
orcid: 0000-0001-7577-5028
depends_on:
- uberon
description: An ontology for the development and anatomy of Amphioxus (Branchiostoma
lanceolatum).
download_obo: http://purl.obolibrary.org/obo/amphx.obo
download_owl: http://purl.obolibrary.org/obo/amphx.owl
example: '1000160'
homepage: https://github.com/EBISPOT/amphx_ontology
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: AMPHX
bioportal: AMPHX
obofoundry: amphx
ols: amphx
ontobee: AMPHX
name: The Amphioxus Development and Anatomy Ontology
pattern: ^\d+$
preferred_prefix: AMPHX
rdf_uri_format: http://purl.obolibrary.org/obo/AMPHX_$1
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_$1
antweb:
description: AntWeb is a website documenting the known species of ants, with records
for each species linked to their geographical distribution, life history, and
includes pictures.
example: casent0106247
homepage: http://www.antweb.org/
keywords:
- anatomy
- classification
- life science
mappings:
biocontext: ANTWEB
fairsharing: FAIRsharing.yk38tw
miriam: antweb
n2t: antweb
ncbi: AntWeb
prefixcommons: antweb
wikidata: P5299
name: AntWeb
pattern: ^casent\d+(\-D\d+)?$
preferred_prefix: antweb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/antweb:$1
publications:
- doi: 10.1038/424242b
pmc: null
pubmed: '12867945'
title: Ants join online colony to boost conservation efforts.
year: 2003
uri_format: http://www.antweb.org/specimen.do?name=$1
anzctr:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: ' The Australian New Zealand Clinical Trials Registry (ANZCTR) is an
online register of clinical trials being undertaken in Australia, New Zealand
and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic
areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle,
devices, treatment and rehabilitation strategies and complementary therapies.
In 2007 the ANZCTR was one of the first three trial registries to be recognised
by the World Health Organization International Clinical Trials Registry Platform
(WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries
if they fulfil certain criteria with respect to data content, quality and validity,
accessibility, unique identification, technical capacity and administration. The
ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials
from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch.
(from website)'
example: ACTRN12623000498695
homepage: https://anzctr.org.au
name: Australian New Zealand Clinical Trials Registry
pattern: ^ACTRN\d+$
preferred_prefix: anzctr
providers:
- code: ''
description: ''
homepage: ''
name: ''
uri_format: https://anzctr.org.au/ACTRN$1.aspx
synonyms:
- ACTRN
uri_format: https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1
aop:
description: International repository of Adverse Outcome Pathways.
example: '98'
homepage: https://aopwiki.org/
mappings:
biocontext: AOP
miriam: aop
n2t: aop
name: AOPWiki
pattern: ^\d+$
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:
contact:
email: awalker@apa.org
github: null
name: Alvin Walker
orcid: 0000-0003-1082-8760
description: An ontology developed by the American Psychological Association (APA).
Note that URIs in this ontology appear to have been generated with erroneous settings
in Protege.
download_owl: http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl
example: Abdomen
homepage: https://bioportal.bioontology.org/ontologies/APAONTO
keywords:
- ontology
- ontology and terminology
- psychology
mappings:
aberowl: APAONTO
bioportal: APAONTO
fairsharing: FAIRsharing.gkw1w8
name: Psychology Ontology
preferred_prefix: apaonto
references:
- https://github.com/biopragmatics/bioregistry/issues/528
uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1
apd:
description: The antimicrobial peptide database (APD) provides information on anticancer,
antiviral, antifungal and antibacterial peptides.
example: '01001'
homepage: http://aps.unmc.edu/AP/
keywords:
- biology
- protein
mappings:
biocontext: APD
fairsharing: FAIRsharing.ctwd7b
miriam: apd
n2t: apd
prefixcommons: apd
re3data: r3d100012901
name: Antimicrobial Peptide Database
pattern: ^\d{5}$
preferred_prefix: apd
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/apd:$1
publications:
- doi: 10.1093/nar/gkv1278
pmc: PMC4702905
pubmed: '26602694'
title: 'APD3: the antimicrobial peptide database as a tool for research and education.'
year: 2015
- doi: 10.1093/nar/gkn823
pmc: PMC2686604
pubmed: '18957441'
title: 'APD2: the updated antimicrobial peptide database and its application in
peptide design.'
year: 2008
- doi: 10.1093/nar/gkh025
pmc: PMC308759
pubmed: '14681488'
title: 'APD: the Antimicrobial Peptide Database.'
year: 2004
uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1
aphidbase.transcript:
description: AphidBase is a centralized bioinformatic resource that was developed
to facilitate community annotation of the pea aphid genome by the International
Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed
to organize and distribute genomic data and annotations for a large international
community. This collection references the transcript report, which describes genomic
location, sequence and exon information.
example: ACYPI000159
homepage: http://www.aphidbase.com/aphidbase
keywords:
- genome
mappings:
biocontext: APHIDBASE.TRANSCRIPT
miriam: aphidbase.transcript
n2t: aphidbase.transcript
prefixcommons: aphidbase
name: AphidBase Transcript
pattern: ^ACYPI\d{6}(-RA)?$
preferred_prefix: aphidbase.transcript
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/aphidbase:$1
publications:
- doi: 10.1111/j.1365-2583.2009.00930.x
pmc: PMC4372297
pubmed: '20482635'
title: 'AphidBase: a centralized bioinformatic resource for annotation of the
pea aphid genome.'
year: 2010
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=$1
apo:
contact:
email: stacia@stanford.edu
github: srengel
name: Stacia R Engel
orcid: 0000-0001-5472-917X
description: A structured controlled vocabulary for the phenotypes of Ascomycete
fungi.
download_obo: http://purl.obolibrary.org/obo/apo.obo
download_owl: http://purl.obolibrary.org/obo/apo.owl
example: 0000184
homepage: http://www.yeastgenome.org/
keywords:
- cell biology
- life science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: APO
biocontext: APO
bioportal: APO
fairsharing: FAIRsharing.dyqz3y
obofoundry: apo
ols: apo
ontobee: APO
name: Ascomycete phenotype ontology
pattern: ^\d{7}$
preferred_prefix: APO
publications:
- doi: 10.1093/database/bap001
pmc: PMC2790299
pubmed: '20157474'
title: New mutant phenotype data curation system in the Saccharomyces Genome Database.
year: 2009
rdf_uri_format: http://purl.obolibrary.org/obo/APO_$1
repository: https://github.com/obophenotype/ascomycete-phenotype-ontology
twitter: yeastgenome
uri_format: https://www.yeastgenome.org/observable/APO:$1
version: '2023-03-25'
apollosv:
appears_in:
- scdo
contact:
email: hoganwr@ufl.edu
github: hoganwr
name: William Hogan
orcid: 0000-0002-9881-1017
description: An OWL2 ontology of phenomena in infectious disease epidemiology and
population biology for use in epidemic simulation.
download_owl: http://purl.obolibrary.org/obo/apollo_sv.owl
example: '00000443'
homepage: https://github.com/ApolloDev/apollo-sv
keywords:
- biomedical science
- ecology
- epidemiology
- obo
- ontology
- population genetics
license: CC-BY-4.0
mappings:
aberowl: APOLLO_SV
bioportal: APOLLO-SV
fairsharing: FAIRsharing.ngv2xx
obofoundry: apollo_sv
ols: apollo_sv
ontobee: APOLLO_SV
name: Apollo Structured Vocabulary
pattern: ^\d{8}$
preferred_prefix: APOLLO_SV
providers:
- code: conflated
description: This might be resulting from properties in Apollo SV actually trying
to use appropriate identifiers
homepage: http://purl.obolibrary.org
name: OBO PURL in Parts
uri_format: http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl#APOLLO_SV_$1
publications:
- doi: 10.1186/s13326-016-0092-y
pmc: PMC4989460
pubmed: '27538448'
title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious
disease epidemiology and population biology for use in epidemic simulation.'
year: 2016
- doi: null
pmc: PMC3900155
pubmed: '24551417'
title: 'Apollo: giving application developers a single point of access to public
health models using structured vocabularies and Web services.'
year: 2013
rdf_uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1
repository: https://github.com/ApolloDev/apollo-sv
uri_format: http://purl.obolibrary.org/obo/APOLLO_SV_$1
version: '2023-01-10'
arachnoserver:
description: ArachnoServer (www.arachnoserver.org) is a manually curated database
providing information on the sequence, structure and biological activity of protein
toxins from spider venoms. It include a molecular target ontology designed specifically
for venom toxins, as well as current and historic taxonomic information.
example: AS000060
homepage: http://www.arachnoserver.org/
keywords:
- drug
- life science
- protein
mappings:
biocontext: ARACHNOSERVER
edam: '2578'
fairsharing: FAIRsharing.c54ywe
miriam: arachnoserver
n2t: arachnoserver
prefixcommons: arachnoserver
re3data: r3d100012902
uniprot: DB-0145
name: ArachnoServer
pattern: ^AS\d{6}$
preferred_prefix: arachnoserver
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/arachnoserver:$1
publications:
- doi: 10.1093/bioinformatics/btx661
pmc: null
pubmed: '29069336'
title: 'ArachnoServer 3.0: an online resource for automated discovery, analysis
and annotation of spider toxins.'
year: 2018
- doi: 10.1093/nar/gkq1058
pmc: PMC3013666
pubmed: '21036864'
title: ArachnoServer 2.0, an updated online resource for spider toxin sequences
and structures.
year: 2010
uri_format: http://www.arachnoserver.org/toxincard.html?id=$1
araport:
description: Website with general information about Arabidopsis and functionalities
such as a genomic viewer
example: AT5G05330
homepage: https://www.araport.org/
mappings:
miriam: tair.name
ncbi: Araport
uniprot: DB-0221
name: Arabidopsis Information Portal
pattern: ^AT.G[0-9]{5}$
preferred_prefix: araport
publications:
- doi: 10.1093/nar/gku1200
pmc: PMC4383980
pubmed: '25414324'
title: 'Araport: the Arabidopsis information portal.'
year: 2014
uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1
archdb:
contact:
email: narcis.fernandez@gmail.com
github: null
name: Narcis Fernandez-Fuentes
orcid: 0000-0002-6421-1080
description: ArchDB is a compilation of structural classifications of loops extracted
from known protein structures. The structural classification is based on the geometry
and conformation of the loop. The geometry is defined by four internal variables
and the type of regular flanking secondary structures, resulting in 10 different
loop types. Loops in ArchDB have been classified using an improved version (Espadaler
et al.) of the original ArchType program published in 1997 by Oliva et al.
example: '39421'
homepage: http://sbi.imim.es/archdb
keywords:
- classification
- life science
- protein
mappings:
fairsharing: FAIRsharing.tp9z4q
prefixcommons: archdb
name: ArchDB
preferred_prefix: archdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/archdb:$1
publications:
- doi: 10.1093/nar/gkt1189
pmc: PMC3964960
pubmed: '24265221'
title: 'ArchDB 2014: structural classification of loops in proteins.'
year: 2013
- doi: 10.1093/nar/gkh002
pmc: PMC308737
pubmed: '14681390'
title: 'ArchDB: automated protein loop classification as a tool for structural
genomics.'
year: 2004
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1
ardb:
description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated
database which characterises genes involved in antibiotic resistance. Each gene
and resistance type is annotated with information, including resistance profile,
mechanism of action, ontology, COG and CDD annotations, as well as external links
to sequence and protein databases. This collection references resistance genes.
example: CAE46076
homepage: http://ardb.cbcb.umd.edu/
mappings:
biocontext: ARDB
miriam: ardb
n2t: ardb
name: Antibiotic Resistance Genes Database
pattern: ^[A-Z_]{3}[0-9]{4,}$
preferred_prefix: ardb
uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1
ark:
banana: ark
contact:
email: jakkbl@gmail.com
github: jkunze
name: John Kunze
orcid: 0000-0001-7604-8041
contributor_extras:
- email: jakkbl@gmail.com
github: jkunze
name: John Kunze
orcid: 0000-0001-7604-8041
- email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Archival Resource Keys (ARKs) serve as persistent identifiers, or stable,
trusted references for information objects. Among other things, they aim to be
web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance
is an open global community supporting the ARK infrastructure on behalf of research
and scholarship. End users, especially researchers, rely on ARKs for long term
access to the global scientific and cultural record. Since 2001 some 8.2 billion
ARKs have been created by over 1000 organizations — libraries, data centers, archives,
museums, publishers, government agencies, and vendors. They identify anything
digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized
persistent identifiers that can be created by an organization as soon as it is
registered with a NAAN (Name Assigning Authority Number). Once registered, an
ARK organization can create unlimited numbers of ARKs and publicize them via the
n2t.net global resolver or via their own local resolver.
example: /53355/cl010066723
homepage: https://arks.org
keywords:
- data management
- subject agnostic
mappings:
biocontext: ARK
fairsharing: FAIRsharing.f928f1
miriam: ark
n2t: ark
mastodon: arks_org@fosstodon.org
name: Archival Resource Key
namespace_in_lui: true
pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$
preferred_prefix: ark
references:
- https://n2t.net/e/about.html
twitter: ARKsInTheOpen
uri_format: http://n2t.net/ark:$1
aro:
appears_in:
- scdo
contact:
email: mcarthua@mcmaster.ca
github: agmcarthur
name: Andrew G. McArthur
orcid: 0000-0002-1142-3063
description: Antibiotic resistance genes and mutations
download_obo: http://purl.obolibrary.org/obo/aro.obo
download_owl: http://purl.obolibrary.org/obo/aro.owl
example: '1000001'
homepage: https://github.com/arpcard/aro
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: ARO
biocontext: ARO
bioportal: ARO
obofoundry: aro
ols: aro
ontobee: ARO
name: Antibiotic Resistance Ontology
pattern: ^\d{7}$
preferred_prefix: ARO
publications:
- doi: 10.1093/nar/gkz935
pmc: PMC7145624
pubmed: '31665441'
title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic
resistance database.'
year: 2020
rdf_uri_format: http://purl.obolibrary.org/obo/ARO_$1
repository: https://github.com/arpcard/aro
uri_format: http://purl.obolibrary.org/obo/ARO_$1
arrayexpress:
description: ArrayExpress is a public repository for microarray data, which is aimed
at storing MIAME-compliant data in accordance with Microarray Gene Expression
Data (MGED) recommendations.
example: E-MEXP-1712
homepage: https://www.ebi.ac.uk/arrayexpress/
keywords:
- expression
- functional genomics
- microarray
- nucleotide
mappings:
biocontext: ARRAYEXPRESS
cellosaurus: ArrayExpress
fairsharing: FAIRsharing.6k0kwd
miriam: arrayexpress
n2t: arrayexpress
prefixcommons: arrayexpress
re3data: r3d100010222
name: ArrayExpress
pattern: ^[AEP]-\w{4}-\d+$
preferred_prefix: arrayexpress
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/arrayexpress:$1
- 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
publications:
- doi: 10.1093/nar/gky964
pmc: PMC6323929
pubmed: '30357387'
title: ArrayExpress update - from bulk to single-cell expression data.
year: 2019
- doi: 10.1093/nar/gku1057
pmc: PMC4383899
pubmed: '25361974'
title: ArrayExpress update--simplifying data submissions.
year: 2014
- doi: 10.1093/nar/gkg091
pmc: PMC165538
pubmed: '12519949'
title: ArrayExpress--a public repository for microarray gene expression data at
the EBI.
year: 2003
twitter: ArrayExpressEBI
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/$1
arraymap:
contact:
email: mbaudis@me.com
github: mbaudis
name: Michael Baudis
orcid: 0000-0002-9903-4248
description: arrayMap is a collection of pre-processed oncogenomic array data sets
and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation
commonly found in cancer genomes. arrayMap data is assembled from public repositories
and supplemented with additional sources, using custom curation pipelines. This
information has been mapped to multiple editions of the reference human genome.
example: icdom:8500_3
homepage: https://www.arraymap.org
keywords:
- bioinformatics
- biomedical science
- genomics
- life science
mappings:
biocontext: ARRAYMAP
fairsharing: FAIRsharing.1fbc5y
miriam: arraymap
n2t: arraymap
re3data: r3d100012630
name: ArrayMap
pattern: ^[\w\-:,]{3,64}$
preferred_prefix: arraymap
publications:
- doi: 10.1093/nar/gkv1310
pmc: PMC4702916
pubmed: '26615188'
title: 'The SIB Swiss Institute of Bioinformatics'' resources: focus on curated
databases.'
year: 2015
- doi: 10.1093/nar/gku1123
pmc: PMC4383937
pubmed: '25428357'
title: 'arrayMap 2014: an updated cancer genome resource.'
year: 2014
- doi: 10.1186/1471-2164-15-82
pmc: PMC3909908
pubmed: '24476156'
title: Chromothripsis-like patterns are recurring but heterogeneously distributed
features in a survey of 22,347 cancer genome screens.
year: 2014
- doi: 10.1371/journal.pone.0036944
pmc: PMC3356349
pubmed: '22629346'
title: 'arrayMap: a reference resource for genomic copy number imbalances in human
malignancies.'
year: 2012
twitter: progenetix
uri_format: https://www.arraymap.org/pgx:$1
arxiv:
description: arXiv is an e-print service in the fields of physics, mathematics,
non-linear science, computer science, and quantitative biology.
example: 0807.4956v1
homepage: https://arxiv.org/
keywords:
- bibliography
mappings:
biocontext: ARXIV
miriam: arxiv
n2t: arxiv
prefixcommons: arxiv
wikidata: P818
name: arXiv
pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$
preferred_prefix: arxiv
providers:
- code: ar5iv
description: Articles from arXiv.org as responsive HTML5 web pages.
homepage: https://ar5iv.labs.arxiv.org/
name: ar5iv
uri_format: https://ar5iv.org/abs/$1
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/arxiv:$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/arxiv/$1
uri_format: https://arxiv.org/abs/$1
asap:
description: ASAP (a systematic annotation package for community analysis of genomes)
stores bacterial genome sequence and functional characterization data. It includes
multiple genome sequences at various stages of analysis, corresponding experimental
data and access to collections of related genome resources.
example: ABE-0009634
homepage: http://asap.ahabs.wisc.edu/asap/home.php
keywords:
- comparative genomics
- developmental biology
- gene expression
- genome
- life science
mappings:
biocontext: ASAP
fairsharing: FAIRsharing.anpa6
go: ASAP
miriam: asap
n2t: asap
ncbi: ASAP
prefixcommons: asap
re3data: r3d100010666
name: A Systematic Annotation Package for Community Analysis of Genomes
pattern: ^[A-Za-z0-9-]+$
preferred_prefix: asap
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/asap:$1
publications:
- doi: 10.1093/nar/gkj164
pmc: PMC1347526
pubmed: '16381899'
title: 'ASAP: a resource for annotating, curating, comparing, and disseminating
genomic data.'
year: 2006
- doi: 10.1093/nar/gkg125
pmc: PMC165572
pubmed: '12519969'
title: ASAP, a systematic annotation package for community analysis of genomes.
year: 2003
uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1
ascl:
description: The Astrophysics Source Code Library (ASCL) is a free online registry
for software that have been used in research that has appeared in, or been submitted
to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics
Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable
by using the unique ascl ID assigned to each code. The ascl ID can be used to
link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).
example: '1801.012'
homepage: http://ascl.net/
keywords:
- astrophysics and astronomy
mappings:
biocontext: ASCL
fairsharing: FAIRsharing.wb0txg
miriam: ascl
n2t: ascl
re3data: r3d100011865
name: Astrophysics Source Code Library
pattern: ^[0-9\.]+$
preferred_prefix: ascl
publications:
- doi: 10.5334/jors.bv
pmc: null
pubmed: null
title: 'Looking before Leaping: Creating a Software Registry'
year: 2015
twitter: asclnet
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/$1
aspgd.locus:
description: The Aspergillus Genome Database (AspGD) is a repository for information
relating to fungi of the genus Aspergillus, which includes organisms of clinical,
agricultural and industrial importance. AspGD facilitates comparative genomics
by providing a full-featured genomics viewer, as well as matched and standardized
sets of genomic information for the sequenced aspergilli. This collection references
gene information.
example: ASPL0000349247
homepage: http://www.aspgd.org/
mappings:
biocontext: ASPGD.LOCUS
biolink: AspGD
go: AspGD_LOCUS
miriam: aspgd.locus
n2t: aspgd.locus
name: Aspergillus Genome Database
pattern: ^[A-Za-z_0-9]+$
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/
keywords:
- genome
- regulation
- rna
mappings:
prefixcommons: asrp
name: Arabidopsis Small RNA Project
preferred_prefix: asrp
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/asrp:$1
publications:
- doi: 10.1093/nar/gkm997
pmc: PMC2238918
pubmed: '17999994'
title: 'Update of ASRP: the Arabidopsis Small RNA Project database.'
year: 2007
- doi: 10.1093/nar/gki127
pmc: PMC540081
pubmed: '15608278'
title: 'ASRP: the Arabidopsis Small RNA Project Database.'
year: 2005
uri_format: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1
astd:
comment: This resource doesn't exist on the web anymore
deprecated: true
description: Identifier of an object from the ASTD database.
example: ENSG00000136147
homepage: http://www.ebi.ac.uk/astd/
keywords:
- alternative splicing
- gene
- transcript
mappings:
edam: '2367'
prefixcommons: astd
name: ASTD
preferred_prefix: astd
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/astd:$1
provides: ensembl
publications:
- doi: 10.1016/j.ygeno.2008.11.003
pmc: null
pubmed: '19059335'
title: 'ASTD: The Alternative Splicing and Transcript Diversity database.'
year: 2008
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.ebi.ac.uk/astd/geneview.html?acc=$1
atc:
contact:
email: whocc@fhi.no
github: null
name: WHO Collaborating Centre for Drug Statistics Methodology
orcid: null
description: The Anatomical Therapeutic Chemical (ATC) classification system, divides
active substances into different groups according to the organ or system on which
they act and their therapeutic, pharmacological and chemical properties. Drugs
are classified in groups at five different levels; Drugs are divided into fourteen
main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The
3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the
5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC)
classification system and the Defined Daily Dose (DDD) is a tool for exchanging
and comparing data on drug use at international, national or local levels.
example: A10BA02
homepage: http://www.whocc.no/atc_ddd_index/
keywords:
- biomedical science
- chemical
- chemical biology
- ontology
- pharmacology
mappings:
aberowl: ATC
bartoc: '449'
biocontext: ATC
bioportal: ATC
edam: '3103'
fairsharing: FAIRsharing.1a27h8
hl7: 2.16.840.1.113883.6.73
miriam: atc
n2t: atc
prefixcommons: atc
wikidata: P267
name: Anatomical Therapeutic Chemical Classification System
pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$
preferred_prefix: atc
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/atc:$1
publications:
- doi: null
pmc: null
pubmed: '7368387'
title: '[New classification of drugs. The Medical list and the Drug catalogue
are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code)
in 1981].'
year: 1980
- doi: 10.1007/s002280000200
pmc: null
pubmed: '11214783'
title: Different versions of the anatomical therapeutic chemical classification
system and the defined daily dose--are drug utilisation data comparable?
year: 2000
synonyms:
- ATC_code
- ATTC
uri_format: http://www.whocc.no/atc_ddd_index/?code=$1
atcc:
description: The American Type Culture Collection (ATCC) is a private, nonprofit
biological resource center whose mission focuses on the acquisition, authentication,
production, preservation, development and distribution of standard reference microorganisms,
cell lines and other materials for research in the life sciences.
example: '11303'
homepage: https://www.lgcstandards-atcc.org
keywords:
- epidemiology
- life science
- virology
mappings:
biocontext: ATCC
cellosaurus: ATCC
fairsharing: FAIRsharing.j0ezpm
hl7: 2.16.840.1.113883.6.77
miriam: atcc
n2t: atcc
ncbi: ATCC
name: American Type Culture Collection
pattern: ^([A-Z]+-)?\d+$
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=$1
ato:
contact:
email: david.c.blackburn@gmail.com
github: null
name: David Blackburn
orcid: 0000-0002-1810-9886
deprecated: true
description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and
genres. It is being integrated into UBERON resource
download_obo: http://aber-owl.net/media/ontologies/ATO/2/ato.obo
example: '0000000'
homepage: http://www.amphibanat.org
keywords:
- obo
- ontology
- taxonomy
mappings:
aberowl: ATO
biocontext: ATO
bioportal: ATO
fairsharing: FAIRsharing.ayjdsm
obofoundry: ato
name: Amphibian taxonomy
pattern: ^\d{7}$
preferred_prefix: ATO
rdf_uri_format: http://purl.obolibrary.org/obo/ATO_$1
uri_format: http://purl.obolibrary.org/obo/ATO_$1
atol:
contact:
email: pylebail@rennes.inra.fr
github: null
name: Pierre-Yves LeBail
orcid: 0000-0002-8310-5195
description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics
defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide
a reference ontology of phenotypic traits of farm animals for the international
scientificand educational - communities, farmers, etc.; - deliver this reference
ontology in a language which can be used by computers in order to support database
management, semantic analysis and modeling; - represent traits as generic as possible
for livestock vertebrates; - make the ATOL ontology as operational as possible
and closely related to measurement techniques; - structure the ontology in relation
to animal production.'
download_owl: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl
example: '0002233'
homepage: http://www.atol-ontology.com
keywords:
- agriculture
- animal husbandry
- life science
- ontology
mappings:
aberowl: ATOL
agroportal: ATOL
bioportal: ATOL
fairsharing: FAIRsharing.wsfk5z
ols: atol
name: Animal Trait Ontology for Livestock
pattern: ^\d{7}$
preferred_prefix: atol
uri_format: http://opendata.inra.fr/ATOL/ATOL_$1
version: '2018-09-13'
autdb:
description: AutDB is a curated database for autism research. It is built on information
extracted from the studies on molecular genetics and biology of Autism Spectrum
Disorders (ASD). The four modules of AutDB include information on Human Genes,
Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively.
It provides an annotated list of ASD candidate genes in the form of reference
dataset for interrogating molecular mechanisms underlying the disorder.
example: ADA
homepage: http://autism.mindspec.org/autdb/
mappings:
biocontext: AUTDB
miriam: autdb
n2t: autdb
name: AutDB
pattern: ^[A-Z]+[A-Z-0-9]{2,}$
preferred_prefix: autdb
uri_format: http://autism.mindspec.org/GeneDetail/$1
bacdive:
contact:
email: contact@bacdive.de
github: null
name: Lorenz Reimer
orcid: 0000-0002-7805-0660
description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked
information on the different aspects of bacterial and archaeal biodiversity.
example: '131392'
homepage: https://bacdive.dsmz.de/
keywords:
- biodiversity
- life science
- microbiology
mappings:
fairsharing: FAIRsharing.aSszvY
miriam: bacdive
n2t: bacdive
re3data: r3d100013060
wikidata: P2946
name: BacDive
pattern: ^[0-9]+$
preferred_prefix: bacdive
publications:
- doi: 10.1093/nar/gky879
pmc: PMC6323973
pubmed: '30256983'
title: 'BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity
analysis.'
year: 2019
- doi: 10.1016/j.jbiotec.2017.05.004
pmc: null
pubmed: '28487186'
title: Mobilization and integration of bacterial phenotypic data-Enabling next
generation biodiversity analysis through the BacDive metadatabase.
year: 2017
- doi: 10.1093/nar/gkv983
pmc: PMC4702946
pubmed: '26424852'
title: BacDive--The Bacterial Diversity Metadatabase in 2016.
year: 2015
- doi: 10.1093/nar/gkt1058
pmc: PMC3965005
pubmed: '24214959'
title: BacDive--the Bacterial Diversity Metadatabase.
year: 2013
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
keywords:
- life science
- protein
mappings:
fairsharing: FAIRsharing.5f5mfm
prefixcommons: bactibase
re3data: r3d100012755
name: Bactibase
preferred_prefix: bactibase
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bactibase:$1
publications:
- doi: 10.1186/1471-2180-10-22
pmc: PMC2824694
pubmed: '20105292'
title: 'BACTIBASE second release: a database and tool platform for bacteriocin
characterization.'
year: 2010
- doi: 10.1186/1471-2180-7-89
pmc: PMC2211298
pubmed: '17941971'
title: 'BACTIBASE: a new web-accessible database for bacteriocin characterization.'
year: 2007
uri_format: http://bactibase.hammamilab.org/$1
bams:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: 'BAMS (Brain Architectural Management System) describes vertebrate
neuroinformatics data at four levels of organization: expressed molecules, neuron
types and classes, brain regions, and networks of brain regions.'
homepage: https://bams1.org
name: Brain Architecture Knowledge Management System Neuroanatomical Ontology
preferred_prefix: bams
references:
- https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full
bao:
contact:
email: sschurer@med.miami.edu
github: null
name: Stephan Schurer
orcid: null
description: The BioAssay Ontology (BAO) describes chemical biology screening assays
and their results including high-throughput screening (HTS) data for the purpose
of categorizing assays and data analysis.
download_owl: http://www.bioassayontology.org/bao/bao_complete.owl
example: 0002989
homepage: http://bioassayontology.org
keywords:
- biochemistry
- biomedical science
- life science
- ontology
mappings:
aberowl: BAO
biocontext: BAO
bioportal: BAO
fairsharing: FAIRsharing.mye76w
miriam: bao
n2t: bao
ols: bao
ontobee: BAO
name: BioAssay Ontology
pattern: ^\d{7}$
preferred_prefix: bao
publications:
- doi: 10.1186/2041-1480-5-s1-s5
pmc: PMC4108877
pubmed: '25093074'
title: 'Evolving BioAssay Ontology (BAO): modularization, integration and applications.'
year: 2014
- doi: 10.1371/journal.pone.0049198
pmc: PMC3498356
pubmed: '23155465'
title: Formalization, annotation and analysis of diverse drug and probe screening
assay datasets using the BioAssay Ontology (BAO).
year: 2012
- doi: 10.1186/1471-2105-12-257
pmc: PMC3149580
pubmed: '21702939'
title: 'BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput
screening results.'
year: 2011
- doi: 10:1371/journal.pone.0049198
pmc: null
pubmed: '10'
title: Digitoxin metabolism by rat liver microsomes.
year: 1975
repository: https://github.com/BioAssayOntology/BAO/wiki
synonyms:
- BAO
uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1
version: 2.7.5
bartoc:
contact:
email: voss@gbv.de
github: nichtich
name: Jakob Voß
orcid: 0000-0002-7613-4123
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
contributor_extras:
- email: voss@gbv.de
github: nichtich
name: Jakob Voß
orcid: 0000-0002-7613-4123
description: 'The Basic Register of Thesauri, Ontologies & Classifications (BARTOC)
is a database of Knowledge Organization Systems and KOS related registries.
The main goal of BARTOC is to list as many Knowledge Organization Systems as possible
at one place in order to achieve greater visibility, highlight their features,
make them searchable and comparable, and foster knowledge sharing. BARTOC includes
any kind of KOS from any subject area, in any language, any publication format,
and any form of accessibility. BARTOC’s search interface is available in 20 European
languages and provides two search options: Basic Search by keywords, and Advanced
Search by taxonomy terms. A circle of editors has gathered around BARTOC from
all across Europe and BARTOC has been approved by the International Society for
Knowledge Organization (ISKO).'
example: '241'
homepage: https://bartoc.org
keywords:
- knowledge and information systems
- ontology and terminology
license: PDDL 1.0
mappings:
bartoc: '2054'
fairsharing: FAIRsharing.f1777e
wikidata: P2689
name: Basic Register of Thesauri, Ontologies & Classifications
owners:
- name: Verbundzentrale des GBV
partnered: false
ror: 048vdhs48
wikidata: null
pattern: ^[1-9][0-9]*$
preferred_prefix: bartoc
rdf_uri_format: https://bartoc.org/en/node/$1
references:
- https://github.com/biopragmatics/bioregistry/issues/783
repository: https://github.com/gbv/bartoc.org
uri_format: https://bartoc.org/en/node/$1
bbkg:
description: Blue Brain Project's published data as knowledge graphs and Web Studios.
example: topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a
homepage: https://portal.bluebrain.epfl.ch
mappings:
miriam: bbkg
name: Blue Brain Project Knowledge Graph
pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$
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:$1
bcgo:
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
deprecated: true
description: An application ontology built for beta cell genomics studies.
download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl
example: '0000015'
homepage: https://github.com/obi-bcgo/bcgo
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: BCGO
biocontext: BCGO
bioportal: BCGO
cellosaurus: BCGO
obofoundry: bcgo
ols: bcgo
ontobee: BCGO
name: Beta Cell Genomics Ontology
pattern: ^\d{7}$
preferred_prefix: BCGO
rdf_uri_format: http://purl.obolibrary.org/obo/BCGO_$1
repository: https://github.com/obi-bcgo/bcgo
uri_format: http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1
version: '2015-07-08'
bcio:
contact:
email: srodriguez142857@gmail.com
github: null
name: Sergio José Rodríguez Méndez
orcid: 0000-0001-7203-8399
description: The Behaviour Change Intervention Ontology is an ontology for all aspects
of human behaviour change interventions and their evaluation.
download_owl: http://humanbehaviourchange.org/ontology/bcio.owl
example: '040000'
homepage: https://www.humanbehaviourchange.org/
keywords:
- ontology
mappings:
aberowl: BCI-O
bioportal: BCI-O
ols: bcio
name: The Behaviour Change Intervention Ontology
pattern: ^\d{6}$
preferred_prefix: bcio
uri_format: https://w3id.org/BCI-ontology#$1
version: '2022-08-24'
bco:
appears_in:
- fovt
contact:
email: rlwalls2008@gmail.com
github: ramonawalls
name: Ramona Walls
orcid: 0000-0001-8815-0078
description: An ontology to support the interoperability of biodiversity data, including
data on museum collections, environmental/metagenomic samples, and ecological
surveys.
download_owl: http://purl.obolibrary.org/obo/bco.owl
example: 0000081
homepage: https://github.com/BiodiversityOntologies/bco
keywords:
- biodiversity
- ecology
- metagenomics
- obo
- ontology
- taxonomy
license: CC0-1.0
mappings:
aberowl: BCO
agroportal: BCO
biocontext: BCO
bioportal: BCO
ecoportal: BCO
fairsharing: FAIRsharing.8ktkqy
obofoundry: bco
ols: bco
ontobee: BCO
name: Biological Collections Ontology
pattern: ^\d{7}$
preferred_prefix: BCO
publications:
- doi: 10.1371/journal.pone.0089606
pmc: PMC3940615
pubmed: '24595056'
title: 'Semantics in support of biodiversity knowledge discovery: an introduction
to the biological collections ontology and related ontologies.'
year: 2014
rdf_uri_format: http://purl.obolibrary.org/obo/BCO_$1
repository: https://github.com/BiodiversityOntologies/bco
uri_format: http://purl.obolibrary.org/obo/BCO_$1
version: '2021-11-14'
bcrc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell line collections
example: '60316'
homepage: https://catalog.bcrc.firdi.org.tw
keywords:
- cell lines
mappings:
cellosaurus: BCRC
name: BCRC Strain Collection Catalog
pattern: ^\d+$
preferred_prefix: bcrc
uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1
bcrj:
description: Cell line collections
example: 0278
homepage: https://bcrj.org.br/pesquisa/
mappings:
cellosaurus: BCRJ
name: Banco de Celulas do Rio de Janeiro
pattern: ^\d{4}$
preferred_prefix: bcrj
uri_format: http://bcrj.org.br/celula/$1
bdgp.est:
description: The BDGP EST database collects the expressed sequence tags (ESTs) derived
from a variety of tissues and developmental stages for Drosophila melanogaster.
All BDGP ESTs are available at dbEST (NCBI).
example: EY223054.1
has_canonical: dbest
homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html
keywords:
- genome
mappings:
biocontext: BDGP.EST
miriam: bdgp.est
n2t: bdgp.est
ncbi: BDGP_EST
prefixcommons: flybase.est
name: Berkeley Drosophila Genome Project EST database
pattern: ^\w+(\.)?(\d+)?$
preferred_prefix: bdgp.est
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/flybase.est:$1
uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
bdgp.insertion:
description: BDGP gene disruption collection provides a public resource of gene
disruptions of Drosophila genes using a single transposable element.
example: KG09531
homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/
keywords:
- gene
- sequence
mappings:
biocontext: BDGP.INSERTION
miriam: bdgp.insertion
n2t: bdgp.insertion
prefixcommons: bdgp
name: BDGP insertion DB
pattern: ^\w+$
preferred_prefix: bdgp.insertion
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bdgp:$1
publications:
- doi: 10.1534/genetics.104.026427
pmc: PMC1470905
pubmed: '15238527'
title: 'The BDGP gene disruption project: single transposon insertions associated
with 40% of Drosophila genes.'
year: 2004
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/$1
beetlebase:
description: BeetleBase is a comprehensive sequence database and community resource
for Tribolium genetics, genomics and developmental biology. It incorporates information
about genes, mutants, genetic markers, expressed sequence tags and publications.
example: TC010103
homepage: http://beetlebase.org/
keywords:
- computational biology
- genome
- life science
mappings:
biocontext: BEETLEBASE
fairsharing: FAIRsharing.h5f091
miriam: beetlebase
n2t: beetlebase
ncbi: BEETLEBASE
prefixcommons: beetlebase
re3data: r3d100010921
name: Tribolium Genome Database -- Insertion
pattern: ^TC\d+$
preferred_prefix: beetlebase
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/beetlebase:$1
publications:
- doi: 10.1093/nar/gkp807
pmc: PMC2808946
pubmed: '19820115'
title: 'BeetleBase in 2010: revisions to provide comprehensive genomic information
for Tribolium castaneum.'
year: 2009
uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1
begdb:
description: The Benchmark Energy & Geometry Database (BEGDB) collects results of
highly accurate quantum mechanics (QM) calculations of molecular structures, energies
and properties. These data can serve as benchmarks for testing and parameterization
of other computational methods.
example: '4214'
homepage: http://www.begdb.com
keywords:
- life science
mappings:
biocontext: BEGDB
fairsharing: FAIRsharing.nbe4fq
miriam: begdb
n2t: begdb
re3data: r3d100011166
name: Benchmark Energy & Geometry Database
pattern: ^[0-9]+$
preferred_prefix: begdb
publications:
- doi: 10.1135/cccc20081261
pmc: null
pubmed: null
title: 'Quantum Chemical Benchmark Energy and Geometry Database for Molecular
Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples'
year: 2008
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
keywords:
- cell lines
mappings:
cellosaurus: BEI_Resources
name: BEI Resources
preferred_prefix: beiresources
synonyms:
- BEI_Resources
uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx
bel:
comment: INDRA uses bel as a catch-all for scomp/sfam
contact:
email: support@bel.bio
github: null
name: William Hayes
orcid: 0000-0003-0728-781X
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Biological Expression Language is a domain-specific language for
describing causal, correlative, and associative relationships between a variety
of biological agents.
example: 9-1-1 Complex
homepage: https://biological-expression-language.github.io/
keywords:
- biology
mappings:
fairsharing: FAIRsharing.dp0jvd
name: Biological Expression Language
preferred_prefix: bel
bfo:
appears_in:
- ado
- agro
- aism
- cdno
- colao
- duo
- ecocore
- epio
- foodon
- fovt
- hso
- lepao
- mco
- ons
- pcl
- pco
- psdo
- rbo
- xpo
- zp
contact:
email: phismith@buffalo.edu
github: phismith
name: Barry Smith
orcid: 0000-0003-1384-116X
description: The upper level ontology upon which OBO Foundry ontologies are built.
download_obo: http://purl.obolibrary.org/obo/bfo.obo
download_owl: http://purl.obolibrary.org/obo/bfo.owl
example: '0000001'
homepage: http://ifomis.org/bfo/
keywords:
- obo
- ontology
- subject agnostic
license: CC-BY-4.0
logo: https://avatars2.githubusercontent.com/u/12972134?v=3&s=200
mappings:
aberowl: BFO
agroportal: BFO
biocontext: BFO
bioportal: BFO
fairsharing: FAIRsharing.wcpd6f
go: BFO
obofoundry: bfo
ols: bfo
ontobee: BFO
name: Basic Formal Ontology
pattern: ^\d{7}$
preferred_prefix: BFO
rdf_uri_format: http://purl.obolibrary.org/obo/BFO_$1
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=$1
bgee.gene:
description: Bgee is a database to retrieve and compare gene expression patterns
in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in
situ hybridization, and EST data). This collection references genes in Bgee.
example: FBgn0000015
homepage: https://bgee.org/
keywords:
- gene expression
mappings:
biocontext: BGEE.GENE
miriam: bgee.gene
n2t: bgee.gene
prefixcommons: bgee
name: Bgee gene
pattern: ^[A-Za-z]+\d+$
preferred_prefix: bgee.gene
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bgee:$1
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
bibo:
contact:
email: fred@fgiasson.com
github: fgiasson
name: Frédérick Giasson
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Bibliographic Ontology Specification provides main concepts and
properties for describing citations and bibliographic references (i.e. quotes,
books, articles, etc) on the Semantic Web.
example: authorList
homepage: https://bibliontology.com/
keywords:
- bibliometrics
name: The Bibliographic Ontology
preferred_prefix: bibo
uri_format: http://purl.org/ontology/bibo/$1
bido:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology that allows the description of numerical and categorical
bibliometric data (e.g., journal impact factor, author h-index, categories describing
research careers) in RDF.
example: CategorialBibliometricData
homepage: http://www.sparontologies.net/ontologies/bido
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.d7f0a9
name: Bibliometric Data Ontology
preferred_prefix: BiDO
repository: https://github.com/sparontologies/bido
twitter: sparontologies
uri_format: http://purl.org/spar/bido/$1
bigg.compartment:
description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically
structured genome-scale metabolic network reconstructions. It more published genome-scale
metabolic networks into a single database with a set of stardized identifiers
called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
and metabolites are linked to many external databases (KEGG, PubChem, and many
more). This collection references model compartments.
example: c
homepage: http://bigg.ucsd.edu/compartments/
mappings:
biocontext: BIGG.COMPARTMENT
miriam: bigg.compartment
n2t: bigg.compartment
name: BiGG Compartment
pattern: ^[a-z_A-Z]+$
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/$1
bila:
contact:
email: henrich@embl.de
github: ThorstenHen
name: Thorsten Henrich
orcid: 0000-0002-1548-3290
deprecated: true
description: This is a record of the Bilateria anatomy terminology and ontology.
We have been unable to find any further information about this resource.
download_owl: http://purl.obolibrary.org/obo/bila.owl
example: '0000000'
homepage: http://4dx.embl.de/4DXpress
keywords:
- anatomy
- gene expression
- obo
- ontology
mappings:
biocontext: BILA
fairsharing: FAIRsharing.eqgjeq
obofoundry: bila
ols: bila
prefixcommons: 4dxpress
name: Bilateria anatomy
pattern: ^\d{7}$
preferred_prefix: BILA
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/4dxpress:$1
publications:
- doi: 10.1093/nar/gkm797
pmc: PMC2238840
pubmed: '17916571'
title: '4DXpress: a database for cross-species expression pattern comparisons.'
year: 2007
rdf_uri_format: http://purl.obolibrary.org/obo/BILA_$1
uri_format: http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1
version: '2019-06-12'
bind:
deprecated: true
description: Accession number of an entry from the BIND database.
example: '98346'
homepage: http://bind.ca
keywords:
- interaction
- pathway
- small molecule
mappings:
biocontext: BIND
edam: '1129'
prefixcommons: bind
name: BIND accession number
preferred_prefix: bind
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bind:$1
publications:
- doi: 10.1093/nar/gkg056
pmc: PMC165503
pubmed: '12519993'
title: 'BIND: the Biomolecular Interaction Network Database.'
year: 2003
- doi: 10.1093/bioinformatics/16.5.465
pmc: null
pubmed: '10871269'
title: BIND--a data specification for storing and describing biomolecular interactions,
molecular complexes and pathways.
year: 2000
uri_format: http://www.bind.ca/Action?identifier=bindid&idsearch=$1
bindingdb:
contact:
email: mgilson@health.ucsd.edu
github: null
name: Michael K. Gilson
orcid: 0000-0002-3375-1738
description: BindingDB is the first public database of protein-small molecule affinity
data.
example: e999
homepage: https://www.bindingdb.org
keywords:
- chemistry
- computational chemistry
- drug discovery
- interaction
- life science
- medicinal chemistry
- protein
mappings:
biocontext: BINDINGDB
fairsharing: FAIRsharing.3b36hk
miriam: bindingdb
n2t: bindingdb
prefixcommons: bindingdb
re3data: r3d100012074
uniprot: DB-0127
name: BindingDB
pattern: ^\w\d+$
preferred_prefix: bindingdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bindingdb:$1
publications:
- doi: 10.1093/nar/gkv1072
pmc: PMC4702793
pubmed: '26481362'
title: 'BindingDB in 2015: A public database for medicinal chemistry, computational
chemistry and systems pharmacology.'
year: 2015
- doi: 10.1093/nar/gkl999
pmc: PMC1751547
pubmed: '17145705'
title: 'BindingDB: a web-accessible database of experimentally determined protein-ligand
binding affinities.'
year: 2006
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/$1
biocatalogue.service:
description: The BioCatalogue provides a common interface for registering, browsing
and annotating Web Services to the Life Science community. Registered services
are monitored, allowing the identification of service problems and changes and
the filtering-out of unavailable or unreliable resources. BioCatalogue is free
to use, for all.
example: '614'
homepage: https://www.biocatalogue.org/
keywords:
- registry
mappings:
biocontext: BIOCATALOGUE.SERVICE
miriam: biocatalogue.service
n2t: biocatalogue.service
prefixcommons: biocatalogue
name: BioCatalogue Service
pattern: ^\d+$
preferred_prefix: biocatalogue.service
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/biocatalogue:$1
publications:
- doi: 10.1093/nar/gkq394
pmc: PMC2896129
pubmed: '20484378'
title: 'BioCatalogue: a universal catalogue of web services for the life sciences.'
year: 2010
uri_format: https://www.biocatalogue.org/services/$1
biocyc:
description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides
an electronic reference source on the genomes and metabolic pathways of sequenced
organisms.
example: ECOLI:CYT-D-UBIOX-CPLX
homepage: http://biocyc.org
keywords:
- genome
- pathway
- sequence
mappings:
biocontext: BIOCYC
edam: '2104'
go: BioCyc
miriam: biocyc
n2t: biocyc
prefixcommons: biocyc
uniprot: DB-0005
name: BioCyc collection of metabolic pathway databases
pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$
preferred_prefix: biocyc
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/biocyc:$1
publications:
- doi: 10.1093/nar/gkv1164
pmc: PMC4702838
pubmed: '26527732'
title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection
of pathway/genome databases.
year: 2015
- doi: 10.1093/nar/gki892
pmc: PMC1266070
pubmed: '16246909'
title: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.
year: 2005
uri_format: http://biocyc.org/getid?id=$1
biofactoid:
contact:
email: jeffvin.wong@utoronto.ca
github: jvwong
name: Jeffrey Wong
orcid: 0000-0002-8912-5699
contributor:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
description: Biofactoid is a web-based system that empowers authors to capture and
share machine-readable summaries of molecular-level interactions described in
their publications.
example: fdb8a927-45c3-48b7-9743-cbb5e16837fa
github_request_issue: 700
homepage: https://biofactoid.org/
keywords:
- biocuration
- database
- relationships
license: CC0-1.0
name: Biofactoid
pattern: ^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
preferred_prefix: biofactoid
publications:
- doi: 10.7554/elife.68292
pmc: PMC8683078
pubmed: '34860157'
title: Author-sourced capture of pathway knowledge in computable form using Biofactoid.
year: 2021
repository: https://github.com/PathwayCommons/factoid
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://biofactoid.org/document/$1
biogrid:
contact:
email: md.tyers@umontreal.ca
github: null
name: Mike Tyers
orcid: 0000-0002-9713-9994
description: BioGRID is a database of physical and genetic interactions in Saccharomyces
cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
Schizosaccharomyces pombe.
example: '31623'
homepage: http://thebiogrid.org/
keywords:
- biochemistry
- bioinformatics
- chemical biology
- cheminformatics
- gene
- interaction
- life science
- protein
- proteomics
- systems biology
mappings:
biocontext: BIOGRID
fairsharing: FAIRsharing.9d5f5r
miriam: biogrid
n2t: biogrid
prefixcommons: biogrid
re3data: r3d100010350
uniprot: DB-0184
name: BioGRID
pattern: ^\d+$
preferred_prefix: biogrid
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/biogrid:$1
publications:
- doi: 10.1002/pro.3978
pmc: PMC7737760
pubmed: '33070389'
title: 'The BioGRID database: A comprehensive biomedical resource of curated protein,
genetic, and chemical interactions.'
year: 2020
- doi: 10.1093/nar/gky1079
pmc: PMC6324058
pubmed: '30476227'
title: 'The BioGRID interaction database: 2019 update.'
year: 2019
- doi: 10.1093/nar/gkq1116
pmc: PMC3013707
pubmed: '21071413'
title: 'The BioGRID Interaction Database: 2011 update.'
year: 2010
- doi: 10.1093/nar/gkj109
pmc: PMC1347471
pubmed: '16381927'
title: 'BioGRID: a general repository for interaction datasets.'
year: 2006
- doi: 10.1186/gb-2003-4-3-r23
pmc: PMC153463
pubmed: '12620108'
title: 'The GRID: the General Repository for Interaction Datasets.'
year: 2003
repository: https://github.com/BioGRID
twitter: biogrid
uri_format: http://thebiogrid.org/$1
biogrid.interaction:
contact:
email: md.tyers@umontreal.ca
github: null
name: Mike Tyers
orcid: 0000-0002-9713-9994
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: BioGRID is a database of physical and genetic interactions in Saccharomyces
cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and
Schizosaccharomyces pombe.
example: '2649230'
homepage: https://thebiogrid.org/
mappings:
edam: '2628'
name: BioGRID Interactions
part_of: biogrid
pattern: ^\d+$
preferred_prefix: biogrid.interaction
twitter: biogrid
uri_format: https://thebiogrid.org/interaction/$1
biokc:
description: BioKC (Biological Knowledge Curation), is a web-based collaborative
platform for the curation and annotation of biomedical knowledge following the
standard data model from Systems Biology Markup Language (SBML).
example: bkc640
homepage: https://wwwen.uni.lu/lcsb
mappings:
miriam: biokc
name: BioKC
pattern: ^bkc[0-9]*$
preferred_prefix: biokc
uri_format: https://biokb.lcsb.uni.lu/fact/$1
biolegend:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: BioLegend is a life sciences supply vendor.
example: '3403'
homepage: https://www.biolegend.com
keywords:
- antibodies
- assays
- life sciences
- reagents
- vendor
name: BioLegend
pattern: ^\d+$
preferred_prefix: biolegend
uri_format: https://www.biolegend.com/Default.aspx?ID=6664&productid=$1
biolink:
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: A high level datamodel of biological entities (genes, diseases, phenotypes,
pathways, individuals, substances, etc) and their associations.
download_owl: http://aber-owl.net/media/ontologies/BIOLINK/52/biolink.owl
example: Gene
homepage: https://biolink.github.io/biolink-model/
keywords:
- biomedical science
- functional genomics
- medical biotechnology
- medical informatics
- ontology
- translational medicine
mappings:
aberowl: BIOLINK
biolink: biolink
bioportal: BIOLINK
fairsharing: FAIRsharing.ad9d85
miriam: biolink
name: Biolink Model
pattern: ^\S+$
preferred_prefix: biolink
repository: https://github.com/biolink/biolink-model
uri_format: https://w3id.org/biolink/vocab/$1
biomagresbank:
description: A repository for Data from NMR Spectroscopy on Proteins, Peptides,
and Nucleic Acids.
example: '10046'
homepage: http://www.bmrb.wisc.edu/
keywords:
- protein
mappings:
prefixcommons: biomagresbank
name: BioMagResBank
preferred_prefix: biomagresbank
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/biomagresbank:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1
biominder:
description: Database of the dielectric properties of biological tissues.
example: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3
homepage: https://datalab.rwth-aachen.de/MINDER
mappings:
biocontext: BIOMINDER
miriam: biominder
n2t: biominder
name: Bio-MINDER Tissue Database
pattern: ^[a-z0-9\-]+$
preferred_prefix: biominder
uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1
biomodels.db:
description: BioModels Database is a data resource that allows biologists to store,
search and retrieve published mathematical models of biological interests.
example: BIOMD0000000048
homepage: https://www.ebi.ac.uk/biomodels/
keywords:
- model
mappings:
biocontext: BIOMODELS.DB
go: BIOMD
miriam: biomodels.db
n2t: biomodels.db
prefixcommons: biomodels
name: BioModels Database
pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
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: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/biomodels:$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
publications:
- doi: 10.1093/nar/gkj092
pmc: PMC1347454
pubmed: '16381960'
title: 'BioModels Database: a free, centralized database of curated, published,
quantitative kinetic models of biochemical and cellular systems.'
year: 2006
synonyms:
- BIOMD
uri_format: https://www.ebi.ac.uk/biomodels/$1
biomodels.kisao:
banana: KISAO
banana_peel: _
contact:
email: jonrkarr@gmail.com
github: jonrkarr
name: Jonathan Karr
orcid: 0000-0002-2605-5080
description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that
describes simulation algorithms and methods used for biological kinetic models,
and the relationships between them. This provides a means to unambiguously refer
to simulation algorithms when describing a simulation experiment.
download_owl: http://purl.obolibrary.org/obo/kisao.owl
example: '0000057'
homepage: https://github.com/SED-ML/KiSAO
keywords:
- bioinformatics
- computer science
- obo
- ontology
license: Artistic License 2.0
mappings:
aberowl: KISAO
biocontext: KISAO
bioportal: KISAO
fairsharing: FAIRsharing.jcg19w
miriam: biomodels.kisao
n2t: biomodels.kisao
obofoundry: kisao
ols: kisao
ontobee: KISAO
prefixcommons: kisao
name: Kinetic Simulation Algorithm Ontology
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: biomodels.kisao
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kisao:$1
- code: legacy
description: This is the URI scheme used in the ontology but it does not resolve.
homepage: https://www.biomodels.net
name: Legacy Biomodels URL
uri_format: https://www.biomodels.net/kisao/KISAO#KISAO_$1
publications:
- doi: 10.1038/msb.2011.77
pmc: PMC3261705
pubmed: '22027554'
title: Controlled vocabularies and semantics in systems biology.
year: 2011
rdf_uri_format: http://purl.obolibrary.org/obo/KISAO_$1
repository: https://github.com/SED-ML/KiSAO
synonyms:
- biomodels.kisao
- kisao
uri_format: https://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=kisao:KISAO_$1
version: '2.30'
biomodels.teddy:
banana: TEDDY
banana_peel: _
contact:
email: biomodels-net-support@lists.sf.net
github: null
name: BioModels.net team
orcid: null
description: The Terminology for Description of Dynamics (TEDDY) is an ontology
for dynamical behaviours, observable dynamical phenomena, and control elements
of bio-models and biological systems in Systems Biology and Synthetic Biology.
download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl
example: '0000066'
homepage: http://teddyontology.sourceforge.net/
keywords:
- neurophysiology
- ontology
- synthetic biology
- systems biology
mappings:
aberowl: TEDDY
biocontext: BIOMODELS.TEDDY
bioportal: TEDDY
fairsharing: FAIRsharing.w9jvbt
miriam: biomodels.teddy
n2t: biomodels.teddy
ols: teddy
prefixcommons: teddy
name: Terminology for Description of Dynamics
pattern: ^\d+$
preferred_prefix: biomodels.teddy
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/teddy:$1
publications:
- doi: 10.1038/msb.2011.77
pmc: PMC3261705
pubmed: '22027554'
title: Controlled vocabularies and semantics in systems biology.
year: 2011
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#$1
bionumbers:
description: BioNumbers is a database of key numberical information that may be
used in molecular biology. Along with the numbers, it contains references to the
original literature, useful comments, and related numeric data.
example: '104674'
homepage: https://bionumbers.hms.harvard.edu
mappings:
biocontext: BIONUMBERS
edam: '2660'
miriam: bionumbers
n2t: bionumbers
prefixcommons: bionumbers
name: BioNumbers
pattern: ^\d+$
preferred_prefix: bionumbers
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bionumbers:$1
uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1
biopixie:
comment: This resource doesn't exist on the web anymore
deprecated: true
description: bioPIXIE is a novel system for biological data integration and visualization.
It allows you to discover interaction networks and pathways in which your gene(s)
(e.g. BNI1, YFL039C) of interest participate.
example: '12'
homepage: http://pixie.princeton.edu/pixie/
keywords:
- gene
- interaction
mappings:
prefixcommons: biopixie
name: biological Process Inference from eXperimental Interaction Evidence/Microarray
Experiment Functional Integration Technology
preferred_prefix: biopixie
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/biopixie:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1
bioportal:
contact:
email: support@bioontology.org
github: null
name: John Graybeal
orcid: 0000-0001-6875-5360
description: BioPortal is an open repository of biomedical ontologies that provides
access via Web services and Web browsers to ontologies developed in OWL, RDF,
OBO format and Protégé frames. BioPortal functionality includes the ability to
browse, search and visualize ontologies.
example: '1046'
example_extras:
- SEPIO
- pseudo
- FBBi
homepage: http://bioportal.bioontology.org/
keywords:
- life science
- ontology
- ontology and terminology
mappings:
biocontext: BIOPORTAL
fairsharing: FAIRsharing.4m97ah
miriam: bioportal
n2t: bioportal
prefixcommons: bioportal
re3data: r3d100012344
name: BioPortal
pattern: ^(\d+)|(\w+)$
preferred_prefix: bioportal
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bioportal:$1
publications:
- doi: 10.1093/nar/gkr469
pmc: PMC3125807
pubmed: '21672956'
title: 'BioPortal: enhanced functionality via new Web services from the National
Center for Biomedical Ontology to access and use ontologies in software applications.'
year: 2011
- doi: 10.1093/nar/gkp440
pmc: PMC2703982
pubmed: '19483092'
title: 'BioPortal: ontologies and integrated data resources at the click of a
mouse.'
year: 2009
repository: http://github.com/ncbo
twitter: bioontology
uri_format: http://bioportal.bioontology.org/ontologies/$1
bioproject:
description: BioProject provides an organizational framework to access metadata
about research projects and the data from the projects that are deposited into
different databases. It provides information about a project’s scope, material,
objectives, funding source and general relevance categories.
example: PRJDB3
has_canonical: ena.embl
homepage: http://trace.ddbj.nig.ac.jp/bioproject/
keywords:
- life science
mappings:
biocontext: BIOPROJECT
fairsharing: FAIRsharing.aqhv1y
miriam: bioproject
n2t: bioproject
re3data: r3d100013330
name: BioProject
pattern: ^PRJ[DEN][A-Z]\d+$
preferred_prefix: bioproject
providers:
- 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
- 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
publications:
- doi: 10.1093/nar/gkr1163
pmc: PMC3245069
pubmed: '22139929'
title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization
of metadata.'
year: 2011
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
keywords:
- bioinformatics
- cheminformatics
- computational biology
- computational chemistry
- life science
- ontology and terminology
mappings:
bartoc: '18951'
fairsharing: FAIRsharing.250a8c
mastodon: bioregistry@fosstodon.org
name: Bioregistry
preferred_prefix: bioregistry
publications:
- doi: 10.1101/2022.07.08.499378
pmc: null
pubmed: null
title: Unifying the Identification of Biomedical Entities with the Bioregistry
year: 2022
repository: https://github.com/biopragmatics/bioregistry
twitter: bioregistry
uri_format: https://bioregistry.io/registry/$1
bioregistry.collection:
contact:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Manually curated collections of resources stored in the bioregistry
example: '0000001'
homepage: https://bioregistry.io/collection
keywords:
- registry
name: Bioregistry Collections
pattern: ^\d{7}$
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/
keywords:
- data integration
- data science
- metaregistry
- registry
name: Bioregistry Metaregistry
preferred_prefix: bioregistry.registry
uri_format: https://bioregistry.io/metaregistry/$1
bioregistry.schema:
contact:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Schema for the export of the Bioregistry as RDF
example: '0000001'
homepage: https://bioregistry.io/schema
keywords:
- registry
name: Bioregistry Schema
pattern: ^\d{7}$
preferred_prefix: bioregistry.schema
uri_format: https://bioregistry.io/schema/#$1
biorxiv:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The bioRxiv is a preprint server for biology
example: 2022.07.08.499378
example_extras:
- 000091
- 000091v1
- 2022.07.08.499378v2
homepage: https://biorxiv.org
keywords:
- preprints
- publishing
mappings:
go: bioRxiv
wikidata: P3951
name: bioRxiv
pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$
preferred_prefix: biorxiv
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/biorxiv/$1
rdf_uri_format: http://dx.doi.org/10.1101/$1
uri_format: https://www.biorxiv.org/content/10.1101/$1
biosample:
description: The BioSample Database stores information about biological samples
used in molecular experiments, such as sequencing, gene expression or proteomics.
It includes reference samples, such as cell lines, which are repeatedly used in
experiments. Accession numbers for the reference samples will be exchanged with
a similar database at NCBI, and DDBJ (Japan). Record access may be affected due
to different release cycles and inter-institutional synchronisation.
example: SAMEA2397676
homepage: https://www.ebi.ac.uk/biosamples/
keywords:
- biology
mappings:
biocontext: BIOSAMPLE
cellosaurus: BioSamples
fairsharing: FAIRsharing.qr6pqk
miriam: biosample
n2t: biosample
re3data: r3d100012828
name: BioSample
pattern: ^SAM[NED](\w)?\d+$
preferred_prefix: biosample
providers:
- code: ddbj
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
- 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
publications:
- doi: 10.1093/nar/gkr1163
pmc: PMC3245069
pubmed: '22139929'
title: 'BioProject and BioSample databases at NCBI: facilitating capture and organization
of metadata.'
year: 2011
synonyms:
- biosamples
uri_format: https://www.ebi.ac.uk/biosamples/sample/$1
bioschemas:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Bioschemas aims to improve the Findability on the Web of life sciences
resources such as datasets, software, and training materials. It does this by
encouraging people in the life sciences to use Schema.org markup in their websites
so that they are indexable by search engines and other services. Bioschemas encourages
the consistent use of markup to ease the consumption of the contained markup across
many sites. This structured information then makes it easier to discover, collate,
and analyse distributed resources. [from BioSchemas.org]
example: Dataset
homepage: https://bioschemas.org
mappings:
biolink: bioschemas
name: BioSchemas
preferred_prefix: bioschemas
repository: https://github.com/BioSchemas/specifications
synonyms:
- bioschema
twitter: bioschemas
uri_format: https://bioschemas.org/profiles/$1
biosimulations:
description: BioSimulations is an open repository of simulation projects, including
simulation experiments, their results, and data visualizations of their results.
BioSimulations supports a broad range of model languages, modeling frameworks,
simulation algorithms, and simulation software tools.
example: Yeast-cell-cycle-Irons-J-Theor-Biol-2009
homepage: https://icahn.mssm.edu/
mappings:
miriam: biosimulations
re3data: r3d100013361
name: biosimulations
pattern: ^[a-zA-Z0-9_-]{3,}$
preferred_prefix: biosimulations
uri_format: https://biosimulations.org/projects/$1
biosimulators:
contact:
email: karr@mssm.edu
github: null
name: Jonathan Karr
orcid: 0000-0002-2605-5080
description: BioSimulators is a registry of containerized simulation tools that
support a common interface. The containers in BioSimulators support a range of
modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete
kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats
(e.g., BGNL, SBML, SED-ML).
example: vcell
homepage: https://biosimulators.org/
keywords:
- computational biology
- systems biology
mappings:
fairsharing: FAIRsharing.pwEima
miriam: biosimulators
re3data: r3d100013432
name: BioSimulators
pattern: ^[a-zA-Z0-9-_]+$
preferred_prefix: biosimulators
repository: https://github.com/biosimulators/Biosimulators/issues/new/choose
uri_format: https://biosimulators.org/simulators/$1
biostudies:
description: The BioStudies database holds descriptions of biological studies, links
to data from these studies in other databases at EMBL-EBI or outside, as well
as data that do not fit in the structured archives at EMBL-EBI. The database can
accept a wide range of types of studies described via a simple format. It also
enables manuscript authors to submit supplementary information and link to it
from the publication.
example: S-EPMC6266652
homepage: https://www.ebi.ac.uk/biostudies/
keywords:
- biomedical science
- life science
mappings:
fairsharing: FAIRsharing.mtjvme
miriam: biostudies
n2t: biostudies
re3data: r3d100012627
name: BioStudies database
pattern: ^S-[A-Z]{4}[\-\_A-Z\d]+$
preferred_prefix: biostudies
publications:
- doi: 10.1093/nar/gkx965
pmc: PMC5753238
pubmed: '29069414'
title: The BioStudies database-one stop shop for all data supporting a life sciences
study.
year: 2018
- doi: 10.15252/msb.20156658
pmc: PMC4704487
pubmed: '26700850'
title: The BioStudies database.
year: 2015
uri_format: https://www.ebi.ac.uk/biostudies/studies/$1
biosystems:
description: The NCBI BioSystems database centralizes and cross-links existing biological
systems databases, increasing their utility and target audience by integrating
their pathways and systems into NCBI resources.
example: '001'
homepage: https://www.ncbi.nlm.nih.gov/biosystems/
keywords:
- biology
- molecules
- pathways
- systems biology
mappings:
biocontext: BIOSYSTEMS
fairsharing: FAIRsharing.w2eeqr
miriam: biosystems
n2t: biosystems
prefixcommons: biosystems
re3data: r3d100011033
name: BioSystems
pattern: ^\d+$
preferred_prefix: biosystems
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/biosystems:$1
publications:
- doi: 10.1093/nar/gkp858
pmc: PMC2808896
pubmed: '19854944'
title: The NCBI BioSystems database.
year: 2009
uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1
biotools:
contact:
email: haiiu@dtu.dk
github: hansioan
name: Hans Ienasescu
orcid: 0000-0001-9727-2544
description: BioTools is a registry of databases and software with tools, services,
and workflows for biological and biomedical research.
example: bioregistry
homepage: https://bio.tools/
keywords:
- bioinformatics
- biology
- biomedical science
mappings:
biocontext: BIOTOOLS
fairsharing: FAIRsharing.63520c
miriam: biotools
n2t: biotools
re3data: r3d100013668
name: BioTools
pattern: ^[-A-Za-z0-9\_]*$
preferred_prefix: biotools
publications:
- doi: 10.1093/nar/gkv1116
pmc: PMC4702812
pubmed: '26538599'
title: 'Tools and data services registry: a community effort to document bioinformatics
resources.'
year: 2015
repository: http://github.com/bio-tools/biotoolsregistry/
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
keywords:
- biologics
- life sciences
- vendor
name: BIOZIL
preferred_prefix: biozil
uri_format: https://www.biozol.de/en/product/$1
birnlex:
comment: Part of the NeuroLex namespace now
contact:
email: wbug@ncmir.ucsd.edu
github: null
name: William Bug
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The BIRN Project lexicon will provide entities for data and database
annotation for the BIRN project, covering anatomy, disease, data collection, project
management and experimental design.
download_owl: http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl
example: '2023'
homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX
keywords:
- anatomy
- biomedical science
- ontology
mappings:
aberowl: BIRNLEX
bioportal: BIRNLEX
fairsharing: FAIRsharing.jedbbt
name: Biomedical Informatics Research Network Lexicon
pattern: ^\d+$
preferred_prefix: birnlex
uri_format: http://uri.neuinfo.org/nif/nifstd/birnlex_$1
biro:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology meant to define bibliographic records, bibliographic references,
and their compilation into bibliographic collections and bibliographic lists,
respectively.
example: BibliographicRecord
homepage: http://www.sparontologies.net/ontologies/biro
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.99da5f
name: Bibliographic Reference Ontology
preferred_prefix: BiRO
repository: https://github.com/sparontologies/biro
twitter: sparontologies
uri_format: http://purl.org/spar/biro/$1
bitbucket:
description: Bitbucket is a Git-based source code repository hosting service owned
by Atlassian.
example: andreadega/systems-biology-compiler
homepage: https://www.atlassian.com/
keywords:
- knowledge and information systems
- software engineering
- subject agnostic
mappings:
fairsharing: FAIRsharing.fc3431
miriam: bitbucket
re3data: r3d100013478
name: Bitbucket
pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$
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=$1
bko:
comment: This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.
contact:
email: adrienrougny@gmail.com
github: adrienrougny
name: Adrien Rougny
orcid: 0000-0002-2118-035X
contributor:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
description: SBGN bricks represent biomolecular or biological concepts. BKO formally
associates bricks with the concepts they represent. BKO includes terms that describe
concepts, the template bricks representing these concepts, and categories that
gather bricks in a broader way.
download_owl: http://aber-owl.net/media/ontologies/BKO/1/bko.owl
example: '0000204'
github_request_issue: 283
homepage: http://www.sbgnbricks.org/
keywords:
- ontology
mappings:
aberowl: BKO
bioportal: BKO
name: SBGN Bricks data and ontology
pattern: ^\d+$
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:$1
bmrb:
description: BMRB collects, annotates, archives, and disseminates (worldwide in
the public domain) the important spectral and quantitative data derived from NMR
spectroscopic investigations of biological macromolecules and metabolites. The
goal is to empower scientists in their analysis of the structure, dynamics, and
chemistry of biological systems and to support further development of the field
of biomolecular NMR spectroscopy.
example: '15000'
homepage: http://www.bmrb.wisc.edu/
keywords:
- structural biology
mappings:
fairsharing: FAIRsharing.p06nme
miriam: bmrb
re3data: r3d100010191
uniprot: DB-0256
name: Biological Magnetic Resonance Data Bank
pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$
preferred_prefix: bmrb
publications:
- doi: 10.1007/s10858-008-9221-y
pmc: PMC2268728
pubmed: '18288446'
title: 'BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB):
new policies affecting biomolecular NMR depositions.'
year: 2008
- doi: 10.1093/nar/gkm957
pmc: PMC2238925
pubmed: '17984079'
title: BioMagResBank.
year: 2007
uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html
bmrb.restraint:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The NMR Restraints Grid contains the original NMR data as collected
for over 2500 protein and nucleic acid structures with corresponding PDB entries.
In addition to the original restraints, most of the distance, dihedral angle and
RDC restraint data (>85%) were parsed, and those in over 500 entries were converted
and filtered. The converted and filtered data sets constitute the DOCR and FRED
databases respectively.
example: '28789'
homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet
keywords:
- chemistry
- nmr
- spectrometry
name: NMR Restraints Grid
pattern: ^\d+$
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=$1
bold.taxonomy:
description: The Barcode of Life Data System (BOLD) is an informatics workbench
aiding the acquisition, storage, analysis and publication of DNA barcode records.
The associated taxonomy browser shows the progress of DNA barcoding and provides
sample collection site distribution, and taxon occurence information.
example: '27267'
homepage: http://www.boldsystems.org/
keywords:
- dna
mappings:
biocontext: BOLD.TAXONOMY
miriam: bold.taxonomy
n2t: bold.taxonomy
ncbi: BOLD
prefixcommons: bold
wikidata: P3606
name: BOLD Systems taxon
pattern: ^\d+$
preferred_prefix: bold.taxonomy
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bold:$1
publications:
- doi: 10.1111/j.1471-8286.2007.01678.x
pmc: PMC1890991
pubmed: '18784790'
title: 'bold: The Barcode of Life Data System (http://www.barcodinglife.org).'
year: 2007
uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1
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
keywords:
- obo
- ontology
mappings:
biocontext: BOOTSTREP
obofoundry: bootstrep
name: Gene Regulation Ontology
preferred_prefix: BOOTSTREP
rdf_uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1
uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1
bpdb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'Database of biopesticides maintained by the University of Hertfordshire '
example: '2404'
homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm
keywords:
- biology
- biopesticides
- pesticides
name: Bio-Pesticides DataBase
pattern: ^\d+$
preferred_prefix: bpdb
uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm
brenda:
description: BRENDA is a collection of enzyme functional data available to the scientific
community. Data on enzyme function are extracted directly from the primary literature
The database covers information on classification and nomenclature, reaction and
specificity, functional parameters, occurrence, enzyme structure and stability,
mutants and enzyme engineering, preparation and isolation, the application of
enzymes, and ligand-related data.
example: 1.1.1.1
homepage: https://www.brenda-enzymes.org/
keywords:
- enzyme
- life science
mappings:
biocontext: BRENDA
fairsharing: FAIRsharing.etp533
go: BRENDA
miriam: brenda
n2t: brenda
prefixcommons: brenda
re3data: r3d100010616
name: BRENDA Enzyme
pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$
preferred_prefix: brenda
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/brenda:$1
provides: eccode
publications:
- doi: s0168-1656(17)30183-9
pmc: null
pubmed: '28438579'
title: The BRENDA enzyme information system-From a database to an expert system.
year: null
- doi: 10.1016/j.jbiotec.2017.04.020
pmc: null
pubmed: '28438579'
title: The BRENDA enzyme information system-From a database to an expert system.
year: 2017
- doi: 10.1093/nar/gku1068
pmc: PMC4383907
pubmed: '25378310'
title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
year: 2014
- doi: 10.1093/nar/gks1049
pmc: PMC3531171
pubmed: '23203881'
title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
improved disease classification: new options and contents in BRENDA.'
year: 2012
- doi: 10.1093/nar/gkq1089
pmc: PMC3013686
pubmed: '21062828'
title: BRENDA, the enzyme information system in 2011.
year: 2010
- doi: 10.1093/nar/gkn820
pmc: PMC2686525
pubmed: '18984617'
title: 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and
tools in 2009.'
year: 2008
- doi: 10.1093/nar/gkl972
pmc: PMC1899097
pubmed: '17202167'
title: 'BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.'
year: 2007
- doi: 10.1093/nar/gkh081
pmc: PMC308815
pubmed: '14681450'
title: 'BRENDA, the enzyme database: updates and major new developments.'
year: 2004
- doi: 10.1016/s1096-7176(03)00008-9
pmc: null
pubmed: '12850129'
title: Review of the BRENDA Database.
year: 2003
- doi: 10.1016/s0968-0004(01)02027-8
pmc: null
pubmed: '11796225'
title: 'BRENDA: a resource for enzyme data and metabolic information.'
year: 2002
- doi: 10.1093/nar/30.1.47
pmc: PMC99121
pubmed: '11752250'
title: BRENDA, enzyme data and metabolic information.
year: 2002
uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1
brenda.ligand:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Information for ligands in the BRENDA database.
example: '278'
homepage: https://www.brenda-enzymes.de/ligand.php
keywords:
- chemistry
- structrual bioinformatics
name: BRENDA Ligand
pattern: ^\d+$
preferred_prefix: brenda.ligand
uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1
brenda.ligandgroup:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Information for ligand groups (chemical classes).
example: '18030'
homepage: https://www.brenda-enzymes.de/ligand.php
keywords:
- chemistry
- grouping
- structrual bioinformatics
name: BRENDA Ligand Group
pattern: ^\d+$
preferred_prefix: brenda.ligandgroup
uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1
bridgedb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A vocabulary about resources, similar to bioregistry.schema, venn,
idot, etc.
example: hasPrimaryUriPattern
homepage: https://bridgedb.org
name: BridgeDb Vocabulary
preferred_prefix: bridgedb
references:
- https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl
uri_format: http://vocabularies.bridgedb.org/ops#$1
broad:
description: Magnaporthe grisea, the causal agent of rice blast disease, is one
of the most devasting threats to food security worldwide and is a model organism
for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe
comparative genomics database provides accesses to multiple fungal genomes from
the Magnaporthaceae family to facilitate the comparative analysis. As part of
the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes
the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies
of Gaeumannomyces graminis var. tritici and M. poae.
example: S7000002168151102
homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/
mappings:
biocontext: BROAD
miriam: broad
n2t: broad
name: Broad Fungal Genome Initiative
pattern: ^S\d+$
preferred_prefix: broad
uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1
bs:
comment: An alernative vocabulary that has been aligned and integrated in Sequence
Ontology (SO).
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: SO is a collaborative ontology project for the definition of sequence
features used in biological sequence annotation. It is part of the Open Biomedical
Ontologies library.
download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo
example: '00042'
homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies
keywords:
- ontology
name: Biosapiens Protein Feature Ontology
pattern: ^\d+$
preferred_prefix: bs
repository: https://github.com/The-Sequence-Ontology/SO-Ontologies
uri_format: https://biopragmatics.github.io/providers/bs/$1
bspo:
appears_in:
- aism
- colao
- fovt
- lepao
- zp
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: An ontology for respresenting spatial concepts, anatomical axes, gradients,
regions, planes, sides and surfaces. These concepts can be used at multiple biological
scales and in a diversity of taxa, including plants, animals and fungi. The BSPO
is used to provide a source of anatomical location descriptors for logically defining
anatomical entity classes in anatomy ontologies.
download_json: http://purl.obolibrary.org/obo/bspo.json
download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo
download_owl: http://purl.obolibrary.org/obo/bspo.owl
example: 0000029
homepage: https://github.com/obophenotype/biological-spatial-ontology
keywords:
- anatomy
- life science
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: BSPO
biocontext: BSPO
bioportal: BSPO
fairsharing: FAIRsharing.newa3z
obofoundry: bspo
ols: bspo
ontobee: BSPO
name: Biological Spatial Ontology
pattern: ^\d{7}$
preferred_prefix: BSPO
publications:
- doi: 10.1186/2041-1480-5-34
pmc: PMC4137724
pubmed: '25140222'
title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity
in the Biological Spatial Ontology.'
year: 2014
rdf_uri_format: http://purl.obolibrary.org/obo/BSPO_$1
repository: https://github.com/obophenotype/biological-spatial-ontology
uri_format: http://purl.obolibrary.org/obo/BSPO_$1
version: '2022-11-16'
bto:
banana: BTO
contact:
email: c.dudek@tu-braunschweig.de
github: chdudek
name: Christian-Alexander Dudek
orcid: 0000-0001-9117-7909
description: The Brenda tissue ontology is a structured controlled vocabulary eastablished
to identify the source of an enzyme cited in the Brenda enzyme database. It comprises
terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular
organisms.
download_json: http://purl.obolibrary.org/obo/bto.json
download_obo: http://purl.obolibrary.org/obo/bto.obo
download_owl: http://purl.obolibrary.org/obo/bto.owl
example: 0000590
homepage: http://www.brenda-enzymes.org
keywords:
- enzymology
- life science
- obo
- ontology
- tissue
license: CC-BY-4.0
mappings:
aberowl: BTO
biocontext: BTO
bioportal: BTO
cellosaurus: BTO
fairsharing: FAIRsharing.1414v8
go: BTO
miriam: bto
n2t: bto
obofoundry: bto
ols: bto
ontobee: BTO
prefixcommons: bto
wikidata: P5501
name: BRENDA Tissue Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: BTO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bto:$1
- code: miriam_obo_legacy
description: An old URI style for MIRIAM
homepage: https://identifiers.org/
name: MIRIAM OBO Legacy
uri_format: http://identifiers.org/obo.bto/BTO:$1
publications:
- doi: 10.1093/nar/gky1048
pmc: PMC6323942
pubmed: '30395242'
title: 'BRENDA in 2019: a European ELIXIR core data resource.'
year: 2019
- doi: 10.1093/nar/gku1068
pmc: PMC4383907
pubmed: '25378310'
title: 'BRENDA in 2015: exciting developments in its 25th year of existence.'
year: 2014
- doi: 10.1093/nar/gks1049
pmc: PMC3531171
pubmed: '23203881'
title: 'BRENDA in 2013: integrated reactions, kinetic data, enzyme function data,
improved disease classification: new options and contents in BRENDA.'
year: 2012
- doi: 10.1093/nar/gkq968
pmc: PMC3013802
pubmed: '21030441'
title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of
all organisms for enzyme sources.'
year: 2010
- doi: 10.1093/nar/gkh081
pmc: PMC308815
pubmed: '14681450'
title: 'BRENDA, the enzyme database: updates and major new developments.'
year: 2004
rdf_uri_format: http://purl.obolibrary.org/obo/BTO_$1
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?action=view&expt_id=$1
bugbase.protocol:
description: BugBase is a MIAME-compliant microbial gene expression and comparative
genomic database. It stores experimental annotation and multiple raw and analysed
data formats, as well as protocols for bacterial microarray designs. This collection
references design protocols.
example: '67'
homepage: http://bugs.sgul.ac.uk/E-BUGS
mappings:
biocontext: BUGBASE.PROTOCOL
miriam: bugbase.protocol
n2t: bugbase.protocol
name: BugBase Protocol
pattern: ^\d+$
preferred_prefix: bugbase.protocol
uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1
bykdb:
description: The bacterial tyrosine kinase database (BYKdb) that collects sequences
of putative and authentic bacterial tyrosine kinases, providing structural and
functional information.
example: A0A009E7X8
homepage: https://bykdb.ibcp.fr/BYKdb/
keywords:
- domain
- life science
- microbial
- sequence
mappings:
biocontext: BYKDB
fairsharing: FAIRsharing.jr30xc
miriam: bykdb
n2t: bykdb
prefixcommons: bykdb
name: Bacterial Tyrosine Kinase Database
pattern: ^[A-Z0-9]+$
preferred_prefix: bykdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/bykdb:$1
provides: uniprot
publications:
- doi: 10.1016/s0378-1119(97)00554-4
pmc: null
pubmed: '9434192'
title: Characterization of a bacterial gene encoding an autophosphorylating protein
tyrosine kinase.
year: 1997
- doi: 10.1093/nar/gkr915
pmc: PMC3245071
pubmed: '22080550'
title: 'BYKdb: the Bacterial protein tYrosine Kinase database.'
year: 2011
- doi: 10.1007/s00726-009-0237-8
pmc: null
pubmed: '19189200'
title: 'Tyrosine-kinases in bacteria: from a matter of controversy to the status
of key regulatory enzymes.'
year: 2009
- doi: 10.1093/bioinformatics/btn462
pmc: null
pubmed: '18772155'
title: Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase)
family signature.
year: 2008
uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html
c4o:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology that permits the number of in-text citations of a cited
source to be recorded, together with their textual citation contexts, along with
the number of citations a cited entity has received globally on a particular date.
example: InTextReferencePointer
homepage: http://www.sparontologies.net/ontologies/c4o
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.beb855
name: Citation Counting and Context Characterisation Ontology
preferred_prefix: C4O
repository: https://github.com/sparontologies/c4o
twitter: sparontologies
uri_format: http://purl.org/spar/c4o/$1
cabri:
contact:
email: paolo.romano@hsanmartino.it
github: null
name: Paolo Romano
orcid: 0000-0003-4694-3883
description: CABRI (Common Access to Biotechnological Resources and Information)
is an online service where users can search a number of European Biological Resource
Centre catalogues. It lists the availability of a particular organism or genetic
resource and defines the set of technical specifications and procedures which
should be used to handle it.
example: dsmz_mutz-id:ACC 291
homepage: http://www.cabri.org/
keywords:
- applied microbiology
- medical microbiology
- microbiology
- molecular biology
- molecular microbiology
- virology
mappings:
biocontext: CABRI
edam: '2380'
fairsharing: FAIRsharing.qx2rvz
miriam: cabri
n2t: cabri
ncbi: CABRI
name: Common Access to Biological Resources and Information Project
pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$
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]
publications:
- doi: 10.1002/cfg.376
pmc: PMC2447341
pubmed: '18629057'
title: Interoperability of CABRI Services and Biochemical Pathways Databases.
year: 2004
- doi: 10.2165/00822942-200594030-00002
pmc: null
pubmed: '16231959'
title: The role of informatics in the coordinated management of biological resources
collections.
year: 2005
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=$1]
caloha:
contact:
email: Paula.Duek@sib.swiss
github: paulacalipho
name: Paula Duek Roggli
orcid: 0000-0002-0819-0473
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: This is a code repository for the SIB - Swiss Institute of Bioinformatics
CALIPHO group neXtProt project, which is a comprehensive human-centric discovery
platform, that offers a integration of and navigation through protein-related
data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies
to help uncover the function of uncharacterized human proteins.
download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo
example: TS-0001
homepage: https://github.com/calipho-sib/controlled-vocabulary
keywords:
- anatomy
- human
- ontology
- physiology
license: CC-BY-4.0
name: CALIPHO Group Ontology of Human Anatomy
pattern: ^TS-\d+$
preferred_prefix: caloha
providers:
- code: biopragmatics
description: A static site generated from the CALOHA OBO flat file
homepage: https://biopragmatics.github.io/providers
name: Biopragmatics Browser
uri_format: https://biopragmatics.github.io/providers/caloha/$1
references:
- https://twitter.com/neXtProt_news/status/1350105997633867781
- https://github.com/biopragmatics/bioregistry/issues/721
repository: https://github.com/calipho-sib/controlled-vocabulary
twitter: neXtProt_news
uri_format: https://www.nextprot.org/term/$1
cameo:
contact:
email: torsten.schwede@unibas.ch
github: null
name: Torsten Schwede
orcid: 0000-0003-2715-335X
description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community
project is to continuously evaluate the accuracy and reliability of protein structure
prediction servers, offering scores on tertiary and quaternary structure prediction,
model quality estimation, accessible surface area prediction, ligand binding site
residue prediction and contact prediction services in a fully automated manner.
These predictions are regularly compared against reference structures from PDB.
example: 2019-08-03_00000089_1
homepage: https://cameo3d.org
keywords:
- life science
mappings:
biocontext: CAMEO
fairsharing: FAIRsharing.dq34p2
miriam: cameo
n2t: cameo
name: Continuous Automated Model Evaluation
pattern: ^[0-9\-_]+$
preferred_prefix: cameo
publications:
- doi: 10.1093/database/bat031
pmc: PMC3889916
pubmed: '23624946'
title: The Protein Model Portal--a comprehensive resource for protein structure
and model information.
year: 2013
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=$1
caro:
appears_in:
- aism
- colao
- ehdaa2
- lepao
- pco
contact:
email: haendel@ohsu.edu
github: mellybelly
name: Melissa Haendel
orcid: 0000-0001-9114-8737
description: The Common Anatomy Reference Ontology (CARO) is being developed to
facilitate interoperability between existing anatomy ontologies for different
species, and will provide a template for building new anatomy ontologies.
download_json: http://purl.obolibrary.org/obo/caro.json
download_obo: http://purl.obolibrary.org/obo/caro.obo
download_owl: http://purl.obolibrary.org/obo/caro.owl
example: '0000000'
homepage: https://github.com/obophenotype/caro/
keywords:
- anatomy
- life science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: CARO
biocontext: CARO
bioportal: CARO
fairsharing: FAIRsharing.3kcgmr
go: CARO
obofoundry: caro
ols: caro
ontobee: CARO
name: Common Anatomy Reference Ontology
pattern: ^\d{7}$
preferred_prefix: CARO
providers:
- code: obo.1
description: This incorrect encoding was found inside IDO-COVID-19
homepage: http://purl.obolibrary.org
name: Nonstandard OBO PURL
uri_format: http://purl.obolibrary.org/obo/ido.owl/CARO_$1
publications:
- doi: 10.1007/978-1-84628-885-2_16
pmc: null
pubmed: null
title: CARO – The Common Anatomy Reference Ontology
year: 2008
rdf_uri_format: http://purl.obolibrary.org/obo/CARO_$1
repository: https://github.com/obophenotype/caro
uri_format: http://purl.obolibrary.org/obo/CARO_$1
version: '2023-03-15'
cas:
description: CAS (Chemical Abstracts Service) is a division of the American Chemical
Society and is the producer of comprehensive databases of chemical information.
example: 50-00-0
homepage: https://commonchemistry.cas.org/
keywords:
- chemical
- cheminformatics
- structure
mappings:
biocontext: CAS
cheminf: '000446'
edam: '1002'
fairsharing: FAIRsharing.r7Kwy7
go: CAS
hl7: 2.16.840.1.113883.6.61
miriam: cas
n2t: cas
prefixcommons: cas
wikidata: P231
name: CAS Registry Number
pattern: ^\d{1,7}\-\d{2}\-\d$
preferred_prefix: cas
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cas:$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/cas/$1
publications:
- doi: 10.1021/acs.jcim.2c00268
pmc: PMC9199008
pubmed: '35559614'
title: 'CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information
for the Scientific Community.'
year: 2022
synonyms:
- CASID
- CAS_RN
- SECONDARY_CAS_RN
- cas_id
uri_format: https://commonchemistry.cas.org/detail?cas_rn=$1
casspc:
comment: Jim Balhoff said that Catalog of Fishes does not publish their data in
a machine readable format, but a long time ago they sent a CSV dump to help in
the development of TTO and VTO. These ontologies are effectively retired and CASSPC
terms are only also used in Phenoscape.
contributor:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
contributor_extras:
- email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
example: '5359'
homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
mappings:
go: CASSPC
name: Eschmeyer's Catalog of Fishes
pattern: ^\d+$
preferred_prefix: casspc
uri_format: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1
cath:
description: CATH is a classification of protein structural domains. We group protein
domains into superfamilies when there is sufficient evidence they have diverged
from a common ancestor. CATH can be used to predict structural and functional
information directly from protein sequence.
example: 1.10.8.10
homepage: http://www.cathdb.info
keywords:
- biology
- classification
- evolutionary biology
- protein
- structure
mappings:
biocontext: CATH
edam: '2700'
fairsharing: FAIRsharing.xgcyyn
miriam: cath
n2t: cath
prefixcommons: cath
re3data: r3d100012629
name: CATH Protein Structural Domain Superfamily
pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$
preferred_prefix: cath
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cath:$1
publications:
- doi: 10.1016/s0969-2126(97)00260-8
pmc: null
pubmed: '9309224'
title: CATH--a hierarchic classification of protein domain structures.
year: 1997
- doi: 10.1093/nar/gkaa1079
pmc: PMC7778904
pubmed: '33237325'
title: 'CATH: increased structural coverage of functional space.'
year: 2021
- doi: 10.1093/nar/gky1097
pmc: PMC6323983
pubmed: '30398663'
title: 'CATH: expanding the horizons of structure-based functional annotations
for genome sequences.'
year: 2019
- doi: 10.1093/nar/gkx1069
pmc: PMC5753370
pubmed: '29112716'
title: 'Gene3D: Extensive prediction of globular domains in proteins.'
year: 2018
- doi: 10.1093/nar/gkw1098
pmc: PMC5210570
pubmed: '27899584'
title: 'CATH: an expanded resource to predict protein function through structure
and sequence.'
year: 2016
- doi: 10.1093/bioinformatics/btw473
pmc: PMC5018379
pubmed: '27477482'
title: 'Functional classification of CATH superfamilies: a domain-based approach
for protein function annotation.'
year: 2016
- doi: 10.1016/j.biochi.2015.08.004
pmc: PMC4678953
pubmed: '26253692'
title: The history of the CATH structural classification of protein domains.
year: 2015
- doi: 10.1093/nar/gku947
pmc: PMC4384018
pubmed: '25348408'
title: 'CATH: comprehensive structural and functional annotations for genome sequences.'
year: 2014
- doi: null
pmc: null
pubmed: '11788987'
title: 'The CATH protein family database: a resource for structural and functional
annotation of genomes.'
year: 2002
twitter: CATHDatabase
uri_format: http://www.cathdb.info/cathnode/$1
cath.domain:
description: The CATH database is a hierarchical domain classification of protein
structures in the Protein Data Bank. Protein structures are classified using a
combination of automated and manual procedures. There are four major levels in
this hierarchy; Class (secondary structure classification, e.g. mostly alpha),
Architecture (classification based on overall shape), Topology (fold family) and
Homologous superfamily (protein domains which are thought to share a common ancestor).
This colelction is concerned with CATH domains.
example: 1cukA01
homepage: http://www.cathdb.info/
mappings:
biocontext: CATH.DOMAIN
edam: '1040'
miriam: cath.domain
n2t: cath.domain
name: CATH domain
pattern: ^\w+$
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/$1
cattleqtldb:
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
designed to house publicly all available QTL and single-nucleotide polymorphism/gene
association data on livestock animal species. This collection references cattle
QTLs.
example: '4685'
homepage: https://www.animalgenome.org/QTLdb
keywords:
- dna
- genome
mappings:
biocontext: CATTLEQTLDB
miriam: cattleqtldb
n2t: cattleqtldb
prefixcommons: cattleqtldb
name: Animal Genome Cattle QTL
part_of: qtldb
pattern: ^\d+$
preferred_prefix: cattleqtldb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cattleqtldb:$1
uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
cazy:
description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized
in enzymes that build and breakdown complex carbohydrates and glycoconjugates.
These enzymes are classified into families based on structural features.
example: GT10
homepage: http://www.cazy.org/
keywords:
- classification
- glycomics
- life science
- polysaccharide
mappings:
biocontext: CAZY
fairsharing: FAIRsharing.ntyq70
go: CAZY
miriam: cazy
n2t: cazy
prefixcommons: cazy
re3data: r3d100012321
uniprot: DB-0136
name: Carbohydrate Active EnZYmes
pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$
preferred_prefix: cazy
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cazy:$1
publications:
- doi: 10.1093/nar/gkt1178
pmc: PMC3965031
pubmed: '24270786'
title: The carbohydrate-active enzymes database (CAZy) in 2013.
year: 2013
- doi: 10.1093/nar/gkn663
pmc: PMC2686590
pubmed: '18838391'
title: 'The Carbohydrate-Active EnZymes database (CAZy): an expert resource for
Glycogenomics.'
year: 2008
uri_format: http://www.cazy.org/$1.html
cba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological
Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available
in MEDLINE.'
example: '375364'
homepage: http://www.cba.ac.cn
keywords:
- bibliography
name: Chinese Biological Abstracts
pattern: ^\d+$
preferred_prefix: cba
uri_format: https://europepmc.org/article/CBA/$1
cbioportal:
contact:
email: gaoj@mskcc.org
github: jjgao
name: Jianjiong Gao
orcid: 0000-0002-5739-1781
description: The cBioPortal for Cancer Genomics provides visualization, analysis
and download of large-scale cancer genomics data sets.
example: laml_tcga_pub
homepage: http://www.cbioportal.org
keywords:
- biomedical science
- genomics
- preclinical studies
- proteomics
mappings:
fairsharing: FAIRsharing.6L6MjA
miriam: cbioportal
n2t: cbioportal
name: The cBioPortal for Cancer Genomics
pattern: ^[a-z0-9\_]+$
preferred_prefix: cbioportal
publications:
- doi: 10.1126/scisignal.2004088
pmc: PMC4160307
pubmed: '23550210'
title: Integrative analysis of complex cancer genomics and clinical profiles using
the cBioPortal.
year: 2013
- doi: 10.1158/2159-8290.cd-12-0095
pmc: PMC3956037
pubmed: '22588877'
title: 'The cBio cancer genomics portal: an open platform for exploring multidimensional
cancer genomics data.'
year: 2012
repository: https://github.com/cBioPortal/cbioportal
twitter: 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:$1&sid=IDORG
ccds:
description: The Consensus CDS (CCDS) project is a collaborative effort to identify
a core set of human and mouse protein coding regions that are consistently annotated
and of high quality. The CCDS set is calculated following coordinated whole genome
annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal
is to support convergence towards a standard set of gene annotations.
example: CCDS13573.1
homepage: http://www.ncbi.nlm.nih.gov/CCDS/
keywords:
- gene
- life science
- protein
mappings:
biocontext: CCDS
fairsharing: FAIRsharing.46s4nt
miriam: ccds
n2t: ccds
prefixcommons: ccds
uniprot: DB-0187
name: Consensus CDS
pattern: ^CCDS\d+\.\d+$
preferred_prefix: ccds
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ccds:$1
publications:
- doi: 10.1101/gr.080531.108
pmc: PMC2704439
pubmed: '19498102'
title: 'The consensus coding sequence (CCDS) project: Identifying a common protein-coding
gene set for the human and mouse genomes.'
year: 2009
uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1
ccle:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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=$1
cco:
banana: CCO
contact:
email: kuiper@bio.ntnu.no
github: makuintnu
name: Martin Kuiper
orcid: 0000-0002-1171-9876
description: The Cell Cycle Ontology is an application ontology that captures and
integrates detailed knowledge on the cell cycle process.
download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo
download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl
example: '0000003'
homepage: http://www.semantic-systems-biology.org/apo
keywords:
- cell cycle
- functional genomics
- genomics
- life science
- obo
- ontology
- proteomics
mappings:
aberowl: CCO
biocontext: CCO
bioportal: CCO
fairsharing: FAIRsharing.xhwrnr
miriam: cco
n2t: cco
ols: cco
prefixcommons: cco
name: Cell Cycle Ontology
namespace_in_lui: true
pattern: ^\w+$
preferred_prefix: cco
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cco:$1
publications:
- doi: 10.1186/gb-2009-10-5-r58
pmc: PMC2718524
pubmed: '19480664'
title: 'The Cell Cycle Ontology: an application ontology for the representation
and integrated analysis of the cell cycle process.'
year: 2009
uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1
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=$1
cdao:
contact:
email: balhoff@renci.org
github: balhoff
name: Jim Balhoff
orcid: 0000-0002-8688-6599
description: The Comparative Data Analysis Ontology (CDAO) provides a framework
for understanding data in the context of evolutionary-comparative analysis. This
comparative approach is used commonly in bioinformatics and other areas of biology
to draw inferences from a comparison of differently evolved versions of something,
such as differently evolved versions of a protein. In this kind of analysis,
the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic
Units). The OTUs can represent biological species, but also may be drawn from
higher or lower in a biological hierarchy, anywhere from molecules to communities. The
features to be compared among OTUs are rendered in an entity-attribute-value model
sometimes referred to as the 'character-state data model'. For a given character,
such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences
between states are understood to emerge by a historical process of evolutionary
transitions in state, represented by a model (or rules) of transitions along with
a phylogenetic tree. CDAO provides the framework for representing OTUs, trees,
transformations, and characters. The representation of characters and transformations
may depend on imported ontologies for a specific type of character.
download_owl: http://purl.obolibrary.org/obo/cdao.owl
example: '0000072'
homepage: https://github.com/evoinfo/cdao
keywords:
- bioinformatics
- biomedical science
- evolutionary biology
- life science
- molecular biology
- obo
- ontology
- phylogenetics
- taxonomy
license: CC0-1.0
mappings:
aberowl: CDAO
agroportal: CDAO
biocontext: CDAO
bioportal: CDAO
fairsharing: FAIRsharing.kay31r
obofoundry: cdao
ols: cdao
ontobee: CDAO
name: Comparative Data Analysis Ontology
pattern: ^\d{7}$
preferred_prefix: CDAO
publications:
- doi: 10.4137/ebo.s2320
pmc: PMC2747124
pubmed: '19812726'
title: Initial implementation of a comparative data analysis ontology.
year: 2009
rdf_uri_format: http://purl.obolibrary.org/obo/CDAO_$1
repository: https://github.com/evoinfo/cdao
uri_format: http://purl.obolibrary.org/obo/CDAO_$1
version: '2022-11-30'
cdd:
description: The Conserved Domain Database (CDD) is a collection of multiple sequence
alignments and derived database search models, which represent protein domains
conserved in molecular evolution.
example: cd00400
homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd
keywords:
- earth science
- geology
- protein
- structure
mappings:
biocontext: CDD
edam: '2666'
fairsharing: FAIRsharing.ea287c
go: CDD
miriam: cdd
n2t: cdd
ncbi: CDD
prefixcommons: cdd
re3data: r3d100012041
uniprot: DB-0214
name: Conserved Domain Database at NCBI
pattern: ^(cd)?\d{5}$
preferred_prefix: cdd
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cdd:$1
publications:
- doi: doi
pmc: PMC4383992
pubmed: '25414356'
title: null
year: null
- doi: 10.1093/nar/gku1221
pmc: PMC4383992
pubmed: '25414356'
title: 'CDD: NCBI''s conserved domain database.'
year: 2014
- doi: 10.1093/nar/gkn845
pmc: PMC2686570
pubmed: '18984618'
title: 'CDD: specific functional annotation with the Conserved Domain Database.'
year: 2008
uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1
cdno:
contact:
email: l.andres.hernandez.18@student.scu.edu.au
github: LilyAndres
name: Liliana Andres Hernandez
orcid: 0000-0002-7696-731X
depends_on:
- bfo
- chebi
- envo
- pato
- ro
description: None
download_obo: http://purl.obolibrary.org/obo/cdno.obo
download_owl: http://purl.obolibrary.org/obo/cdno.owl
example: '0000013'
homepage: https://cdno.info/
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: CDNO
agroportal: CDNO
bioportal: CDNO
obofoundry: cdno
ols: cdno
ontobee: CDNO
name: Compositional Dietary Nutrition Ontology
pattern: ^\d{7}$
preferred_prefix: CDNO
publications:
- doi: 10.1002/csc2.20092
pmc: null
pubmed: null
title: Knowledge representation and data sharing to unlock crop variation for
nutritional food security
year: 2020
rdf_uri_format: http://purl.obolibrary.org/obo/CDNO_$1
repository: https://github.com/Southern-Cross-Plant-Science/cdno
uri_format: http://purl.obolibrary.org/obo/CDNO_$1
version: '2022-12-23'
cdpd:
description: The Canadian Drug Product Database (DPD) contains product specific
information on drugs approved for use in Canada, and includes human pharmaceutical
and biological drugs, veterinary drugs and disinfectant products. This information
includes 'brand name', 'route of administration' and a Canadian 'Drug Identification
Number' (DIN).
example: '63250'
homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp
mappings:
biocontext: CDPD
miriam: cdpd
n2t: cdpd
name: Canadian Drug Product Database
pattern: ^\d+$
preferred_prefix: cdpd
uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1
cdt:
appears_in:
- ohd
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Code on Dental Procedures and Nomenclature (the CDT Code) assures
consistency in documenting dental treatment.
download_owl: https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl
example: '1000001'
homepage: https://www.ada.org/publications/CDT
keywords:
- ontology
mappings:
bartoc: '20299'
hl7: 2.16.840.1.113883.6.116
name: Current Dental Terminology
pattern: ^\d{7}$
preferred_prefix: cdt
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: https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/
mappings:
cellosaurus: CBA
name: CellBank Australia
preferred_prefix: cellbank.australia
uri_format: https://www.cellbankaustralia.com/$1.html
cellimage:
description: 'The Cell: An Image Library™ is a freely accessible, public repository
of reviewed and annotated images, videos, and animations of cells from a variety
of organisms, showcasing cell architecture, intracellular functionalities, and
both normal and abnormal processes.'
example: '24801'
homepage: http://cellimagelibrary.org/
keywords:
- cell biology
- image
- life science
mappings:
biocontext: CELLIMAGE
fairsharing: FAIRsharing.8t18te
miriam: cellimage
n2t: cellimage
prefixcommons: cellimage
re3data: r3d100000023
name: Cell Image Library
pattern: ^\d+$
preferred_prefix: cellimage
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cellimage:$1
publications:
- doi: 10.1093/nar/gks1257
pmc: PMC3531121
pubmed: '23203874'
title: 'The cell: an image library-CCDB: a curated repository of microscopy data.'
year: 2012
twitter: CellImageLibrar
uri_format: http://cellimagelibrary.org/images/$1
cellopub:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cellosaurus identifeirs for publications, like Pubmed
example: CLPUB00496
homepage: https://web.expasy.org/cellosaurus/
mappings:
cellosaurus: CelloPub
name: Cellosaurus Publication
pattern: ^CLPUB\d+$
preferred_prefix: cellopub
uri_format: https://web.expasy.org/cellosaurus/cellopub/$1
cellosaurus:
banana: CVCL
banana_peel: _
contact:
email: Amos.Bairoch@sib.swiss
github: AmosBairoch
name: Amos Bairoch
orcid: 0000-0003-2826-6444
description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts
to describe all cell lines used in biomedical research. Its scope includes: Immortalized
cell lines; naturally immortal cell lines (example: stem cell lines); finite life
cell lines when those are distributed and used widely; vertebrate cell line with
an emphasis on human, mouse and rat cell lines; and invertebrate (insects and
ticks) cell lines. Its scope does not include primary cell lines (with the exception
of the finite life cell lines described above) and plant cell lines.'
download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo
example: '0440'
homepage: https://cellosaurus.org
keywords:
- life science
- ontology
mappings:
biocontext: CELLOSAURUS
cellosaurus: Cellosaurus
fairsharing: FAIRsharing.hkk309
miriam: cellosaurus
n2t: cellosaurus
re3data: r3d100013293
wikidata: P3289
mastodon: cellosaurus@fediscience.org
name: Cellosaurus
pattern: ^[A-Z0-9]{4}$
preferred_prefix: cellosaurus
providers:
- code: legacy
description: The legacy URI for the Cellosaurus website, updated on August 30,
2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).
homepage: https://web.expasy.org/cellosaurus
name: Legacy Endpoint
uri_format: https://web.expasy.org/cellosaurus/CVCL_$1
- code: nextprot
description: The neXtProt endpoint for exploring Cellosaurus
homepage: https://www.nextprot.org/
name: neXtProt Cellosaurus Browser
uri_format: https://www.nextprot.org/term/CVCL_$1
publications:
- doi: 10.1002/ijc.32639
pmc: null
pubmed: '31444973'
title: 'CLASTR: The Cellosaurus STR similarity search tool - A precious help for
cell line authentication.'
year: 2019
- doi: 10.7171/jbt.18-2902-002
pmc: PMC5945021
pubmed: '29805321'
title: The Cellosaurus, a Cell-Line Knowledge Resource.
year: 2018
synonyms:
- CVCL
twitter: cellosaurus
uri_format: https://www.cellosaurus.org/CVCL_$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/
keywords:
- cell lines
- cells
- registry
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/$1
cemo:
contact:
email: n.queralt_rosinach@lumc.nl
github: NuriaQueralt
name: Núria Queralt Rosinach
orcid: 0000-0003-0169-8159
contributor:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
description: The covid-19 epidemiology and monitoring ontology (cemo) provides a
common ontological model to make epidemiological quantitative data for monitoring
the covid-19 outbreak machine-readable and interoperable to facilitate its exchange,
integration and analysis, to eventually support evidence-based rapid response.
download_json: https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json
download_owl: https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl
example: secondary_attack_rate
github_request_issue: 593
homepage: https://github.com/NuriaQueralt/covid19-epidemiology-ontology
keywords:
- ontology
license: CC0-1.0
name: The COVID-19 epidemiology and monitoring ontology
pattern: ^[0-9a-z_-]+$
preferred_prefix: cemo
providers:
- code: obo
description: This represents misconfigured base IRIs, even though this ontology
isn't an OBO Foundry ontology
homepage: http://purl.obolibrary.org/obo/
name: Legacy OBO PURL
uri_format: http://purl.obolibrary.org/obo/cemo.owl#$1
repository: https://github.com/NuriaQueralt/covid19-epidemiology-ontology
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://biopragmatics.github.io/providers/cemo/$1
ceph:
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
deprecated: true
description: An anatomical and developmental ontology for cephalopods
download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo
download_owl: http://purl.obolibrary.org/obo/ceph.owl
example: 0000109
homepage: https://github.com/obophenotype/cephalopod-ontology
keywords:
- anatomy
- fisheries science
- obo
- ontology
- zoology
license: CC-BY-3.0
mappings:
aberowl: CEPH
biocontext: CEPH
bioportal: CEPH
fairsharing: FAIRsharing.p58bm4
obofoundry: ceph
ols: ceph
ontobee: CEPH
name: Cephalopod Ontology
pattern: ^\d{7}$
preferred_prefix: CEPH
rdf_uri_format: http://purl.obolibrary.org/obo/CEPH_$1
repository: https://github.com/obophenotype/cephalopod-ontology
uri_format: http://purl.obolibrary.org/obo/CEPH_$1
version: '2016-01-12'
cgd:
description: The Candida Genome Database (CGD) provides access to genomic sequence
data and manually curated functional information about genes and proteins of the
human pathogen Candida albicans. It collects gene names and aliases, and assigns
gene ontology terms to describe the molecular function, biological process, and
subcellular localization of gene products.
example: CAL0003079
homepage: http://www.candidagenome.org/
keywords:
- eukaryotic
- genome
- life science
- nucleotide
mappings:
biocontext: CGD
fairsharing: FAIRsharing.j7j53
go: CGD
miriam: cgd
n2t: cgd
ncbi: CGD
prefixcommons: cgd
re3data: r3d100010617
uniprot: DB-0126
name: Candida Genome Database
pattern: ^CAL\d{7}$
preferred_prefix: cgd
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cgd:$1
publications:
- doi: 10.1093/nar/gkw924
pmc: PMC5210628
pubmed: '27738138'
title: 'The Candida Genome Database (CGD): incorporation of Assembly 22, systematic
identifiers and visualization of high throughput sequencing data.'
year: 2016
- doi: 10.1093/nar/gkr945
pmc: PMC3245171
pubmed: '22064862'
title: 'The Candida genome database incorporates multiple Candida species: multispecies
search and analysis tools with curated gene and protein information for Candida
albicans and Candida glabrata.'
year: 2011
- doi: 10.1093/nar/gki003
pmc: PMC539957
pubmed: '15608216'
title: The Candida Genome Database (CGD), a community resource for Candida albicans
gene and protein information.
year: 2005
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=$1&aid=%t&lang=en
cgnc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Nomenclature Consortium around Chicken genes (analogous to the HGNC
for humans)
example: '10087'
homepage: http://birdgenenames.org/cgnc/
keywords:
- gene
mappings:
prefixcommons: cgnc
re3data: r3d100012429
name: Chicken Gene Nomenclature Consortium
pattern: ^\d+$
preferred_prefix: cgnc
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cgnc:$1
publications:
- doi: 10.1186/1471-2164-10-s2-s5
pmc: PMC2966335
pubmed: '19607656'
title: The Chicken Gene Nomenclature Committee report.
year: 2009
synonyms:
- BirdBase
- CGNC
uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1
cgsc:
description: The CGSC Database of E. coli genetic information includes genotypes
and reference information for the strains in the CGSC collection, the names, synonyms,
properties, and map position for genes, gene product information, and information
on specific mutations and references to primary literature.
example: '74'
homepage: http://cgsc.biology.yale.edu/index.php
keywords:
- gene
- life science
mappings:
biocontext: CGSC
fairsharing: FAIRsharing.1tbrdz
go: CGSC
miriam: cgsc
n2t: cgsc
prefixcommons: cgsc
re3data: r3d100010585
name: Coli Genetic Stock Center
pattern: ^\d+$
preferred_prefix: cgsc
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cgsc:$1
publications:
- doi: 10.1016/s0076-6879(06)21001-2
pmc: null
pubmed: '17352909'
title: Strain collections and genetic nomenclature.
year: 2007
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/$1
chebi:
appears_in:
- cdno
- chiro
- cl
- ecocore
- ecto
- envo
- fobi
- foodon
- genepio
- maxo
- mco
- ons
- pcl
- proco
- scdo
- uberon
- xpo
banana: CHEBI
contact:
email: amalik@ebi.ac.uk
github: amalik01
name: Adnan Malik
orcid: 0000-0001-8123-5351
description: Chemical Entities of Biological Interest (ChEBI) is a freely available
dictionary of molecular entities focused on 'small' chemical compounds.
download_obo: http://purl.obolibrary.org/obo/chebi.obo
download_owl: http://purl.obolibrary.org/obo/chebi.owl
example: '24867'
homepage: http://www.ebi.ac.uk/chebi
keywords:
- biochemistry
- chemical
- chemistry
- obo
- ontology
license: CC-BY-4.0
logo: https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png
mappings:
aberowl: CHEBI
bartoc: '558'
biocontext: CHEBI
bioportal: CHEBI
cellosaurus: ChEBI
cheminf: '000407'
edam: '1174'
fairsharing: FAIRsharing.62qk8w
go: CHEBI
miriam: chebi
n2t: chebi
obofoundry: chebi
ols: chebi
ontobee: CHEBI
prefixcommons: chebi
re3data: r3d100012626
wikidata: P683
name: Chemical Entities of Biological Interest
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: CHEBI
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/chebi:$1
- 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
publications:
- doi: 10.1093/nar/gkv1031
pmc: PMC4702775
pubmed: '26467479'
title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.'
year: 2015
- doi: 10.1093/nar/gks1146
pmc: PMC3531142
pubmed: '23180789'
title: 'The ChEBI reference database and ontology for biologically relevant chemistry:
enhancements for 2013.'
year: 2012
- doi: 10.1093/nar/gkp886
pmc: PMC2808869
pubmed: '19854951'
title: 'Chemical Entities of Biological Interest: an update.'
year: 2009
- doi: 10.1002/0471250953.bi1409s26
pmc: null
pubmed: '19496059'
title: 'ChEBI: an open bioinformatics and cheminformatics resource.'
year: 2009
- doi: 10.1093/nar/gkm791
pmc: PMC2238832
pubmed: '17932057'
title: 'ChEBI: a database and ontology for chemical entities of biological interest.'
year: 2007
rdf_uri_format: http://purl.obolibrary.org/obo/CHEBI_$1
repository: https://github.com/ebi-chebi/ChEBI
synonyms:
- CHEBI
- CHEBIID
- ChEBI
twitter: chebit
uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1
version: '219'
chembank:
comment: This resource doesn't exist on the web anymore
deprecated: true
description: ChemBank is a public, web-based informatics environment created by
the Broad Institute's Chemical Biology Program and funded in large part by the
National Cancer Institute's Initiative for Chemical Genetics (ICG).
example: '1000000'
homepage: http://chembank.broad.harvard.edu
keywords:
- chemical
- metabolite
mappings:
biocontext: CHEMBANK
biolink: ChemBank
prefixcommons: chembank
name: ChemBank
preferred_prefix: chembank
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/chembank:$1
publications:
- doi: 10.1093/nar/gkm843
pmc: PMC2238881
pubmed: '17947324'
title: 'ChemBank: a small-molecule screening and cheminformatics resource database.'
year: 2007
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1
chembl:
contact:
email: dmendez@ebi.ac.uk
github: nclopezo
name: David Mendez Lopez
orcid: 0000-0002-0294-5484
description: ChEMBL is a database of bioactive compounds, their quantitative properties
and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
abstracted and curated from the primary scientific literature.
example: CHEMBL4303805
homepage: https://www.ebi.ac.uk/chembl
keywords:
- biochemistry
- drug discovery
- genomics
- medicinal chemistry
- molecules
license: CC-BY-4.0
mappings:
cheminf: '000412'
fairsharing: FAIRsharing.m3jtpg
miriam: chembl
prefixcommons: chembl
re3data: r3d100010539
uniprot: DB-0174
name: ChEMBL
pattern: ^CHEMBL\d+$
preferred_prefix: chembl
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/chembl:$1
publications:
- doi: 10.1093/nar/gky1075
pmc: PMC6323927
pubmed: '30398643'
title: 'ChEMBL: towards direct deposition of bioassay data.'
year: 2019
- doi: 10.1093/nar/gkw1074
pmc: PMC5210557
pubmed: '27899562'
title: The ChEMBL database in 2017.
year: 2016
- doi: 10.1093/nar/gkt1031
pmc: PMC3965067
pubmed: '24214965'
title: 'The ChEMBL bioactivity database: an update.'
year: 2013
- doi: 10.1093/nar/gkr777
pmc: PMC3245175
pubmed: '21948594'
title: 'ChEMBL: a large-scale bioactivity database for drug discovery.'
year: 2011
repository: https://github.com/chembl/GLaDOS
synonyms:
- ChEMBL
- ChEMBL_ID
- chembl
twitter: chembl
uri_format: https://www.ebi.ac.uk/chembl/entity/$1
chembl.cell:
contact:
email: dmendez@ebi.ac.uk
github: nclopezo
name: David Mendez Lopez
orcid: 0000-0002-0294-5484
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
keywords:
- bioactivities
- cell lines
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/$1
chembl.compound:
contact:
email: dmendez@ebi.ac.uk
github: nclopezo
name: David Mendez Lopez
orcid: 0000-0002-0294-5484
description: ChEMBL is a database of bioactive compounds, their quantitative properties
and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
abstracted and curated from the primary scientific literature.
example: CHEMBL465070
homepage: https://www.ebi.ac.uk/chembldb/
license: CC-BY-4.0
mappings:
biocontext: CHEMBL.COMPOUND
edam: '2646'
miriam: chembl.compound
n2t: chembl.compound
wikidata: P592
name: ChEMBL
part_of: chembl
pattern: ^CHEMBL\d+$
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
rdf_uri_format: http://rdf.ebi.ac.uk/resource/chembl/molecule/$1
uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1
chembl.target:
contact:
email: dmendez@ebi.ac.uk
github: nclopezo
name: David Mendez Lopez
orcid: 0000-0002-0294-5484
description: ChEMBL is a database of bioactive compounds, their quantitative properties
and bioactivities (binding constants, pharmacology and ADMET, etc). The data is
abstracted and curated from the primary scientific literature.
example: CHEMBL3467
homepage: https://www.ebi.ac.uk/chembldb/
license: CC-BY-4.0
mappings:
biocontext: CHEMBL.TARGET
cellosaurus: ChEMBL-Targets
miriam: chembl.target
n2t: chembl.target
name: ChEMBL target
part_of: chembl
pattern: ^CHEMBL\d+$
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/$1
chemdb:
description: ChemDB is a chemical database containing commercially available small
molecules, important for use as synthetic building blocks, probes in systems biology
and as leads for the discovery of drugs and other useful compounds.
example: '3966782'
homepage: http://cdb.ics.uci.edu/
keywords:
- biochemistry
- biomedical science
- life science
- preclinical studies
- small molecule
- systems biology
mappings:
biocontext: CHEMDB
fairsharing: FAIRsharing.dstf7h
miriam: chemdb
n2t: chemdb
prefixcommons: chemdb
name: ChemDB
pattern: ^\d+$
preferred_prefix: chemdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/chemdb:$1
publications:
- doi: 10.1093/bioinformatics/btm341
pmc: null
pubmed: '17599932'
title: ChemDB update--full-text search and virtual chemical space.
year: 2007
- doi: 10.1093/bioinformatics/bti683
pmc: null
pubmed: '16174682'
title: 'ChemDB: a public database of small molecules and related chemoinformatics
resources.'
year: 2005
uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1
chemidplus:
description: ChemIDplus is a web-based search system that provides access to structure
and nomenclature authority files used for the identification of chemical substances
cited in National Library of Medicine (NLM) databases. It also provides structure
searching and direct links to many biomedical resources at NLM and on the Internet
for chemicals of interest.
example: 57-27-2
homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp
keywords:
- biomedical science
- chemistry
- molecules
- structure
mappings:
biocontext: CHEMIDPLUS
edam: '2658'
fairsharing: FAIRsharing.5949vn
miriam: chemidplus
n2t: chemidplus
prefixcommons: chemidplus
name: ChemIDplus
pattern: ^\d+\-\d+\-\d+$
preferred_prefix: chemidplus
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/chemidplus:$1
publications:
- doi: 10.1300/j115v21n01_04
pmc: null
pubmed: '11989279'
title: ChemIDplus-super source for chemical and drug information.
year: 2002
synonyms:
- ChemIDplus
uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1
cheminf:
appears_in:
- proco
contact:
email: egon.willighagen@gmail.com
github: egonw
name: Egon Willighagen
orcid: 0000-0001-7542-0286
description: Includes terms for the descriptors commonly used in cheminformatics
software applications and the algorithms which generate them.
download_owl: https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl
example: '000410'
homepage: https://github.com/semanticchemistry/semanticchemistry
keywords:
- biochemistry
- chemistry
- life science
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: CHEMINF
biocontext: CHEMINF
bioportal: CHEMINF
fairsharing: FAIRsharing.sjhvyy
obofoundry: cheminf
ols: cheminf
ontobee: CHEMINF
name: Chemical Information Ontology
pattern: ^\d{6}$
preferred_prefix: CHEMINF
providers:
- code: semanticscience
description: Legacy URLs before conversion of CHEMINF to OBO PURLs
homepage: http://semanticscience.org
name: Semantic Science
uri_format: http://semanticscience.org/resource/CHEMINF_$1
publications:
- doi: 10.1371/journal.pone.0025513
pmc: PMC3184996
pubmed: '21991315'
title: 'The chemical information ontology: provenance and disambiguation for chemical
data on the biological semantic web.'
year: 2011
rdf_uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1
repository: https://github.com/semanticchemistry/semanticchemistry
uri_format: https://semanticscience.org/resource/CHEMINF_$1
version: '2.0'
chemrof:
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: CHEMROF is an ontological framework for Chemical Entities Mixtures
Reactions Ontological Framework. This OWL ontology is an automated Translation
of the source LinkML schema, https://w3id.org/chemrof
download_owl: http://aber-owl.net/media/ontologies/CHEMROF/2/chemrof.owl
example: FullySpecifiedAtom
homepage: https://chemkg.github.io/chemrof/
keywords:
- ontology
mappings:
aberowl: CHEMROF
bioportal: CHEMROF
name: Chemical Entity Materials and Reactions Ontological Framework
preferred_prefix: ChEMROF
uri_format: https://chemkg.github.io/chemrof/$1
chemspider:
contact:
email: pencehe@oneonta.edu
github: null
name: Harry E. Pence
orcid: 0000-0002-0412-9018
description: ChemSpider is a collection of compound data from across the web, which
aggregates chemical structures and their associated information into a single
searchable repository entry. These entries are supplemented with additional properties,
related information and links back to original data sources.
example: '56586'
homepage: http://www.chemspider.com/
keywords:
- chemistry
- life science
- molecules
- structure
mappings:
biocontext: CHEMSPIDER
cheminf: '000405'
edam: '1173'
fairsharing: FAIRsharing.96f3gm
miriam: chemspider
n2t: chemspider
prefixcommons: chemspider
re3data: r3d100010205
wikidata: P661
name: ChemSpider
pattern: ^\d+$
preferred_prefix: chemspider
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/chemspider:$1
publications:
- doi: 10.1021/ed100697w
pmc: null
pubmed: null
title: 'ChemSpider: An Online Chemical Information Resource'
year: 2010
rdf_uri_format: http://rdf.chemspider.com/$1
synonyms:
- ChemSpiderID
- Chemspider
twitter: ChemSpider
uri_format: http://www.chemspider.com/Chemical-Structure.$1.html
chickenqtldb:
description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is
designed to house publicly all available QTL and single-nucleotide polymorphism/gene
association data on livestock animal species. This collection references chicken
QTLs.
example: '14362'
homepage: https://www.animalgenome.org/QTLdb
keywords:
- dna
- genome
mappings:
biocontext: CHICKENQTLDB
miriam: chickenqtldb
n2t: chickenqtldb
prefixcommons: chickenqtldb
name: Animal Genome Chicken QTL
part_of: qtldb
pattern: ^\d+$
preferred_prefix: chickenqtldb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/chickenqtldb:$1
uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1
chictr:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Established in 2005 by professor Wu Taixiang and Li Youping team, West
China Hospital, Sichuan University, and the Ministry of Health of China assigned
it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical
Trial Registry provides the services include register for trials, consultation
for trial design, central randomization for an allocation sequence, peer review
for draft articles and training for peer reviewers. (from website)
example: ChiCTR2300070727
homepage: https://www.chictr.org.cn
logo: https://www.chictr.org.cn/images/top.jpg
name: Chinese Clinical Trial Registry
pattern: ^ChiCTR\d+$
preferred_prefix: chictr
references:
- https://www.chictr.org.cn/showproj.html?proj=187605
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
keywords:
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: CHIRO
bioportal: CHIRO
obofoundry: chiro
ols: chiro
ontobee: CHIRO
name: ChEBI Integrated Role Ontology
no_own_terms: true
preferred_prefix: CHIRO
publications:
- doi: 10.26434/chemrxiv.12591221
pmc: null
pubmed: null
title: Extension of Roles in the ChEBI Ontology
year: 2020
rdf_uri_format: http://purl.obolibrary.org/obo/CHIRO_$1
repository: https://github.com/obophenotype/chiro
uri_format: http://purl.obolibrary.org/obo/CHIRO_$1
version: '2015-11-23'
chmo:
appears_in:
- rbo
- scdo
contact:
email: batchelorc@rsc.org
github: batchelorc
name: Colin Batchelor
orcid: 0000-0001-5985-7429
description: CHMO, the chemical methods ontology, describes methods used to collect
data in chemical experiments, such as mass spectrometry and electron microscopy
prepare and separate material for further analysis, such as sample ionisation,
chromatography, and electrophoresis synthesise materials, such as epitaxy and
continuous vapour deposition It also describes the instruments used in these experiments,
such as mass spectrometers and chromatography columns. It is intended to be complementary
to the Ontology for Biomedical Investigations (OBI).
download_obo: http://purl.obolibrary.org/obo/chmo.obo
download_owl: http://purl.obolibrary.org/obo/chmo.owl
example: 0002902
homepage: https://github.com/rsc-ontologies/rsc-cmo
keywords:
- chemistry
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: CHMO
biocontext: CHMO
bioportal: CHMO
fairsharing: FAIRsharing.9j4wh2
obofoundry: chmo
ols: chmo
ontobee: CHMO
name: Chemical Methods Ontology
pattern: ^\d{7}$
preferred_prefix: CHMO
rdf_uri_format: http://purl.obolibrary.org/obo/CHMO_$1
repository: https://github.com/rsc-ontologies/rsc-cmo
uri_format: http://purl.obolibrary.org/obo/CHMO_$1
version: '2022-04-19'
cido:
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven
open-source biomedical ontology in the area of coronavirus infectious disease.
The CIDO is developed to provide standardized human- and computer-interpretable
annotation and representation of various coronavirus infectious diseases, including
their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.
download_owl: https://github.com/CIDO-ontology/cido/raw/master/cido.owl
example: '0000005'
homepage: https://github.com/cido-ontology/cido
keywords:
- bioinformatics
- drug discovery
- drug repositioning
- epidemiology
- obo
- ontology
- virology
license: CC-BY-4.0
mappings:
aberowl: CIDO
bioportal: CIDO
fairsharing: FAIRsharing.aVmpKl
obofoundry: cido
ols: cido
ontobee: CIDO
name: Coronavirus Infectious Disease Ontology
pattern: ^\d{7}$
preferred_prefix: CIDO
publications:
- doi: 10.1186/s13326-022-00279-z
pmc: PMC9585694
pubmed: '36271389'
title: 'A comprehensive update on CIDO: the community-based coronavirus infectious
disease ontology.'
year: 2022
- doi: 10.1038/s41597-020-0523-6
pmc: PMC7293349
pubmed: '32533075'
title: CIDO, a community-based ontology for coronavirus disease knowledge and
data integration, sharing, and analysis.
year: 2020
rdf_uri_format: http://purl.obolibrary.org/obo/CIDO_$1
repository: https://github.com/cido-ontology/cido
uri_format: http://purl.obolibrary.org/obo/CIDO_$1
version: 1.0.337
cio:
contact:
email: frederic.bastian@unil.ch
github: fbastian
name: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: An ontology to capture confidence information about annotations.
download_obo: http://purl.obolibrary.org/obo/cio.obo
download_owl: http://purl.obolibrary.org/obo/cio.owl
example: '0000040'
homepage: https://github.com/BgeeDB/confidence-information-ontology
keywords:
- biology
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: CIO
biocontext: CIO
bioportal: CIO
fairsharing: FAIRsharing.e3t0yw
obofoundry: cio
ols: cio
ontobee: CIO
name: Confidence Information Ontology
pattern: ^\d{7}$
preferred_prefix: CIO
publications:
- doi: 10.1093/database/bav043
pmc: PMC4425939
pubmed: '25957950'
title: 'The Confidence Information Ontology: a step towards a standard for asserting
confidence in annotations.'
year: 2015
rdf_uri_format: http://purl.obolibrary.org/obo/CIO_$1
repository: https://github.com/BgeeDB/confidence-information-ontology
uri_format: http://purl.obolibrary.org/obo/CIO_$1
version: '2015-03-10'
citexplore:
contact:
email: maria.taboada@usc.es
github: null
name: Maria Taboada
orcid: 0000-0002-2353-596X
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/
keywords:
- biomedical science
- genetics
- preclinical studies
mappings:
fairsharing: FAIRsharing.619eqr
prefixcommons: citexplore
name: CiteXplore
preferred_prefix: citexplore
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/citexplore:$1
publications:
- doi: 10.1097/mol.0b013e328362df13
pmc: null
pubmed: '23759795'
title: Cerebrotendinous xanthomatosis.
year: 2013
references:
- https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/
synonyms:
- CTX
uri_format: https://europepmc.org/article/CTX/$1
cito:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology that enables characterization of the nature or type of
citations, both factually and rhetorically.
example: sharesAuthorInstitutionWith
homepage: http://www.sparontologies.net/ontologies/cito
keywords:
- knowledge and information systems
mappings:
fairsharing: FAIRsharing.b220d4
name: Citation Typing Ontology
preferred_prefix: CiTO
publications:
- doi: 10.1016/j.websem.2012.08.001
pmc: null
pubmed: null
title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
citations'
year: 2012
repository: https://github.com/sparontologies/cito
twitter: sparontologies
uri_format: http://purl.org/spar/cito/$1
civic.aid:
description: 'A CIViC assertion classifies the clinical significance of a variant-disease
relationship under recognized guidelines. The CIViC Assertion (AID) summarizes
a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic,
prognostic or predisposing clinical information for a variant in a specific cancer
context. CIViC currently has two main types of Assertions: those based on variants
of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic)
and those based on variants of primarily germline origin (predisposing). When
the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence
Items (EIDs) in CIViC sufficiently cover what is known for a particular variant
and cancer type, then a corresponding assertion be created in CIViC.'
example: '3'
homepage: https://civicdb.org/
mappings:
miriam: civic.aid
name: CIViC Assertion
part_of: civic
pattern: ^[0-9]+$
preferred_prefix: civic.aid
uri_format: https://civicdb.org/links/assertions/$1
civic.did:
description: Within the CIViC database, the disease should be the cancer or cancer
subtype that is a result of the described variant. The disease selected should
be as specific as possible should reflect the disease type used in the source
that supports the evidence statement.
example: '46'
homepage: https://civicdb.org/
mappings:
miriam: civic.did
name: CIViC Disease
part_of: civic
pattern: ^[0-9]+$
preferred_prefix: civic.did
uri_format: https://civicdb.org/links/diseases/$1
civic.eid:
description: Evidence Items are the central building block of the Clinical Interpretation
of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece
of information that has been manually curated from trustable medical literature
about a Variant or genomic ‘event’ that has implications in cancer Predisposition,
Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy,
Oncogenicity or protein Function. For example, an Evidence Item might describe
a line of evidence supporting the notion that tumors with a somatic BRAF V600
mutation generally respond well to the drug dabrafenib. A Variant may be a single
nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a
chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc.
Each clinical Evidence statement corresponds to a single citable Source (a publication
or conference abstract).
example: '1199'
homepage: https://civicdb.org/
mappings:
miriam: civic.eid
name: CIViC Evidence
part_of: civic
pattern: ^[0-9]+$
preferred_prefix: civic.eid
uri_format: https://civicdb.org/links/evidence/$1
civic.gid:
description: A CIViC Gene Summary is created to provide a high-level overview of
clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus
on emphasizing the clinical relevance from a molecular perspective rather than
describing the biological function of the gene unless necessary to contextualize
its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes,
specific treatments for the gene’s associated variants, pathway interactions,
functional alterations caused by the variants in the gene, and normal/abnormal
functions of the gene with associated roles in oncogenesis
example: '272'
homepage: https://civicdb.org/
mappings:
miriam: civic.gid
wikidata: P11277
name: CIViC gene
part_of: civic
pattern: ^[0-9]+$
preferred_prefix: civic.gid
uri_format: https://civicdb.org/links/gene/$1
civic.mpid:
description: CIViC Molecular Profiles are combinations of one or more CIViC variants.
Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single
variant. In most cases, these can be considered equivalent to the CIViC concept
of a Variant. However, increasingly clinical significance must be considered in
the context of multiple variants simultaneously. Complex Molecular Profiles in
CIViC allow for curation of such variant combinations. Regardless of the nature
of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic,
Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered
in CIViC.
example: '559'
homepage: https://civicdb.org/
mappings:
miriam: civic.mpid
name: CIViC Molecular Profile
pattern: ^[0-9]+$
preferred_prefix: civic.mpid
uri_format: https://civicdb.org/links/molecular_profile/$1
civic.sid:
description: In CIViC, each Evidence Item must be associated with a Source Type
and Source ID, which link the Evidence Item to the original source of information
supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed
OR abstracts published through the American Society of Clinical Oncology (ASCO).
Each such source entered into CIViC is assigned a unique identifier and expert
curators can curate guidance that assists future curators in the interpretation
of information from this source.
example: '62'
homepage: https://civicdb.org/
mappings:
miriam: civic.sid
name: CIViC Source
part_of: civic
pattern: ^[0-9]+$
preferred_prefix: civic.sid
uri_format: https://civicdb.org/links/sources/$1
civic.tid:
description: Therapies (often drugs) in CIViC are associated with Predictive Evidence
Types, which describe sensitivity, resistance or adverse response to therapies
when a given variant is present. The Therapy field may also be used to describe
more general treatment types and regimes, such as FOLFOX or Radiation, as long
as the literature derived Evidence Item makes a scientific association between
the Therapy (treatment type) and the presence of the variant.
example: '14'
homepage: https://civicdb.org/
mappings:
miriam: civic.tid
name: CIViC Therapy
part_of: civic
pattern: ^[0-9]+$
preferred_prefix: civic.tid
uri_format: https://civicdb.org/links/drugs/$1
civic.vgid:
description: Variant Groups in CIViC provide user-defined grouping of Variants within
and between genes based on unifying characteristics. CIViC curators are required
to define a cohesive rationale for grouping these variants together, summarize
their relevance to cancer diagnosis, prognosis or treatment and highlight any
treatments or cancers of particular relevance
example: '16'
homepage: https://civicdb.org/
mappings:
miriam: civic.vgid
name: CIViC Variant Group
pattern: ^[0-9]+$
preferred_prefix: civic.vgid
uri_format: https://civicdb.org/links/variant_group/$1
civic.vid:
description: CIViC variants are usually genomic alterations, including single nucleotide
variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s
such as amplification or deletion), structural variants (SVs such as translocations
and inversions), and other events that differ from the “normal” genome. In some
cases a CIViC variant may represent events of the transcriptome or proteome. For
example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the
variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic,
or Functional relevance that is clinical in nature to be entered in CIViC. i.e.
There must be some rationale for why curation of this variant could ultimately
aid clinical decision making.
example: '12'
homepage: https://civicdb.org/
mappings:
miriam: civic.vid
wikidata: P3329
name: CIViC variant
part_of: civic
pattern: ^[0-9]+$
preferred_prefix: civic.vid
uri_format: https://civicdb.org/links/variant/$1
cl:
appears_in:
- clo
- ecao
- ehdaa2
- go
- mco
- pcl
- uberon
- xpo
banana: CL
contact:
email: addiehl@buffalo.edu
github: addiehl
name: Alexander Diehl
orcid: 0000-0001-9990-8331
depends_on:
- chebi
- go
- ncbitaxon
- pato
- pr
- ro
- uberon
description: The Cell Ontology is designed as a structured controlled vocabulary
for cell types. The ontology was constructed for use by the model organism and
other bioinformatics databases, incorporating cell types from prokaryotes to mammals,
and includes plants and fungi.
download_obo: https://github.com/obophenotype/cell-ontology/raw/master/cl.obo
download_owl: http://purl.obolibrary.org/obo/cl.owl
example: '0000062'
homepage: https://obophenotype.github.io/cell-ontology/
keywords:
- anatomy
- cell
- cell biology
- life science
- obo
- ontology
license: CC-BY-4.0
logo: https://obofoundry.org/images/CL-logo.jpg
mappings:
aberowl: CL
agroportal: CL
biocontext: CL
bioportal: CL
cellosaurus: CL
fairsharing: FAIRsharing.j9y503
go: CL
miriam: cl
n2t: cl
obofoundry: cl
ols: cl
ontobee: CL
prefixcommons: cl
wikidata: P7963
name: Cell Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: CL
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cl:$1
- code: cellxgene
description: Explore single cell data through the CZ CELLxGENE portal
homepage: https://onto.cellxgene-labs.prod.si.czi.technology
name: CELLxGENE
uri_format: https://onto.cellxgene-labs.prod.si.czi.technology/a/ontology/CL/CL:$1
publications:
- doi: 10.1186/s13326-016-0088-7
pmc: PMC4932724
pubmed: '27377652'
title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology
interoperability.'
year: 2016
- doi: 10.1186/1471-2105-12-6
pmc: PMC3024222
pubmed: '21208450'
title: Logical development of the cell ontology.
year: 2011
rdf_uri_format: http://purl.obolibrary.org/obo/CL_$1
repository: https://github.com/obophenotype/cell-ontology
twitter: CellOntology
uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1
version: '2023-04-20'
clao:
contact:
email: lagonzalezmo@unal.edu.co
github: luis-gonzalez-m
name: Luis González-Montaña
orcid: 0000-0002-9136-9932
depends_on:
- ro
description: 'CLAO is an ontology of anatomical terms employed in morphological
descriptions for the Class Collembola (Arthropoda: Hexapoda).'
download_obo: http://purl.obolibrary.org/obo/clao.obo
download_owl: http://purl.obolibrary.org/obo/clao.owl
example: 0000088
homepage: https://github.com/luis-gonzalez-m/Collembola
keywords:
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: CLAO
bioportal: CLAO
obofoundry: clao
ols: clao
ontobee: CLAO
name: Collembola Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: CLAO
rdf_uri_format: http://purl.obolibrary.org/obo/CLAO_$1
repository: https://github.com/luis-gonzalez-m/Collembola
uri_format: http://purl.obolibrary.org/obo/CLAO_$1
version: '2021-09-27'
classyfire:
banana: C
comment: There's a mismatch between the MIRIAM URI format string, which has a C
prefix in front of class identifiers and the ontology which does not use them.
description: ClassyFire is a web-based application for automated structural classification
of chemical entities. This application uses a rule-based approach that relies
on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire
provides a hierarchical chemical classification of chemical entities (mostly small
molecules and short peptide sequences), as well as a structure-based textual description,
based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes
of organic and inorganic compounds. Moreover, ClassyFire allows for text-based
search via its web interface. It can be accessed via the web interface or via
the ClassyFire API.
download_obo: http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip
example: 0004828
homepage: http://classyfire.wishartlab.com/
keywords:
- ontology
mappings:
miriam: classyfire
name: ClassyFire
pattern: ^\d{7}$
preferred_prefix: classyfire
synonyms:
- CHEMONTID
uri_format: http://classyfire.wishartlab.com/tax_nodes/C$1
clb:
description: ChecklistBank is an index and repository for taxonomic and nomenclatural
datasets
example: '1010'
homepage: https://www.checklistbank.org
mappings:
miriam: clb
name: ChecklistBank
pattern: ^[0-9]+(LR)?$
preferred_prefix: clb
uri_format: https://www.checklistbank.org/dataset/$1
cldb:
description: The Cell Line Data Base (CLDB) is a reference information source for
human and animal cell lines. It provides the characteristics of the cell lines
and their availability through distributors, allowing cell line requests to be
made from collections and laboratories.
example: cl3603
homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html
mappings:
biocontext: CLDB
cellosaurus: CLDB
miriam: cldb
n2t: cldb
name: Cell Line Database
pattern: ^(cl|tum)\d+$
preferred_prefix: cldb
synonyms:
- hypercldb
uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html
clingene:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
contributor_extras:
- email: null
github: sierra-moxon
name: Sierra Moxon
orcid: 0000-0002-8719-7760
description: The allele registry provides and maintains identifiers for genetic
variants
example: CA981206459
homepage: https://reg.clinicalgenome.org
keywords:
- alleles
- genetics
- mutations
mappings:
biolink: CAID
name: ClinGen Allele Registry
pattern: ^CA\d+$
preferred_prefix: clingene
references:
- https://github.com/biopragmatics/bioregistry/issues/647
synonyms:
- CAID
uri_format: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1
clinicaltrials:
description: ClinicalTrials.gov provides free access to information on clinical
studies for a wide range of diseases and conditions. Studies listed in the database
are conducted in 175 countries
example: NCT00222573
homepage: https://clinicaltrials.gov/
keywords:
- disease
- drug
- human
mappings:
biocontext: CLINICALTRIALS
miriam: clinicaltrials
n2t: clinicaltrials
prefixcommons: clinicaltrials
wikidata: P3098
name: ClinicalTrials.gov
pattern: ^NCT\d{8}$
preferred_prefix: clinicaltrials
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/clinicaltrials:$1
- code: smartpatients
description: Smart Patients is an online community for patients and their families.
Join us to talk with other patients about the latest research for your condition.
homepage: https://www.smartpatients.com
name: Smart Patients
uri_format: https://www.smartpatients.com/trials/$1
synonyms:
- NCT
- clinicaltrial
uri_format: https://clinicaltrials.gov/ct2/show/$1
clinvar:
description: ClinVar archives reports of relationships among medically important
variants and phenotypes. It records human variation, interpretations of the relationship
specific variations to human health, and supporting evidence for each interpretation.
Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
of the same variation and condition from one or more submitters. Submissions for
individual variation/phenotype combinations (SCV identifier) are also collected
and made available separately. This collection references the Variant identifier.
example: '12345'
homepage: http://www.ncbi.nlm.nih.gov/clinvar/
keywords:
- biomedical science
- clinical studies
- genomics
- preclinical studies
mappings:
biocontext: ClinVarVariant
biolink: CLINVAR
cellosaurus: ClinVar
fairsharing: FAIRsharing.wx5r6f
hl7: 2.16.840.1.113883.6.319
miriam: clinvar
n2t: clinvar
re3data: r3d100013331
wikidata: P1929
name: ClinVar Variation
pattern: ^\d+$
preferred_prefix: clinvar
publications:
- doi: 10.1093/nar/gkt1113
pmc: PMC3965032
pubmed: '24234437'
title: 'ClinVar: public archive of relationships among sequence variation and
human phenotype.'
year: 2013
synonyms:
- clinvar.variant
- clinvar.variation
uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1
clinvar.record:
description: ClinVar archives reports of relationships among medically important
variants and phenotypes. It records human variation, interpretations of the relationship
specific variations to human health, and supporting evidence for each interpretation.
Each ClinVar record (RCV identifier) represents an aggregated view of interpretations
of the same variation and condition from one or more submitters. Submissions
for individual variation/phenotype combinations (SCV identifier) are also collected
and made available separately. This collection references the Record Report, based
on RCV accession.
example: RCV000033555.3
homepage: http://www.ncbi.nlm.nih.gov/clinvar/
mappings:
biocontext: CLINVAR.RECORD
miriam: clinvar.record
n2t: clinvar.record
name: ClinVar Record
part_of: clinvar
pattern: ^RCV\d+(\.\d+)?$
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/$1
clo:
appears_in:
- mco
contact:
email: siiraa@umich.edu
github: siiraa
name: Sirarat Sarntivijai
orcid: 0000-0002-2548-641X
depends_on:
- cl
- doid
- ncbitaxon
- uberon
description: The Cell Line Ontology is a community-based ontology of cell lines.
The CLO is developed to unify publicly available cell line entry data from multiple
sources to a standardized logically defined format based on consensus design patterns.
download_owl: http://purl.obolibrary.org/obo/clo.owl
example: 0000091
homepage: http://www.clo-ontology.org
keywords:
- cell biology
- life science
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: CLO
biocontext: CLO
bioportal: CLO
cellosaurus: CLO
fairsharing: FAIRsharing.4dvtcz
miriam: clo
obofoundry: clo
ols: clo
ontobee: CLO
prefixcommons: clo
wikidata: P2158
name: Cell Line Ontology
pattern: ^\d{7}$
preferred_prefix: CLO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/clo:$1
- code: bioportal
description: Our vision is that all biomedical knowledge and data are disseminated
on the Internet using principled ontologies in such a way that the knowledge
and data are semantically interoperable and useful for furthering biomedical
science and clinical care. Our mission is to create software and support services
for the application of principled ontologies in biomedical science and clinical
care, ranging from tools for application developers to software for end-users.
homepage: https://bioportal.bioontology.org
name: Center for Biomedical Informatics Research, Stanford
uri_format: https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1
publications:
- doi: 10.1186/2041-1480-5-37
pmc: PMC4387853
pubmed: '25852852'
title: 'CLO: The cell line ontology.'
year: 2014
- doi: 10.1186/gb-2005-6-2-r21
pmc: PMC551541
pubmed: '15693950'
title: An ontology for cell types.
year: 2005
rdf_uri_format: http://purl.obolibrary.org/obo/CLO_$1
repository: https://github.com/CLO-Ontology/CLO
synonyms:
- CLO
uri_format: https://www.ebi.ac.uk/ols/ontologies/clo/terms?short_form=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://cls.shop/$1
clyh:
contact:
email: lucas.leclere@obs-vlfr.fr
github: L-Leclere
name: Lucas Leclere
orcid: 0000-0002-7440-0467
depends_on:
- iao
- ro
- uberon
description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish
- of the cnidarian hydrozoan species, Clytia hemiphaerica.
download_obo: http://purl.obolibrary.org/obo/clyh.obo
download_owl: http://purl.obolibrary.org/obo/clyh.owl
example: '1000100'
homepage: https://github.com/EBISPOT/clyh_ontology
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: CLYH
bioportal: CLYH
obofoundry: clyh
ols: clyh
ontobee: CLYH
name: Clytia hemisphaerica Development and Anatomy Ontology
pattern: ^\d+$
preferred_prefix: CLYH
rdf_uri_format: http://purl.obolibrary.org/obo/CLYH_$1
repository: https://github.com/EBISPOT/clyh_ontology
uri_format: http://purl.obolibrary.org/obo/CLYH_$1
version: '2020-05-29'
cmecs:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Use this database to browse the CMECS classification and to get definitions
for individual CMECS Units. This database contains the units that were published
in the Coastal and Marine Ecological Classification Standard.
example: '595'
homepage: https://cmecscatalog.org/cmecs
keywords:
- ecology
- marine ecology
name: Costal and Marine Ecological Classification Standard
pattern: ^\d+$
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:
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/
keywords:
- obo
- ontology
mappings:
aberowl: CMF
biocontext: CMF
obofoundry: cmf
ontobee: CMF
name: CranioMaxilloFacial ontology
preferred_prefix: CMF
rdf_uri_format: http://purl.obolibrary.org/obo/CMF_$1
uri_format: http://purl.obolibrary.org/obo/CMF_$1
cmo:
appears_in:
- scdo
contact:
email: jrsmith@mcw.edu
github: jrsjrs
name: Jennifer Smith
orcid: 0000-0002-6443-9376
description: Morphological and physiological measurement records generated from
clinical and model organism research and health programs.
download_obo: http://purl.obolibrary.org/obo/cmo.obo
download_owl: http://purl.obolibrary.org/obo/cmo.owl
example: '0001350'
homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
keywords:
- biomedical science
- life science
- obo
- ontology
- preclinical studies
license: CC0-1.0
logo: http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif
mappings:
aberowl: CMO
biocontext: CMO
bioportal: CMO
fairsharing: FAIRsharing.dq78pn
obofoundry: cmo
ols: cmo
ontobee: CMO
name: Clinical measurement ontology
pattern: ^\d{7}$
preferred_prefix: CMO
publications:
- doi: 10.1186/2041-1480-4-26
pmc: PMC3882879
pubmed: '24103152'
title: 'The clinical measurement, measurement method and experimental condition
ontologies: expansion, improvements and new applications.'
year: 2013
- doi: 10.3389/fgene.2012.00087
pmc: PMC3361058
pubmed: '22654893'
title: Three ontologies to define phenotype measurement data.
year: 2012
rdf_uri_format: http://purl.obolibrary.org/obo/CMO_$1
repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology
twitter: ratgenome
uri_format: http://purl.obolibrary.org/obo/CMO_$1
version: '2019-02-19'
cmpo:
contact:
email: jupp@ebi.ac.uk
github: null
name: Simon Jupp
orcid: 0000-0002-0643-3144
description: CMPO is a species neutral ontology for describing general phenotypic
observations relating to the whole cell, cellular components, cellular processes
and cell populations.
download_owl: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl
example: '0000435'
homepage: http://www.ebi.ac.uk/cmpo
keywords:
- cell biology
- ontology
mappings:
aberowl: CMPO
bioportal: CMPO
fairsharing: FAIRsharing.knp11s
ols: cmpo
name: Cellular Microscopy Phenotype Ontology
pattern: ^\d{7}$
preferred_prefix: cmpo
publications:
- doi: 10.1186/s13326-016-0074-0
pmc: PMC4870745
pubmed: '27195102'
title: The cellular microscopy phenotype ontology.
year: 2016
repository: https://github.com/EBISPOT/CMPO
twitter: EBIOLS
uri_format: http://www.ebi.ac.uk/cmpo/CMPO_$1
version: '2017-12-19'
cnrs:
comment: Motivated to add because of appearance in ROR
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: identifier for an academic research group issued by the CNRS
example: UMR7315
homepage: https://annuaire.cnrs.fr
mappings:
wikidata: P4550
name: French National Center for Scientific Research - Research Group Identifier
pattern: ^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\d+$
preferred_prefix: cnrs
uri_format: https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u
co_320:
contact:
email: j.detras@cgiar.org
github: null
name: Jeffrey A. Detras
orcid: 0000-0002-6680-578X
description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based
on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping
Network variables
download_owl: https://cropontology.org/ontology/CO_320/Rice/owl
example: 0000618
homepage: https://cropontology.org/ontology/CO_320/Rice
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_320
cropoct: CO_320
fairsharing: FAIRsharing.2jkxp5
ols: co_320
name: Rice ontology
pattern: ^\d{7}$
preferred_prefix: CO_320
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_320:$1
version: '2019-10-09'
co_321:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Rosemary Shrestha
orcid: 0000-0002-9399-8003
description: July 2018
download_owl: https://cropontology.org/ontology/CO_321/Wheat/owl
example: 0000449
homepage: https://cropontology.org/ontology/CO_321/Wheat
keywords:
- agriculture
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_321
cropoct: CO_321
fairsharing: FAIRsharing.czzmpg
ols: co_321
name: Wheat ontology
pattern: ^\d{7}$
preferred_prefix: CO_321
publications:
- doi: 10.1093/aobpla/plq008
pmc: PMC3000699
pubmed: '22476066'
title: 'Multifunctional crop trait ontology for breeders'' data: field book, annotation,
data discovery and semantic enrichment of the literature.'
year: 2010
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_321:$1
version: '2019-10-09'
co_322:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016
download_owl: https://cropontology.org/ontology/CO_322/Maize/owl
example: '0000773'
homepage: https://cropontology.org/ontology/CO_322/Maize
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_322
cropoct: CO_322
fairsharing: FAIRsharing.eeyne8
ols: co_322
name: Maize ontology
pattern: ^\d{7}$
preferred_prefix: CO_322
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_322:$1
version: '2019-10-09'
co_323:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Ramesh Verna
orcid: null
description: ICARDA - TDv5 - Sept 2018
download_owl: https://cropontology.org/ontology/CO_323/Barley/owl
example: '0000252'
homepage: https://cropontology.org/ontology/CO_323/Barley
keywords:
- agriculture
- botany
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_323
cropoct: CO_323
fairsharing: FAIRsharing.f69084
ols: co_323
name: Barley ontology
pattern: ^\d{7}$
preferred_prefix: CO_323
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_323:$1
version: '2019-11-20'
co_324:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Sorghum TDv5 - Oct 2019
download_owl: https://cropontology.org/ontology/CO_324/Sorghum/owl
example: '0000111'
homepage: https://cropontology.org/ontology/CO_324/Sorghum
keywords:
- agriculture
- botany
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_324
cropoct: CO_324
fairsharing: FAIRsharing.dxx0c
ols: co_324
name: Sorghum ontology
pattern: ^\d{7}$
preferred_prefix: CO_324
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_324:$1
version: '2019-10-09'
co_325:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Elizabeth Arnaud
orcid: 0000-0002-6020-5919
description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019
download_owl: https://cropontology.org/ontology/CO_325/Banana/owl
example: 0000519
homepage: https://cropontology.org/ontology/CO_325/Banana
keywords:
- agriculture
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_325
cropoct: CO_325
fairsharing: FAIRsharing.gdszhh
ols: co_325
name: Banana ontology
pattern: ^\d{7}$
preferred_prefix: CO_325
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_325:$1
version: '2019-10-09'
co_326:
description: Draft version
download_owl: https://cropontology.org/ontology/CO_326/Coconut/owl
example: '0000254'
homepage: https://cropontology.org/ontology/CO_326/Coconut
keywords:
- ontology
license: CC-BY-4.0
mappings:
cropoct: CO_326
ols: co_326
name: Coconut ontology
pattern: ^\d{7}$
preferred_prefix: CO_326
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_326:$1
co_327:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April
2016
download_owl: http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl
example: 0000095
homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet
keywords:
- agriculture
- botany
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_327
cropoct: CO_327
fairsharing: FAIRsharing.4e3qh9
ols: co_327
name: Pearl millet ontology
pattern: ^\d{7}$
preferred_prefix: CO_327
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_327:$1
co_330:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: CIP - potato ontology - december 2018
download_owl: https://cropontology.org/ontology/CO_330/Potato/owl
example: '0000106'
homepage: https://cropontology.org/ontology/CO_330/Potato
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_330
cropoct: CO_330
fairsharing: FAIRsharing.4fa657
ols: co_330
name: Potato ontology
pattern: ^\d{7}$
preferred_prefix: CO_330
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_330:$1
version: '2019-10-09'
co_331:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Vilma Hualla Mamani
orcid: 0000-0003-0595-5271
description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019
download_owl: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl
example: 0000088
homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_331
cropoct: CO_331
fairsharing: FAIRsharing.4g5qcw
ols: co_331
name: Sweet Potato ontology
pattern: ^\d{7}$
preferred_prefix: CO_331
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_331:$1
co_333:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: 'This ontology was built as part of the AKER project. It describes
variables used in beet phenotyping (experimental properties and measurement scale)
for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez).
Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez)
- First submission in November 2017.'
download_owl: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl
example: '3000045'
homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology
keywords:
- agriculture
- botany
- life science
- ontology
- plant breeding
license: CC-BY-4.0
mappings:
agroportal: CO_333
cropoct: CO_333
fairsharing: FAIRsharing.af5655
ols: co_333
name: Beet Ontology ontology
pattern: ^\d+$
preferred_prefix: CO_333
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_333:$1
co_334:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated
in February 2016
download_owl: https://cropontology.org/ontology/CO_334/Cassava/owl
example: '0000070'
homepage: https://cropontology.org/ontology/CO_334/Cassava
keywords:
- agriculture
- botany
- nutritional science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_334
cropoct: CO_334
fairsharing: FAIRsharing.v06c4q
ols: co_334
name: Cassava ontology
pattern: ^\d{7}$
preferred_prefix: CO_334
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_334:$1
version: '2019-10-09'
co_335:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: CIAT Common bean trait dictionary - version August 2014
download_owl: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl
example: 0000189
homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean
keywords:
- agriculture
- botany
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_335
cropoct: CO_335
fairsharing: FAIRsharing.a14123
ols: co_335
name: Common Bean ontology
pattern: ^\d{7}$
preferred_prefix: CO_335
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_335:$1
co_336:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Elizabeth Arnaud
orcid: 0000-0002-6020-5919
description: Soybean Trait Dictionary in template v5 - IITA - July 2015
download_owl: https://cropontology.org/ontology/CO_336/Soybean/owl
example: 0000339
homepage: https://cropontology.org/ontology/CO_336/Soybean
keywords:
- agriculture
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_336
cropoct: CO_336
fairsharing: FAIRsharing.j75srj
ols: co_336
name: Soybean ontology
pattern: ^\d{7}$
preferred_prefix: CO_336
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_336:$1
co_337:
contact:
email: tm.shah@cgiar.org
github: null
name: Trushar Shah
orcid: 0000-0002-0091-7981
description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept
2015
download_owl: https://cropontology.org/ontology/CO_337/Groundnut/owl
example: '0000054'
homepage: https://cropontology.org/ontology/CO_337/Groundnut
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_337
cropoct: CO_337
fairsharing: FAIRsharing.ge8y23
ols: co_337
name: Groundnut ontology
pattern: ^\d{7}$
preferred_prefix: CO_337
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_337:$1
version: '2019-10-09'
co_338:
contact:
email: tm.shah@cgiar.org
github: null
name: Trushar Shah
orcid: 0000-0002-0091-7981
description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015
download_owl: https://cropontology.org/ontology/CO_338/Chickpea/owl
example: 0000138
homepage: https://cropontology.org/ontology/CO_338/Chickpea
keywords:
- agriculture
- botany
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_338
cropoct: CO_338
fairsharing: FAIRsharing.js20q3
ols: co_338
name: Chickpea ontology
pattern: ^\d{7}$
preferred_prefix: CO_338
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_338:$1
version: '2019-10-09'
co_339:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015
download_owl: https://cropontology.org/ontology/CO_339/Lentil/owl
example: '0000032'
homepage: https://cropontology.org/ontology/CO_339/Lentil
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_339
cropoct: CO_339
fairsharing: FAIRsharing.ry1ezg
ols: co_339
name: Lentil ontology
pattern: ^\d{7}$
preferred_prefix: CO_339
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_339:$1
version: '2019-10-09'
co_340:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Cowpea Trait Dictionary in template v5 - IITA - August 2015
download_owl: https://cropontology.org/ontology/CO_340/Cowpea/owl
example: 0000639
homepage: https://cropontology.org/ontology/CO_340/Cowpea
keywords:
- agriculture
- botany
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_340
cropoct: CO_340
fairsharing: FAIRsharing.31apg2
ols: co_340
name: Cowpea ontology
pattern: ^\d{7}$
preferred_prefix: CO_340
publications:
- doi: 10.3389/fphys.2012.00326
pmc: PMC3429094
pubmed: '22934074'
title: Bridging the phenotypic and genetic data useful for integrated breeding
through a data annotation using the Crop Ontology developed by the crop communities
of practice.
year: 2012
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_340:$1
version: '2019-10-09'
co_341:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Elizabeth Arnaud
orcid: 0000-0002-6020-5919
description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015
download_owl: https://cropontology.org/ontology/CO_341/Pigeonpea/owl
example: '0000140'
homepage: https://cropontology.org/ontology/CO_341/Pigeonpea
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_341
cropoct: CO_341
fairsharing: FAIRsharing.ehe3yp
ols: co_341
name: Pigeonpea ontology
pattern: ^\d{7}$
preferred_prefix: CO_341
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_341:$1
version: '2019-11-18'
co_343:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: version 2019 - pvs
download_owl: https://cropontology.org/ontology/CO_343/Yam/owl
example: '0100010'
homepage: https://cropontology.org/ontology/CO_343/Yam
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_343
cropoct: CO_343
fairsharing: FAIRsharing.7e9cff
ols: co_343
name: Yam ontology
pattern: ^\d{7}$
preferred_prefix: CO_343
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_343:$1
version: '2019-10-09'
co_345:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Brachiaria (forages) ontology TD v5 - Version Oct 2016
download_owl: https://cropontology.org/ontology/CO_345/Brachiaria/owl
example: '0000127'
homepage: https://cropontology.org/ontology/CO_345/Brachiaria
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_345
cropoct: CO_345
fairsharing: FAIRsharing.9e9683
ols: co_345
name: Brachiaria ontology
pattern: ^\d{7}$
preferred_prefix: CO_345
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_345:$1
version: '2019-10-09'
co_346:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: oct 2016
download_owl: https://cropontology.org/ontology/CO_346/Mungbean/owl
example: 0000199
homepage: https://cropontology.org/ontology/CO_346/Mungbean
keywords:
- agriculture
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_346
cropoct: CO_346
fairsharing: FAIRsharing.fgd5gq
ols: co_346
name: Mungbean ontology
pattern: ^\d{7}$
preferred_prefix: CO_346
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_346:$1
version: '2019-10-09'
co_347:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: 'March 2017 version '
download_owl: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl
example: 0000108
homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_347
cropoct: CO_347
fairsharing: FAIRsharing.qrrvyk
ols: co_347
name: Castor bean ontology
pattern: ^\d{7}$
preferred_prefix: CO_347
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_347:$1
co_348:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: helpdesk cropontology
orcid: null
description: Brassica Trait Ontology (BRaTO) hosts trait information to describe
brassica crop data. Terms are collected from various projects including OREGIN,
RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute
(UK), Southern Cross University (Australia) and INRA (France).
download_owl: https://cropontology.org/ontology/CO_348/Brassica/owl
example: '1100107'
homepage: https://cropontology.org/ontology/CO_348/Brassica
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_348
cropoct: CO_348
fairsharing: FAIRsharing.af7a2d
ols: co_348
name: Brassica ontology
pattern: ^\d+$
preferred_prefix: CO_348
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_348:$1
version: '2019-11-29'
co_350:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Jean-Luc Jannink
orcid: 0000-0003-4849-628X
description: Oat trait dictionary started by Oat Global (http://oatglobal.org/)
and improved by NIAB and PepsiCo
download_owl: https://cropontology.org/ontology/CO_350/Oat/owl
example: '0000215'
homepage: https://cropontology.org/ontology/CO_350/Oat
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_350
cropoct: CO_350
fairsharing: FAIRsharing.35e1c3
ols: co_350
name: Oat ontology
pattern: ^\d{7}$
preferred_prefix: CO_350
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_350:$1
version: '2019-10-09'
co_356:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Grape Ontology including OIV and bioversity descriptors. INRA July
2017
download_owl: https://cropontology.org/ontology/CO_356/Vitis/owl
example: '4000027'
homepage: https://cropontology.org/ontology/CO_356/Vitis
keywords:
- agriculture
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_356
cropoct: CO_356
fairsharing: FAIRsharing.c7f4d7
ols: co_356
name: Vitis ontology
pattern: ^\d+$
preferred_prefix: CO_356
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_356:$1
version: '2019-11-29'
co_357:
contact:
email: celia.michotey@inrae.fr
github: null
name: Célia Michotey
orcid: 0000-0003-1877-1703
description: 'This ontology lists all variables used for woody plant observations.
Terms are collected from various sources (past and ongoing projects at national
and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET)
- Version 2 submitted on Jun 2020 by INRAE.'
download_owl: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl
example: '1000290'
homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology
keywords:
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_357
cropoct: CO_357
fairsharing: FAIRsharing.2b04ae
ols: co_357
name: Woody Plant Ontology ontology
pattern: ^\d+$
preferred_prefix: CO_357
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_357:$1
co_358:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Cotton ontology from CottonGen database - June 2019
download_owl: https://cropontology.org/ontology/CO_358/Cotton/owl
example: 0000139
homepage: https://cropontology.org/ontology/CO_358/Cotton
keywords:
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_358
cropoct: CO_358
ols: co_358
name: Cotton ontology
pattern: ^\d{7}$
preferred_prefix: CO_358
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_358:$1
version: '2020-01-03'
co_359:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: December 2019
download_owl: https://cropontology.org/ontology/CO_359/Sunflower/owl
example: 0000947
homepage: https://cropontology.org/ontology/CO_359/Sunflower
keywords:
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_359
cropoct: CO_359
ols: co_359
name: Sunflower ontology
pattern: ^\d{7}$
preferred_prefix: CO_359
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_359:$1
co_360:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: Sugar Kelp trait ontology
download_owl: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl
example: '0000071'
homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait
keywords:
- botany
- life science
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_360
cropoct: CO_360
fairsharing: FAIRsharing.1c1738
ols: co_360
name: Sugar Kelp trait ontology
pattern: ^\d{7}$
preferred_prefix: CO_360
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_360:$1
co_365:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: ICARDA Ethiopia
orcid: null
description: developed by ICARDA - Dec 2018
download_owl: https://cropontology.org/ontology/CO_365/Fababean/owl
example: '0000205'
homepage: https://cropontology.org/ontology/CO_365/Fababean
keywords:
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_365
cropoct: CO_365
ols: co_365
name: Fababean ontology
pattern: ^\d{7}$
preferred_prefix: CO_365
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_365:$1
version: '2019-10-15'
co_366:
contact:
email: helpdesk@cropontology-curationtool.org
github: null
name: Crop Ontology Helpdesk
orcid: null
description: version Dec 2019
download_owl: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl
example: '0000072'
homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut
keywords:
- ontology
license: CC-BY-4.0
mappings:
agroportal: CO_366
cropoct: CO_366
ols: co_366
name: Bambara groundnut ontology
pattern: ^\d{7}$
preferred_prefix: CO_366
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_366:$1
co_367:
description: 'Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah
University of Science and Technology; Contributing Scientists or Crop expert group:
The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021'
example: '0000004'
homepage: https://cropontology.org/term/CO_367:ROOT
license: CC-BY-4.0
mappings:
cropoct: CO_367
name: Quinoa Ontology ontology
pattern: ^\d{7}$
preferred_prefix: CO_367
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_367:$1
co_370:
contact:
email: ekaterina.chuprikova@eurac.edu
github: null
name: Ekaterina Chuprikova
orcid: 0000-0002-8981-0442
description: Apple (Malus domestica) defines crop traits and variables to support
the standardisation of apple breeding databases providing description of agronomic,
morphological, physiological, quality traits, its methods and scales.
example: 0000890
homepage: https://cropontology.org/term/CO_370:ROOT
license: CC-BY-4.0
mappings:
agroportal: CO_370
cropoct: CO_370
name: Apple Ontology
pattern: ^\d{7}$
preferred_prefix: CO_370
repository: https://github.com/bioversity/Crop-Ontology
uri_format: https://cropontology.org/rdf/CO_370:$1
cob:
contact:
email: bpeters@lji.org
github: bpeters42
name: Bjoern Peters
orcid: 0000-0002-8457-6693
description: COB brings together key terms from a wide range of OBO projects to
improve interoperability.
download_owl: http://purl.obolibrary.org/obo/cob.owl
example: 0000080
homepage: https://obofoundry.org/COB/
keywords:
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: COB
bioportal: COB
obofoundry: cob
ols: cob
ontobee: COB
name: Core Ontology for Biology and Biomedicine
pattern: ^\d{7}$
preferred_prefix: COB
rdf_uri_format: http://purl.obolibrary.org/obo/COB_$1
repository: https://github.com/OBOFoundry/COB
uri_format: http://purl.obolibrary.org/obo/COB_$1
version: '2022-11-02'
coconut:
comment: '@mSorok is the dev of the resource, hope I got it right!'
contributor:
email: adriano.rutz@ik.me
github: adafede
name: Adriano Rutz
orcid: 0000-0003-0443-9902
description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source
project for Natural Products (NPs) storage, search and analysis. It gathers data
from over 50 open NP resources and is available free of charge and without any
restriction. Each entry corresponds to a "flat" NP structure, and is associated,
when available, to their known stereochemical forms, literature, organisms that
produce them, natural geographical presence and diverse pre-computed molecular
properties.
example: CNP0171505
github_request_issue: 221
homepage: https://coconut.naturalproducts.net
keywords:
- chemistry
- natural producs
- organic chemistry
name: COlleCtion of Open Natural ProdUcTs
pattern: ^CNP\d{7}$
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/$1
codelink:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray
targets most of the known and predictive genes of the human genome as it is described
today in the public domain. It is comprised of approximately 55,000 30-mer probes
designed to conserved exons across the transcripts of targeted genes. These 55,000
probes represent well annotated, full length, and partial human gene sequences
from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human
Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build
#165, RefSeq database (January 5, 2004 release) and dbEST database (January 8,
2004 release).'
example: GE86325
homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt
keywords:
- microarray
- transcriptomics
name: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
pattern: ^GE\d+$
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
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/
keywords:
- genome
- life science
- protein
mappings:
biolink: COG
fairsharing: FAIRsharing.djsbw2
go: COG_Cluster
prefixcommons: cog
name: Cluster of orthologous genes
pattern: ^COG\d+$
preferred_prefix: cog
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cog:$1
publications:
- doi: 10.1126/science.278.5338.631
pmc: null
pubmed: '9381173'
title: A genomic perspective on protein families.
year: 1997
- doi: 10.1093/nar/gku1223
pmc: PMC4383993
pubmed: '25428365'
title: Expanded microbial genome coverage and improved protein family annotation
in the COG database.
year: 2014
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/
keywords:
- pathways
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
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/$1
cohd:
comment: not really sure where the source is. this also links to a system called
athena. I was not able to figure out what COHD stands for.
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: MIMIC-III is a dataset comprising health-related data associated with
over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess
Medical Center between 2001 and 2012
homepage: https://github.com/MIT-LCP/mimic-omop
keywords:
- clinical data
- clinical trials
- health
- health sciences
name: MIMIC III Database
no_own_terms: true
preferred_prefix: cohd
repository: https://github.com/MIT-LCP/mimic-omop
col:
description: Identifier of a taxon or synonym in the Catalogue of Life
example: 4QHKG
homepage: https://www.checklistbank.org
mappings:
bartoc: '1915'
miriam: col
name: Catalogue of Life
pattern: ^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$
preferred_prefix: col
providers:
- code: col
description: The Catalogue of Life website providing a view onto the latest release
of the COL Checklist.
homepage: https://www.catalogueoflife.org
name: Catalogue of Life (COL)
uri_format: https://www.catalogueoflife.org/data/taxon/$1
uri_format: https://www.checklistbank.org/dataset/3LR/taxon/$1
col.taiwan:
contributor:
email: meghan.balk@gmail.com
github: megbalk
name: Meghan Balk
orcid: 0000-0003-2699-3066
description: Identifier (name code) for a taxon in the catalogue of life in taiwan
example: '431472'
github_request_issue: 466
homepage: http://taibnet.sinica.edu.tw/home.php
mappings:
wikidata: P3088
name: Catalogue of Life in Taiwan
pattern: ^[1-9]\d{5}$
preferred_prefix: col.taiwan
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1
colao:
contact:
email: entiminae@gmail.com
github: JCGiron
name: Jennifer C. Giron
orcid: 0000-0002-0851-6883
depends_on:
- aism
- bfo
- bspo
- caro
- pato
- ro
- uberon
description: The Coleoptera Anatomy Ontology contains terms used for describing
the anatomy and phenotype of beetles in biodiversity research.
download_obo: http://purl.obolibrary.org/obo/colao.obo
download_owl: http://purl.obolibrary.org/obo/colao.owl
example: '0000000'
homepage: https://github.com/insect-morphology/colao
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: COLAO
bioportal: COLAO
obofoundry: colao
ols: colao
ontobee: COLAO
name: Coleoptera Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: COLAO
rdf_uri_format: http://purl.obolibrary.org/obo/COLAO_$1
repository: https://github.com/insect-morphology/colao
uri_format: http://purl.obolibrary.org/obo/COLAO_$1
version: '2023-04-08'
collagenmutdb:
description: This database aims to record all published accounts of variants resulting
in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP,
FKBP10, LEPRE1 and PPIB genes.
example: COL3A1
homepage: http://www.le.ac.uk/genetics/collagen/
keywords:
- gene
mappings:
prefixcommons: cmd
name: Collagen Mutation Database
preferred_prefix: collagenmutdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cmd:$1
provides: hgnc.symbol
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://eds.gene.le.ac.uk/home.php?select_db=$1
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=$1
combine.specifications:
description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative
to coordinate the development of the various community standards and formats for
computational models, initially in Systems Biology and related fields. This collection
pertains to specifications of the standard formats developed by the Computational
Modeling in Biology Network.
example: sed-ml.level-1.version-1
homepage: https://co.mbine.org/standards/
mappings:
biocontext: COMBINE.SPECIFICATIONS
miriam: combine.specifications
n2t: combine.specifications
name: COMBINE specifications
pattern: ^\w+(\-|\.|\w)*$
preferred_prefix: combine.specifications
uri_format: https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md
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
keywords:
- protein
mappings:
prefixcommons: come
name: The Bioinorganic Motif Database
preferred_prefix: come
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/come:$1
uri_format: https://www.flymine.org/come/entry?gn=$1
commoncoreontology:
contact:
email: mpjensen@buffalo.edu
github: mark-jensen
name: Mark Jensen
orcid: 0000-0001-9228-8838
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The Common Core Ontologies (CCO) comprise twelve ontologies that are
designed to represent and integrate taxonomies of generic classes and relations
across all domains of interest.
CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology
framework widely used to structure and integrate ontologies in the biomedical
domain (Arp, et al., 2015). BFO aims to represent the most generic categories
of entity and the most generic types of relations that hold between them, by defining
a small number of classes and relations. CCO then extends from BFO in the sense
that every class in CCO is asserted to be a subclass of some class in BFO, and
that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and
Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained
by the BFO framework, from which it inherits much of its basic semantic relationships.'
example: DirectiveInformationContentEntity
homepage: http://www.ontologyrepository.com
keywords:
- ontology
- upper-level ontology
license: CC-BY-4.0
name: Common Core Ontologies
preferred_prefix: commoncoreontology
repository: https://github.com/CommonCoreOntology/CommonCoreOntologies
uri_format: http://www.ontologyrepository.com/CommonCoreOntologies/$1
complexportal:
description: A database that describes manually curated macromolecular complexes
and provides links to details about these complexes in other databases.
example: CPX-263
homepage: https://www.ebi.ac.uk/complexportal
mappings:
biocontext: COMPLEXPORTAL
biolink: ComplexPortal
go: ComplexPortal
miriam: complexportal
n2t: complexportal
re3data: r3d100013295
uniprot: DB-0228
wikidata: P7718
name: Complex Portal
pattern: ^CPX-[0-9]+$
preferred_prefix: complexportal
publications:
- doi: 10.1093/nar/gku975
pmc: PMC4384031
pubmed: '25313161'
title: The complex portal--an encyclopaedia of macromolecular complexes.
year: 2014
synonyms:
- ComplexPortal
uri_format: https://www.ebi.ac.uk/complexportal/complex/$1
comptox:
description: The Chemistry Dashboard is a part of a suite of databases and web applications
developed by the US Environmental Protection Agency's Chemical Safety for Sustainability
Research Program. These databases and apps support EPA's computational toxicology
research efforts to develop innovative methods to change how chemicals are currently
evaluated for potential health risks.
example: DTXSID2021028
homepage: https://comptox.epa.gov/dashboard
mappings:
biocontext: COMPTOX
miriam: comptox
n2t: comptox
wikidata: P3117
name: DSSTox substance
pattern: ^DTXSID\d+$
preferred_prefix: comptox
uri_format: https://comptox.epa.gov/dashboard/$1
compulyeast:
description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis
federated database. This collection references a subset of Uniprot, and contains
general information about the protein record.
example: O08709
homepage: http://compluyeast2dpage.dacya.ucm.es/
keywords:
- protein
mappings:
biocontext: COMPULYEAST
fairsharing: FAIRsharing.rbjs3e
miriam: compulyeast
n2t: compulyeast
prefixcommons: compluyeast2dpage
name: Compluyeast-2D-DB
pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9])$
preferred_prefix: compulyeast
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/compluyeast2dpage:$1
provides: uniprot
uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1
conference:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The conference-ontology is a new self-contained ontology for modelleing
knowledge about conferences. The conference-ontology adopts best ontology design
practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and
guarantees interoperability with SWC ontology and all other pertinent vocabularies.
(from homepage)
download_owl: https://w3id.org/scholarlydata/ontology/conference-ontology.owl
example: isDocumentRelatedTo
homepage: http://www.scholarlydata.org/ontology/doc/
keywords:
- ontology
license: CC-BY-3.0
name: Conference Ontology
preferred_prefix: conference
uri_format: https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1
confident.event:
contact:
email: Philip.Stroemert@tib.eu
github: StroemPhi
name: Philip Strömert
orcid: 0000-0002-1595-3213
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Confident makes descriptive metadata on conferences and other formats
of scientific events permanently accessible in a high quality through automated
processes and scientific data curating.
example: 37af84f2-bfd7-4653-b608-eaff44febba6
github_request_issue: 519
homepage: https://www.confident-conference.org/index.php/Category:Event
keywords:
- conferences
- meetings
- metascience
name: ConfIDent Event
pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
preferred_prefix: confident.event
uri_format: https://www.confident-conference.org/index.php/Event:$1
confident.series:
contact:
email: Philip.Stroemert@tib.eu
github: StroemPhi
name: Philip Strömert
orcid: 0000-0002-1595-3213
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Confident makes descriptive metadata on conferences and other formats
of scientific events permanently accessible in a high quality through automated
processes and scientific data curating.
example: AAC
github_request_issue: 519
homepage: https://www.confident-conference.org/index.php/Category:Event_Series
keywords:
- conferences
- grouping
- meetings
- metascience
name: ConfIDent Event Series
preferred_prefix: confident.series
uri_format: https://www.confident-conference.org/index.php/Event_Series:$1
conoserver:
contact:
email: d.craik@imb.uq.edu.au
github: null
name: David Craik
orcid: 0000-0003-0007-6796
description: ConoServer is a database specialized in the sequence and structures
of conopeptides, which are peptides expressed by carnivorous marine cone snails.
example: '2639'
homepage: http://www.conoserver.org/
keywords:
- life science
- neurophysiology
- statistics
- synthetic biology
mappings:
biocontext: CONOSERVER
fairsharing: FAIRsharing.y00hz4
miriam: conoserver
n2t: conoserver
uniprot: DB-0156
name: ConoServer
pattern: ^\d+$
preferred_prefix: conoserver
publications:
- doi: 10.1093/nar/gkr886
pmc: PMC3245185
pubmed: '22058133'
title: 'ConoServer: updated content, knowledge, and discovery tools in the conopeptide
database.'
year: 2011
- doi: 10.1016/j.toxicon.2010.03.002
pmc: null
pubmed: '20211197'
title: 'Conopeptide characterization and classifications: an analysis using ConoServer.'
year: 2010
- doi: 10.1093/bioinformatics/btm596
pmc: null
pubmed: '18065428'
title: ConoServer, a database for conopeptide sequences and structures.
year: 2007
- doi: 10.1021/cb700091j
pmc: null
pubmed: '17649970'
title: Chemical modification of conotoxins to improve stability and activity.
year: 2007
- doi: 10.1152/physrev.00020.2003
pmc: null
pubmed: '14715910'
title: 'Conus venoms: a rich source of novel ion channel-targeted peptides.'
year: 2004
uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1
conso:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology describing phenomena encountered in the literature surrounding
neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's
disease, tauopathies, and related protein aggregation diseases.
example: CONSO00010
homepage: https://pharmacome.github.io/conso/
keywords:
- biology
- life science
- neurodegeneration
- neuroscience
- ontology
name: Curation of Neurodegeneration Supporting Ontology
pattern: ^CONSO\d{5}$
preferred_prefix: conso
uri_format: https://pharmacome.github.io/conso/$1
cordis.article:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Community Research and Development Information Service (CORDIS)
is the European Commission's primary source of results from the projects funded
by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
example: '436605'
homepage: https://cordis.europa.eu/
name: CORDIS Article
pattern: ^\d+$
preferred_prefix: cordis.article
uri_format: https://cordis.europa.eu/article/id/$1
cordis.project:
contributor:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
description: The Community Research and Development Information Service (CORDIS)
is the European Commission's primary source of results from the projects funded
by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).
example: '817732'
github_request_issue: 450
homepage: https://cordis.europa.eu/
name: CORDIS Project
pattern: ^\d+$
preferred_prefix: cordis.project
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://cordis.europa.eu/project/id/$1
coriell:
description: The Coriell Cell Repositories provide essential research reagents to
the scientific community by establishing, verifying, maintaining, and distributing
cell cultures and DNA derived from cell cultures. These collections, supported
by funds from the National Institutes of Health (NIH) and several foundations,
are extensively utilized by research scientists around the world.
example: GM17027
homepage: http://ccr.coriell.org/
mappings:
biocontext: Coriell
cellosaurus: Coriell
go: CORIELL
miriam: coriell
n2t: coriell
name: Coriell Institute for Medical Research
pattern: ^[A-Z]{2}\d+$
preferred_prefix: coriell
uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1
corrdb:
contact:
email: zhu@iastate.edu
github: null
name: Zhiliang Hu
orcid: 0000-0002-6704-7538
description: A genetic correlation is the proportion of shared variance between
two traits that is due to genetic causes; a phenotypic correlation is the degree
to which two traits co-vary among individuals in a population. In the genomics
era, while gene expression, genetic association, and network analysis provide
unprecedented means to decode the genetic basis of complex phenotypes, it is important
to recognize the possible effects genetic progress in one trait can have on other
traits. This database is designed to collect all published livestock genetic/phenotypic
trait correlation data, aimed at facilitating genetic network analysis or systems
biology studies.
example: '37232'
homepage: https://www.animalgenome.org
keywords:
- animal genetics
- genetics
- life science
- systems biology
mappings:
fairsharing: FAIRsharing.IziuCK
miriam: corrdb
re3data: r3d100011496
name: CorrDB
pattern: ^[0-9]+$
preferred_prefix: corrdb
uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1
corum:
contact:
email: andreas.ruepp@helmholtz-muenchen.de
github: null
name: Andreas Ruepp
orcid: 0000-0003-1705-3515
description: The CORUM database provides a resource of manually annotated protein
complexes from mammalian organisms. Annotation includes protein complex function,
localization, subunit composition, literature references and more. All information
is obtained from individual experiments published in scientific articles, data
from high-throughput experiments is excluded.
example: '100'
homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/
keywords:
- bioinformatics
- biology
- protein
mappings:
biocontext: CORUM
fairsharing: FAIRsharing.ohbpNw
go: CORUM
miriam: corum
n2t: corum
prefixcommons: corum
uniprot: DB-0224
name: Comprehensive Resource of Mammalian protein complexes
pattern: ^\d+$
preferred_prefix: corum
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/corum:$1
publications:
- doi: 10.1093/nar/gky973
pmc: PMC6323970
pubmed: '30357367'
title: 'CORUM: the comprehensive resource of mammalian protein complexes-2019.'
year: 2019
uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1
cosmic:
description: COSMIC is a comprehensive global resource for information on somatic
mutations in human cancer, combining curation of the scientific literature with
tumor resequencing data from the Cancer Genome Project at the Sanger Institute,
U.K. This collection references genes.
example: BRAF
homepage: http://cancer.sanger.ac.uk/cosmic/
keywords:
- biomedical science
- genetics
mappings:
biocontext: COSMIC
cellosaurus: Cosmic
edam: '3264'
fairsharing: FAIRsharing.s5zmbp
miriam: cosmic
n2t: cosmic
name: COSMIC Gene
pattern: ^[A-Z0-9]+$
preferred_prefix: cosmic
publications:
- doi: 10.1093/nar/gky1015
pmc: PMC6323903
pubmed: '30371878'
title: 'COSMIC: the Catalogue Of Somatic Mutations In Cancer.'
year: 2019
- doi: 10.1093/nar/gku1075
pmc: PMC4383913
pubmed: '25355519'
title: 'COSMIC: exploring the world''s knowledge of somatic mutations in human
cancer.'
year: 2014
- doi: 10.1093/nar/gkq929
pmc: PMC3013785
pubmed: '20952405'
title: 'COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations
in Cancer.'
year: 2010
- doi: 10.1038/sj.bjc.6601894
pmc: PMC2409828
pubmed: '15188009'
title: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website.
year: 2004
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=$1
covid19:
contact:
email: dylan.mcgagh@magd.ox.ac.uk
github: null
name: Dylan McGagh
orcid: 0000-0002-6772-2775
description: Curated contextual database gathering samples related to SARS-CoV-2
virus and covid-19 disease.
download_owl: http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl
example: SFB_COVID19_MW286762
homepage: https://covid19.sfb.uit.no
keywords:
- ontology
mappings:
aberowl: COVID19
bioportal: COVID19
miriam: covid19
name: COVID-19 Surveillance Ontology
pattern: ^\w+_COVID19_[-\w]+$
preferred_prefix: covid19
uri_format: https://covid19.sfb.uit.no/api/records/$1
covoc:
contact:
email: zmp@ebi.ac.uk
github: zoependlington
name: Zoë May Pendlington
orcid: 0000-0002-4071-8397
description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related
to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity,
gene and gene products, barrier gestures, treatments and more.
download_json: https://github.com/EBISPOT/covoc/releases/download/current/covoc.json
download_obo: https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo
download_owl: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl
example: '0010034'
homepage: https://github.com/EBISPOT/covoc
keywords:
- ontology
mappings:
ols: covoc
name: CoVoc Coronavirus Vocabulary
pattern: ^\d{7}$
preferred_prefix: covoc
repository: https://github.com/EBISPOT/covoc
uri_format: http://purl.obolibrary.org/obo/COVOC_$1
version: '2022-10-26'
cp:
appears_in:
- cl
comment: Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
name: Cellular Phenotypes
preferred_prefix: cp
cpc:
description: The Cooperative Patent Classification (CPC) is a patent classification
system, developed jointly by the European Patent Office (EPO) and the United States
Patent and Trademark Office (USPTO). It is based on the previous European classification
system (ECLA), which itself was a version of the International Patent Classification
(IPC) system. The CPC patent classification system has been used by EPO and USPTO
since 1st January, 2013.
example: A01M1/026
homepage: https://worldwide.espacenet.com/classification
keywords:
- atmospheric science
- earth science
- geodesy
- geography
- hydrogeology
- meteorology
mappings:
biocontext: CPC
fairsharing: FAIRsharing.e08886
miriam: cpc
n2t: cpc
name: Cooperative Patent Classification
pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H,
Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$
preferred_prefix: cpc
uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1
cpt:
contact:
email: Intellectual.PropertyServices@ama-assn.org
github: null
name: American Medical Association
orcid: null
contributor:
email: null
github: sierra-moxon
name: Sierra Moxon
orcid: 0000-0002-8719-7760
contributor_extras:
- email: null
github: colleenXu
name: Colleen Xu
orcid: 0000-0003-2975-882X
description: Current Procedural Terminology, more commonly known as CPT®, refers
to a medical code set created and maintained by the American Medical Association
— and used by physicians, allied health professionals, nonphysician practitioners,
hospitals, outpatient facilities, and laboratories to represent the services and
procedures they perform. No provider of outpatient services gets paid without
reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]
example: '00103'
github_request_issue: 357
homepage: https://www.aapc.com
keywords:
- biomedical science
- health science
- medicine
- ontology
mappings:
aberowl: CPT
biolink: CPT
bioportal: CPT
fairsharing: FAIRsharing.wpxab1
name: Current Procedural Terminology
pattern: ^\d+$
preferred_prefix: cpt
publications:
- doi: 10.1136/neurintsurg-2014-011156
pmc: null
pubmed: '24589819'
title: Current procedural terminology; a primer.
year: 2014
- doi: 10.1016/j.jacr.2007.10.004
pmc: null
pubmed: '18359442'
title: 'CPT: an open system that describes all that you do.'
year: 2008
references:
- 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
synonyms:
- ama-cpt
uri_format: https://www.aapc.com/codes/cpt-codes/$1
credit:
contact:
email: info@casrai.org
github: null
name: Liz Allen
orcid: 0000-0002-9298-3168
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/
keywords:
- data quality
- ontology and terminology
- subject agnostic
mappings:
fairsharing: FAIRsharing.fe4816
name: CASRAI Contributor Roles Taxonomy
preferred_prefix: credit
publications:
- doi: 10.1038/d41586-019-01715-4
pmc: null
pubmed: '31164773'
title: Credit data generators for data reuse.
year: 2019
- doi: 10.1038/508312a
pmc: null
pubmed: '24745070'
title: 'Publishing: Credit where credit is due.'
year: 2014
- doi: 10.3789/ansi.niso.z39.104-2022
pmc: null
pubmed: null
title: ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy
year: null
- doi: 10.1087/20150211
pmc: null
pubmed: null
title: 'Beyond authorship: attribution, contribution, collaboration, and credit'
year: 2015
- doi: 10.1002/leap.1210
pmc: null
pubmed: null
title: How can we ensure visibility and diversity in research contributions? How
the Contributor Role Taxonomy (CRediT) is helping the shift from authorship
to contributorship
year: 2019
twitter: contrib_roles
crisprdb:
contact:
email: Christine.Pourcel@u-psud.fr
github: null
name: Christine Pourcel
orcid: 0000-0002-8951-466X
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/
keywords:
- life science
mappings:
biocontext: CRISPRDB
fairsharing: FAIRsharing.7sfedh
miriam: crisprdb
n2t: crisprdb
name: CRISPRdb
pattern: ^[0-9]+$
preferred_prefix: crisprdb
publications:
- doi: 10.1093/nar/gkn228
pmc: PMC2447796
pubmed: '18442988'
title: 'CRISPRcompar: a website to compare clustered regularly interspaced short
palindromic repeats.'
year: 2008
- doi: 10.1093/nar/gkm360
pmc: PMC1933234
pubmed: '17537822'
title: 'CRISPRFinder: a web tool to identify clustered regularly interspaced short
palindromic repeats.'
year: 2007
- doi: 10.1186/1471-2105-8-172
pmc: PMC1892036
pubmed: '17521438'
title: The CRISPRdb database and tools to display CRISPRs and to generate dictionaries
of spacers and repeats.
year: 2007
uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1
cro:
contact:
email: whimar@ohsu.edu
github: marijane
name: Marijane White
orcid: 0000-0001-5059-4132
description: A classification of the diverse roles performed in the work leading
to a published research output in the sciences. Its purpose to provide transparency
in contributions to scholarly published work, to enable improved systems of attribution,
credit, and accountability.
download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo
download_owl: http://purl.obolibrary.org/obo/cro.owl
example: 0000038
homepage: https://github.com/data2health/contributor-role-ontology
keywords:
- obo
- ontology
license: CC BY 2.0
mappings:
aberowl: CRO
biocontext: CRO
bioportal: CRO
obofoundry: cro
ols: cro
ontobee: CRO
name: Contributor Role Ontology
pattern: ^\d{7}$
preferred_prefix: CRO
rdf_uri_format: http://purl.obolibrary.org/obo/CRO_$1
repository: https://github.com/data2health/contributor-role-ontology
uri_format: http://purl.obolibrary.org/obo/CRO_$1
version: '2019-12-11'
crop2ml:
description: CropMRespository is a database of soil and crop biophysical process
models.
example: '000000001'
homepage: http://www.crop2ml.org
mappings:
miriam: crop2ml
name: CropMRepository
pattern: ^[0-9]{9}$
preferred_prefix: crop2ml
uri_format: http://www.crop2ml.org/cropmdb/$1
cryoem:
contact:
email: isanchez@cnb.csic.es
github: null
name: Carlos Oscar S. Sorzano
orcid: 0000-0002-9473-283X
description: Ontology that describes data types and image processing operations
in Cryo Electron Microscopy of Single Particles
download_owl: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl
example: '0000052'
homepage: http://scipion.i2pc.es/ontology/cryoem
keywords:
- ontology
- structural biology
mappings:
aberowl: CRYOEM
bioportal: CRYOEM
fairsharing: FAIRsharing.q47I0t
ols: cryoem
name: Cryo Electron Microscopy ontology
pattern: ^\d{7}$
preferred_prefix: cryoem
uri_format: http://scipion.i2pc.es/ontology/CRYOEM_$1
version: '2021-03-09'
cryptodb:
contact:
email: jkissing@uga.edu
github: null
name: Jessica Kissinger
orcid: 0000-0003-4446-6200
description: CryptoDB is one of the databases that can be accessed through the EuPathDB
(http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of
the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: cgd7_230
homepage: https://cryptodb.org/cryptodb/
keywords:
- functional genomics
- genome
- genomics
- parasitology
mappings:
biocontext: CRYPTODB
fairsharing: FAIRsharing.t3nprm
miriam: cryptodb
n2t: cryptodb
prefixcommons: cryptodb
re3data: r3d100012265
name: CryptoDB
pattern: ^\w+$
preferred_prefix: cryptodb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cryptodb:$1
publications:
- doi: 10.1007/978-1-4939-9748-0_10
pmc: null
pubmed: '31452162'
title: Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.
year: 2020
- doi: 10.1093/nar/gkj078
pmc: PMC1347441
pubmed: '16381902'
title: 'CryptoDB: a Cryptosporidium bioinformatics resource update.'
year: 2006
twitter: VEuPathDB
uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1
csa:
contact:
email: nickf@ebi.ac.uk
github: null
name: Nicholas Furnham
orcid: 0000-0002-7532-1269
description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active
sites and catalytic residues in enzymes of 3D structure. It uses a defined classification
for catalytic residues which includes only those residues thought to be directly
involved in some aspect of the reaction catalysed by an enzyme.
example: 1a05
homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/
keywords:
- enzyme
- life science
- structure
mappings:
biocontext: CSA
fairsharing: FAIRsharing.2ajtcf
miriam: csa
n2t: csa
prefixcommons: csa
name: Catalytic Site Atlas
pattern: ^[0-9][A-Za-z0-9]{3}$
preferred_prefix: csa
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/csa:$1
publications:
- doi: 10.1093/nar/gkt1243
pmc: PMC3964973
pubmed: '24319146'
title: 'The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues
identified in enzymes.'
year: 2013
- doi: 10.1093/nar/gkh028
pmc: PMC308762
pubmed: '14681376'
title: 'The Catalytic Site Atlas: a resource of catalytic sites and residues identified
in enzymes using structural data.'
year: 2004
uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1
csd:
contact:
email: support@ccdc.cam.ac.uk
github: null
name: Support Email
orcid: 0000-0002-6062-7492
description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive
collection of small-molecule crystal structures. Entries curated into the CSD
are identified by a CSD Refcode.
example: PELNAW
homepage: https://www.ccdc.cam.ac.uk/
keywords:
- biochemistry
- chemistry
- organic chemistry
- organic molecular chemistry
mappings:
fairsharing: FAIRsharing.vs7865
miriam: csd
re3data: r3d100010197
name: Cambridge Structural Database
pattern: ^[A-Z]{6}(\d{2})?$
preferred_prefix: csd
publications:
- doi: 10.1107/s2052520616003954
pmc: PMC4822653
pubmed: '27048719'
title: The Cambridge Structural Database.
year: 2016
- doi: 10.1107/s0108768102003890
pmc: null
pubmed: '12037359'
title: 'The Cambridge Structural Database: a quarter of a million crystal structures
and rising.'
year: 2002
twitter: ccdc_cambridge
uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG
csp:
contact:
email: af8d@nih.gov
github: null
name: Anita Ghebeles
orcid: null
deprecated: true
description: CRISP is a terminology used for indexing biomedical information. CRISP
contains over 8,000 preferred terms that are grouped hierarchically into 11 domains.
example: 2004-2820
homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm
keywords:
- anatomy
- biology
- biomedical science
- chemical biology
- medicine
- ontology
- social science
mappings:
aberowl: CRISP
bioportal: CRISP
fairsharing: FAIRsharing.1evfpc
hl7: 2.16.840.1.113883.6.120
name: Computer Retrieval of Information on Science Projects Thesaurus
preferred_prefix: csp
publications:
- doi: null
pmc: null
pubmed: '8718842'
title: Taking a bite out of CRISP. Strategies on using and conducting searches
in the Computer Retrieval of Information on Scientific Projects database.
year: 1996
synonyms:
- CRISP
- CRISP Thesaurus
- CRISP Thesaurus, 2006
- CSP2005
uri_format: http://purl.bioontology.org/ontology/CSP/$1
cst:
description: Cell Signaling Technology is a commercial organisation which provides
a pathway portal to showcase their phospho-antibody products. This collection
references pathways.
example: Akt_PKB
homepage: http://www.cellsignal.com/pathways/index.html
keywords:
- biomedical science
- life science
mappings:
biocontext: CST
fairsharing: FAIRsharing.n8pxvx
hl7: 2.16.840.1.113883.6.62
miriam: cst
n2t: cst
name: Cell Signaling Technology Pathways
pattern: ^[A-Za-z0-9_-]+$
preferred_prefix: cst
uri_format: http://www.cellsignal.com/reference/pathway/$1.html
cst.ab:
description: Cell Signaling Technology is a commercial organisation which provides
a pathway portal to showcase their phospho-antibody products. This collection
references antibody products.
example: '3305'
homepage: http://www.cellsignal.com/catalog/index.html
keywords:
- pathway
mappings:
biocontext: CST.AB
miriam: cst.ab
n2t: cst.ab
prefixcommons: cst
name: Cell Signaling Technology Antibody
pattern: ^\d+$
preferred_prefix: cst.ab
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cst:$1
uri_format: http://www.cellsignal.com/products/$1.html
cstr:
description: 'CSTR is an identifier for Common Science and Technology Resources,
to provide persistent identification services for the positioning, traceability,
citation, statistics and evaluation of science and technology resources. '
example: 31253.11.sciencedb.j00001.00123
homepage: https://www.cstr.cn/en/
mappings:
miriam: cstr
name: Common Science and Technology Resources
pattern: ^\w{5}\.\d{2}\..*$
preferred_prefix: cstr
uri_format: https://cstr.cn/$1
ctcae:
appears_in:
- oae
contact:
email: ncictcaehelp@mail.nih.gov
github: null
name: CTCAE Help
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly
called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for
the standardized classification of adverse effects of drugs used in cancer therapy.
The CTCAE system is a product of the US National Cancer Institute (NCI).
download_owl: http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl
example: E12768
homepage: https://evs.nci.nih.gov/ftp1/CTCAE/About.html
keywords:
- ontology
mappings:
aberowl: CTCAE
bioportal: CTCAE
name: Common Terminology Criteria for Adverse Events
pattern: ^E\d+$
preferred_prefix: ctcae
publications:
- doi: null
pmc: PMC5977606
pubmed: '29854250'
title: 'Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping
and OAE-based representation and analysis of adverse events in patients treated
with cancer drugs.'
year: 2018
references:
- https://github.com/OAE-ontology/OAE/issues/8
- https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events
synonyms:
- CTCAE
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=$1
ctd.gene:
description: The Comparative Toxicogenomics Database (CTD) presents scientifically
reviewed and curated information on chemicals, relevant genes and proteins, and
their interactions in vertebrates and invertebrates. It integrates sequence, reference,
species, microarray, and general toxicology information to provide a unique centralized
resource for toxicogenomic research. The database also provides visualization
capabilities that enable cross-species comparisons of gene and protein sequences.
example: '101'
homepage: http://ctdbase.org/
mappings:
biocontext: CTD.GENE
biolink: CTD.GENE
miriam: ctd.gene
n2t: ctd.gene
uniprot: DB-0140
name: CTD Gene
part_of: ctd
pattern: ^\d+$
preferred_prefix: ctd.gene
provides: ncbigene
publications:
- doi: 10.1093/nar/gkaa891
pmc: PMC7779006
pubmed: '33068428'
title: 'Comparative Toxicogenomics Database (CTD): update 2021.'
year: 2021
uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1
cteno:
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
depends_on:
- ro
- uberon
description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo
download_owl: http://purl.obolibrary.org/obo/cteno.owl
example: '0000047'
homepage: https://github.com/obophenotype/ctenophore-ontology
keywords:
- anatomy
- developmental biology
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: CTENO
biocontext: CTENO
bioportal: CTENO
fairsharing: FAIRsharing.mgxgza
obofoundry: cteno
ols: cteno
ontobee: CTENO
name: Ctenophore Ontology
pattern: ^\d{7}$
preferred_prefix: CTENO
rdf_uri_format: http://purl.obolibrary.org/obo/CTENO_$1
repository: https://github.com/obophenotype/ctenophore-ontology
uri_format: http://purl.obolibrary.org/obo/CTENO_$1
version: '2016-10-19'
ctis:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: This website supports the undertaking and oversight of clinical trials
in the European Union (EU) and European Economic Area (EEA). It is part of a broad
initiative to transform the EU/EEA clinical trials environment in support of large
clinical trials in multiple European countries, to the benefit of medical innovation
and patients. (from homepage)
example: 2023-503698-40-00
homepage: https://euclinicaltrials.eu/
name: Clinical Trials Information System
pattern: ^\d{4}-\d+-\d+-\d+$
preferred_prefix: ctis
uri_format: https://euclinicaltrials.eu/app/#/view/$1
cto:
contact:
email: alpha.tom.kodamullil@scai.fraunhofer.de
github: akodamullil
name: Dr. Alpha Tom Kodamullil
orcid: 0000-0001-9896-3531
description: The core Ontology of Clinical Trials (CTO) will serve as a structured
resource integrating basic terms and concepts in the context of clinical trials.
Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to
generate extended versions for specific applications such as annotation of variables
in study documents from clinical trials.
download_owl: http://purl.obolibrary.org/obo/cto.owl
example: '0000022'
homepage: https://github.com/ClinicalTrialOntology/CTO/
keywords:
- biomedical science
- neurobiology
- obo
- ontology
- preclinical studies
license: CC-BY-4.0
mappings:
aberowl: CTO
bioportal: CTO
fairsharing: FAIRsharing.qp211a
obofoundry: cto
ols: cto
ontobee: CTO
name: Clinical Trials Ontology
pattern: ^\d{7}$
preferred_prefix: CTO
rdf_uri_format: http://purl.obolibrary.org/obo/CTO_$1
repository: https://github.com/ClinicalTrialOntology/CTO
uri_format: http://purl.obolibrary.org/obo/CTO_$1
version: 1.0.0
ctri:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The mission of the Clinical Trials Registry-India (CTRI) is to ensure
that all clinical trials conducted in India are prospectively registered, i.e.
before the enrolment of the first participant. Additionally, post-marketing surveillance
studies, BA/BE studies as well as clinical studies as part of PG thesis are also
expected to be registered in the CTRI. (from homepage)
Note that the identifier in this semantic space is not the one used in the webpages'
example: CTRI/2023/04/052053
homepage: https://ctri.nic.in
name: India Clinical Trials Registry
pattern: ^CTRI/\d{4}/\d{2}/\d+$
preferred_prefix: ctri
references:
- https://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=82487
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/
cutg:
description: Codon usage in individual genes has been calculated using the nucleotide
sequence data obtained from the GenBank Genetic Sequence Database. The compilation
of codon usage is synchronized with each major release of GenBank.
example: '9606'
homepage: http://www.kazusa.or.jp/codon/
keywords:
- dna
- gene
mappings:
prefixcommons: cutg
name: Codon Usage Tabulated from GenBank
preferred_prefix: cutg
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/cutg:$1
provides: ncbitaxon
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1
cvdo:
contact:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
description: An ontology to describe entities related to cardiovascular diseases
download_owl: http://purl.obolibrary.org/obo/cvdo.owl
example: '0000546'
homepage: https://github.com/OpenLHS/CVDO
keywords:
- cardiology
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: CVDO
biocontext: CVDO
bioportal: CVDO
fairsharing: FAIRsharing.2basyz
obofoundry: cvdo
ols: cvdo
ontobee: CVDO
name: Cardiovascular Disease Ontology
pattern: ^\d{7}$
preferred_prefix: CVDO
rdf_uri_format: http://purl.obolibrary.org/obo/CVDO_$1
repository: https://github.com/OpenLHS/CVDO
uri_format: http://purl.obolibrary.org/obo/CVDO_$1
version: '2020-03-05'
cvx:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The CDC's National Center of Immunization and Respiratory Diseases
(NCIRD) developed and maintains the CVX (vaccine administered) code set. The table
below has the most up to date values. It includes both active and inactive vaccines
available in the US. CVX codes for inactive vaccines allow transmission of historical
immunization records.
example: '54'
homepage: https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx
mappings:
hl7: 2.16.840.1.113883.6.59
name: Vaccine administered code set
pattern: ^\d+$
preferred_prefix: cvx
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
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/dailymed:$1
uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1
dandi:
contact:
email: yoh@dartmouth.edu
github: null
name: Yaroslav Halchenko
orcid: 0000-0003-3456-2493
description: 'DANDI works with BICCN and other BRAIN Initiative awardees to curate
data using community data standards such as NWB and BIDS, and to make data and
software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable,
and Reusable).
DANDI references electrical and optical cellular neurophysiology recordings and
associated MRI and/or optical imaging data.
These data will help scientists uncover and understand cellular level mechanisms
of brain function. Scientists will study the formation of neural networks, how
cells and networks enable functions such as learning and memory, and how these
functions are disrupted in neurological disorders.'
example: '000017'
homepage: https://dandiarchive.org/
keywords:
- neurophysiology
mappings:
fairsharing: FAIRsharing.f2c119
miriam: dandi
re3data: r3d100013638
name: Distributed Archives for Neurophysiology Data Integration
pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$
preferred_prefix: dandi
repository: https://github.com/dandi/dandiarchive
twitter: dandiarchive
uri_format: https://dandiarchive.org/dandiset/$1
darc:
description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM
(electron microscopy) data and atomic coordinates of ribosomal particles from
the PDB, which are aligned within a common coordinate system. The aligned coordinate
system simplifies direct visualization of conformational changes in the ribosome,
such as subunit rotation and head-swiveling, as well as direct comparison of bound
ligands, such as antibiotics or translation factors.
example: '1250'
homepage: http://darcsite.genzentrum.lmu.de/darc/index.php
keywords:
- life science
mappings:
biocontext: DARC
fairsharing: FAIRsharing.evfe2s
miriam: darc
n2t: darc
name: Database of Aligned Ribosomal Complexes
pattern: ^\d+$
preferred_prefix: darc
publications:
- doi: 10.1093/nar/gkr824
pmc: PMC3245104
pubmed: '22009674'
title: 'The DARC site: a database of aligned ribosomal complexes.'
year: 2011
uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1
dashr:
contact:
email: dashr@lisanwanglab.org
github: null
name: Li-San Wang
orcid: 0000-0002-3684-0031
description: DASHR reports the annotation, expression and evidence for specific
RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor
and mature sncRNA products across different human tissues and cell types. DASHR
integrates information from multiple existing annotation resources for small non-coding
RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs),
nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs),
and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human
tissues and cell types and were generated for studying or profiling small non-coding
RNAs. This collection references RNA records.
example: hsa-mir-200a
homepage: http://lisanwanglab.org/DASHR/
keywords:
- life science
mappings:
biocontext: DASHR
fairsharing: FAIRsharing.ztvs34
miriam: dashr
n2t: dashr
name: Database of small human noncoding RNAs
pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$
preferred_prefix: dashr
publications:
- doi: 10.1093/nar/gkv1188
pmc: PMC4702848
pubmed: '26553799'
title: 'DASHR: database of small human noncoding RNAs.'
year: 2015
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
datacite:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology that enables the metadata properties of the DataCite Metadata
Schema Specification (i.e., a list of metadata properties for the accurate and
consistent identification of a resource for citation and retrieval purposes) to
be described in RDF.
download_owl: http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl
example: AgentIdentifierScheme
homepage: http://www.sparontologies.net/ontologies/datacite
keywords:
- ontology
- subject agnostic
mappings:
aberowl: DATACITE
bioportal: DATACITE
fairsharing: FAIRsharing.c06f1e
name: DataCite Ontology
preferred_prefix: DataCite
repository: https://github.com/sparontologies/datacite
twitter: datacite
uri_format: http://purl.org/spar/datacite/$1
datacommons:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A large RDF store built from American governmental data. This semantic
space has a mixture of direct terms and subspaces.
example: Gene
homepage: https://datacommons.org
mappings:
biolink: dcid
name: Data Commons
preferred_prefix: datacommons
repository: https://github.com/datacommonsorg/website
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://datacommons.org/browser/$1
datanator.gene:
description: Datanator is an integrated database of genomic and biochemical data
designed to help investigators find data about specific molecules and reactions
in specific organisms and specific environments for meta-analyses and mechanistic
models. Datanator currently includes metabolite concentrations, RNA modifications
and half-lives, protein abundances and modifications, and reaction kinetics integrated
from several databases and numerous publications. The Datanator website and REST
API provide tools for extracting clouds of data about specific molecules and reactions
in specific organisms and specific environments, as well as data about similar
molecules and reactions in taxonomically similar organisms.
example: K00973
homepage: https://datanator.info/
mappings:
miriam: datanator.gene
name: Datanator Gene
part_of: datanator
pattern: ^K[0-9]+$
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/$1
datf:
deprecated: true
description: DATF contains known and predicted Arabidopsis transcription factors
(1827 genes in 56 families) with the unique information of 1177 cloned sequences
and many other features including 3D structure templates, EST expression information,
transcription factor binding sites and nuclear location signals.
example: AT1G01030.1
homepage: http://datf.cbi.pku.edu.cn/
keywords:
- regulation
mappings:
biocontext: DATF
miriam: datf
n2t: datf
prefixcommons: datf
name: Database of Arabidopsis Transcription Factors
pattern: ^AT[1-5]G\d{5}(\.\d+)?$
preferred_prefix: datf
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/datf:$1
uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1
dbd:
description: The DBD (transcription factor database) provides genome-wide transcription
factor predictions for organisms across the tree of life. The prediction method
identifies sequence-specific DNA-binding transcription factors through homology
using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY.
It does not include basal transcription factors or chromatin-associated proteins.
example: '0045310'
homepage: http://www.transcriptionfactor.org/
keywords:
- genome
- regulation
mappings:
biocontext: DBD
edam: '2716'
miriam: dbd
n2t: dbd
prefixcommons: dbd
name: Transcription Factor Database
pattern: ^\d+$
preferred_prefix: dbd
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/dbd:$1
uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD
dbest:
description: The dbEST contains sequence data and other information on "single-pass"
cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
example: BP100000
homepage: https://www.ncbi.nlm.nih.gov/nucest
keywords:
- bioinformatics
- dna
- life science
mappings:
biocontext: DBEST
edam: '1105'
fairsharing: FAIRsharing.v9fya8
miriam: dbest
n2t: dbest
ncbi: dbEST
prefixcommons: dbest
re3data: r3d100010648
name: EST database maintained at the NCBI.
pattern: ^([A-Z]+)?\d+(\.\d+)?$
preferred_prefix: dbest
providers:
- 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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/dbest:$1
- 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
publications:
- doi: 10.1038/ng0893-332
pmc: null
pubmed: '8401577'
title: dbEST--database for "expressed sequence tags".
year: 1993
uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1
dbg2introns:
description: The Database for Bacterial Group II Introns provides a catalogue of
full-length, non-redundant group II introns present in bacterial DNA sequences
in GenBank.
example: Cu.me.I1
homepage: http://webapps2.ucalgary.ca/~groupii/
keywords:
- dna
mappings:
biocontext: DBG2INTRONS
miriam: dbg2introns
n2t: dbg2introns
prefixcommons: mgiid
name: DBG2 Introns
pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$
preferred_prefix: dbg2introns
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/mgiid:$1
publications:
- doi: 10.1093/nar/gkr1043
pmc: PMC3245105
pubmed: '22080509'
title: Database for bacterial group II introns.
year: 2011
uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1
dbgap:
description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes
the results of studies that have investigated the interaction of genotype and
phenotype.
example: phs000768.v2.p1
homepage: https://www.ncbi.nlm.nih.gov/projects/gap
keywords:
- biomedical science
- epigenetics
- genetics
mappings:
biocontext: DBGAP
cellosaurus: dbGAP
fairsharing: FAIRsharing.88v2k0
miriam: dbgap
n2t: dbgap
name: Database of Genotypes and Phenotypes
pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$
preferred_prefix: dbgap
publications:
- doi: 10.1093/nar/gkt1211
pmc: PMC3965052
pubmed: '24297256'
title: 'NCBI''s Database of Genotypes and Phenotypes: dbGaP.'
year: 2013
- doi: 10.1038/ng1007-1181
pmc: PMC2031016
pubmed: '17898773'
title: The NCBI dbGaP database of genotypes and phenotypes.
year: 2007
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
dbo:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: This ontology is generated from the manually created specifications
in the dbpedia mappings wiki. each release of this ontology corresponds to a new
release of the dbpedia data set which contains instance data extracted from the
different language versions of wikipedia. for information regarding changes in
this ontology, please refer to the dbpedia mappings wiki.
example: careerPrizeMoney
github_request_issue: 515
homepage: https://dbpedia.org/ontology
keywords:
- dbpedia
- ontology
name: DBPedia Ontology
preferred_prefix: dbo
uri_format: https://dbpedia.org/ontology/$1
dbprobe:
description: The NCBI Probe Database is a public registry of nucleic acid reagents
designed for use in a wide variety of biomedical research applications, together
with information on reagent distributors, probe effectiveness, and computed sequence
similarities.
example: '1000000'
homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe
keywords:
- nucleotide
mappings:
biocontext: DBPROBE
edam: '2719'
miriam: dbprobe
n2t: dbprobe
ncbi: dbProbe
prefixcommons: dbprobe
name: NCBI Probe database Public registry of nucleic acid reagents
pattern: ^\d+$
preferred_prefix: dbprobe
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/dbprobe:$1
uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1
dbsnp:
description: The dbSNP database is a repository for both single base nucleotide
subsitutions and short deletion and insertion polymorphisms.
example: rs121909098
homepage: https://www.ncbi.nlm.nih.gov/snp/
keywords:
- genome
- life science
mappings:
biocontext: dbSNP
cellosaurus: dbSNP
edam: '1106'
fairsharing: FAIRsharing.edxb58
go: dbSNP
hl7: 2.16.840.1.113883.6.284
miriam: dbsnp
n2t: dbsnp
ncbi: dbSNP
prefixcommons: dbsnp
re3data: r3d100010652
uniprot: DB-0013
wikidata: P6861
name: dbSNP Reference SNP number
pattern: ^rs\d+$
preferred_prefix: dbsnp
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/dbsnp:$1
- 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
publications:
- doi: 10.1093/nar/gkl1031
pmc: PMC1781113
pubmed: '17170002'
title: Database resources of the National Center for Biotechnology Information.
year: 2006
- doi: 10.1093/nar/29.1.308
pmc: PMC29783
pubmed: '11125122'
title: 'dbSNP: the NCBI database of genetic variation.'
year: 2001
repository: https://github.com/ncbi/dbsnp/tree/master/tutorials
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:
contact:
email: kdurante@stanford.edu
github: null
name: Kim Durante
orcid: 0000-0001-9052-2854
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: 'Metadata terms maintained by the Dublin Core Metadata Initiative,
including properties, vocabulary encoding schemes, syntax encoding schemes, and
classes.
**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported
indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`)
([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).'
download_owl: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf
example: contributor
homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
keywords:
- biomedical science
- life science
- ontology
- subject agnostic
mappings:
aberowl: dcelements
biocontext: dc
bioportal: DC
fairsharing: FAIRsharing.3nx7t
ols: dc
name: Dublin Core Elements (1.1)
preferred_prefix: dc
synonyms:
- dc.elements
- dc11
- dce
uri_format: http://purl.org/dc/elements/1.1/$1
dc_cl:
contact:
email: Lindsay.Cowell@utsouthwestern.edu
github: null
name: Lindsay Cowell
orcid: 0000-0003-1617-8244
deprecated: true
example: '0000003'
homepage: http://www.dukeontologygroup.org/Projects.html
keywords:
- obo
- ontology
mappings:
biocontext: DC_CL
obofoundry: dc_cl
name: Dendritic cell
pattern: ^\d{7}$
preferred_prefix: DC_CL
rdf_uri_format: http://purl.obolibrary.org/obo/DC_CL_$1
uri_format: http://purl.obolibrary.org/obo/DC_CL_$1
dcat:
contact:
email: kdurante@stanford.edu
github: null
name: Kim Durante
orcid: 0000-0001-9052-2854
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: DCAT is an RDF vocabulary designed to facilitate interoperability between
data catalogs published on the Web
download_owl: http://aber-owl.net/media/ontologies/DCAT/2/dcat.owl
example: Dataset
homepage: https://www.w3.org/ns/dcat
keywords:
- data management
- ontology
- subject agnostic
mappings:
aberowl: DCAT
biocontext: dcat
biolink: dcat
bioportal: DCAT
fairsharing: FAIRsharing.h4j3qm
name: Data Catalog
preferred_prefix: dcat
repository: https://github.com/w3c/dxwg/
uri_format: http://www.w3.org/ns/dcat#$1
dcterms:
contact:
email: futo@stanford.edu
github: null
name: Michelle Futornick
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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.
download_owl: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf
example: title
homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
keywords:
- ontology
- subject agnostic
mappings:
aberowl: dcterms
biocontext: dcterms
biolink: dct
bioportal: DCTERMS
fairsharing: FAIRsharing.9vtwjs
ols: dcterms
name: Dublin Core Metadata Initiative Terms
preferred_prefix: dcterms
synonyms:
- dc.terms
- dct
uri_format: http://purl.org/dc/terms/$1
dctypes:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/$1
ddanat:
contact:
email: pfey@northwestern.edu
github: pfey03
name: Petra Fey
orcid: 0000-0002-4532-2703
description: A structured controlled vocabulary of the anatomy of the slime-mold
Dictyostelium discoideum
download_obo: http://purl.obolibrary.org/obo/ddanat.obo
download_owl: http://purl.obolibrary.org/obo/ddanat.owl
example: '0000006'
homepage: http://dictybase.org/
keywords:
- anatomy
- life science
- obo
- ontology
- slime-mould
license: CC0-1.0
mappings:
aberowl: DDANAT
biocontext: DDANAT
bioportal: DDANAT
fairsharing: FAIRsharing.z656ab
go: DDANAT
obofoundry: ddanat
ols: ddanat
ontobee: DDANAT
prefixcommons: ddanat
name: Dictyostelium discoideum anatomy
pattern: ^\d{7}$
preferred_prefix: DDANAT
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ddanat:$1
publications:
- doi: 10.1186/1471-2164-9-130
pmc: PMC2323390
pubmed: '18366659'
title: An anatomy ontology to represent biological knowledge in Dictyostelium
discoideum.
year: 2008
rdf_uri_format: http://purl.obolibrary.org/obo/DDANAT_$1
repository: https://github.com/dictyBase/migration-data
twitter: dictybase
uri_format: http://purl.obolibrary.org/obo/DDANAT_$1
version: '2020-04-13'
ddinter.drug:
contact:
email: oriental-cds@163.com
github: null
name: Dongsheng Cao
orcid: 0000-0003-3604-3785
contributor:
email: null
github: sierra-moxon
name: Sierra Moxon
orcid: 0000-0002-8719-7760
description: Ddinter is a comprehensive, professional, and open-access database
specific to drug-drug interactions. it provides abundant annotations for each
ddi association including mechanism description, risk levels, management strategies,
alternative medications, etc. to improve clinical decision-making and patient
safety.
example: DDInter20
github_request_issue: 492
homepage: http://ddinter.scbdd.com
keywords:
- chemistry
- drugs
- relationships
license: CC-BY-NC-SA-4.0
name: Curated Drug-Drug Interactions Database - Drug
pattern: ^DDInter\d+$
preferred_prefix: ddinter.drug
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://ddinter.scbdd.com/ddinter/drug-detail/$1
ddinter.interaction:
contact:
email: oriental-cds@163.com
github: null
name: Dongsheng Cao
orcid: 0000-0003-3604-3785
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Ddinter is a comprehensive, professional, and open-access database
specific to drug-drug interactions. it provides abundant annotations for each
ddi association including mechanism description, risk levels, management strategies,
alternative medications, etc. to improve clinical decision-making and patient
safety.
example: '1122888'
github_request_issue: 492
homepage: http://ddinter.scbdd.com
keywords:
- chemistry
- drug-drug interactions
- drugs
- relationships
license: CC-BY-NC-SA-4.0
name: Curated Drug-Drug Interactions Database - Interaction
pattern: ^\d+$
preferred_prefix: ddinter.interaction
uri_format: http://ddinter.scbdd.com/ddinter/interact/$1
ddpheno:
contact:
email: pfey@northwestern.edu
github: pfey03
name: Petra Fey
orcid: 0000-0002-4532-2703
description: A structured controlled vocabulary of phenotypes of the slime-mould
Dictyostelium discoideum.
download_json: http://purl.obolibrary.org/obo/ddpheno.json
download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo
download_owl: http://purl.obolibrary.org/obo/ddpheno.owl
example: '0001417'
homepage: http://dictybase.org/
keywords:
- life science
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: DDPHENO
biocontext: DDPHENO
bioportal: DDPHENO
fairsharing: FAIRsharing.9c1p18
obofoundry: ddpheno
ols: ddpheno
ontobee: DDPHENO
name: Dictyostelium discoideum phenotype ontology
pattern: ^\d{7}$
preferred_prefix: DDPHENO
publications:
- doi: 10.1387/ijdb.190226pf
pmc: PMC7409682
pubmed: '31840793'
title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report.
year: 2019
- doi: 10.1007/978-1-62703-302-2_4
pmc: PMC3762881
pubmed: '23494302'
title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock
Center in 2012.'
year: 2013
rdf_uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1
repository: https://github.com/obophenotype/dicty-phenotype-ontology
twitter: dictybase
uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1
version: '2023-02-19'
debio:
contact:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A repository for the TSV-based, decentralized, community-curated curation
of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph
JSON.
download_json: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.json
download_obo: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.obo
download_owl: https://raw.githubusercontent.com/biopragmatics/debio/main/releases/current/debio.owl
example: '0000001'
homepage: https://biopragmatics.github.io/debio
keywords:
- ontology
name: Decentralized Biomedical Ontology
pattern: ^\d{7}$
preferred_prefix: DeBiO
providers:
- code: obo2
description: Because it's not possible to configure the base URI with ROBOT/OWLAPI,
this pops out
homepage: http://purl.obolibrary.org
name: Placeholder OBO PURL
uri_format: http://purl.obolibrary.org/obo/debio_$1
uri_format: https://biopragmatics.github.io/debio/$1
decipher:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: CNV syndromes in the DECIPHER genomics database that are linked to
Human Phenotype Ontology terms
example: '1'
homepage: https://www.deciphergenomics.org/
keywords:
- biomedical science
- life science
mappings:
biocontext: DECIPHER
fairsharing: FAIRsharing.l8Sf5x
name: DECIPHER CNV Syndromes
pattern: ^\d+$
preferred_prefix: decipher
publications:
- doi: 10.1093/nar/gkt937
pmc: PMC3965078
pubmed: '24150940'
title: 'DECIPHER: database for the interpretation of phenotype-linked plausibly
pathogenic sequence and copy-number variation.'
year: 2013
- doi: 10.1016/j.ajhg.2009.03.010
pmc: PMC2667985
pubmed: '19344873'
title: 'DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using
Ensembl Resources.'
year: 2009
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
deo:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology that provides a structured vocabulary for rhetorical elements
within documents (e.g., Introduction, Discussion, Acknowledgements, Reference
List, Figures, Appendix). It is imported by DoCO.
example: Reference
homepage: http://www.sparontologies.net/ontologies/deo
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.39fd58
name: Discourse Elements Ontology
preferred_prefix: DEO
publications:
- doi: 10.3233/sw-150177
pmc: null
pubmed: null
title: The Document Components Ontology (DoCO)
year: 2016
repository: https://github.com/sparontologies/deo
twitter: sparontologies
uri_format: http://purl.org/spar/deo/$1
depmap:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE
Cells.
example: ACH-000001
homepage: https://depmap.org/portal
mappings:
cellosaurus: DepMap
name: DepMap Cell Lines
pattern: ^ACH-\d+$
preferred_prefix: depmap
uri_format: https://depmap.org/portal/cell_line/$1
depod:
contact:
email: depod@embl.de
github: null
name: General Enquiries
orcid: 0000-0003-3562-7869
description: The human DEPhOsphorylation Database (DEPOD) contains information on
known human active phosphatases and their experimentally verified protein and
nonprotein substrates. Reliability scores are provided for dephosphorylation interactions,
according to the type of assay used, as well as the number of laboratories that
have confirmed such interaction. Phosphatase and substrate entries are listed
along with the dephosphorylation site, bioassay type, and original literature,
and contain links to other resources.
example: PTPN1
homepage: http://www.depod.bioss.uni-freiburg.de
keywords:
- life science
mappings:
biocontext: DEPOD
fairsharing: FAIRsharing.q9j2e3
miriam: depod
n2t: depod
re3data: r3d100011936
uniprot: DB-0190
name: Human Dephosphorylation Database
pattern: ^[A-Z0-9]+$
preferred_prefix: depod
provides: hgnc.symbol
publications:
- doi: doi
pmc: PMC6911163
pubmed: '31836896'
title: null
year: null
- doi: 10.1093/database/baz133
pmc: PMC6911163
pubmed: '31836896'
title: 'The human DEPhOsphorylation Database DEPOD: 2019 update.'
year: 2019
- doi: 10.1093/nar/gku1009
pmc: PMC4383878
pubmed: '25332398'
title: 'The human DEPhOsphorylation database DEPOD: a 2015 update.'
year: 2014
- doi: 10.1126/scisignal.2003203
pmc: null
pubmed: '23674824'
title: Elucidating human phosphatase-substrate networks.
year: 2013
uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1
dermo:
contact:
email: pns12@hermes.cam.ac.uk
github: PaulNSchofield
name: Paul Schofield
orcid: 0000-0002-5111-7263
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: DermO is an ontology with broad coverage of the domain of dermatologic
disease and we demonstrate here its utility for text mining and investigation
of phenotypic relationships between dermatologic disorders
download_obo: http://aber-owl.net/media/ontologies/DERMO/10/dermo.obo
example: '0000000'
homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x
keywords:
- dermatology
- ontology
mappings:
aberowl: DERMO
bioportal: DERMO
fairsharing: FAIRsharing.k008w7
name: Human Dermatological Disease Ontology
pattern: ^\d{7}$
preferred_prefix: dermo
publications:
- doi: 10.1186/s13326-016-0085-x
pmc: PMC4907256
pubmed: '27296450'
title: DermO; an ontology for the description of dermatologic disease.
year: 2016
uri_format: http://purl.obolibrary.org/obo/DERMO_$1
dev.ga4ghdos:
description: Assists in resolving data across cloud resources.
example: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00
homepage: http://github.com/ga4gh/data-object-service-schemas
mappings:
biocontext: DEV.GA4GHDOS
miriam: dev.ga4ghdos
n2t: dev.ga4ghdos
name: Development Data Object Service
pattern: ^[a-zA-Z0-9\-:#\.]+$
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=$1
dhba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
developing human brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo
example: '10153'
homepage: https://www.brainspan.org/
keywords:
- ontology
name: Developing Human Brain Atlas
pattern: ^\d+$
preferred_prefix: DHBA
uri_format: https://biopragmatics.github.io/providers/dhba/$1
dicom:
contact:
email: dclunie@dclunie.com
github: null
name: David Clunie
orcid: 0000-0002-2406-1145
description: DICOM Controlled Terminology
download_owl: ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl
example: '109082'
homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html
keywords:
- anatomy
- biomedical science
- medicine
- ontology
mappings:
bioportal: DCM
fairsharing: FAIRsharing.b7z8by
hl7: 1.2.840.10008.2.16.4
ols: dicom
name: DICOM Controlled Terminology
pattern: ^\d+$
preferred_prefix: dicom
publications:
- doi: 10.1007/s10278-013-9577-8
pmc: PMC3705029
pubmed: '23404629'
title: 'Multi-series DICOM: an extension of DICOM that stores a whole study in
a single object.'
year: 2013
- doi: 10.1016/j.crad.2005.07.003
pmc: null
pubmed: '16223609'
title: 'DICOM demystified: a review of digital file formats and their use in radiological
practice.'
year: 2005
uri_format: http://dicom.nema.org/resources/ontology/DCM/$1
version: 2023b_20230403
dictybase:
description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics
example: DDB0191090
homepage: http://dictybase.org
keywords:
- anatomy
- comparative genomics
- genome
- life science
mappings:
biocontext: dictyBase
fairsharing: FAIRsharing.4shj9c
go: dictyBase
ncbi: dictyBase
prefixcommons: dictybase
re3data: r3d100010586
uniprot: DB-0015
name: dictyBase
preferred_prefix: dictybase
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/dictybase:$1
publications:
- doi: 10.1007/978-1-62703-302-2_4
pmc: PMC3762881
pubmed: '23494302'
title: 'One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock
Center in 2012.'
year: 2013
- doi: 10.1093/nar/gks1064
pmc: PMC3531180
pubmed: '23172289'
title: 'DictyBase 2013: integrating multiple Dictyostelid species.'
year: 2012
- doi: 10.1093/nar/gkh138
pmc: PMC308872
pubmed: '14681427'
title: 'dictyBase: a new Dictyostelium discoideum genome database.'
year: 2004
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:$1
dideo:
contact:
email: mbrochhausen@gmail.com
github: mbrochhausen
name: Mathias Brochhausen
orcid: 0000-0003-1834-3856
description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction
Evidence Ontology
download_owl: http://purl.obolibrary.org/obo/dideo.owl
example: 00000180
homepage: https://github.com/DIDEO/DIDEO
keywords:
- biochemistry
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: DIDEO
biocontext: DIDEO
bioportal: DIDEO
fairsharing: FAIRsharing.9y8f0n
obofoundry: dideo
ols: dideo
ontobee: DIDEO
name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
pattern: ^\d{8}$
preferred_prefix: DIDEO
publications:
- doi: 10.1186/s13326-018-0183-z
pmc: PMC5944177
pubmed: '29743102'
title: Extending the DIDEO ontology to include entities from the natural product
drug interaction domain of discourse.
year: 2018
- doi: null
pmc: PMC5765984
pubmed: '29295242'
title: Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies
to Improve Evidence Base Curation.
year: 2017
- doi: 10.1016/j.knosys.2016.10.006
pmc: null
pubmed: null
title: 'Conceptual models of drug-drug interactions: A summary of recent efforts'
year: 2016
rdf_uri_format: http://purl.obolibrary.org/obo/DIDEO_$1
repository: https://github.com/DIDEO/DIDEO
uri_format: http://purl.obolibrary.org/obo/DIDEO_$1
version: '2022-06-14'
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
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: DINTO
biocontext: DINTO
bioportal: DINTO
obofoundry: dinto
ontobee: DINTO
name: The Drug-Drug Interactions Ontology
preferred_prefix: DINTO
publications:
- doi: 10.1021/acs.jcim.5b00119
pmc: null
pubmed: '26147071'
title: 'DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions
and Their Mechanisms.'
year: 2015
rdf_uri_format: http://purl.obolibrary.org/obo/DINTO_$1
repository: https://github.com/labda/DINTO
uri_format: http://purl.obolibrary.org/obo/DINTO_$1
dip:
description: The database of interacting protein (DIP) database stores experimentally
determined interactions between proteins. It combines information from a variety
of sources to create a single, consistent set of protein-protein interactions
example: DIP-743N
homepage: https://dip.doe-mbi.ucla.edu/
keywords:
- biology
- interaction
- protein
mappings:
biocontext: DIP
edam: '2616'
fairsharing: FAIRsharing.qje0v8
miriam: dip
n2t: dip
prefixcommons: dip
re3data: r3d100010670
uniprot: DB-0016
name: Database of Interacting Proteins
pattern: ^DIP(\:)?\-\d{1,}[ENXS]$
preferred_prefix: dip
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/dip:$1
publications:
- doi: 10.1093/nar/gkh086
pmc: PMC308820
pubmed: '14681454'
title: 'The Database of Interacting Proteins: 2004 update.'
year: 2004
- doi: 10.1093/nar/30.1.303
pmc: PMC99070
pubmed: '11752321'
title: 'DIP, the Database of Interacting Proteins: a research tool for studying
cellular networks of protein interactions.'
year: 2002
- doi: 10.1093/nar/29.1.239
pmc: PMC29798
pubmed: '11125102'
title: 'DIP: The Database of Interacting Proteins: 2001 update.'
year: 2001
- doi: 10.1093/nar/28.1.289
pmc: PMC102387
pubmed: '10592249'
title: 'DIP: the database of interacting proteins.'
year: 2000
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=$1&searchmode=exact
disdriv:
contact:
email: lynn.schriml@gmail.com
github: lschriml
name: Lynn Schriml
orcid: 0000-0001-8910-9851
description: Drivers of human diseases including environmental, maternal and social
exposures.
download_owl: http://purl.obolibrary.org/obo/disdriv.owl
example: '0000000'
homepage: http://www.disease-ontology.org
keywords:
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: DISDRIV
bioportal: DISDRIV
obofoundry: disdriv
ols: disdriv
ontobee: DISDRIV
name: Disease Drivers Ontology
pattern: ^\d+$
preferred_prefix: DISDRIV
rdf_uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1
repository: https://github.com/DiseaseOntology/DiseaseDriversOntology
twitter: diseaseontology
uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1
diseaseclass:
appears_in:
- efo
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: Legacy disease classes that later became MONDO
download_obo: https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo
example: 0000598
keywords:
- ontology
name: Disease Class
pattern: ^\d{7}$
preferred_prefix: diseaseclass
uri_format: https://biopragmatics.github.io/providers/diseaseclass/$1
diseasesdb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The Diseases Database is a cross-referenced index of human disease,
medications, symptoms, signs, abnormal investigation findings etc. This site provides
a medical textbook-like index and search portal covering areas including: internal
medical disorders, symptoms and signs, congenital and inherited disorders, infectious
diseases and organisms, drugs and medications, common haematology and biochemistry
investigation abnormalities.'
example: '1784'
homepage: http://www.diseasesdatabase.com/
mappings:
wikidata: P557
name: Diseases Database
pattern: ^\d+$
preferred_prefix: diseasesdb
uri_format: https://www.diseasesdatabase.com/ddb$1.htm
disprot:
contact:
email: silvio.tosatto@unipd.it
github: null
name: Silvio C.E. Tosatto
orcid: 0000-0003-4525-7793
description: DisProt is a database of intrinsically disordered proteins and protein
disordered regions, manually curated from literature.
example: DP00003
homepage: https://disprot.org/
keywords:
- biology
- biomedical science
- protein
- structural biology
- structure
mappings:
biocontext: DISPROT
edam: '2723'
fairsharing: FAIRsharing.dt9z89
go: DisProt
miriam: disprot
n2t: disprot
prefixcommons: disprot
re3data: r3d100010561
uniprot: DB-0017
name: DisProt
pattern: ^DP\d{5}$
preferred_prefix: disprot
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/disprot:$1
publications:
- doi: 10.1093/nar/gkab1082
pmc: PMC8728214
pubmed: '34850135'
title: 'DisProt in 2022: improved quality and accessibility of protein intrinsic
disorder annotation.'
year: 2022
- doi: 10.1093/nar/gkz975
pmc: PMC7145575
pubmed: '31713636'
title: 'DisProt: intrinsic protein disorder annotation in 2020.'
year: 2020
- doi: 10.1093/nar/gkw1056
pmc: PMC5210544
pubmed: '27899601'
title: 'DisProt 7.0: a major update of the database of disordered proteins.'
year: 2016
- doi: 10.1093/nar/gkl893
pmc: PMC1751543
pubmed: '17145717'
title: 'DisProt: the Database of Disordered Proteins.'
year: 2006
- doi: 10.1093/bioinformatics/bth476
pmc: null
pubmed: '15310560'
title: 'DisProt: a database of protein disorder.'
year: 2004
repository: https://disprot.github.io/
twitter: disprot_db
uri_format: https://disprot.org/$1
disprot.region:
description: DisProt is a database of intrisically disordered proteins and protein
disordered regions, manually curated from literature.
example: DP00086r013
homepage: https://www.disprot.org
mappings:
miriam: disprot.region
name: DisProt region
part_of: disprot
pattern: ^DP\d{5}r\d{3}$
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/$1
dmba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
developing mouse brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo
example: '15567'
homepage: https://developingmouse.brain-map.org/
keywords:
- ontology
name: Developing Mouse Brain Atlas
pattern: ^\d+$
preferred_prefix: DMBA
uri_format: https://biopragmatics.github.io/providers/dmba/$1
doap:
contact:
email: edd@usefulinc.com
github: ewilderj
name: Edd Wilder-James
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: DOAP is a project to create an XML/RDF vocabulary to describe software
projects, and in particular open source projects.
download_rdf: http://usefulinc.com/ns/doap
example: Project
homepage: https://github.com/ewilderj/doap/wiki
keywords:
- metadata
- rdf
- semantic web
name: Description of a Project
preferred_prefix: doap
references:
- https://en.wikipedia.org/wiki/DOAP
repository: https://github.com/ewilderj/doap
uri_format: http://usefulinc.com/ns/doap#$1
doco:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology that provides a structured vocabulary written of document
components, both structural (e.g., block, inline, paragraph, section, chapter)
and rhetorical (e.g., introduction, discussion, acknowledgements, reference list,
figure, appendix).
example: Paragraph
homepage: http://www.sparontologies.net/ontologies/doco
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.162003
name: Document Components Ontology
preferred_prefix: DoCO
publications:
- doi: 10.3233/sw-150177
pmc: null
pubmed: null
title: The Document Components Ontology (DoCO)
year: 2016
repository: https://github.com/sparontologies/doco
twitter: sparontologies
uri_format: http://purl.org/spar/doco/$1
doi:
banana: doi
comment: 'The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html)
specifies that `https://doi.org/DOI` is the preferred format:
> Users may resolve DOI names that are structured to use the DOI system Proxy
Server (https://doi.org (preferred)). The resolution of the DOI name in this case
depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would
be resolved from the address: "https://doi.org/10.123/456". Any standard browser
encountering a DOI name in this form will be able to resolve it. The proxy service
(both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible
over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**)
as well as HTTP requests.'
contributor_extras:
- email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
- email: null
github: dhimmel
name: Daniel Himmelstein
orcid: 0000-0002-3012-7446
description: The Digital Object Identifier System is for identifying content objects
in the digital environment.
example: 10.1038/s41597-022-01807-3
example_extras:
- 10.21/FQSQT4T3
- 10.1333/s00897980202a
- 10.1139/z02-135
- 10.1016/j.foodchem.2008.11.065
- 10.1093/acprof:oso/9780195159561.001.1
homepage: https://www.doi.org/
keywords:
- bibliography
- knowledge and information systems
mappings:
biocontext: DOI
biolink: doi
cellosaurus: DOI
edam: '1188'
fairsharing: FAIRsharing.hFLKCn
go: DOI
miriam: doi
n2t: doi
prefixcommons: doi
wikidata: P356
name: Digital Object Identifier
pattern: ^10.\d{2,9}/.*$
preferred_prefix: doi
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/doi:$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: 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: miriam_legacy
description: A legacy MIRIAM URI that does not follow the standard pattern
homepage: https://identifiers.org
name: Legacy MIRIAM URI
uri_format: http://identifiers.org/DOI/$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
rdf_uri_format: http://dx.doi.org/$1
references:
- https://github.com/biopragmatics/bioregistry/issues/287
- https://github.com/biopragmatics/bioregistry/pull/316
uri_format: https://doi.org/$1
doid:
appears_in:
- clo
- scdo
banana: DOID
contact:
email: lynn.schriml@gmail.com
github: lschriml
name: Lynn Schriml
orcid: 0000-0001-8910-9851
description: The Disease Ontology has been developed as a standardized ontology
for human disease with the purpose of providing the biomedical community with
consistent, reusable and sustainable descriptions of human disease terms, phenotype
characteristics and related medical vocabulary disease concepts.
download_json: http://purl.obolibrary.org/obo/doid.json
download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo
download_owl: http://purl.obolibrary.org/obo/doid.owl
example: 0110974
homepage: http://www.disease-ontology.org
keywords:
- biomedical science
- disease
- human
- life science
- obo
- ontology
license: CC0-1.0
logo: http://www.disease-ontology.org/media/images/DO_logo.jpg
mappings:
aberowl: DOID
bartoc: '576'
biocontext: DOID
bioportal: DOID
fairsharing: FAIRsharing.8b6wfq
miriam: doid
n2t: doid
obofoundry: doid
ols: doid
ontobee: DOID
prefixcommons: do
wikidata: P699
name: Human Disease Ontology
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: DOID
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/do:$1
- 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
- code: purl
description: Legacy PURLs found in OAE
homepage: http://purl.org/obo/owl/
name: Legacy PURL
uri_format: http://purl.org/obo/owl/DOID#DOID_$1
publications:
- doi: 10.1093/nar/gkab1063
pmc: PMC8728220
pubmed: '34755882'
title: The Human Disease Ontology 2022 update.
year: 2022
- doi: 10.1093/bib/bbab191
pmc: PMC8195003
pubmed: '34015823'
title: COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker
data model.
year: 2021
- doi: 10.7554/elife.52614
pmc: PMC7077981
pubmed: '32180547'
title: Wikidata as a knowledge graph for the life sciences.
year: 2020
- doi: 10.1093/nar/gky1036
pmc: PMC6323956
pubmed: '30407590'
title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
information.'
year: 2019
- doi: 10.1093/nar/gky1032
pmc: PMC6323977
pubmed: '30407550'
title: 'Human Disease Ontology 2018 update: classification, content and workflow
expansion.'
year: 2019
- doi: 10.1242/dmm.032839
pmc: PMC5897730
pubmed: '29590633'
title: 'Disease Ontology: improving and unifying disease annotations across species.'
year: 2018
- doi: 10.1093/database/baw015
pmc: PMC4795929
pubmed: '26989148'
title: Wikidata as a semantic framework for the Gene Wiki initiative.
year: 2016
- doi: 10.1016/j.ajhg.2015.05.020
pmc: PMC4572507
pubmed: '26119816'
title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
Disease.'
year: 2015
- doi: 10.1007/s00335-015-9576-9
pmc: PMC4602048
pubmed: '26093607'
title: 'The Disease Ontology: fostering interoperability between biological and
clinical human disease-related data.'
year: 2015
- doi: 10.1093/database/bav032
pmc: PMC4385274
pubmed: '25841438'
title: Generating a focused view of disease ontology cancer terms for pan-cancer
data integration and analysis.
year: 2015
- doi: 10.1093/nar/gku1011
pmc: PMC4383880
pubmed: '25348409'
title: 'Disease Ontology 2015 update: an expanded and updated database of human
diseases for linking biomedical knowledge through disease data.'
year: 2014
- doi: 10.1093/nar/gkr972
pmc: PMC3245088
pubmed: '22080554'
title: 'Disease Ontology: a backbone for disease semantic integration.'
year: 2011
- doi: 10.1186/1471-2164-10-s1-s6
pmc: PMC2709267
pubmed: '19594883'
title: Annotating the human genome with Disease Ontology.
year: 2009
- doi: 10.1093/bioinformatics/btp193
pmc: PMC2687947
pubmed: '19478018'
title: 'From disease ontology to disease-ontology lite: statistical methods to
adapt a general-purpose ontology for the test of gene-ontology associations.'
year: 2009
rdf_uri_format: http://purl.obolibrary.org/obo/DOID_$1
repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
synonyms:
- do
twitter: diseaseontology
uri_format: https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1
version: '2023-03-31'
dolce:
comment: This resource doesn't exist anymore
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
description: DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering)
is a foundational ontology developed as part of the WonderWeb Foundational Ontologies
Library (WFOL). The development of this library has been guided by the need of
a reliable set of foundational ontologies that can serve as 1) astarting point
for building other ontologies, 2) a reference point for easy and rigorous comparisons
among different ontological approaches, and 3) a rigorous basis for analyzing,
harmonizing and integrating existing ontologies and metadata standards (by manually
mapping them into some general module(s) in the library). DOLCE is the first module
of WFOL and it is not a candidate for a universal standard ontology. Rather, it
is intended as a starting point for comparing and elucidating the relationships
with the other modules of the library, and also for clarifying the hidden assumptions
underlying existing ontologies or linguistic resources such as WordNet. As reflected
by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at
capturing the ontological categories underlying natural language and human commonsense.
DOLCE is an ontology that focuses on particulars in the sense that its domain
of discourse is restricted to them. The project is complete, though the ontology
remains available for use.
homepage: http://www.loa.istc.cnr.it/dolce/overview.html
keywords:
- computer science
- knowledge and information systems
- linguistics
- subject agnostic
mappings:
fairsharing: FAIRsharing.ae8hpt
name: Descriptive Ontology for Linguistic and Cognitive Engineering
preferred_prefix: dolce
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/$1
door:
description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted
operons of all the sequenced prokaryotic genomes. It includes operons for RNA
genes.
example: '1398574'
homepage: http://csbl.bmb.uga.edu/DOOR/operon.php
keywords:
- dna
mappings:
biocontext: DOOR
miriam: door
n2t: door
prefixcommons: door
re3data: r3d100014113
name: Database for Prokaryotic Operons
pattern: ^\d+$
preferred_prefix: door
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/door:$1
uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1
doqcs.model:
description: The Database of Quantitative Cellular Signaling is a repository of
models of signaling pathways. It includes reaction schemes, concentrations, rate
constants, as well as annotations on the models. The database provides a range
of search, navigation, and comparison functions. This datatype provides access
to specific models.
example: '57'
homepage: http://doqcs.ncbs.res.in/
keywords:
- model
mappings:
biocontext: DOQCS.MODEL
miriam: doqcs.model
n2t: doqcs.model
prefixcommons: doqcs.model
name: 'Database of Quantitative Cellular Signaling: Model'
part_of: doqcs
pattern: ^\d+$
preferred_prefix: doqcs.model
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/doqcs.model:$1
publications:
- doi: 10.1093/bioinformatics/btf860
pmc: null
pubmed: '12584128'
title: 'The Database of Quantitative Cellular Signaling: management and analysis
of chemical kinetic models of signaling networks.'
year: 2003
uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1
doqcs.pathway:
description: The Database of Quantitative Cellular Signaling is a repository of
models of signaling pathways. It includes reaction schemes, concentrations, rate
constants, as well as annotations on the models. The database provides a range
of search, navigation, and comparison functions. This datatype provides access
to pathways.
example: '131'
homepage: http://doqcs.ncbs.res.in/
keywords:
- pathway
mappings:
biocontext: DOQCS.PATHWAY
miriam: doqcs.pathway
n2t: doqcs.pathway
prefixcommons: doqcs.pathway
name: 'Database of Quantitative Cellular Signaling: Pathway'
part_of: doqcs
pattern: ^\d+$
preferred_prefix: doqcs.pathway
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/doqcs.pathway:$1
publications:
- doi: 10.1093/bioinformatics/btf860
pmc: null
pubmed: '12584128'
title: 'The Database of Quantitative Cellular Signaling: management and analysis
of chemical kinetic models of signaling networks.'
year: 2003
uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1
dpo:
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
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: DPO
bioportal: DPO
obofoundry: dpo
ols: dpo
ontobee: DPO
name: Drosophila Phenotype Ontology
no_own_terms: true
part_of: fbcv
preferred_prefix: DPO
publications:
- doi: 10.1186/2041-1480-4-30
pmc: PMC3816596
pubmed: '24138933'
title: The Drosophila phenotype ontology.
year: 2013
rdf_uri_format: http://purl.obolibrary.org/obo/FBcv_$1
repository: https://github.com/FlyBase/drosophila-phenotype-ontology
uri_format: http://purl.obolibrary.org/obo/FBcv_$1
version: '2023-02-09'
dpv:
description: Description of Plant Viruses (DPV) provides information about viruses,
viroids and satellites of plants, fungi and protozoa. It provides taxonomic information,
including brief descriptions of each family and genus, and classified lists of
virus sequences. The database also holds detailed information for all sequences
of viruses, viroids and satellites of plants, fungi and protozoa that are complete
or that contain at least one complete gene.
example: '100'
homepage: http://www.dpvweb.net/
keywords:
- classification
- gene
mappings:
biocontext: DPV
miriam: dpv
n2t: dpv
prefixcommons: dpvweb
name: Description of Plant Viruses
pattern: ^\d+$
preferred_prefix: dpv
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/dpvweb:$1
publications:
- doi: 10.1093/nar/gkj023
pmc: PMC1347386
pubmed: '16381892'
title: 'DPVweb: a comprehensive database of plant and fungal virus genes and genomes.'
year: 2006
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
drduke:
description: identifier for chemicals linked to information on occurrence in plants
example: '19'
homepage: https://phytochem.nal.usda.gov/phytochem/search/list
mappings:
wikidata: P10074
name: Dr. Duke's Phytochemical and Ethnobotanical Databases chemical
preferred_prefix: drduke
uri_format: https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1
drks:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The German Clinical Trials Register (DRKS) is the German WHO primary
registry. It is competent for the registration of all patient-oriented clinical
trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently,
around 2,000 studies are added annually. (from website)
example: DRKS00031815
homepage: http://drks.de
name: German Clinical Trials Register
pattern: ^DRKS\d+$
preferred_prefix: drks
providers:
- code: alt1
description: German Language Provider
homepage: http://drks.de
name: German Language Provider
uri_format: https://drks.de/search/de/trial/$1
- code: alt2
description: Legacy Provider
homepage: http://drks.de
name: Legacy Provider
uri_format: http://drks.de/en/trial/$1
uri_format: https://drks.de/search/en/trial/$1
dron:
appears_in:
- scdo
contact:
email: hoganwr@gmail.com
github: hoganwr
name: William Hogan
orcid: 0000-0002-9881-1017
description: We built this ontology primarily to support comparative effectiveness
researchers studying claims data. They need to be able to query U.S. National
Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade),
physiological effect (diuresis), and therapeutic intent (anti-hypertensive).
download_json: http://purl.obolibrary.org/obo/dron.json
download_obo: http://purl.obolibrary.org/obo/dron.obo
download_owl: http://purl.obolibrary.org/obo/dron.owl
example: '00023232'
homepage: https://github.com/ufbmi/dron
keywords:
- biomedical science
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: DRON
biocontext: DRON
bioportal: DRON
fairsharing: FAIRsharing.w5ntfd
obofoundry: dron
ols: dron
ontobee: DRON
name: The Drug Ontology
pattern: ^\d{8}$
preferred_prefix: DRON
publications:
- doi: 10.1186/s13326-017-0121-5
pmc: PMC5335794
pubmed: '28253937'
title: 'Therapeutic indications and other use-case-driven updates in the drug
ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large
term request.'
year: 2017
- doi: 10.1186/s13326-016-0048-2
pmc: PMC4836073
pubmed: '27096073'
title: An accurate and precise representation of drug ingredients.
year: 2016
- doi: 10.1186/2041-1480-4-44
pmc: PMC3931349
pubmed: '24345026'
title: Building a drug ontology based on RxNorm and other sources.
year: 2013
rdf_uri_format: http://purl.obolibrary.org/obo/DRON_$1
repository: https://github.com/ufbmi/dron
uri_format: http://purl.obolibrary.org/obo/DRON_$1
version: '2023-03-10'
drsc:
description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of
reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen
results. It maintains a list of Drosophila gene names, identifiers, symbols and
synonyms and provides information for cell-based or in vivo RNAi reagents, other
types of reagents, screen results, etc. corresponding for a given gene.
example: DRSC05221
homepage: http://flyrnai.org/
mappings:
biocontext: DRSC
miriam: drsc
n2t: drsc
name: Drosophila RNAi Screening Center
pattern: ^DRSC\d+$
preferred_prefix: drsc
uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1
drugbank:
contact:
email: david.wishart@ualberta.ca
github: null
name: David Wishart
orcid: 0000-0002-3207-2434
description: The DrugBank database is a bioinformatics and chemoinformatics resource
that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical)
data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
This collection references drug information.
example: DB14938
homepage: http://www.drugbank.ca
keywords:
- biomedical science
- drug
- life science
- protein
mappings:
bartoc: '18377'
biocontext: DrugBank
cellosaurus: DrugBank
cheminf: '000406'
edam: '2326'
fairsharing: FAIRsharing.353yat
miriam: drugbank
n2t: drugbank
prefixcommons: drugbank
re3data: r3d100010544
uniprot: DB-0019
wikidata: P715
name: DrugBank
pattern: ^DB\d{5}$
preferred_prefix: drugbank
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/drugbank:$1
publications:
- doi: 10.1093/nar/gkt1068
pmc: PMC3965102
pubmed: '24203711'
title: 'DrugBank 4.0: shedding new light on drug metabolism.'
year: 2013
- doi: 10.1093/nar/gkq1126
pmc: PMC3013709
pubmed: '21059682'
title: 'DrugBank 3.0: a comprehensive resource for ''omics'' research on drugs.'
year: 2010
- doi: 10.1093/nar/gkm958
pmc: PMC2238889
pubmed: '18048412'
title: 'DrugBank: a knowledgebase for drugs, drug actions and drug targets.'
year: 2007
- doi: 10.1093/nar/gkj067
pmc: PMC1347430
pubmed: '16381955'
title: 'DrugBank: a comprehensive resource for in silico drug discovery and exploration.'
year: 2006
synonyms:
- DRUGBANK_ID
- DrugBank
twitter: DrugBankDB
uri_format: http://www.drugbank.ca/drugs/$1
drugbank.category:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Close to 5K Categorizations for drugs, similar to ATCC.
example: DBCAT000600
homepage: https://go.drugbank.com/categories
keywords:
- chemistry
- drugs
- metascience
- topics
name: DrugBank Drug Category
part_of: drugbank
pattern: ^DBCAT\d+$
preferred_prefix: drugbank.category
uri_format: https://www.drugbank.ca/categories/$1
drugbank.salt:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: DrugBank is a web-enabled database containing comprehensive molecular
information about drugs, their mechanisms, their interactions and their targets.
example: DBSALT001211
homepage: http://www.drugbank.ca
mappings:
biocontext: DRUGBANK.TARGET
name: DrugBank Salts
part_of: drugbank
pattern: ^DBSALT\d{6}$
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/$1
drugcentral:
contact:
email: toprea@salud.unm.edu
github: null
name: Tudor Oprea
orcid: 0000-0002-6195-6976
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: DrugCentral provides information on active ingredients chemical entities,
pharmaceutical products, drug mode of action, indications, pharmacologic action.
example: '307'
homepage: http://drugcentral.org
keywords:
- biomedical science
- drug development
- drug discovery
- drug repositioning
- pharmacology
- pharmacy
license: CC-BY-SA-4.0
mappings:
biolink: DrugCentral
fairsharing: FAIRsharing.3me82d
miriam: drugcentral
uniprot: DB-0239
wikidata: P11198
name: Drug Central
pattern: ^\d+$
preferred_prefix: drugcentral
publications:
- doi: 10.1093/nar/gky963
pmc: PMC6323925
pubmed: '30371892'
title: 'DrugCentral 2018: an update.'
year: 2019
- doi: 10.1093/nar/gkw993
pmc: PMC5210665
pubmed: '27789690'
title: 'DrugCentral: online drug compendium.'
year: 2016
synonyms:
- Drug_Central
uri_format: http://drugcentral.org/drugcard/$1
dsm4:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A terminology published by the American Psychiatric Association (APA)
for the classification of mental disorders using a common language and standard
criteria. [wikipedia]
example: '315.1'
example_extras:
- '291.89'
homepage: https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)
mappings:
hl7: 2.16.840.1.113883.6.126
wikidata: P663
name: Diagnostic and Statistical Manual of Mental Disorders (4th Edition)
pattern: ^\d+\.\d+$
preferred_prefix: dsm4
synonyms:
- dsm-iv
dsm5:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A terminology published by the American Psychiatric Association (APA)
for the classification of mental disorders using a common language and standard
criteria. [wikipedia]
example: '312.33'
homepage: https://en.wikipedia.org/wiki/DSM-5
mappings:
hl7: 2.16.840.1.113883.6.344
wikidata: P1930
name: Diagnostic and Statistical Manual of Mental Disorders (5th Edition)
pattern: ^\d{3}\.\d{2}$
preferred_prefix: dsm5
references:
- https://archive.org/details/diagnosticstatis0005unse
synonyms:
- dsm-v
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
re3data: r3d100010219
name: Deutsche Sammlung von Mikroorganismen und Zellkulturen
preferred_prefix: dsmz
uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1
dso:
contact:
email: evan@epatters.org
github: epatters
name: Evan Patterson
orcid: 0000-0002-8600-949X
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Data Science Ontology is a research project of IBM Research AI
and Stanford University Statistics. Its long-term objective is to improve the
efficiency and transparency of collaborative, data-driven science.
example: classification-model
homepage: https://www.datascienceontology.org/
keywords:
- data science
- ontology
name: Data Science Ontology
preferred_prefix: dso
repository: https://github.com/IBM/datascienceontology
uri_format: https://www.datascienceontology.org/concept/$1
dto:
appears_in:
- pr
contact:
email: sschurer@med.miami.edu
github: null
name: Stephan Schurer
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'DTO integrates and harmonizes knowledge of the most important druggable
protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.'
download_owl: http://aber-owl.net/media/ontologies/DTO/4/dto.owl
example: '90000018'
homepage: https://github.com/DrugTargetOntology/DTO
keywords:
- biomedical science
- drug discovery
- ontology
mappings:
aberowl: DTO
bioportal: DTO
fairsharing: FAIRsharing.tke3y2
name: Drug Target Ontology
pattern: ^\d+$
preferred_prefix: dto
publications:
- doi: 10.1186/s13326-017-0161-x
pmc: PMC5679337
pubmed: '29122012'
title: Drug target ontology to classify and integrate drug discovery data.
year: 2017
repository: https://github.com/DrugTargetOntology/DTO
uri_format: http://www.drugtargetontology.org/dto/DTO_$1
duo:
appears_in:
- scdo
contact:
email: mcourtot@gmail.com
github: mcourtot
name: Melanie Courtot
orcid: 0000-0002-9551-6370
depends_on:
- bfo
- iao
description: DUO is an ontology which represent data use conditions.
download_owl: http://purl.obolibrary.org/obo/duo.owl
example: '0000046'
homepage: https://github.com/EBISPOT/DUO
keywords:
- biomedical science
- obo
- ontology
- subject agnostic
license: CC-BY-4.0
mappings:
aberowl: DUO
biocontext: DUO
bioportal: DUO
fairsharing: FAIRsharing.5dnjs2
obofoundry: duo
ols: duo
ontobee: DUO
name: Data Use Ontology
pattern: ^\d{7}$
preferred_prefix: DUO
publications:
- doi: 10.1016/j.xgen.2021.100028
pmc: PMC8591903
pubmed: '34820659'
title: The Data Use Ontology to streamline responsible access to human biomedical
datasets.
year: 2021
rdf_uri_format: http://purl.obolibrary.org/obo/DUO_$1
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
re3data: r3d100011564
name: eagle-i
preferred_prefix: eaglei
uri_format: http://hawaii.eagle-i.net/i/$1
easychair.cfp:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Conferences in EasyChair
example: SysBioCancer2022
homepage: https://easychair.org/cfp/
keywords:
- conferences
- metascience
name: EasyChair Call for Paper
preferred_prefix: easychair.cfp
uri_format: https://easychair.org/cfp/$1
easychair.topic:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Call for paper topics in EasyChair
example: '27106865'
homepage: https://easychair.org/cfp/
keywords:
- metascience
- topics
name: EasyChair Topic
pattern: ^\d+$
preferred_prefix: easychair.topic
uri_format: https://easychair.org/cfp/topic.cgi?tid=$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/$1
ecacc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The European Collection of Authenticated Cell Cultures (ECACC) is one
of four Culture Collections of Public Health England. We supply authenticated
and quality controlled cell lines, nucleic acids and induced Pluripotent Stem
Cells (iPSCs).
example: '90062901'
homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx
mappings:
cellosaurus: ECACC
name: European Collection of Authenticated Cell Culture
pattern: ^\d+$
preferred_prefix: ecacc
uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1
ecao:
contact:
email: ettensohn@cmu.edu
github: ettensohn
name: Charles Ettensohn
orcid: 0000-0002-3625-0955
depends_on:
- cl
- ro
- uberon
description: None
download_obo: http://purl.obolibrary.org/obo/ecao.obo
download_owl: http://purl.obolibrary.org/obo/ecao.owl
example: 0107180
homepage: https://github.com/echinoderm-ontology/ecao_ontology
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: ECAO
bioportal: ECAO
obofoundry: ecao
ols: ecao
ontobee: ECAO
name: The Echinoderm Anatomy and Development Ontology
pattern: ^\d{7}$
preferred_prefix: ECAO
rdf_uri_format: http://purl.obolibrary.org/obo/ECAO_$1
repository: https://github.com/echinoderm-ontology/ecao_ontology
uri_format: http://purl.obolibrary.org/obo/ECAO_$1
version: '2020-05-22'
eccode:
contact:
email: kristian.axelsen@sib.swiss
github: kaxelsen
name: Kristian Axelsen
orcid: 0000-0003-3889-2879
description: The Enzyme Classification contains the recommendations of the Nomenclature
Committee of the International Union of Biochemistry and Molecular Biology on
the nomenclature and classification of enzyme-catalysed reactions.
example: 1.1.1.1
example_decoys:
- '100'
- '2.'
- 2.n1
- 2.3.
- 2.3.n1
- 2.3.1.
- 2.3.1.n
- 2.3.4.1.
example_extras:
- '2'
- '2.3'
- 2.3.1
- 2.3.1.n12
- 3.1.26.n2
homepage: https://www.enzyme-database.org/
keywords:
- biochemistry
- classification
- enzyme
- enzymology
mappings:
bartoc: '671'
biocontext: EC-CODE
edam: '1011'
fairsharing: FAIRsharing.rfLD2u
go: EC
miriam: ec-code
n2t: ec-code
prefixcommons: intenz
re3data: r3d100010803
uniprot: DB-0024
wikidata: P591
name: Enzyme Commission Code
pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$
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: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/intenz:$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
- 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
publications:
- doi: 10.1093/nar/28.1.304
pmc: PMC102465
pubmed: '10592255'
title: The ENZYME database in 2000.
year: 2000
references:
- https://github.com/biopragmatics/bioregistry/issues/681
synonyms:
- EC
- EC number
- EC-CODE
- ECCODE
- EC_CODE
- ec-code
- intenz
uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1
ecg:
contact:
email: rwinslow@jhu.edu
github: null
name: Raimond Winslow
orcid: 0000-0003-1719-1651
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Electrocardiography (ECG) Ontology is a Driving Biological Project
of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms,
their capture method(s) and their waveforms.
download_owl: http://aber-owl.net/media/ontologies/ECG/12/ecg.owl
example: 000000159
homepage: https://bioportal.bioontology.org/ontologies/ECG
keywords:
- biomedical science
- ontology
mappings:
aberowl: ECG
bioportal: ECG
fairsharing: FAIRsharing.azr389
name: Electrocardiogram Ontology
pattern: ^\d+$
preferred_prefix: ecg
publications:
- doi: 10.1016/j.jbi.2010.08.007
pmc: null
pubmed: '20800107'
title: Using an ECG reference ontology for semantic interoperability of ECG data.
year: 2010
synonyms:
- ECGOntology
uri_format: http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1
echinobase:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Echinobase supports the international research community by providing
a centralized, integrated and easy to use web based resource to access the diverse
and rich, functional genomics data of echinoderm species.
example: '23159291'
homepage: https://www.echinobase.org
name: Echinobase
pattern: ^\d+$
preferred_prefix: echinobase
uri_format: https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1
echobase:
description: EchoBASE is a database designed to contain and manipulate information
from post-genomic experiments using the model bacterium Escherichia coli K-12.
The database is built on an enhanced annotation of the updated genome sequence
of strain MG1655 and the association of experimental data with the E.coli genes
and their products.
example: EB0170
homepage: http://www.york.ac.uk/
keywords:
- gene
- gene expression
mappings:
biocontext: ECHOBASE
go: EchoBASE
miriam: echobase
n2t: echobase
prefixcommons: echobase
re3data: r3d100011646
uniprot: DB-0020
name: EchoBASE post-genomic database for Escherichia coli
pattern: ^EB\d+$
preferred_prefix: echobase
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/echobase:$1
publications:
- doi: 10.1093/nar/gki028
pmc: PMC539982
pubmed: '15608209'
title: 'EchoBASE: an integrated post-genomic database for Escherichia coli.'
year: 2005
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/$1
ecn:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: identifier for a chemical compound per EINECS or ELINCS
example: 200-003-9
homepage: https://echa.europa.eu/information-on-chemicals
mappings:
cheminf: '000447'
wikidata: P232
name: EC number
pattern: ^\d{3}-\d{3}-\d$
preferred_prefix: ecn
references:
- https://github.com/biopragmatics/bioregistry/issues/257
- https://en.wikipedia.org/wiki/European_Community_number
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://www.evidenceontology.org
keywords:
- computational biology
- life science
- obo
- ontology
license: CC0-1.0
logo: https://avatars1.githubusercontent.com/u/12802432
mappings:
aberowl: ECO
bartoc: '1028'
biocontext: ECO
bioportal: ECO
fairsharing: FAIRsharing.wvpgwn
go: ECO
miriam: eco
n2t: eco
obofoundry: eco
ols: eco
ontobee: ECO
prefixcommons: eco
wikidata: P3811
name: Evidence ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: ECO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/eco:$1
publications:
- doi: 10.1093/nar/gkab1025
pmc: PMC8728134
pubmed: '34986598'
title: 'ECO: the Evidence and Conclusion Ontology, an update for 2022.'
year: 2022
- doi: 10.1093/nar/gky1036
pmc: PMC6323956
pubmed: '30407590'
title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence
information.'
year: 2019
- doi: 10.1007/978-1-4939-3743-1_18
pmc: PMC6377151
pubmed: '27812948'
title: 'The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.'
year: 2017
- doi: 10.1093/database/bau075
pmc: PMC4105709
pubmed: '25052702'
title: Standardized description of scientific evidence using the Evidence Ontology
(ECO).
year: 2014
- doi: 10.1142/9789812704856_0019
pmc: null
pubmed: '14992503'
title: An evidence ontology for use in pathway/genome databases.
year: 2004
rdf_uri_format: http://purl.obolibrary.org/obo/ECO_$1
repository: https://github.com/evidenceontology/evidenceontology
uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1
version: '2023-04-07'
ecocore:
contact:
email: p.buttigieg@gmail.com
github: pbuttigieg
name: Pier Luigi Buttigieg
orcid: 0000-0002-4366-3088
depends_on:
- bfo
- chebi
- envo
- go
- iao
- pato
- pco
- po
- ro
- uberon
description: Ecocore is a community ontology for the concise and controlled description
of ecological traits of organisms.
download_obo: http://purl.obolibrary.org/obo/ecocore.obo
download_owl: http://purl.obolibrary.org/obo/ecocore.owl
example: '00000001'
homepage: https://github.com/EcologicalSemantics/ecocore
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: ECOCORE
biocontext: ECOCORE
bioportal: ECOCORE
obofoundry: ecocore
ols: ecocore
ontobee: ECOCORE
name: An ontology of core ecological entities
pattern: ^\d+$
preferred_prefix: ECOCORE
rdf_uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1
repository: https://github.com/EcologicalSemantics/ecocore
uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1
version: '2022-03-09'
ecocyc:
contributor_extras:
- email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
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: https://ecocyc.org/
keywords:
- biology
mappings:
fairsharing: FAIRsharing.65dmtr
go: EcoCyc
ncbi: ECOCYC
re3data: r3d100011277
name: EcoCyc
preferred_prefix: ecocyc
publications:
- doi: 10.3389/fmicb.2021.711077
pmc: PMC8357350
pubmed: '34394059'
title: The EcoCyc Database in 2021.
year: 2021
- doi: 10.1093/nar/gkw1003
pmc: PMC5210515
pubmed: '27899573'
title: 'The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.'
year: 2016
- doi: 10.1128/ecosalplus.esp-0009-2013
pmc: PMC4243172
pubmed: '26442933'
title: The EcoCyc Database.
year: 2014
- doi: 10.1093/nar/gks1027
pmc: PMC3531154
pubmed: '23143106'
title: 'EcoCyc: fusing model organism databases with systems biology.'
year: 2012
uri_format: https://ecocyc.org/gene?id=$1
ecogene:
description: The EcoGene database contains updated information about the E. coli
K-12 genome and proteome sequences, including extensive gene bibliographies. A
major EcoGene focus has been the re-evaluation of translation start sites.
example: EG10173
homepage: http://ecogene.org/
keywords:
- genome
- protein
mappings:
biocontext: EcoGene
fairsharing: FAIRsharing.3q3kvn
miriam: ecogene
n2t: ecogene
ncbi: EcoGene
prefixcommons: ecogene
re3data: r3d100010546
name: Database of Escherichia coli Sequence and Function
pattern: ^EG\d+$
preferred_prefix: ecogene
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ecogene:$1
publications:
- doi: 10.1093/nar/28.1.60
pmc: PMC102481
pubmed: '10592181'
title: 'EcoGene: a genome sequence database for Escherichia coli K-12.'
year: 2000
uri_format: http://www.ecogene.org/gene/$1
ecolexicon:
comment: No resolution - everything is in a single page app
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: EcoLexicon represents the conceptual structure of the specialized domain
of the Environment in the form of a visual thesaurus. This thesaurus has been
elaborated according to the theoretical premises of Frame-Based Terminology.
example: canal
homepage: http://ecolexicon.ugr.es/en/index.htm
keywords:
- ecology
- environmental science
name: EcoLexicon
preferred_prefix: ecolexicon
ecoliwiki:
description: EcoliWiki is a wiki-based resource to store information related to
non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This
collection references genes.
example: aaeA
homepage: http://ecoliwiki.net/colipedia/
keywords:
- bioinformatics
- genomics
- life science
- ontology and terminology
mappings:
biocontext: ECOLIWIKI
fairsharing: FAIRsharing.tx95wa
go: EcoliWiki
miriam: ecoliwiki
n2t: ecoliwiki
name: EcoliWiki from EcoliHub
pattern: ^[A-Za-z0-9-]+$
preferred_prefix: ecoliwiki
publications:
- doi: 10.1016/j.tim.2009.04.004
pmc: PMC3575750
pubmed: '19576778'
title: What we can learn about Escherichia coli through application of Gene Ontology.
year: 2009
uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene
ecso:
contact:
email: brycemecum@gmail.com
github: amoeba
name: Bryce Mecum
orcid: 0000-0002-0381-3766
description: DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use
Cases
download_owl: https://raw.githubusercontent.com/DataONEorg/sem-prov-ontologies/run4/observation/d1-ECSO.owl
example: '00000532'
homepage: https://github.com/DataONEorg/sem-prov-ontologies
keywords:
- ontology
mappings:
bioportal: ECSO
name: The Ecosystem Ontology
pattern: ^\d+$
preferred_prefix: ecso
repository: https://github.com/DataONEorg/sem-prov-ontologies
uri_format: http://purl.dataone.org/odo/ECSO_$1
ecto:
contact:
email: annethessen@gmail.com
github: diatomsRcool
name: Anne Thessen
orcid: 0000-0002-2908-3327
depends_on:
- chebi
- envo
- exo
- go
- iao
- maxo
- nbo
- ncbitaxon
- ncit
- pato
- ro
- uberon
- xco
description: ECTO describes exposures to experimental treatments of plants and model
organisms (e.g. exposures to modification of diet, lighting levels, temperature);
exposures of humans or any other organisms to stressors through a variety of routes,
for purposes of public health, environmental monitoring etc, stimuli, natural
and experimental, any kind of environmental condition or change in condition that
can be experienced by an organism or population of organisms on earth. The scope
is very general and can include for example plant treatment regimens, as well
as human clinical exposures (although these may better be handled by a more specialized
ontology).
download_json: http://purl.obolibrary.org/obo/ecto.json
download_obo: http://purl.obolibrary.org/obo/ecto.obo
download_owl: http://purl.obolibrary.org/obo/ecto.owl
example: '0000001'
homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology
keywords:
- obo
- ontology
license: CC0-1.0
logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png
mappings:
aberowl: ECTO
biolink: ECTO
bioportal: ECTO
obofoundry: ecto
ols: ecto
ontobee: ECTO
name: Environmental conditions, treatments and exposures ontology
pattern: ^\d{7}$
preferred_prefix: ECTO
rdf_uri_format: http://purl.obolibrary.org/obo/ECTO_$1
repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology
uri_format: http://purl.obolibrary.org/obo/ECTO_$1
version: '2023-02-14'
ecyano.entity:
description: E-cyanobacterium.org is a web-based platform for public sharing, annotation,
analysis, and visualisation of dynamical models and wet-lab experiments related
to cyanobacteria. It allows models to be represented at different levels of abstraction
— as biochemical reaction networks or ordinary differential equations.It provides
concise mappings of mathematical models to a formalised consortium-agreed biochemical
description, with the aim of connecting the world of biological knowledge with
benefits of mathematical description of dynamic processes. This collection references
entities.
example: '23'
homepage: http://www.e-cyanobacterium.org/bcs/entity/
mappings:
biocontext: ECYANO.ENTITY
miriam: ecyano.entity
n2t: ecyano.entity
name: E-cyanobacterium entity
part_of: ecyano
pattern: ^\d+$
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/$1
edam:
contact:
email: matus.kalas@uib.no
github: matuskalas
name: Matúš Kalaš
orcid: 0000-0002-1509-4981
description: 'EDAM is an ontology of general bioinformatics concepts, including
topics, data types, formats, identifiers and operations. EDAM provides a controlled
vocabulary for the description, in semantic terms, of things such as: web services
(e.g. WSDL files), applications, tool collections and packages, work-benches and
workflow software, databases and ontologies, XSD data schema and data objects,
data syntax and file formats, web portals and pages, resource catalogues and documents
(such as scientific publications).'
download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
download_owl: https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl
example: data_1664
homepage: http://edamontology.org
keywords:
- bioinformatics
- life science
- obo
- ontology
mappings:
aberowl: EDAM
agroportal: EDAM
biocontext: EDAM
bioportal: EDAM
fairsharing: FAIRsharing.a6r7zs
miriam: edam
n2t: edam
ols: edam
ontobee: EDAM
prefixcommons: edam
name: Bioinformatics operations, data types, formats, identifiers and topics
pattern: ^(data|topic|operation|format)\_\d{4}$
preferred_prefix: edam
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/edam:$1
publications:
- doi: 10.1093/bioinformatics/btt113
pmc: PMC3654706
pubmed: '23479348'
title: 'EDAM: an ontology of bioinformatics operations, types of data and identifiers,
topics and formats.'
year: 2013
repository: https://github.com/edamontology/edamontology
twitter: edamontology
uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1
edam.data:
contact:
email: matus.kalas@uib.no
github: matuskalas
name: Matúš Kalaš
orcid: 0000-0002-1509-4981
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Information, represented in an information artefact (data record) that
is 'understandable' by dedicated computational tools that can use the data as
input or produce it as output.
download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
example: '1664'
homepage: http://edamontology.org
keywords:
- ontology
mappings:
biolink: EDAM-DATA
name: EDAM Data
part_of: edam
pattern: ^\d+$
preferred_prefix: edam.data
repository: https://github.com/edamontology/edamontology
twitter: edamontology
uri_format: http://edamontology.org/data_$1
edam.format:
contact:
email: matus.kalas@uib.no
github: matuskalas
name: Matúš Kalaš
orcid: 0000-0002-1509-4981
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A defined way or layout of representing and structuring data in a computer
file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats
as means of structuring data exchanged between different tools or resources. The
serialisation, compression, or encoding of concrete data formats/models is not
in scope of EDAM. Format 'is format of' Data.
download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
example: '1915'
homepage: http://edamontology.org
keywords:
- ontology
mappings:
biolink: EDAM-FORMAT
name: EDAM Format
part_of: edam
pattern: ^\d+$
preferred_prefix: edam.format
repository: https://github.com/edamontology/edamontology
twitter: edamontology
uri_format: http://edamontology.org/format_$1
edam.operation:
contact:
email: matus.kalas@uib.no
github: matuskalas
name: Matúš Kalaš
orcid: 0000-0002-1509-4981
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'A function that processes a set of inputs and results in a set of
outputs, or associates arguments (inputs) with values (outputs). Special cases
are: a) An operation that consumes no input (has no input arguments). Such operation
is either a constant function, or an operation depending only on the underlying
state. b) An operation that may modify the underlying state but has no output.
c) The singular-case operation with no input or output, that still may modify
the underlying state.'
download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
example: '0004'
homepage: http://edamontology.org
keywords:
- ontology
mappings:
biolink: EDAM-OPERATION
name: EDAM Operation
part_of: edam
pattern: ^\d+$
preferred_prefix: edam.operation
repository: https://github.com/edamontology/edamontology
twitter: edamontology
uri_format: http://edamontology.org/operation_$1
edam.topic:
contact:
email: matus.kalas@uib.no
github: matuskalas
name: Matúš Kalaš
orcid: 0000-0002-1509-4981
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A category denoting a rather broad domain or field of interest, of
study, application, work, data, or technology. Topics have no clearly defined
borders between each other.
download_obo: https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo
example: '0003'
homepage: http://edamontology.org
keywords:
- ontology
mappings:
biolink: EDAM-TOPIC
name: EDAM Topic
part_of: edam
pattern: ^\d+$
preferred_prefix: edam.topic
repository: https://github.com/edamontology/edamontology
twitter: edamontology
uri_format: http://edamontology.org/topic_$1
edda:
contact:
email: tanja.bekhuis@tcbinfosci.com
github: null
name: Tanja Bekhuis
orcid: 0000-0002-8537-9077
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.
download_owl: http://aber-owl.net/media/ontologies/EDDA/11/edda.owl
example: health_care_quality_assessment
homepage: https://bioportal.bioontology.org/ontologies/EDDA
keywords:
- medicine
- ontology
mappings:
aberowl: EDDA
bioportal: EDDA
fairsharing: FAIRsharing.2ffmsb
name: EDDA Study Designs Taxonomy
preferred_prefix: edda
uri_format: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1
efo:
contact:
email: plwhetzel@gmail.com
github: twhetzel
name: Trish Whetzel
orcid: 0000-0002-3458-4839
description: The Experimental Factor Ontology (EFO) provides a systematic description
of many experimental variables available in EBI databases. It combines parts of
several biological ontologies, such as anatomy, disease and chemical compounds.
The scope of EFO is to support the annotation, analysis and visualization of data
handled by the EBI Functional Genomics Team.
download_obo: http://www.ebi.ac.uk/efo/efo.obo
download_owl: http://www.ebi.ac.uk/efo/efo.owl
example: '0005147'
homepage: http://www.ebi.ac.uk/efo
keywords:
- functional genomics
- ontology
license: Apache-2.0
mappings:
aberowl: EFO
agroportal: EFO
biocontext: EFO
biolink: EFO
bioportal: EFO
cellosaurus: EFO
fairsharing: FAIRsharing.1gr4tz
miriam: efo
n2t: efo
ols: efo
ontobee: EFO
name: Experimental Factor Ontology
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^\d{7}$
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
publications:
- doi: 10.1093/bioinformatics/btq099
pmc: PMC2853691
pubmed: '20200009'
title: Modeling sample variables with an Experimental Factor Ontology.
year: 2010
repository: https://github.com/EBISPOT/efo/
uri_format: http://www.ebi.ac.uk/efo/EFO_$1
version: 3.53.0
ega.dataset:
description: The EGA is a service for permanent archiving and sharing of all types
of personally identifiable genetic and phenotypic data resulting from biomedical
research projects. The EGA contains exclusive data collected from individuals
whose consent agreements authorize data release only for specific research use
or to bona fide researchers. Strict protocols govern how information is managed,
stored and distributed by the EGA project. This collection references 'Datasets'.
example: EGAD00000000001
homepage: https://ega-archive.org/
keywords:
- biology
- biomedical science
- clinical studies
- genomics
- phenomics
mappings:
biocontext: EGA.DATASET
fairsharing: FAIRsharing.mya1ff
miriam: ega.dataset
n2t: ega.dataset
re3data: r3d100011242
name: European Genome-phenome Archive Dataset
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^EGAD\d{11}$
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
publications:
- doi: 10.1093/nar/gkab1059
pmc: PMC8728218
pubmed: '34791407'
title: The European Genome-phenome Archive in 2021.
year: 2022
- doi: 10.1038/ng.3312
pmc: PMC5426533
pubmed: '26111507'
title: The European Genome-phenome Archive of human data consented for biomedical
research.
year: 2015
twitter: EGAarchive
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
uri_format: https://www.ebi.ac.uk/ega/studies/$1
eggnog:
description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous
Groups) is a database of orthologous groups of genes. The orthologous groups are
annotated with functional description lines (derived by identifying a common denominator
for the genes based on their various annotations), with functional categories
(i.e derived from the original COG/KOG categories).'
example: veNOG12876
homepage: http://eggnog.embl.de/version_3.0/
keywords:
- gene
- life science
mappings:
biocontext: EGGNOG
fairsharing: FAIRsharing.j1wj7d
miriam: eggnog
n2t: eggnog
prefixcommons: eggnog
uniprot: DB-0152
name: eggNOG
pattern: ^\w+$
preferred_prefix: eggnog
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/eggnog:$1
publications:
- doi: 10.1093/nar/gkp951
pmc: PMC2808932
pubmed: '19900971'
title: 'eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced
non-supervised orthologous groups, species and functional annotations.'
year: 2009
- doi: 10.1093/nar/gkm796
pmc: PMC2238944
pubmed: '17942413'
title: 'eggNOG: automated construction and annotation of orthologous groups of
genes.'
year: 2007
uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1
ehda:
contact:
email: J.Bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
deprecated: true
description: A structured controlled vocabulary of stage-specific anatomical structures
of the human. It has been designed to mesh with the mouse anatomy and incorporates
each Carnegie stage of development (CS1-20). The timed version of the human developmental
anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of
human development (1-20) linked by a part-of rule. Each term is mentioned only
once so that the embryo at each stage can be seen as the simple sum of its parts.
Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are
only mentioned once.
download_obo: http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo
example: '1'
homepage: http://genex.hgu.mrc.ac.uk/
keywords:
- anatomy
- development
- human
- obo
- ontology
mappings:
aberowl: EHDA
biocontext: EHDA
bioportal: EHDA
obofoundry: ehda
prefixcommons: ehda
name: Human developmental anatomy, timed version
pattern: ^\d+$
preferred_prefix: EHDA
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ehda:$1
rdf_uri_format: http://purl.obolibrary.org/obo/EHDA_$1
uri_format: http://purl.obolibrary.org/obo/EHDA_$1
ehdaa:
contact:
email: J.Bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
deprecated: true
description: A structured controlled vocabulary of stage-specific anatomical structures
of the human. It has been designed to mesh with the mouse anatomy and incorporates
each Carnegie stage of development (CS1-20). The abstract version of the human
developmental anatomy ontology compresses all the tissues present over Carnegie
stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie
Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In
the abstract mouse, it has a single ID so that the abstract term given as just
heart really means heart (CS 9-20). Timing details will be added
to the abstract version of the ontology in a future release.
download_obo: http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo
example: '1'
homepage: http://genex.hgu.mrc.ac.uk/
keywords:
- anatomy
- development
- human
- obo
- ontology
mappings:
aberowl: EHDAA
biocontext: EHDAA
bioportal: EHDAA
obofoundry: ehdaa
prefixcommons: ehdaa
name: Human developmental anatomy, abstract version
pattern: ^\d+$
preferred_prefix: EHDAA
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ehdaa:$1
rdf_uri_format: http://purl.obolibrary.org/obo/EHDAA_$1
uri_format: http://purl.obolibrary.org/obo/EHDAA_$1
ehdaa2:
contact:
email: J.Bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
depends_on:
- aeo
- caro
- cl
deprecated: true
description: A structured controlled vocabulary of stage-specific anatomical structures
of the developing human.
download_obo: http://purl.obolibrary.org/obo/ehdaa2.obo
download_owl: http://purl.obolibrary.org/obo/ehdaa2.owl
example: '0000000'
homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology
keywords:
- anatomy
- biomedical science
- life science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: EHDAA2
biocontext: EHDAA2
bioportal: EHDAA2
fairsharing: FAIRsharing.7zxrs6
obofoundry: ehdaa2
ols: ehdaa2
ontobee: EHDAA2
name: Human developmental anatomy, abstract
pattern: ^\d{7}$
preferred_prefix: EHDAA2
publications:
- doi: 10.1111/j.1469-7580.2012.01566.x
pmc: PMC3482348
pubmed: '22973865'
title: A new ontology (structured hierarchy) of human developmental anatomy for
the first 7 weeks (Carnegie stages 1-20).
year: 2012
rdf_uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1
repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
synonyms:
- EHDAA2_RETIRED
- HDAA2
- RETIRED_EHDAA2
uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1
version: '2013-07-04'
elm:
description: Linear motifs are short, evolutionarily plastic components of regulatory
proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif
resource (ELM) is a database of curated motif classes and instances.
example: CLV_MEL_PAP_1
homepage: http://elm.eu.org/
keywords:
- life science
mappings:
biocontext: ELM
fairsharing: FAIRsharing.rj3kj5
miriam: elm
n2t: elm
uniprot: DB-0223
name: Eukaryotic Linear Motif Resource
pattern: ^[A-Za-z_0-9]+$
preferred_prefix: elm
publications:
- doi: 10.1093/nar/gkz1030
pmc: PMC7145657
pubmed: '31680160'
title: ELM-the eukaryotic linear motif resource in 2020.
year: 2020
- doi: 10.1093/nar/gkv1291
pmc: PMC4702912
pubmed: '26615199'
title: ELM 2016--data update and new functionality of the eukaryotic linear motif
resource.
year: 2015
- doi: 10.1093/nar/gkr1064
pmc: PMC3245074
pubmed: '22110040'
title: ELM--the database of eukaryotic linear motifs.
year: 2011
- doi: 10.1093/nar/gkg545
pmc: PMC168952
pubmed: '12824381'
title: 'ELM server: A new resource for investigating short functional sites in
modular eukaryotic proteins.'
year: 2003
uri_format: http://elm.eu.org/elms/elmPages/$1.html
emap:
contact:
email: Terry.Hayamizu@jax.org
github: tfhayamizu
name: Terry Hayamizu
orcid: 0000-0002-0956-8634
deprecated: true
description: A structured controlled vocabulary of stage-specific anatomical structures
of the mouse (Mus).
download_owl: http://purl.obolibrary.org/obo/emap.owl
example: '1'
homepage: http://emouseatlas.org
keywords:
- anatomy
- development
- mouse
- obo
- ontology
mappings:
biocontext: EMAP
bioportal: EMAP
obofoundry: emap
ols: emap
prefixcommons: emap.ontology
name: Mouse gross anatomy and development, timed
pattern: ^\d+$
preferred_prefix: EMAP
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/emap.ontology:$1
rdf_uri_format: http://purl.obolibrary.org/obo/EMAP_$1
uri_format: http://purl.obolibrary.org/obo/EMAP_$1
version: '2020-04-13'
emapa:
contact:
email: Terry.Hayamizu@jax.org
github: tfhayamizu
name: Terry Hayamizu
orcid: 0000-0002-0956-8634
description: An ontology for mouse anatomy covering embryonic development and postnatal
stages.
download_obo: http://purl.obolibrary.org/obo/emapa.obo
download_owl: http://purl.obolibrary.org/obo/emapa.owl
example: '26753'
homepage: http://www.informatics.jax.org/expression.shtml
keywords:
- anatomy
- developmental biology
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: EMAPA
bartoc: '549'
biocontext: EMAPA
bioportal: EMAPA
fairsharing: FAIRsharing.j0fa1d
go: EMAPA
obofoundry: emapa
ols: emapa
ontobee: EMAPA
name: Mouse Developmental Anatomy Ontology
pattern: ^\d+$
preferred_prefix: EMAPA
publications:
- doi: 10.1016/s0925-4773(98)00069-0
pmc: null
pubmed: '9651497'
title: An internet-accessible database of mouse developmental anatomy based on
a systematic nomenclature.
year: 1998
- doi: 10.1007/s00335-015-9584-9
pmc: PMC4602063
pubmed: '26208972'
title: 'Mouse anatomy ontologies: enhancements and tools for exploring and integrating
biomedical data.'
year: 2015
- doi: 10.1186/2041-1480-4-15
pmc: PMC3851555
pubmed: '23972281'
title: 'EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update.'
year: 2013
- doi: 10.1016/b978-0-12-800043-4.00023-3
pmc: null
pubmed: null
title: Textual Anatomics
year: 2016
rdf_uri_format: http://purl.obolibrary.org/obo/EMAPA_$1
repository: https://github.com/obophenotype/mouse-anatomy-ontology
synonyms:
- EMAPA_RETIRED
uri_format: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1
version: '2022-11-04'
emaps:
contact:
email: Terry.Hayamizu@jax.org
github: tfhayamizu
name: Terry Hayamizu
orcid: 0000-0002-0956-8634
contributor:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
depends_on:
- emapa
description: EMAPA identifiers refer to developmental stage-independent mouse anatomical
features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental
Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different
developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed
such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number.
For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823
example: '3517823'
github_request_issue: 747
homepage: https://www.informatics.jax.org/vocab/gxd/anatomy/
name: Mouse Developmental Anatomy Ontology with Theiler Stage
pattern: ^\d+$
preferred_prefix: EMAPS
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1
emdb:
contact:
email: help@emdatabank.org
github: null
name: Ardan Patwardhan
orcid: 0000-0001-7663-9028
description: The Electron Microscopy Data Bank (EMDB) is a public repository for
electron microscopy density maps of macromolecular complexes and subcellular structures.
It covers a variety of techniques, including single-particle analysis, electron
tomography, and electron (2D) crystallography. The EMDB map distribution format
follows the CCP4 definition, which is widely recognized by software packages used
by the structural biology community.
example: EMD-1001
homepage: https://www.ebi.ac.uk/pdbe/emdb/
keywords:
- epidemiology
- structural biology
- virology
mappings:
biocontext: EMDB
edam: '1146'
fairsharing: FAIRsharing.651n9j
miriam: emdb
n2t: emdb
re3data: r3d100010562
name: Electron Microscopy Data Bank
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^EMD-\d{4,5}$
preferred_prefix: emdb
publications:
- doi: 10.1093/nar/gkv1126
pmc: PMC4702818
pubmed: '26578576'
title: EMDataBank unified data resource for 3DEM.
year: 2015
- doi: 10.1093/nar/gkq880
pmc: PMC3013769
pubmed: '20935055'
title: 'EMDataBank.org: unified data resource for CryoEM.'
year: 2010
- doi: 10.1016/s0968-0004(02)02176-x
pmc: null
pubmed: '12417136'
title: New electron microscopy database and deposition system.
year: 2002
uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1
emmo:
banana: EMMO
banana_peel: _
contact:
email: jesper.friis@sintef.no
github: jesper-friis
name: Jesper Friis
orcid: 0000-0002-1560-809X
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: EMMO is a multidisciplinary effort to develop a standard representational
framework (the ontology) for applied sciences. It is based on physics, analytical
philosophy and information and communication technologies. It has been instigated
by materials science to provide a framework for knowledge capture that is consistent
with scientific principles and methodologies. (from GitHub)
download_rdf: https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
example: 03212fd7_abfd_4828_9c8e_62c293052d4b
homepage: https://emmo-repo.github.io
license: CC-BY-4.0
name: Elementary Multiperspective Material Ontology
preferred_prefix: emmo
repository: https://github.com/emmo-repo/EMMO
uri_format: http://emmo.info/emmo#EMMO_$1
emmo.cif:
contact:
email: jesper.friis@sintef.no
github: jesper-friis
name: Jesper Friis
orcid: 0000-0002-1560-809X
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A crystallography domain ontology based on EMMO and the CIF core dictionary.
It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)
download_rdf: https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/ontology/cif-core.ttl
example: _space_group_symop.operation_xyz
example_extras:
- o12
homepage: https://www.iucr.org/resources/cif
name: Crystallographic Information Framework
preferred_prefix: emmo.cif
repository: https://github.com/emmo-repo/CIF-ontology
uri_format: http://emmo.info/emmo/cif-core#$1
emolecules:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Catalog of purchasable reagents and building blocks
example: '491187'
homepage: https://reaxys.emolecules.com
keywords:
- chemistry
- reagents
- vendor
name: Reaxys eMolecules
pattern: ^\d+$
preferred_prefix: emolecules
uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1
empiar:
banana: EMPIAR
banana_peel: '-'
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource
for raw, 2D electron microscopy images. Here, you can browse, upload and download
the raw images used to build a 3D structure
example: '10595'
homepage: https://www.ebi.ac.uk/pdbe/emdb
keywords:
- bioinformatics
- biology
mappings:
fairsharing: FAIRsharing.dff3ef
miriam: empiar
name: Electron Microscopy Public Image Archive
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^\d+$
preferred_prefix: empiar
publications:
- doi: 10.1038/nmeth.3806
pmc: null
pubmed: '27067018'
title: 'EMPIAR: a public archive for raw electron microscopy image data.'
year: 2016
uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1
emsl.project:
contact:
email: montana.smith@pnnl.gov
github: mslarae13
name: Montana Smith
orcid: 0000-0002-8683-0050
contributor:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: 'As a scientific user facility, the Environmental Molecular Sciences
Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects
each year. Current and past projects supported through a variety of EMSL user
proposal avenues are publicly searchable on the EMSL website. Project pages provide
details including:
- Research team and institution
- The EMSL project DOI
- Link to project data available in EMSLs Data Portal
- Project type'
example: '60141'
github_request_issue: 835
homepage: https://www.emsl.pnnl.gov/projects
name: Environmental Molecular Sciences Laboratory Project
pattern: ^\d+$
preferred_prefix: emsl.project
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://www.emsl.pnnl.gov/project/$1
ena.embl:
contact:
email: datasubs@ebi.ac.uk
github: null
name: Guy Cochrane
orcid: 0000-0001-7954-7057
description: The European Nucleotide Archive (ENA) captures and presents information
relating to experimental workflows that are based around nucleotide sequencing.
ENA is made up of a number of distinct databases that includes EMBL-Bank, the
Sequence Read Archive (SRA) and the Trace Archive each with their own data formats
and standards. This collection references Embl-Bank identifiers.
example: BN000065
homepage: https://www.ebi.ac.uk/ena/
keywords:
- biodiversity
- bioinformatics
- data management
- dna
- functional genomics
- genomics
- metagenomics
- transcriptomics
mappings:
biocontext: ENA.EMBL
fairsharing: FAIRsharing.dj8nt8
go: ENA
miriam: ena.embl
n2t: ena.embl
prefixcommons: ena
re3data: r3d100010527
uniprot: DB-0022
name: European Nucleotide Archive
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^[A-Z]+[0-9]+(\.\d+)?$
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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ena:$1
publications:
- doi: 10.1093/nar/gkaa1028
pmc: PMC7778925
pubmed: '33175160'
title: The European Nucleotide Archive in 2020.
year: 2021
- doi: 10.1093/nar/gkw1106
pmc: PMC5210577
pubmed: '27899630'
title: European Nucleotide Archive in 2016.
year: 2016
- doi: 10.1093/nar/gkv1323
pmc: PMC4702924
pubmed: '26657633'
title: The International Nucleotide Sequence Database Collaboration.
year: 2015
- doi: 10.1093/nar/gkv1311
pmc: PMC4702917
pubmed: '26615190'
title: Biocuration of functional annotation at the European nucleotide archive.
year: 2015
- doi: 10.1093/nar/gku1129
pmc: PMC4383942
pubmed: '25404130'
title: Content discovery and retrieval services at the European Nucleotide Archive.
year: 2014
- doi: 10.1093/nar/gks1175
pmc: PMC3531187
pubmed: '23203883'
title: Facing growth in the European Nucleotide Archive.
year: 2012
- doi: 10.1093/nar/gkh120
pmc: PMC308854
pubmed: '14681351'
title: The EMBL Nucleotide Sequence Database.
year: 2004
synonyms:
- ena
twitter: enasequence
uri_format: https://www.ebi.ac.uk/ena/browser/view/$1
encode:
contact:
email: gabdank@stanford.edu
github: null
name: Idan Gabdank
orcid: 0000-0001-5025-5886
description: The ENCODE Consortium is integrating multiple technologies and approaches
in a collective effort to discover and define the functional elements encoded
in the human genome, including genes, transcripts, and transcriptional regulatory
regions, together with their attendant chromatin states and DNA methylation patterns.
example: ENCSR163RYW
homepage: https://www.encodeproject.org
keywords:
- epigenetics
- functional genomics
mappings:
biocontext: ENCODE
cellosaurus: ENCODE
fairsharing: FAIRsharing.v0hbjs
miriam: encode
n2t: encode
re3data: r3d100013051
name: Encyclopedia of DNA Elements
pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$
preferred_prefix: encode
publications:
- doi: 10.1038/s41586-020-2493-4
pmc: PMC7410828
pubmed: '32728249'
title: Expanded encyclopaedias of DNA elements in the human and mouse genomes.
year: 2020
- doi: 10.1038/s41586-020-2449-8
pmc: PMC7410827
pubmed: '32728248'
title: Perspectives on ENCODE.
year: 2020
- doi: 10.1002/cpbi.89
pmc: PMC7307447
pubmed: '31751002'
title: The ENCODE Portal as an Epigenomics Resource.
year: 2019
- doi: 10.1093/nar/gkz1062
pmc: PMC7061942
pubmed: '31713622'
title: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.
year: 2020
- doi: 10.1093/nar/gkx1081
pmc: PMC5753278
pubmed: '29126249'
title: 'The Encyclopedia of DNA elements (ENCODE): data portal update.'
year: 2018
- doi: 10.1371/journal.pone.0175310
pmc: PMC5389787
pubmed: '28403240'
title: 'SnoVault and encodeD: A novel object-based storage system and applications
to ENCODE metadata.'
year: 2017
- doi: 10.1093/database/baw001
pmc: PMC4792520
pubmed: '26980513'
title: Principles of metadata organization at the ENCODE data coordination center.
year: 2016
- doi: 10.1093/nar/gkv1160
pmc: PMC4702836
pubmed: '26527727'
title: ENCODE data at the ENCODE portal.
year: 2015
- doi: 10.1093/database/bav010
pmc: PMC4360730
pubmed: '25776021'
title: Ontology application and use at the ENCODE DCC.
year: 2015
- doi: 10.1093/nar/gks1172
pmc: PMC3531152
pubmed: '23193274'
title: 'ENCODE data in the UCSC Genome Browser: year 5 update.'
year: 2012
- doi: 10.1093/nar/gkr1012
pmc: PMC3245183
pubmed: '22075998'
title: 'ENCODE whole-genome data in the UCSC Genome Browser: update 2012.'
year: 2011
- doi: 10.1093/nar/gkq1017
pmc: PMC3013645
pubmed: '21037257'
title: ENCODE whole-genome data in the UCSC genome browser (2011 update).
year: 2010
- doi: 10.1093/nar/gkp961
pmc: PMC2808953
pubmed: '19920125'
title: ENCODE whole-genome data in the UCSC Genome Browser.
year: 2009
- doi: 10.1093/nar/gkl1017
pmc: PMC1781110
pubmed: '17166863'
title: The ENCODE Project at UC Santa Cruz.
year: 2006
- doi: 10.1126/science.1105136
pmc: null
pubmed: '15499007'
title: The ENCODE (ENCyclopedia Of DNA Elements) Project.
year: 2004
uri_format: https://www.encodeproject.org/$1
enm:
contact:
email: egon.willighagen@maastrichtuniversity.nl
github: null
name: Egon Willighagen
orcid: 0000-0001-7542-0286
description: The eNanoMapper project (https://www.enanomapper.net/), NanoCommons
project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/)
are creating a pan-European computational infrastructure for toxicological data
management for ENMs, based on semantic web standards and ontologies. This ontology
is an application ontology targeting the full domain of nanomaterial safety assessment.
It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO.
download_owl: http://enanomapper.github.io/ontologies/releases/9.0/enanomapper.owl
example: '8000221'
homepage: http://www.enanomapper.net/
keywords:
- health science
- ontology
mappings:
aberowl: ENM
bioportal: ENM
fairsharing: FAIRsharing.2gpf81
ols: enm
name: eNanoMapper ontology
pattern: ^\d+$
preferred_prefix: enm
publications:
- doi: 10.1186/s13326-015-0005-5
pmc: PMC4374589
pubmed: '25815161'
title: 'eNanoMapper: harnessing ontologies to enable data integration for nanomaterial
risk assessment.'
year: 2015
uri_format: http://purl.enanomapper.org/onto/ENM_$1
version: '9.0'
ensembl:
description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to
develop a software system which produces and maintains automatic annotation on
selected eukaryotic genomes. This collections also references outgroup organisms.
example: ENSG00000139618
example_extras:
- ENSG00000049246.14
- ENSG00000109819.9
- ENSG00000132326.12
- ENSG00000179094.16
- ENST00000264867.7
homepage: https://www.ensembl.org/
keywords:
- biomedical science
- comparative genomics
- genome
- genomics
mappings:
biocontext: ENSEMBL
edam: '2610'
fairsharing: FAIRsharing.fx0mw7
go: ENSEMBL
miriam: ensembl
n2t: ensembl
ncbi: ENSEMBL
prefixcommons: ensembl
re3data: r3d100010228
uniprot: DB-0023
wikidata: P594
mastodon: ensembl@genomic.social
name: Ensembl Gene
pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$
preferred_prefix: ensembl
providers:
- code: 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
- 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: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ensembl:$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
publications:
- doi: 10.1093/nar/gkab1049
pmc: PMC8728283
pubmed: '34791404'
title: Ensembl 2022.
year: 2022
- doi: 10.1093/nar/gkz966
pmc: PMC7145704
pubmed: '31691826'
title: Ensembl 2020.
year: 2020
- doi: 10.1093/nar/gky1113
pmc: PMC6323964
pubmed: '30407521'
title: Ensembl 2019.
year: 2019
- doi: 10.1093/nar/gkw1104
pmc: PMC5210575
pubmed: '27899575'
title: Ensembl 2017.
year: 2016
- doi: 10.1093/database/baw093
pmc: PMC4919035
pubmed: '27337980'
title: The Ensembl gene annotation system.
year: 2016
- doi: 10.1186/s13059-016-0974-4
pmc: PMC4893825
pubmed: '27268795'
title: The Ensembl Variant Effect Predictor.
year: 2016
- doi: 10.1093/database/baw053
pmc: PMC4852398
pubmed: '27141089'
title: Ensembl comparative genomics resources.
year: 2016
- doi: 10.1093/database/bav127
pmc: PMC4792531
pubmed: '26980512'
title: ncRNA orthologies in the vertebrate lineage.
year: 2016
- doi: 10.1093/database/bav096
pmc: PMC4761110
pubmed: '26896847'
title: Ensembl comparative genomics resources.
year: 2016
- doi: 10.1093/database/bav119
pmc: PMC4756621
pubmed: '26888907'
title: Ensembl regulation resources.
year: 2016
- doi: 10.1093/nar/gkv1157
pmc: PMC4702834
pubmed: '26687719'
title: Ensembl 2016.
year: 2015
- doi: 10.1186/s13059-015-0621-5
pmc: PMC4407537
pubmed: '25887522'
title: The ensembl regulatory build.
year: 2015
- doi: doi:10.1093/nar/gku1010
pmc: PMC4383879
pubmed: '25352552'
title: Ensembl 2015
year: null
- doi: 10.1093/nar/gku1010
pmc: PMC4383879
pubmed: '25352552'
title: Ensembl 2015.
year: 2014
- doi: 10.1093/bioinformatics/btu613
pmc: PMC4271150
pubmed: '25236461'
title: 'The Ensembl REST API: Ensembl Data for Any Language.'
year: 2014
- doi: 10.1093/bioinformatics/btt737
pmc: PMC3967112
pubmed: '24363377'
title: 'WiggleTools: parallel processing of large collections of genome-wide datasets
for visualization and statistical analysis.'
year: 2013
- doi: 10.1093/nar/gkt1196
pmc: PMC3964975
pubmed: '24316576'
title: Ensembl 2014.
year: 2013
- doi: 10.1093/nar/gks1236
pmc: PMC3531136
pubmed: '23203987'
title: Ensembl 2013.
year: 2012
- doi: 10.1101/gr.135350.111
pmc: PMC3431492
pubmed: '22955987'
title: 'GENCODE: the reference human genome annotation for The ENCODE Project.'
year: 2012
- doi: 10.1101/gr.137901.112
pmc: PMC3460200
pubmed: '22798491'
title: Incorporating RNA-seq data into the zebrafish Ensembl genebuild.
year: 2012
- doi: 10.1093/nar/gkr991
pmc: PMC3245178
pubmed: '22086963'
title: Ensembl 2012.
year: 2011
- doi: 10.1093/database/bar030
pmc: PMC3170168
pubmed: '21785142'
title: 'Ensembl BioMarts: a hub for data retrieval across taxonomic space.'
year: 2011
- doi: 10.1002/0471142905.hg0611s69
pmc: PMC3099348
pubmed: '21400687'
title: Disease and phenotype data at Ensembl.
year: 2011
- doi: 10.1093/nar/gkq1064
pmc: PMC3013672
pubmed: '21045057'
title: Ensembl 2011.
year: 2010
- doi: 10.1093/bioinformatics/btq330
pmc: PMC2916720
pubmed: '20562413'
title: Deriving the consequences of genomic variants with the Ensembl API and
SNP Effect Predictor.
year: 2010
- doi: 10.1186/1471-2105-11-240
pmc: PMC2885371
pubmed: '20459813'
title: 'eHive: an artificial intelligence workflow system for genomic analysis.'
year: 2010
- doi: 10.1186/1471-2105-11-238
pmc: PMC2882931
pubmed: '20459810'
title: A database and API for variation, dense genotyping and resequencing data.
year: 2010
- doi: 10.1186/1471-2164-11-295
pmc: PMC2894802
pubmed: '20459808'
title: 'Touring Ensembl: a practical guide to genome browsing.'
year: 2010
- doi: 10.1186/1471-2164-11-293
pmc: PMC2894800
pubmed: '20459805'
title: Ensembl variation resources.
year: 2010
- doi: 10.1093/nar/gkp972
pmc: PMC2808936
pubmed: '19906699'
title: Ensembl's 10th year.
year: 2009
- doi: 10.1093/nar/gkn828
pmc: PMC2686571
pubmed: '19033362'
title: Ensembl 2009.
year: 2008
- doi: 10.1101/gr.073585.107
pmc: PMC2652215
pubmed: '19029536'
title: 'EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees
in vertebrates.'
year: 2008
- doi: 10.1101/gr.076521.108
pmc: PMC2577868
pubmed: '18849525'
title: Genome-wide nucleotide-level mammalian ancestor reconstruction.
year: 2008
- doi: 10.1093/nar/gkm988
pmc: PMC2238821
pubmed: '18000006'
title: Ensembl 2008.
year: 2007
- doi: 10.1093/bfgp/elm025
pmc: null
pubmed: '17967807'
title: 'Genome browsing with Ensembl: a practical overview.'
year: 2007
- doi: 10.1093/nar/gkl996
pmc: PMC1761443
pubmed: '17148474'
title: Ensembl 2007.
year: 2006
- doi: 10.1038/ng0806-853a
pmc: PMC2610433
pubmed: '16874317'
title: 'TranscriptSNPView: a genome-wide catalog of mouse coding variation.'
year: 2006
- doi: 10.1093/nar/gkj133
pmc: PMC1347495
pubmed: '16381931'
title: Ensembl 2006.
year: 2006
- doi: 10.1093/nar/gki138
pmc: PMC540092
pubmed: '15608235'
title: Ensembl 2005.
year: 2005
- doi: 10.1016/j.tig.2004.04.002
pmc: null
pubmed: '15145580'
title: Genome information resources - developments at Ensembl.
year: 2004
- doi: 10.1101/gr.1862204
pmc: PMC479129
pubmed: '15123595'
title: 'ESTGenes: alternative splicing from ESTs in Ensembl.'
year: 2004
- doi: 10.1101/gr.1866304
pmc: PMC479128
pubmed: '15123594'
title: The Ensembl computing architecture.
year: 2004
- doi: 10.1101/gr.1863004
pmc: PMC479125
pubmed: '15123591'
title: 'The Ensembl Web site: mechanics of a genome browser.'
year: 2004
- doi: 10.1101/gr.1858004
pmc: PMC479124
pubmed: '15123590'
title: The Ensembl automatic gene annotation system.
year: 2004
- doi: 10.1101/gr.1859804
pmc: PMC479123
pubmed: '15123589'
title: The Ensembl analysis pipeline.
year: 2004
- doi: 10.1101/gr.1857204
pmc: PMC479122
pubmed: '15123588'
title: The Ensembl core software libraries.
year: 2004
- doi: 10.1093/nar/gkg083
pmc: PMC165530
pubmed: '12519943'
title: 'Ensembl 2002: accommodating comparative genomics.'
year: 2003
- doi: 10.1093/nar/30.1.38
pmc: PMC99161
pubmed: '11752248'
title: The Ensembl genome database project.
year: 2002
rdf_uri_format: http://rdf.ebi.ac.uk/resource/ensembl/$1
synonyms:
- Ensembl
twitter: ensembl
uri_format: https://www.ensembl.org/id/$1
ensembl.bacteria:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with bacterial
genomes.
example: MU9_3181
homepage: https://bacteria.ensembl.org/
keywords:
- comparative genomics
- genome
- genomics
mappings:
biocontext: ENSEMBL.BACTERIA
fairsharing: FAIRsharing.zsgmvd
miriam: ensembl.bacteria
n2t: ensembl.bacteria
prefixcommons: ensembl.bacteria
re3data: r3d100011195
uniprot: DB-0147
name: Ensembl Bacteria
part_of: ensembl
pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$
preferred_prefix: ensembl.bacteria
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ensembl.bacteria:$1
publications:
- doi: 10.1093/nar/gkz890
pmc: PMC6943047
pubmed: '31598706'
title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
year: 2020
- doi: 10.1093/nar/gkv1209
pmc: PMC4702859
pubmed: '26578574'
title: 'Ensembl Genomes 2016: more genomes, more complexity.'
year: 2015
- doi: 10.1093/nar/gkp871
pmc: PMC2808935
pubmed: '19884133'
title: 'Ensembl Genomes: extending Ensembl across the taxonomic space.'
year: 2009
twitter: ensemblgenomes
uri_format: https://bacteria.ensembl.org/id/$1
ensembl.fungi:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes.
example: CADAFLAT00006211
homepage: https://fungi.ensembl.org/
keywords:
- comparative genomics
- genome
- genomics
mappings:
biocontext: ENSEMBL.FUNGI
fairsharing: FAIRsharing.bg5xqs
go: EnsemblFungi
miriam: ensembl.fungi
n2t: ensembl.fungi
prefixcommons: ensembl.fungi
re3data: r3d100011196
uniprot: DB-0148
name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi.
part_of: ensembl
pattern: ^[A-Z-a-z0-9]+$
preferred_prefix: ensembl.fungi
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ensembl.fungi:$1
publications:
- doi: 10.1093/nar/gkz890
pmc: PMC6943047
pubmed: '31598706'
title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
year: 2020
- doi: 10.1093/nar/gkv1209
pmc: PMC4702859
pubmed: '26578574'
title: 'Ensembl Genomes 2016: more genomes, more complexity.'
year: 2015
twitter: ensemblgenomes
uri_format: https://fungi.ensembl.org/id/$1
ensembl.metazoa:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes.
example: FBtr0084214
homepage: https://metazoa.ensembl.org/
keywords:
- comparative genomics
- genome
- genomics
mappings:
biocontext: ENSEMBL.METAZOA
fairsharing: FAIRsharing.c23cqq
go: EnsemblMetazoa
miriam: ensembl.metazoa
n2t: ensembl.metazoa
prefixcommons: ensembl.metazoa
re3data: r3d100011198
uniprot: DB-0149
name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from
non-vertebrate metazoa.
pattern: ^\w+(\.)?\d+$
preferred_prefix: ensembl.metazoa
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ensembl.metazoa:$1
publications:
- doi: 10.1093/nar/gkz890
pmc: PMC6943047
pubmed: '31598706'
title: Ensembl Genomes 2020-enabling non-vertebrate genomic research.
year: 2020
- doi: 10.1093/nar/gkv1209
pmc: PMC4702859
pubmed: '26578574'
title: 'Ensembl Genomes 2016: more genomes, more complexity.'
year: 2015
twitter: ensemblgenomes
uri_format: https://metazoa.ensembl.org/id/$1
ensembl.plant:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with plant genomes.
example: AT1G73965
homepage: https://plants.ensembl.org/
keywords:
- genome
mappings:
biocontext: ENSEMBL.PLANT
miriam: ensembl.plant
n2t: ensembl.plant
prefixcommons: ensembl.plant
name: Ensembl Plants
pattern: ^\w+(\.\d+)?(\.\d+)?$
preferred_prefix: ensembl.plant
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ensembl.plant:$1
uri_format: https://plants.ensembl.org/id/$1
ensembl.protist:
description: Ensembl Genomes consists of five sub-portals (for bacteria, protists,
fungi, plants and invertebrate metazoa) designed to complement the availability
of vertebrate genomes in Ensembl. This collection is concerned with protist genomes.
example: PF3D7_1328700
homepage: https://protists.ensembl.org
keywords:
- genome
mappings:
biocontext: ENSEMBL.PROTIST
miriam: ensembl.protist
n2t: ensembl.protist
prefixcommons: ensembl.protist
name: Ensembl Protists
pattern: ^\w+$
preferred_prefix: ensembl.protist
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ensembl.protist:$1
uri_format: https://protists.ensembl.org/id/$1
ensemblglossary:
description: The Ensembl glossary lists the terms, data types and file types that
are used in Ensembl and describes how they are used.
download_owl: http://ensembl.org/glossary/ensembl-glossary/releases/2023-01-04/ensembl-glossary.owl
example: 0000198
homepage: http://ensembl.org/glossary
keywords:
- ontology
mappings:
ols: ensemblglossary
name: Ensembl Glossary
pattern: ^\d{7}$
preferred_prefix: ensemblglossary
uri_format: http://ensembl.org/glossary/ENSGLOSSARY_$1
version: '2023-01-04'
envipath:
contact:
email: admin@envipath.org
github: null
name: Jörg Wicker
orcid: 0000-0003-0533-3368
description: enviPath is a database and prediction system for the microbial biotransformation
of organic environmental contaminants. The database provides the possibility to
store and view experimentally observed biotransformation pathways. The pathway
prediction system provides different relative reasoning models to predict likely
biotransformation pathways and products.
example: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea
homepage: https://envipath.org/
keywords:
- environmental science
mappings:
fairsharing: FAIRsharing.g0c5qn
miriam: envipath
re3data: r3d100012715
name: enviPath
pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$
preferred_prefix: envipath
publications:
- doi: 10.1186/s13321-021-00543-x
pmc: PMC8414759
pubmed: '34479624'
title: 'Holistic evaluation of biodegradation pathway prediction: assessing multi-step
reactions and intermediate products.'
year: 2021
- doi: 10.1039/c6em00697c
pmc: null
pubmed: '28229138'
title: 'Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide
soil biodegradation pathways and half-life data.'
year: 2017
- doi: 10.1093/nar/gkv1229
pmc: PMC4702869
pubmed: '26582924'
title: enviPath--The environmental contaminant biotransformation pathway resource.
year: 2015
twitter: envipath
uri_format: https://envipath.org/package/$1
envo:
appears_in:
- agro
- cdno
- ecocore
- ecto
- foodon
- ons
- pco
- rbo
- scdo
banana: ENVO
contact:
email: pier.buttigieg@awi.de
github: pbuttigieg
name: Pier Luigi Buttigieg
orcid: 0000-0002-4366-3088
depends_on:
- chebi
- foodon
- go
- ncbitaxon
- pco
- po
- ro
- uberon
description: The Environment Ontology is a resource and research target for the
semantically controlled description of environmental entities. The ontology's
initial aim was the representation of the biomes, environmental features, and
environmental materials pertinent to genomic and microbiome-related investigations.
download_json: http://purl.obolibrary.org/obo/envo.json
download_obo: http://purl.obolibrary.org/obo/envo.obo
download_owl: http://purl.obolibrary.org/obo/envo.owl
example: 09200010
homepage: http://environmentontology.org/
keywords:
- ecology
- environmental science
- epidemiology
- life science
- nutritional science
- obo
- ontology
license: CC0-1.0
logo: https://obofoundry.org/images/envo.png
mappings:
aberowl: ENVO
agroportal: ENVO
biocontext: ENVO
bioportal: ENVO
fairsharing: FAIRsharing.azqskx
miriam: envo
n2t: envo
obofoundry: envo
ols: envo
ontobee: ENVO
name: Environment Ontology
namespace_in_lui: true
pattern: ^\d{7,8}$
preferred_prefix: ENVO
publications:
- doi: 10.1186/s13326-016-0097-6
pmc: PMC5035502
pubmed: '27664130'
title: 'The environment ontology in 2016: bridging domains with increased scope,
semantic density, and interoperation.'
year: 2016
- doi: 10.1093/database/baw005
pmc: PMC4761108
pubmed: '26896844'
title: 'EXTRACT: interactive extraction of environment metadata and term suggestion
for metagenomic sample annotation.'
year: 2016
- doi: 10.7717/peerj.1470
pmc: PMC4690371
pubmed: '26713234'
title: Emerging semantics to link phenotype and environment.
year: 2015
- doi: 10.1186/2041-1480-4-43
pmc: PMC3904460
pubmed: '24330602'
title: 'The environment ontology: contextualising biological and biomedical entities.'
year: 2013
rdf_uri_format: http://purl.obolibrary.org/obo/ENVO_$1
repository: https://github.com/EnvironmentOntology/envo
twitter: envoTweets
uri_format: https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1
version: '2023-02-13'
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
keywords:
- antibodies
- life sciences
- vendor
name: Enzo Life Sciences
preferred_prefix: enzo
synonyms:
- Enzo Life Sciences
uri_format: https://www.enzolifesciences.com/$1
eo:
appears_in:
- foodon
banana: EO
contact:
email: jaiswalp@science.oregonstate.edu
github: jaiswalp
name: Pankaj Jaiswal
orcid: 0000-0002-1005-8383
deprecated: true
description: The Plant Environment Ontology is a set of standardized controlled
vocabularies to describe various types of treatments given to an individual plant
/ a population or a cultured tissue and/or cell type sample to evaluate the response
on its exposure. It also includes the study types, where the terms can be used
to identify the growth study facility. Each growth facility such as field study,
growth chamber, green house etc is a environment on its own it may also involve
instances of biotic and abiotic environments as supplemental treatments used in
these studies.
download_obo: http://purl.obolibrary.org/obo/eo.obo
download_owl: http://purl.obolibrary.org/obo/eo.owl
example: '0007404'
homepage: http://planteome.org/
keywords:
- obo
- ontology
- plant
license: CC-BY-4.0
logo: http://planteome.org/sites/default/files/garland_logo.PNG
mappings:
aberowl: EO
agroportal: EO
biocontext: EO
miriam: eo
n2t: eo
obofoundry: eo
prefixcommons: eo
name: Plant Environment Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: EO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/eo:$1
publications:
- doi: 10.3732/ajb.1200222
pmc: PMC3492881
pubmed: '22847540'
title: Ontologies as integrative tools for plant science.
year: 2012
rdf_uri_format: http://purl.obolibrary.org/obo/EO_$1
repository: https://github.com/Planteome/plant-environment-ontology
uri_format: http://archive.gramene.org/db/ontology/search?query=EO:$1
eol:
contact:
email: pylebail@rennes.inra.fr
github: null
name: Pierre-Yves LeBail
orcid: 0000-0002-8310-5195
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The EOL ontology describes environmental conditions of livestock farms.
More specifically, it describes the feeding modalities, the environment, the structure
of livestock farms and rearing systems.
download_owl: http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl
example: 0001927
homepage: http://www.atol-ontology.com
keywords:
- agriculture
- animal husbandry
- environmental science
- ontology
mappings:
aberowl: EOL
agroportal: EOL
bioportal: EOL
fairsharing: FAIRsharing.w7bw2y
ols: eol
re3data: r3d100011663
name: Environment Ontology for Livestock
pattern: ^\d{7}$
preferred_prefix: eol
uri_format: http://purl.org/obo/owlEOL_$1
version: '2018-09-13'
eolife:
contact:
email: secretariat@eol.org
github: null
name: EOL Secretariat
orcid: 0000-0002-9943-2342
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A collaborative project intended to create an encyclopedia documenting
all living species known to science
example: '1044544'
homepage: https://eol.org
keywords:
- biodiversity
- biology
- ecology
- taxonomy
mappings:
fairsharing: FAIRsharing.3J6NYn
re3data: r3d100010229
wikidata: P830
name: Encyclopedia of Life
pattern: ^\d+$
preferred_prefix: eolife
twitter: eol
uri_format: https://eol.org/pages/$1
epcc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Collection of European paediatric cardiac coding files
homepage: https://www.aepc.org/european-paediatric-cardiac-coding
name: European Paediatric Cardiac Codes
preferred_prefix: epcc
proprietary: true
references:
- https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE
epd:
contact:
email: Philipp.Bucher@sib.swiss
github: null
name: Philipp Bucher
orcid: 0000-0002-0816-7775
contributor_extras:
- email: sebastien.moretti@sib.swiss
github: smoretti
name: Sebastien Moretti
orcid: 0000-0003-3947-488X
description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant
collection of eukaryotic POL II promoters, for which the transcription start site
has been determined experimentally. Access to promoter sequences is provided by
pointers to positions in nucleotide sequence entries. The annotation part of an
entry includes description of the initiation site mapping data, cross-references
to other databases, and bibliographic references. EPD is structured in a way that
facilitates dynamic extraction of biologically meaningful promoter subsets for
comparative sequence analysis.
example: TA_H3
homepage: https://epd.expasy.org/epd/
keywords:
- bioinformatics
- biology
mappings:
biocontext: EPD
edam: '2386'
fairsharing: FAIRsharing.yk1krv
miriam: epd
n2t: epd
ncbi: EPD
uniprot: DB-0205
name: Eukaryotic Promoter Database
pattern: ^[A-Z-_0-9]+$
preferred_prefix: epd
publications:
- doi: 10.1093/nar/27.1.307
pmc: PMC148166
pubmed: '9847211'
title: 'The Eukaryotic Promoter Database (EPD): recent developments.'
year: 1999
- doi: 10.1093/nar/26.1.353
pmc: PMC147208
pubmed: '9399872'
title: The Eukaryotic Promoter Database EPD.
year: 1998
- doi: 10.1093/nar/14.24.10009
pmc: PMC341352
pubmed: '3808945'
title: Compilation and analysis of eukaryotic POL II promoter sequences.
year: 1986
- doi: 10.1093/nar/gkx807
pmc: PMC5753345
pubmed: '28981707'
title: 'The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics.'
year: 2018
- doi: 10.1093/nar/gkw1069
pmc: PMC5210552
pubmed: '27899657'
title: 'The eukaryotic promoter database in its 30th year: focus on non-vertebrate
organisms.'
year: 2016
- doi: 10.1093/nar/gku1111
pmc: PMC4383928
pubmed: '25378343'
title: 'The Eukaryotic Promoter Database: expansion of EPDnew and new promoter
analysis tools.'
year: 2014
- doi: 10.1093/nar/gks1233
pmc: PMC3531148
pubmed: '23193273'
title: EPD and EPDnew, high-quality promoter resources in the next-generation
sequencing era.
year: 2012
- doi: 10.1093/nar/gkj146
pmc: PMC1347508
pubmed: '16381980'
title: 'EPD in its twentieth year: towards complete promoter coverage of selected
model organisms.'
year: 2006
- doi: 10.1093/nar/gkh122
pmc: PMC308856
pubmed: '14681364'
title: 'The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.'
year: 2004
- doi: 10.1093/nar/30.1.322
pmc: PMC99099
pubmed: '11752326'
title: 'The Eukaryotic Promoter Database, EPD: new entry types and links to gene
expression data.'
year: 2002
- doi: 10.1093/nar/28.1.302
pmc: PMC102462
pubmed: '10592254'
title: The eukaryotic promoter database (EPD).
year: 2000
uri_format: https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1
epio:
contact:
email: alpha.tom.kodamullil@scai.fraunhofer.de
github: akodamullil
name: Alpha Tom Kodamullil
orcid: 0000-0001-9896-3531
depends_on:
- bfo
description: A application driven Epilepsy Ontology with official terms from the
ILAE.
download_owl: http://purl.obolibrary.org/obo/epio.owl
example: '0000011'
homepage: https://github.com/SCAI-BIO/EpilepsyOntology
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: EPIO
bioportal: EPIO
obofoundry: epio
ontobee: EPIO
name: Epilepsy Ontology
pattern: ^\d{7}$
preferred_prefix: EPIO
rdf_uri_format: http://purl.obolibrary.org/obo/EPIO_$1
repository: https://github.com/SCAI-BIO/EpilepsyOntology
uri_format: http://purl.obolibrary.org/obo/EPIO_$1
epo:
contributor_extras:
- email: null
github: djinnome
name: Jeremy Zucker
orcid: 0000-0002-7276-9009
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/
keywords:
- obo
- ontology
mappings:
biocontext: EPO
obofoundry: epo
ontobee: EPO
name: Epidemiology Ontology
preferred_prefix: EPO
rdf_uri_format: http://purl.obolibrary.org/obo/EPO_$1
uri_format: http://purl.obolibrary.org/obo/EPO_$1
epso:
contact:
email: satyasahoo@ieee.org
github: null
name: Satya S. Sahoo
orcid: 0000-0001-9190-4256
description: 'The Epilepsy and Seizure Ontology (EpSO) is an application ontology
developed to support epilepsy focused informatics tools for patient care and clinical
research. '
download_owl: http://aber-owl.net/media/ontologies/EPSO/3/epso.owl
example: '0000400'
homepage: http://prism.case.edu/prism/index.php/EpilepsyOntology
keywords:
- neurology
- ontology
mappings:
aberowl: EPSO
bioportal: EPSO
fairsharing: FAIRsharing.ttprgy
ontobee: EPSO
name: Epilepsy and Seizure Ontology
pattern: ^\d{7}$
preferred_prefix: epso
publications:
- doi: 10.1136/amiajnl-2013-001696
pmc: PMC3912711
pubmed: '23686934'
title: 'Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure
for clinical research and patient care.'
year: 2013
uri_format: http://www.case.edu/EpilepsyOntology.owl#$1
erm:
contact:
email: egon.willighagen@gmail.com
github: egonw
name: Egon Willighagen
orcid: 0000-0001-7542-0286
description: The European Registry of Materials is a simple registry with the sole
purpose to mint material identifiers to be used by research projects throughout
the life cycle of their project.
download_rdf: https://nanocommons.github.io/identifiers/registry
example: ERM00000044
homepage: https://nanocommons.github.io/identifiers/
keywords:
- materials informatics
- nanotechnology
mappings:
cheminf: 000569
fairsharing: FAIRsharing.c26a4e
miriam: erm
n2t: erm
name: European Registry of Materials
pattern: ^ERM[0-9]{8}$
preferred_prefix: erm
publications:
- doi: 10.1186/s13321-022-00614-7
pmc: PMC9400299
pubmed: '36002868'
title: 'European Registry of Materials: global, unique identifiers for (undisclosed)
nanomaterials.'
year: 2022
twitter: nanocommons
uri_format: https://nanocommons.github.io/identifiers/registry#$1
ero:
contact:
email: Marc_Ciriello@hms.harvard.edu
github: null
name: Marc Ciriello
orcid: 0000-0002-3734-1859
deprecated: true
description: An ontology of research resources such as instruments. protocols, reagents,
animal models and biospecimens.
download_owl: http://purl.obolibrary.org/obo/ero.owl
example: '0001655'
homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
keywords:
- biomedical science
- life science
- obo
- ontology
license: CC BY 2.0
mappings:
aberowl: ERO
biocontext: ERO
bioportal: ERO
fairsharing: FAIRsharing.nwgynk
obofoundry: ero
ols: ero
ontobee: ERO
name: eagle-i resource ontology
pattern: ^\d{7}$
preferred_prefix: ERO
publications:
- doi: 10.1109/jcdl.2017.7991571
pmc: PMC5868434
pubmed: '29599662'
title: 'Automating data citation: the eagle-i experience.'
year: 2017
- doi: 10.1093/database/bar067
pmc: PMC3308157
pubmed: '22434835'
title: 'Research resources: curating the new eagle-i discovery system.'
year: 2012
rdf_uri_format: http://purl.obolibrary.org/obo/ERO_$1
uri_format: http://purl.obolibrary.org/obo/ERO_$1
version: '2016-07-27'
eropmoscow:
description: EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence
database which strives to provide a high level of annotations (such as descriptions
of the structure of an oligopeptide, its source and function, post-translational
modifications, etc.).
example: E00002
homepage: http://erop.inbi.ras.ru
keywords:
- protein
mappings:
prefixcommons: eropmoscow
name: Endogenous Regulatory OligoPeptide knowledgebase-Moscow
preferred_prefix: eropmoscow
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/eropmoscow:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://erop.inbi.ras.ru/result2.php?PepName=$1
erv:
description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a
typical mammalian genome contains tens to hundreds of thousands of ERV elements.
Most ERVs are evolutionarily old and have accumulated multiple mutations, playing
important roles in physiology and disease processes. The Human Endogenous Retrovirus
Database (hERV) is compiled from the human genome nucleotide sequences obtained
from Human Genome Projects, and screens those sequences for hERVs, whilst continuously
improving classification and characterization of retroviral families. It provides
access to individual reconstructed HERV elements, their sequence, structure and
features.
example: THE1B
homepage: https://herv.img.cas.cz/
mappings:
biocontext: ERV
miriam: erv
n2t: erv
name: Human Endogenous Retrovirus Database
pattern: ^[A-Za-z0-9\-\_]+$
preferred_prefix: erv
uri_format: https://herv.img.cas.cz/s/$1
esldb:
description: eSLDB is a database of protein subcellular localization annotation
for eukaryotic organisms. It contains experimental annotations derived from primary
protein databases, homology based annotations and computational predictions.
example: HS000015122
homepage: http://gpcr.biocomp.unibo.it/esldb
keywords:
- protein
mappings:
prefixcommons: esldb
name: eukaryotic Subcellular Localization database
preferred_prefix: esldb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/esldb:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1
estdab:
comment: Website is dead
deprecated: true
description: Cell line databases/resources
example: '046'
homepage: https://www.ebi.ac.uk/ipd/estdab/
mappings:
cellosaurus: ESTDAB
name: European Searchable Tumour Line Database
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^\d{3}$
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
synonyms:
- EUCTR
uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1
eugenes:
contact:
email: eugenes@iubio.bio.indiana.edu
github: null
name: Don Gilbert
orcid: 0000-0002-6646-7274
description: euGenes provides a common summary of gene and genomic information from
eukaryotic organism databases including gene symbol and full name, chromosome,
genetic and molecular map information, Gene Ontology (Function/Location/Process)
and gene homology, product information.
example: MGgn0008978
homepage: http://eugenes.org/
keywords:
- genome
- life science
- ontology
mappings:
fairsharing: FAIRsharing.7fc5y6
prefixcommons: eugenes
name: Eukaryotic Genes
preferred_prefix: eugenes
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/eugenes:$1
publications:
- doi: 10.1093/nar/30.1.145
pmc: PMC99146
pubmed: '11752277'
title: 'euGenes: a eukaryote genome information system.'
year: 2002
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://eugenes.org:7072/.bin/fbidq.html?$1
eupath:
appears_in:
- scdo
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
description: The VEuPathDB ontology is an application ontology developed to encode
our understanding of what data is about in the public resources developed and
maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB;
https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB
ontology prior to EuPathDB joining with VectorBase.The ontology was built based
on the Ontology of Biomedical Investigations (OBI) with integration of other OBO
ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the
VEuPath ontology is primarily intended to be used for support of the VEuPathDB
sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will
be submitted to OBO Foundry ontologies for subsequent import and replacement of
those terms when they are available.
download_owl: http://purl.obolibrary.org/obo/eupath.owl
example: '0010316'
homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
keywords:
- biomedical science
- epidemiology
- functional genomics
- obo
- ontology
- population genetics
license: CC-BY-4.0
logo: https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png
mappings:
aberowl: EUPATH
biocontext: EUPATH
bioportal: EUPATH
fairsharing: FAIRsharing.9rhr9j
obofoundry: eupath
ols: eupath
ontobee: EUPATH
name: VEuPathDB ontology
pattern: ^\d{7}$
preferred_prefix: EUPATH
publications:
- doi: 10.5281/zenodo.6685957
pmc: null
pubmed: null
title: Malaria study data integration and information retrieval based on OBO Foundry
ontologies
year: 2016
rdf_uri_format: http://purl.obolibrary.org/obo/EUPATH_$1
repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
uri_format: http://purl.obolibrary.org/obo/EUPATH_$1
version: '2023-03-20'
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
contact:
email: evoc@sanbi.ac.za
github: null
name: eVOC mailing list
orcid: null
deprecated: true
description: Provides structured controlled vocabularies for the annotation of expressed
sequences with respect to anatomical system, cell type, developmental stage, experimental
technique, microarray platform, pathology, pooling, tissue preparation and treatment.
example: EV_0100011
homepage: http://www.evocontology.org/
keywords:
- anatomy
- cell
- development
- experiment
- obo
- ontology
mappings:
biocontext: EV
obofoundry: ev
prefixcommons: evoc
name: eVOC (Expressed Sequence Annotation for Humans)
preferred_prefix: EV
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/evoc:$1
rdf_uri_format: http://purl.obolibrary.org/obo/EV_$1
references:
- https://twitter.com/Bgeedb/status/1350124337815281664
uri_format: http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1
evm:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
name: eVOC mouse development stage
preferred_prefix: evm
references:
- https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229
exac.gene:
description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators
seeking to aggregate and harmonize exome sequencing data from a variety of large-scale
sequencing projects, and to make summary data available for the wider scientific
community. The data pertains to unrelated individuals sequenced as part of various
disease-specific and population genetic studies and serves as a reference set
of allele frequencies for severe disease studies. This collection references gene
information.
example: ENSG00000169174
homepage: http://exac.broadinstitute.org/
mappings:
biocontext: EXAC.GENE
miriam: exac.gene
n2t: exac.gene
name: ExAC Gene
pattern: ^ENSG\d{11}$
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/$1
exo:
appears_in:
- ecto
- scdo
contact:
email: annethessen@gmail.com
github: diatomsRcool
name: Anne Thessen
orcid: 0000-0002-2908-3327
description: ExO is intended to bridge the gap between exposure science and diverse
environmental health disciplines including toxicology, epidemiology, disease surveillance,
and epigenetics.
download_obo: http://purl.obolibrary.org/obo/exo.obo
download_owl: http://purl.obolibrary.org/obo/exo.owl
example: 0000078
homepage: https://github.com/CTDbase/exposure-ontology
keywords:
- environmental science
- epigenetics
- obo
- ontology
- toxicology
license: CC-BY-4.0
mappings:
aberowl: EXO
biocontext: EXO
biolink: ExO
bioportal: EXO
fairsharing: FAIRsharing.6hna78
obofoundry: exo
ols: exo
ontobee: ExO
name: Exposure ontology
pattern: ^\d{7}$
preferred_prefix: ExO
publications:
- doi: 10.1021/es2033857
pmc: PMC3314380
pubmed: '22324457'
title: 'Providing the missing link: the exposure science ontology ExO.'
year: 2012
rdf_uri_format: http://purl.obolibrary.org/obo/ExO_$1
repository: https://github.com/CTDbase/exposure-ontology
synonyms:
- ExO
uri_format: http://purl.obolibrary.org/obo/ExO_$1
version: '2022-06-29'
fabio:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
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.
download_owl: http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl
example: d4e2515
homepage: https://github.com/sparontologies/fabio
keywords:
- ontology
- subject agnostic
mappings:
aberowl: FaBiO
biolink: fabio
fairsharing: FAIRsharing.2f3180
name: FaBiO, the FRBR-aligned Bibliographic Ontology
preferred_prefix: fabio
providers:
- code: rdf
description: A persistent URL for FaBiO
homepage: https://github.com/sparontologies/fabio
name: FABIO PURL
uri_format: http://purl.org/spar/fabio/$1
publications:
- doi: 10.1016/j.websem.2012.08.001
pmc: null
pubmed: null
title: 'FaBiO and CiTO: Ontologies for describing bibliographic resources and
citations'
year: 2012
repository: https://github.com/sparontologies/fabio
twitter: sparontologies
uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1
facebase:
description: FaceBase is a collaborative NIDCR-funded consortium to generate data
in support of advancing research into craniofacial development and malformation.
It serves as a community resource by generating large datasets of a variety of
types and making them available to the wider research community via this website.
Practices emphasize a comprehensive and multidisciplinary approach to understanding
the developmental processes that create the face. The data offered spotlights
high-throughput genetic, molecular, biological, imaging and computational techniques.
One of the missions of this consortium is to facilitate cooperation and collaboration
between projects.
example: FB00000917
homepage: https://www.facebase.org
keywords:
- anatomy
- developmental biology
- epigenetics
- genetics
- medicine
mappings:
biocontext: FACEBASE
fairsharing: FAIRsharing.mqvqde
miriam: facebase
n2t: facebase
re3data: r3d100013263
name: FaceBase Data Repository
pattern: ^FB\d{8}$
preferred_prefix: facebase
publications:
- doi: 10.1242/dev.191213
pmc: PMC7522026
pubmed: '32958507'
title: 'FaceBase 3: analytical tools and FAIR resources for craniofacial and dental
research.'
year: 2020
uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1
fairsharing:
contact:
email: allyson.lister@oerc.ox.ac.uk
github: null
name: Allyson Lister
orcid: 0000-0002-7702-4495
description: The web-based FAIRSharing catalogues aim to centralize bioscience data
policies, reporting standards and links to other related portals. This collection
references bioinformatics data exchange standards, which includes 'Reporting Guidelines',
Format Specifications and Terminologies.
example: bsg-000052
example_extras:
- FAIRsharing.CugtbQ
homepage: https://fairsharing.org/
keywords:
- agriculture
- biomedical science
- data governance
- database management
- earth science
- environmental science
- humanities
- life science
- natural science
- ontology and terminology
- policy
mappings:
biocontext: FAIRSHARING
fairsharing: FAIRsharing.2abjs5
miriam: fairsharing
n2t: fairsharing
re3data: r3d100010142
mastodon: fairsharing@fediscience.org
name: FAIRsharing
pattern: ^(bsg-[dscp]?\d{6})|(FAIRsharing\.\w+)$
preferred_prefix: fairsharing
publications:
- doi: 10.1038/s41587-019-0080-8
pmc: PMC6785156
pubmed: '30940948'
title: FAIRsharing as a community approach to standards, repositories and policies.
year: 2019
- doi: 10.1093/database/baw075
pmc: PMC4869797
pubmed: '27189610'
title: 'BioSharing: curated and crowd-sourced metadata standards, databases and
data policies in the life sciences.'
year: 2016
- doi: 10.5281/zenodo.5106255
pmc: null
pubmed: null
title: FAIRsharing, a FAIR-enabling service for repositories, standards and policies
year: 2021
repository: https://github.com/FAIRsharing
twitter: fairsharing_org
uri_format: https://fairsharing.org/$1
fairsharing.organization:
contact:
email: allyson.lister@oerc.ox.ac.uk
github: allysonlister
name: Allyson Lister
orcid: 0000-0002-7702-4495
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An organization in FAIRsharing, including universities, labs, etc.
example: '3851'
homepage: https://fairsharing.org
name: FAIRsharing Organization
part_of: fairsharing
pattern: ^\d+$
preferred_prefix: fairsharing.organization
uri_format: https://fairsharing.org/organisations/$1
fairsharing.user:
contact:
email: allyson.lister@oerc.ox.ac.uk
github: allysonlister
name: Allyson Lister
orcid: 0000-0002-7702-4495
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A user of FAIRsharing
example: '5112'
homepage: https://fairsharing.org
name: FAIRsharing User
part_of: fairsharing
pattern: ^\d+$
preferred_prefix: fairsharing.user
uri_format: https://fairsharing.org/users/$1
faldo:
contact:
email: faldo@googlegroups.com
github: null
name: FALDO group
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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
download_owl: http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl
example: ForwardStrandPosition
homepage: http://biohackathon.org/resource/faldo
keywords:
- genetics
- ontology
mappings:
aberowl: FALDO
agroportal: FALDO
biocontext: faldo
bioportal: FALDO
fairsharing: FAIRsharing.haxp7g
name: 'Feature Annotation Location Description Ontology '
preferred_prefix: faldo
publications:
- doi: 10.1186/s13326-016-0067-z
pmc: PMC4907002
pubmed: '27296299'
title: 'FALDO: a semantic standard for describing the location of nucleotide and
protein feature annotation.'
year: 2016
repository: https://github.com/OBF/FALDO
uri_format: http://biohackathon.org/resource/faldo#$1
fao:
contact:
email: vw253@cam.ac.uk
github: ValWood
name: Val Wood
orcid: 0000-0001-6330-7526
description: A structured controlled vocabulary for the anatomy of fungi.
download_obo: http://purl.obolibrary.org/obo/fao.obo
download_owl: http://purl.obolibrary.org/obo/fao.owl
example: '0000001'
homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
keywords:
- anatomy
- fungi
- life science
- microbiology
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: FAO
biocontext: FAO
bioportal: FAO
fairsharing: FAIRsharing.xs6t67
obofoundry: fao
ols: fao
ontobee: FAO
prefixcommons: fao
name: Fungal gross anatomy
pattern: ^\d{7}$
preferred_prefix: FAO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/fao:$1
rdf_uri_format: http://purl.obolibrary.org/obo/FAO_$1
repository: https://github.com/obophenotype/fungal-anatomy-ontology
uri_format: http://purl.obolibrary.org/obo/FAO_$1
version: '2020-05-07'
fbbi:
contact:
email: wawong@gmail.com
github: wawong
name: Willy Wong
orcid: 0000-0002-8841-5870
description: A structured controlled vocabulary of sample preparation, visualization
and imaging methods used in biomedical research.
download_obo: http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo
download_owl: http://purl.obolibrary.org/obo/fbbi.owl
example: 00000268
homepage: http://cellimagelibrary.org/
keywords:
- biomedical science
- experiment
- imaging
- life science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: FBbi
biocontext: FBbi
bioportal: FBbi
fairsharing: FAIRsharing.ny3z9j
obofoundry: fbbi
ols: fbbi
ontobee: FBbi
prefixcommons: fbbi
name: Biological Imaging Methods Ontology
pattern: ^\d+$
preferred_prefix: FBbi
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/fbbi:$1
rdf_uri_format: http://purl.obolibrary.org/obo/FBbi_$1
repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology
synonyms:
- FBbi
uri_format: http://purl.obolibrary.org/obo/FBbi_$1
version: '2020-11-06'
fbbt:
contact:
email: cp390@cam.ac.uk
github: Clare72
name: Clare Pilgrim
orcid: 0000-0002-1373-1705
description: An ontology of Drosophila melanogaster anatomy.
download_json: http://purl.obolibrary.org/obo/fbbt.json
download_obo: http://purl.obolibrary.org/obo/fbbt.obo
download_owl: http://purl.obolibrary.org/obo/fbbt.owl
example: 00007294
homepage: http://purl.obolibrary.org/obo/fbbt
keywords:
- anatomy
- developmental biology
- fly
- life science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: FBBT
biocontext: FBbt
bioportal: FB-BT
fairsharing: FAIRsharing.y2qkst
go: FBbt
obofoundry: fbbt
ols: fbbt
ontobee: FBbt
prefixcommons: fbbt
name: Drosophila gross anatomy
part_of: flybase
pattern: ^\d{8}$
preferred_prefix: FBbt
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/fbbt:$1
publications:
- doi: 10.1186/2041-1480-4-32
pmc: PMC4015547
pubmed: '24139062'
title: The Drosophila anatomy ontology.
year: 2013
- doi: 10.1093/bioinformatics/bts113
pmc: null
pubmed: '22402613'
title: A strategy for building neuroanatomy ontologies.
year: 2012
- doi: 10.1093/bioinformatics/btr677
pmc: null
pubmed: '22180411'
title: The Virtual Fly Brain browser and query interface.
year: 2011
- doi: 10.1093/nar/gkj068
pmc: PMC1347431
pubmed: '16381917'
title: 'FlyBase: anatomical data, images and queries.'
year: 2006
rdf_uri_format: http://purl.obolibrary.org/obo/FBbt_$1
repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology
synonyms:
- FBbt
- FBbt_root
uri_format: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1
version: '2023-02-08'
fbcv:
appears_in:
- ontoavida
contact:
email: cp390@cam.ac.uk
github: Clare72
name: Clare Pilgrim
orcid: 0000-0002-1373-1705
description: A miscellaneous ontology of terms used for curation in FlyBase, including
the DPO.
download_json: http://purl.obolibrary.org/obo/fbcv.json
download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo
download_owl: http://purl.obolibrary.org/obo/fbcv.owl
example: 0000586
homepage: http://purl.obolibrary.org/obo/fbcv
keywords:
- descriptor
- fly
- life science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: FBCV
biocontext: FBcv
bioportal: FB-CV
fairsharing: FAIRsharing.6tgyxf
obofoundry: fbcv
ols: fbcv
ontobee: FBcv
prefixcommons: fbcv
name: FlyBase Controlled Vocabulary
part_of: flybase
pattern: ^\d{7}$
preferred_prefix: FBcv
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/fbcv:$1
publications:
- doi: 10.1186/2041-1480-4-30
pmc: PMC3816596
pubmed: '24138933'
title: The Drosophila phenotype ontology.
year: 2013
rdf_uri_format: http://purl.obolibrary.org/obo/FBcv_$1
repository: https://github.com/FlyBase/flybase-controlled-vocabulary
synonyms:
- FBcv
uri_format: http://purl.obolibrary.org/obo/FBcv_$1
version: '2023-02-09'
fbdv:
contact:
email: cp390@cam.ac.uk
github: Clare72
name: Clare Pilgrim
orcid: 0000-0002-1373-1705
description: An ontology of Drosophila melanogaster developmental stages.
download_json: http://purl.obolibrary.org/obo/fbdv.json
download_obo: http://purl.obolibrary.org/obo/fbdv.obo
download_owl: http://purl.obolibrary.org/obo/fbdv.owl
example: '00000000'
homepage: http://purl.obolibrary.org/obo/fbdv
keywords:
- development
- developmental biology
- fly
- life science
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: FBDV
biocontext: FBdv
bioportal: FB-DV
fairsharing: FAIRsharing.p52pzj
obofoundry: fbdv
ols: fbdv
ontobee: FBdv
prefixcommons: fbdv
name: Drosophila development
pattern: ^\d{8}$
preferred_prefix: FBdv
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/fbdv:$1
rdf_uri_format: http://purl.obolibrary.org/obo/FBdv_$1
repository: https://github.com/FlyBase/drosophila-developmental-ontology
synonyms:
- FBdv
uri_format: http://purl.obolibrary.org/obo/FBdv_$1
version: '2023-02-08'
fbol:
comment: Website down, checked on 2021-10-07
deprecated: true
description: DNA barcoding is the use of short standardised segments of the genome
for identification of species in all the Kingdoms of Life. The goal of the Fungal
Barcoding site is to promote the DNA barcoding of fungi and other fungus-like
organisms.
example: '2224'
homepage: http://www.fungalbarcoding.org/
mappings:
biocontext: FBOL
miriam: fbol
n2t: fbol
ncbi: FBOL
name: International Fungal Working Group Fungal Barcoding.
pattern: ^\d+$
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$1
fbsp:
contact:
email: cp390@cam.ac.uk
github: Clare72
name: Clare Pilgrim
orcid: 0000-0002-1373-1705
deprecated: true
description: The taxonomy of the family Drosophilidae (largely after Baechli)
and of other taxa referred to in FlyBase.
download_obo: http://aber-owl.net/media/ontologies/FB-SP/7/fb-sp.obo
download_owl: http://purl.obolibrary.org/obo/fbsp.owl
example: '00000000'
homepage: http://www.flybase.org/
keywords:
- obo
- ontology
mappings:
aberowl: FB-SP
biocontext: FBSP
bioportal: FB-SP
obofoundry: fbsp
ols: fbsp
name: Fly taxonomy
part_of: flybase
pattern: ^\d{8}$
preferred_prefix: FBSP
rdf_uri_format: http://purl.obolibrary.org/obo/FBSP_$1
uri_format: http://purl.obolibrary.org/obo/FBSP_$1
version: '2017-11-19'
fbtc:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The cell line vocabulary inside FlyBase
example: 0000190
homepage: https://flybase.org
name: Flybase Cell Line
part_of: flybase
pattern: ^\d{7}$
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
fhir.implementation:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A set of guides on implementing various processes within hospitals
or healthcare systems.
example: immds
homepage: https://hl7.org/fhir/us/
name: FHIR United States Implementation Guides
preferred_prefix: fhir.implementation
uri_format: https://hl7.org/fhir/us/$1
fideo:
contact:
email: georgeta.bordea@u-bordeaux.fr
github: getbordea
name: Georgeta Bordea
orcid: 0000-0001-9921-8234
description: Food-Drug interactions automatically extracted from scientific literature
download_owl: http://purl.obolibrary.org/obo/fideo.owl
example: '00000021'
homepage: https://gitub.u-bordeaux.fr/erias/fideo
keywords:
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: FIDEO
bioportal: FIDEO
obofoundry: fideo
ols: fideo
ontobee: FIDEO
name: Food Interactions with Drugs Evidence Ontology
pattern: ^\d{8}$
preferred_prefix: FIDEO
rdf_uri_format: http://purl.obolibrary.org/obo/FIDEO_$1
repository: https://gitub.u-bordeaux.fr/erias/fideo
uri_format: http://purl.obolibrary.org/obo/FIDEO_$1
version: '2023-02-01'
fishbase.species:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'Global biodiversity database on finfishes. It offers a wide range
of information on all species currently known in the world: taxonomy, biology,
trophic ecology, life history, and uses, as well as historical data reaching back
to 250 years.'
example: '6472'
homepage: http://fishbase.org
mappings:
re3data: r3d100010912
wikidata: P938
name: FishBase
pattern: ^\d+$
preferred_prefix: fishbase.species
synonyms:
- fishbase
uri_format: https://www.fishbase.ca/summary/$1
fivestars:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology written in OWL 2 DL to enable characterization of the five
attributes of an online journal article - peer review, open access, enriched content,
available datasets and machine-readable metadata.
example: hasOpenAccessRating
homepage: http://www.sparontologies.net/ontologies/fivestars
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.6dfe9b
name: Five Stars of Online Research Articles Ontology
preferred_prefix: FiveStars
publications:
- doi: 10.1045/january2012-shotton
pmc: null
pubmed: null
title: The Five Stars of Online Journal Articles - a Framework for Article Evaluation
year: 2012
repository: https://github.com/sparontologies/fivestars
twitter: sparontologies
fix:
contact:
email: chebi-help@ebi.ac.uk
github: null
name: chEBI
orcid: null
deprecated: true
description: An ontology of physico-chemical methods and properties.
download_obo: http://purl.obolibrary.org/obo/fix.obo
download_owl: http://purl.obolibrary.org/obo/fix.owl
example: 0000390
homepage: https://www.ebi.ac.uk/chebi/
keywords:
- chemistry
- experiment
- obo
- ontology
- property
mappings:
aberowl: FIX
biocontext: FIX
bioportal: FIX
fairsharing: FAIRsharing.wwy1ns
obofoundry: fix
ols: fix
ontobee: FIX
prefixcommons: fix
name: Physico-chemical methods and properties
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
part_of: chebi
pattern: ^\d{7}$
preferred_prefix: FIX
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/fix:$1
rdf_uri_format: http://purl.obolibrary.org/obo/FIX_$1
uri_format: http://purl.obolibrary.org/obo/FIX_$1
version: '2020-04-13'
flopo:
contact:
email: robert.hoehndorf@kaust.edu.sa
github: leechuck
name: Robert Hoehndorf
orcid: 0000-0001-8149-5890
description: Traits and phenotypes of flowering plants occurring in digitized Floras
download_owl: http://purl.obolibrary.org/obo/flopo.owl
example: '0005250'
homepage: https://github.com/flora-phenotype-ontology/flopoontology
keywords:
- biodiversity
- botany
- obo
- ontology
- plant anatomy
license: CC0-1.0
mappings:
aberowl: FLOPO
agroportal: FLOPO
biocontext: FLOPO
bioportal: FLOPO
fairsharing: FAIRsharing.ny9vnm
obofoundry: flopo
ols: flopo
ontobee: FLOPO
name: Flora Phenotype Ontology
pattern: ^\d{7}$
preferred_prefix: FLOPO
publications:
- doi: 10.1186/s13326-016-0107-8
pmc: PMC5109718
pubmed: '27842607'
title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological
traits and phenotypes of vascular plants.'
year: 2016
- doi: 10.3897/bdj.2.e1125
pmc: PMC4092319
pubmed: '25057255'
title: Enriched biodiversity data as a resource and service.
year: 2014
rdf_uri_format: http://purl.obolibrary.org/obo/FLOPO_$1
repository: https://github.com/flora-phenotype-ontology/flopoontology
uri_format: http://purl.obolibrary.org/obo/FLOPO_$1
flowrepository:
contact:
email: rbrinkman@bccrc.ca
github: null
name: Ryan Brinkman
orcid: 0000-0002-9765-2990
description: FlowRepository is a database of flow cytometry experiments where you
can query and download data collected and annotated according to the MIFlowCyt
standard. It is primarily used as a data deposition place for experimental findings
published in peer-reviewed journals in the flow cytometry field.
example: FR-FCM-ZYGW
homepage: https://flowrepository.org/
keywords:
- biology
- cell biology
- life science
mappings:
fairsharing: FAIRsharing.veg2d6
miriam: flowrepository
n2t: flowrepository
re3data: r3d100011280
name: FlowRepository
pattern: ^FR\-FCM\-\w{4}$
preferred_prefix: flowrepository
publications:
- doi: 10.1002/cyto.a.22106
pmc: null
pubmed: '22887982'
title: 'FlowRepository: a resource of annotated flow cytometry datasets associated
with peer-reviewed publications.'
year: 2012
- doi: 10.1002/0471142956.cy1018s61
pmc: null
pubmed: '22752950'
title: Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt)
compliant manuscript using the International Society for Advancement of Cytometry
(ISAC) FCS file repository (FlowRepository.org).
year: 2012
uri_format: https://flowrepository.org/id/$1
flu:
contact:
email: burkesquires@gmail.com
github: null
name: R. Burke Squires
orcid: 0000-0001-9666-6285
deprecated: true
description: Starting in the fall of 2007, a collaborative group of influenza researchers
have established an influenza ontology. The influenza ontology is an application
ontology. Consolidated influenza sequence and surveillance terms from resources
such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense
and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in
Influenza Research and Surveillance (CEIRS)
download_owl: http://purl.obolibrary.org/obo/flu.owl
example: '0000404'
homepage: http://purl.obolibrary.org/obo/flu/
keywords:
- obo
- ontology
mappings:
aberowl: FLU
biocontext: FLU
bioportal: FLU
obofoundry: flu
name: Influenza Ontology
pattern: ^\d{7}$
preferred_prefix: FLU
rdf_uri_format: http://purl.obolibrary.org/obo/FLU_$1
uri_format: http://purl.obolibrary.org/obo/FLU_$1
flybase:
description: FlyBase is the database of the Drosophila Genome Projects and of associated
literature.
example: FBgn0011293
homepage: http://flybase.org/
keywords:
- anatomy
- bioinformatics
- comparative genomics
- dna
- functional genomics
- genetics
- genome
- genomics
- interaction
- life science
- molecular biology
- molecular genetics
mappings:
biocontext: FlyBase
cellosaurus: FlyBase
edam: '1089'
fairsharing: FAIRsharing.wrvze3
go: FB
miriam: fb
n2t: fb
ncbi: FLYBASE
prefixcommons: flybase
re3data: r3d100010591
uniprot: DB-0026
wikidata: P3852
name: FlyBase Gene
pattern: ^FB\w{2}\d{7}$
preferred_prefix: FlyBase
providers:
- 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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/flybase:$1
publications:
- doi: 10.1093/nar/27.1.85
pmc: PMC148103
pubmed: '9847148'
title: The FlyBase database of the Drosophila Genome Projects and community literature.
year: 1999
- doi: 10.1093/nar/26.1.85
pmc: PMC147222
pubmed: '9399806'
title: 'FlyBase: a Drosophila database.'
year: 1998
- doi: 10.1093/nar/25.1.63
pmc: PMC146418
pubmed: '9045212'
title: 'FlyBase: a Drosophila database. The FlyBase consortium.'
year: 1997
- doi: 10.1093/nar/24.1.53
pmc: PMC145580
pubmed: '8594600'
title: 'FlyBase: the Drosophila database.'
year: 1996
- doi: 10.1093/nar/22.17.3456
pmc: PMC308301
pubmed: '7937045'
title: FlyBase--the Drosophila database. The FlyBase Consortium.
year: 1994
- doi: 10.1242/dev.120.7.2077
pmc: null
pubmed: '7925011'
title: FlyBase--the Drosophila genetic database.
year: 1994
- doi: 10.1093/nar/gkaa1026
pmc: PMC7779046
pubmed: '33219682'
title: 'FlyBase: updates to the Drosophila melanogaster knowledge base.'
year: 2021
- doi: 10.1093/nar/gky1003
pmc: PMC6323960
pubmed: '30364959'
title: 'FlyBase 2.0: the next generation.'
year: 2019
- doi: 10.1007/978-1-4939-7737-6_16
pmc: PMC5996772
pubmed: '29761468'
title: Using FlyBase to Find Functionally Related Drosophila Genes.
year: 2018
- doi: 10.1002/cpbi.19
pmc: PMC5152691
pubmed: '27930807'
title: Exploring FlyBase Data Using QuickSearch.
year: 2016
- doi: 10.1093/nar/gkw1016
pmc: PMC5210523
pubmed: '27799470'
title: 'FlyBase at 25: looking to the future.'
year: 2016
- doi: 10.1242/dmm.023317
pmc: PMC4826978
pubmed: '26935103'
title: FlyBase portals to human disease research using Drosophila models.
year: 2016
- doi: 10.1093/nar/gkv1046
pmc: PMC4702782
pubmed: '26467478'
title: 'FlyBase: establishing a Gene Group resource for Drosophila melanogaster.'
year: 2015
- doi: 10.1534/g3.115.018929
pmc: PMC4528329
pubmed: '26109357'
title: 'Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput
Data.'
year: 2015
- doi: 10.1534/g3.115.018937
pmc: PMC4528330
pubmed: '26109356'
title: 'Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.'
year: 2015
- doi: 10.1093/nar/gku1099
pmc: PMC4383921
pubmed: '25398896'
title: 'FlyBase: introduction of the Drosophila melanogaster Release 6 reference
genome assembly and large-scale migration of genome annotations.'
year: 2014
- doi: 10.1093/nar/gkt1092
pmc: PMC3964969
pubmed: '24234449'
title: FlyBase 102--advanced approaches to interrogating FlyBase.
year: 2013
- doi: 10.1093/database/bas024
pmc: PMC3342516
pubmed: '22554788'
title: Directly e-mailing authors of newly published papers encourages community
curation.
year: 2012
- doi: 10.1093/nar/gkr1030
pmc: PMC3245098
pubmed: '22127867'
title: FlyBase 101--the basics of navigating FlyBase.
year: 2011
- doi: 10.1093/nar/gkn788.
pmc: PMC2686450
pubmed: '18948289'
title: 'FlyBase: enhancing Drosophila Gene Ontology annotations.'
year: null
- doi: 10.1093/nar/gkn788
pmc: PMC2686450
pubmed: '18948289'
title: 'FlyBase: enhancing Drosophila Gene Ontology annotations.'
year: 2008
- doi: 10.1007/978-1-59745-583-1_3
pmc: null
pubmed: '18641940'
title: 'FlyBase : a database for the Drosophila research community.'
year: 2008
- doi: 10.1093/nar/gkm930
pmc: PMC2238994
pubmed: '18160408'
title: 'FlyBase: integration and improvements to query tools.'
year: 2007
- doi: 10.1093/nar/gkl827
pmc: PMC1669768
pubmed: '17099233'
title: 'FlyBase: genomes by the dozen.'
year: 2006
- doi: 10.1093/nar/gkj068
pmc: PMC1347431
pubmed: '16381917'
title: 'FlyBase: anatomical data, images and queries.'
year: 2006
- doi: 10.1093/nar/gki046
pmc: PMC540000
pubmed: '15608223'
title: 'FlyBase: genes and gene models.'
year: 2005
- doi: 10.1093/nar/gkg094
pmc: PMC165541
pubmed: '12519974'
title: The FlyBase database of the Drosophila genome projects and community literature.
year: 2003
- doi: 10.1093/nar/30.1.106
pmc: PMC99082
pubmed: '11752267'
title: The FlyBase database of the Drosophila genome projects and community literature.
year: 2002
synonyms:
- FB
- FlyBase
twitter: flybasedotorg
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
flymine.chromosome:
description: FlyMine is an integrated database of genomic, expression and protein
data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible
to run sophisticated data mining queries that span domains of biological knowledge.
example: '1047874'
homepage: http://www.flymine.org/
keywords:
- gene expression
- genome
- protein
mappings:
prefixcommons: flymine
name: FlyMine Chromosome Band
preferred_prefix: flymine.chromosome
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/flymine:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://www.flymine.org/flymine/report/ChromosomeBand/$1
fma:
banana: FMA
contact:
email: mejino@u.washington.edu
github: null
name: Onard Mejino
orcid: null
deprecated: true
description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics
ontology. It is concerned with the representation of classes or types and relationships
necessary for the symbolic representation of the phenotypic structure of the human
body. Specifically, the FMA is a domain ontology that represents a coherent body
of explicit declarative knowledge about human anatomy.
download_owl: http://purl.obolibrary.org/obo/fma.owl
example: '63189'
homepage: http://si.washington.edu/projects/fma
keywords:
- anatomy
- biomedical science
- human
- obo
- ontology
- owl
- radiology
license: CC-BY-3.0
mappings:
aberowl: FMA
bartoc: '571'
biocontext: FMA
bioportal: FMA
edam: '1182'
fairsharing: FAIRsharing.x56jsy
go: FMA
hl7: 2.16.840.1.113883.6.119
miriam: fma
n2t: fma
obofoundry: fma
ols: fma
ontobee: FMA
prefixcommons: fma
wikidata: P1402
name: Foundational Model of Anatomy
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: FMA
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/fma:$1
publications:
- doi: 10.1016/j.artmed.2016.04.003
pmc: PMC4915823
pubmed: '27235801'
title: 'From frames to OWL2: Converting the Foundational Model of Anatomy.'
year: 2016
- doi: 10.1016/j.websem.2007.12.001
pmc: PMC2500209
pubmed: '18688289'
title: Translating the Foundational Model of Anatomy into OWL.
year: 2008
- doi: 10.1016/j.websem.2006.05.007
pmc: PMC2270940
pubmed: '18360535'
title: 'The foundational model of anatomy in OWL: Experience and perspectives.'
year: 2006
- doi: 10.1109/iembs.2004.1404513
pmc: null
pubmed: '17271570'
title: 'The foundational model of anatomy: a template for the symbolic representation
of multi-scale physiological functions.'
year: 2004
- doi: null
pmc: PMC1560487
pubmed: '16779026'
title: 'Challenges in converting frame-based ontology into OWL: the Foundational
Model of Anatomy case-study.'
year: 2005
- doi: 10.1016/j.jbi.2003.11.007
pmc: null
pubmed: '14759820'
title: 'A reference ontology for biomedical informatics: the Foundational Model
of Anatomy.'
year: 2003
rdf_uri_format: http://purl.obolibrary.org/obo/FMA_$1
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:
contact:
email: rafael.goncalves@stanford.edu
github: null
name: Rafael Gonçalves
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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.'
download_owl: http://aber-owl.net/media/ontologies/foaf/1/foaf.owl
example: familyName
homepage: http://xmlns.com/foaf/spec/
keywords:
- ontology
mappings:
aberowl: foaf
biocontext: foaf
biolink: foaf
bioportal: FOAF
name: Friend of a Friend
preferred_prefix: foaf
uri_format: http://xmlns.com/foaf/0.1/$1
fobi:
contact:
email: polcaes@gmail.com
github: pcastellanoescuder
name: Pol Castellano Escuder
orcid: 0000-0001-6466-877X
depends_on:
- chebi
- foodon
description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake
data and associate it with metabolomic data
download_owl: http://purl.obolibrary.org/obo/fobi.owl
example: 030719
example_extras:
- '0142'
- '07504'
homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: FOBI
agroportal: FOBI
bioportal: FOBI
obofoundry: fobi
ols: fobi
ontobee: FOBI
name: Food-Biomarker Ontology
pattern: ^\d{4,6}$
preferred_prefix: FOBI
providers:
- code: fobi.legacy
description: An incorrect encoding of OBO purls
homepage: http://purl.obolibrary.org/obo/fobi
name: FOBI Hash
uri_format: http://purl.obolibrary.org/obo/fobi.owl#FOBI:$1
publications:
- doi: 10.1093/bioinformatics/btab626
pmc: null
pubmed: '34601570'
title: 'The fobitools framework: the first steps towards food enrichment analysis.'
year: 2021
- doi: 10.1093/databa/baaa033
pmc: PMC7298227
pubmed: '32556148'
title: 'FOBI: an ontology to represent food intake data and associate it with
metabolomic data.'
year: 2020
rdf_uri_format: http://purl.obolibrary.org/obo/FOBI_$1
repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology
uri_format: http://purl.obolibrary.org/obo/FOBI_$1
foodb.compound:
description: FooDB is resource on food and its constituent compounds. It includes
data on the compound’s nomenclature, its description, information on its structure,
chemical class, its physico-chemical data, its food source(s), its color, its
aroma, its taste, its physiological effect, presumptive health effects (from published
studies), and concentrations in various foods. This collection references compounds.
example: FDB002100
homepage: https://foodb.ca/
mappings:
biocontext: FOODB.COMPOUND
biolink: foodb.compound
miriam: foodb.compound
n2t: foodb.compound
re3data: r3d100012152
wikidata: P8117
name: FooDB compound
pattern: ^FDB\d+$
preferred_prefix: foodb.compound
synonyms:
- foodb
uri_format: http://foodb.ca/compounds/$1
foodb.food:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Foods in FooDB
example: FOOD00020
homepage: https://foodb.ca/foods
mappings:
biolink: foodb.food
name: FooDB Food
pattern: ^FOOD\d+$
preferred_prefix: foodb.food
uri_format: https://foodb.ca/foods/$1
foodex2:
contact:
email: datex@efsa.europa.eu
github: null
name: European Food Safety Authority
orcid: null
description: FoodEx2 is a comprehensive food classification and description system
aimed at covering the need to describe food in data collections across different
food safety domains.
example: A0TMC
homepage: http://www.efsa.europa.eu/
mappings:
agroportal: FOODEX2
name: Food classification and description system
preferred_prefix: foodex2
uri_format: http://data.food.gov.uk/codes/foodtype/id/$1
foodon:
appears_in:
- agro
- envo
- fobi
- maxo
- one
- ons
banana: FOODON
contact:
email: damion_dooley@sfu.ca
github: ddooley
name: Damion Dooley
orcid: 0000-0002-8844-9165
depends_on:
- bfo
- chebi
- envo
- eo
- ncbitaxon
- obi
- ro
- uberon
description: FoodOn is a comprehensive and easily accessible global farm-to-fork
ontology about food that accurately and consistently describes foods commonly
known in cultures from around the world. It is a consortium-driven project built
to interoperate with the The Open Biological and Biomedical Ontology Foundry library
of ontologies.
download_obo: http://purl.obolibrary.org/obo/foodon.obo
download_owl: http://purl.obolibrary.org/obo/foodon.owl
example: 03307879
homepage: https://foodon.org/
keywords:
- agriculture
- botany
- environmental science
- medicine
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: FOODON
agroportal: FOODON
biocontext: FOODON
bioportal: FOODON
fairsharing: FAIRsharing.dzxae
miriam: foodon
n2t: foodon
obofoundry: foodon
ols: foodon
ontobee: FOODON
name: The Food Ontology
namespace_in_lui: true
pattern: ^[0-9]{8}$
preferred_prefix: FOODON
publications:
- doi: 10.1038/s41538-018-0032-6
pmc: PMC6550238
pubmed: '31304272'
title: 'FoodOn: a harmonized food ontology to increase global food traceability,
quality control and data integration.'
year: 2018
- doi: 10.3389/fmicb.2017.01068
pmc: PMC5483436
pubmed: '28694792'
title: 'Context Is Everything: Harmonization of Critical Food Microbiology Descriptors
and Metadata for Improved Food Safety and Surveillance.'
year: 2017
rdf_uri_format: http://purl.obolibrary.org/obo/FOODON_$1
repository: https://github.com/FoodOntology/foodon
uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1
version: '2023-02-17'
fossilworks.journal:
contributor:
email: meghan.balk@gmail.com
github: megbalk
name: Meghan Balk
orcid: 0000-0003-2699-3066
description: Identifier for a journal article in the fossilworks website
example: '61467'
github_request_issue: 468
homepage: http://fossilworks.org
mappings:
wikidata: P7720
name: Fossilworks Journal
part_of: fossilworks
pattern: ^\d+$
preferred_prefix: fossilworks.journal
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://fossilworks.org/?a=referenceInfo&reference_no=$1
fossilworks.taxon:
contributor:
email: meghan.balk@gmail.com
github: megbalk
name: Meghan Balk
orcid: 0000-0003-2699-3066
description: Identifier for an animal, plant, or microorganism from the fossilworks
website
example: '40565'
github_request_issue: 469
homepage: http://www.fossilworks.org
mappings:
wikidata: P842
name: Fossilworks Taxon
part_of: fossilworks
pattern: ^[1-9]\d{0,5}$
preferred_prefix: fossilworks.taxon
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1
fovt:
contact:
email: meghan.balk@gmail.com
github: megbalk
name: Meghan Balk
orcid: 0000-0003-2699-3066
depends_on:
- bco
- bfo
- bspo
- iao
- oba
- pato
- ro
- uberon
description: These are the terms that are improted for FOVT to describe vertebrate
traits.
download_obo: http://purl.obolibrary.org/obo/fovt.obo
download_owl: http://purl.obolibrary.org/obo/fovt.owl
example: 0000009
homepage: https://github.com/futres/fovt
keywords:
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: FOVT
bioportal: FOVT
obofoundry: fovt
ols: fovt
ontobee: FOVT
name: FuTRES Ontology of Vertebrate Traits
pattern: ^\d{7}$
preferred_prefix: FOVT
rdf_uri_format: http://purl.obolibrary.org/obo/FOVT_$1
repository: https://github.com/futres/fovt
uri_format: http://purl.obolibrary.org/obo/FOVT_$1
version: '2021-11-10'
fplx:
contact:
email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
description: FamPlex is a collection of resources for grounding biological entities
from text and describing their hierarchical relationships.
example: GPIb_IX_V
homepage: https://sorgerlab.github.io/famplex/
keywords:
- ontology
mappings:
aberowl: FPLX
biocontext: FPLX
bioportal: FPLX
miriam: fplx
n2t: fplx
name: FamPlex
pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$
preferred_prefix: fplx
publications:
- doi: 10.1186/s12859-018-2211-5
pmc: PMC6022344
pubmed: '29954318'
title: 'FamPlex: a resource for entity recognition and relationship resolution
of human protein families and complexes in biomedical text mining.'
year: 2018
synonyms:
- famplex
uri_format: https://sorgerlab.github.io/famplex/$1
fr:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology that enables the description of reviews of scientific articles
and other scholarly resources.
example: ReviewVersion
homepage: http://www.sparontologies.net/ontologies/fr
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.e7e609
name: FAIR* Reviews Ontology
preferred_prefix: FR
repository: https://github.com/sparontologies/fr
twitter: sparontologies
frapo:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology for describing the administrative information of research
projects, e.g., grant applications, funding bodies, project partners, etc.
example: Grant
homepage: http://www.sparontologies.net/ontologies/frapo
keywords:
- subject agnostic
mappings:
aberowl: FRAPO
fairsharing: FAIRsharing.0a2576
name: Funding, Research Administration and Projects Ontology
preferred_prefix: FRAPO
repository: https://github.com/sparontologies/frapo
twitter: sparontologies
uri_format: http://purl.org/cerif/frapo/$1
frbr:
contact:
email: silvio.peroni@unibo.it
github: essepuntato
name: Silvio Peroni
orcid: 0000-0003-0530-4305
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL
2 DL of the basic concepts and relations described in the IFLA report on the Functional
Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF
vocabulary. It is imported by FaBiO and BiRO.
example: Expression
homepage: http://www.sparontologies.net/ontologies/frbr
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.b34b43
name: Functional Requirements for Bibliographic Records
preferred_prefix: FRBR
repository: https://github.com/sparontologies/frbr
twitter: sparontologies
uri_format: http://purl.org/vocab/frbr/core#$1
frbrer:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: This is the element set of native RDF classes and properties described
in the current text (Feb 2009) of the Functional Requirements for Bibliographic
Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)
download_rdf: http://iflastandards.info/ns/fr/frbr/frbrer.jsonld
example: '1001'
homepage: https://www.iflastandards.info/fr/frbr/frbrer
name: Functional Requirements for Bibliographic Records Entity-Relationship Model
part_of: frbr
preferred_prefix: frbrer
uri_format: http://iflastandards.info/ns/fr/frbr/frbrer/$1
fsnp:
description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates
information obtained from databases about the functional effects of SNPs. These
effects are predicted and indicated at the splicing, transcriptional, translational
and post-translational level. In particular, users can retrieve SNPs that disrupt
genomic regions known to be functional, including splice sites and transcriptional
regulatory regions. Users can also identify non-synonymous SNPs that may have
deleterious effects on protein structure or function, interfere with protein translation
or impede post-translational modification.
example: rs17852708
homepage: http://compbio.cs.queensu.ca/F-SNP/
keywords:
- dna
- protein
mappings:
biocontext: FSNP
miriam: fsnp
n2t: fsnp
prefixcommons: fsnp
name: F-SNP
pattern: ^rs\d+$
preferred_prefix: fsnp
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/fsnp:$1
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
providers:
- code: crossref.api
description: Access funder data through the Crossref API
homepage: https://api.crossref.org
name: Crossref API
uri_format: https://api.crossref.org/funders/$1
- code: doi
description: Access funder data through a DOI for crossref funders.
homepage: https://doi.org
name: DOI
uri_format: https://dx.doi.org/10.13039/501100000995
synonyms:
- FundRef
- crossref.funder
uri_format: http://data.crossref.org/fundingdata/funder/10.13039/$1
fungidb:
contact:
email: jason.stajich@ucr.edu
github: null
name: Jason E. Stajich
orcid: 0000-0002-7591-0020
description: FungiDB is a genomic resource for fungal genomes. It contains contains
genome sequence and annotation from several fungal classes, including the Ascomycota
classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota
orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage
Mucormycotina.
example: CNBG_0001
homepage: https://fungidb.org/fungidb
keywords:
- genomics
mappings:
biocontext: FUNGIDB
fairsharing: FAIRsharing.xf30yc
miriam: fungidb
n2t: fungidb
re3data: r3d100011906
name: FungiDB
pattern: ^[A-Za-z_0-9]+$
preferred_prefix: fungidb
publications:
- doi: 10.1016/j.fgb.2016.04.002
pmc: null
pubmed: '27259951'
title: Database whiplash, crowdsourcing, and FungiDB.
year: 2016
- doi: 10.1128/ec.00083-14
pmc: PMC4135733
pubmed: '24813190'
title: Literature-based gene curation and proposed genetic nomenclature for cryptococcus.
year: 2014
- doi: 10.1093/nar/gkr918
pmc: PMC3245123
pubmed: '22064857'
title: 'FungiDB: an integrated functional genomics database for fungi.'
year: 2011
twitter: fungidb
uri_format: https://fungidb.org/fungidb/app/record/gene/$1
fungorum:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: identifier for a fungus taxon in Index Fungorum
example: '154022'
homepage: http://www.indexfungorum.org
mappings:
ncbi: Fungorum
wikidata: P1391
name: Index Fungorum
pattern: ^[1-9]\d{0,5}$
preferred_prefix: fungorum
uri_format: http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1
fyeco:
comment: Rather than admitting FYECO to the OBO foundry, we secure the prefix here
at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere
you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to
other OBO ontologies, but this is way ahead in the future.
contact:
email: vw253@cam.ac.uk
github: ValWood
name: Val Wood
orcid: 0000-0001-6330-7526
contributor:
email: vw253@cam.ac.uk
github: ValWood
name: Val Wood
orcid: 0000-0001-6330-7526
description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO
contains experimental conditions relevant to fission yeast biology. The FYECO
namespace shows up in data ingests from PomBase.
example: '0000003'
github_request_issue: 268
homepage: https://github.com/pombase/fypo
mappings:
biolink: FYECO
name: Fission Yeast Experimental Conditions Ontology
pattern: ^\d{7}$
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:
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_json: http://purl.obolibrary.org/obo/fypo.json
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
keywords:
- genetics
- life science
- obo
- ontology
- phylogenetics
license: CC-BY-4.0
logo: https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png
mappings:
aberowl: FYPO
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
publications:
- doi: 10.1093/bioinformatics/btt266
pmc: PMC3694669
pubmed: '23658422'
title: 'FYPO: the fission yeast phenotype ontology.'
year: 2013
rdf_uri_format: http://purl.obolibrary.org/obo/FYPO_$1
repository: https://github.com/pombase/fypo
uri_format: http://purl.obolibrary.org/obo/FYPO_$1
version: '2023-03-08'
ga4ghdos:
description: Assists in resolving data across cloud resources.
example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d
homepage: http://github.com/ga4gh/data-object-service-schemas
mappings:
biocontext: GA4GHDOS
miriam: ga4ghdos
n2t: ga4ghdos
name: Data Object Service
pattern: ^[a-zA-Z0-9\-:#/\.]+$
preferred_prefix: ga4ghdos
uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1
gabi:
description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database)
constitutes a repository for a wide array of heterogeneous data from high-throughput
experiments in several plant species. These data (i.e. genomics, transcriptomics,
proteomics and metabolomics), originating from different model or crop species,
can be accessed through a central gene 'Green Card'.
example: '2679240'
homepage: http://www.gabipd.org/
keywords:
- gene
- genome
- plant
mappings:
biocontext: GABI
miriam: gabi
n2t: gabi
ncbi: GABI
prefixcommons: gabi
name: Network of Different Plant Genomic Research Projects
pattern: ^\w+$
preferred_prefix: gabi
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/gabi:$1
publications:
- doi: 10.1093/nar/gkn611
pmc: PMC2686513
pubmed: '18812395'
title: 'GabiPD: the GABI primary database--a plant integrative ''omics'' database.'
year: 2008
uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject
gainesville.core:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Describes typical Computational Chemistry experiments, including Molecular
Publications, Molecular Systems, Molecular Calculations
download_owl: http://ontologies.makolab.com/gc06/gc.owl
example: Aromatic
homepage: http://ontologies.makolab.com/gc06/gc.html
keywords:
- ontology
license: CC-BY-3.0
name: Gainesville Core Ontology
preferred_prefix: gainesville.core
references:
- http://ontologies.makolab.com/gc/
uri_format: http://purl.org/gc/$1
galen:
comment: I really tried, but could not figure out what GALEN stands for
contact:
email: j@deltaflow.com
github: null
name: Julian Seidenberg
orcid: null
deprecated: true
description: A translation of the full Galen ontology (from the OpenGALEN project)
into the OWL description logic.
download_owl: http://aber-owl.net/media/ontologies/GALEN/1/galen.owl
example: MagnitudeValueType
homepage: https://www.opengalen.org
keywords:
- ontology
mappings:
aberowl: GALEN
bioportal: GALEN
name: GALEN
preferred_prefix: galen
uri_format: http://www.co-ode.org/ontologies/galen#$1
gard:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Database of rare diseases and related terms, including symptoms, healthcare
resources, and organizations supporting research of the disease.
example: '6038'
homepage: https://rarediseases.info.nih.gov/diseases
mappings:
wikidata: P4317
name: Genetic and Rare Diseases Information Center
pattern: ^\d+$
preferred_prefix: gard
synonyms:
- GARD
- Genetic and Rare Diseases Information Center
uri_format: https://rarediseases.info.nih.gov/diseases/$1/index
gateway:
description: The Health Data Research Innovation Gateway (the 'Gateway') provides
a common entry point to discover and enquire about access to UK health datasets
for research and innovation. It provides detailed information about the datasets,
which are held by members of the UK Health Data Research Alliance, such as a description,
size of the population, and the legal basis for access.
example: fd8d0743-344a-4758-bb97-f8ad84a37357
homepage: https://www.hdruk.ac.uk
mappings:
miriam: gateway
name: Health Data Research Innovation Gateway
pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$
preferred_prefix: gateway
uri_format: https://web.www.healthdatagateway.org/dataset/$1
gaz:
appears_in:
- scdo
contact:
email: lschriml@som.umaryland.edu
github: lschriml
name: Lynn Schriml
orcid: 0000-0001-8910-9851
deprecated: true
description: A gazetteer constructed on ontological principles
download_obo: http://purl.obolibrary.org/obo/gaz.obo
download_owl: http://purl.obolibrary.org/obo/gaz.owl
example: '00620027'
homepage: http://environmentontology.github.io/gaz/
keywords:
- environmental science
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: GAZ
biocontext: GAZ
bioportal: GAZ
fairsharing: FAIRsharing.wkdjpb
obofoundry: gaz
ols: gaz
ontobee: GAZ
wikidata: P6778
name: Gazetteer
pattern: ^\d{8}$
preferred_prefix: GAZ
rdf_uri_format: http://purl.obolibrary.org/obo/GAZ_$1
repository: https://github.com/EnvironmentOntology/gaz
uri_format: http://purl.obolibrary.org/obo/GAZ_$1
gbif:
contact:
email: timrobertson100@gmail.com
github: timrobertson100
name: Tim Robertson
orcid: 0000-0001-6215-3617
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity\
\ Information Facility—is international network and data infrastructure funded\
\ by the world's governments and aimed at providing anyone, anywhere, open access\
\ to data about all types of life on Earth."
example: '4238'
homepage: https://www.gbif.org/species
keywords:
- biodiversity
- bioinformatics
- marine biology
- metagenomics
- natural history
- natural science
- taxonomy
mappings:
fairsharing: FAIRsharing.zv11j3
re3data: r3d100000039
wikidata: P846
name: Global Biodiversity Information Facility
pattern: ^\d+$
preferred_prefix: gbif
publications:
- doi: 10.1371/journal.pone.0102623
pmc: PMC4123864
pubmed: '25099149'
title: 'The GBIF integrated publishing toolkit: facilitating the efficient publishing
of biodiversity data on the internet.'
year: 2014
repository: https://github.com/gbif/
twitter: 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$1
gcst:
description: The GWAS Catalog provides a consistent, searchable, visualisable and
freely available database of published SNP-trait associations, which can be easily
integrated with other resources, and is accessed by scientists, clinicians and
other users worldwide.
example: GCST000035
homepage: https://www.ebi.ac.uk
mappings:
miriam: gcst
n2t: gcst
name: GWAS Catalog
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^GCST\d{6}\d*$
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/$1
gear:
contact:
email: jorvis@gmail.com
github: jorvis
name: Joshua Orvis
orcid: 0000-0002-5705-5710
contributor:
email: jorvis@gmail.com
github: jorvis
name: Joshua Orvis
orcid: 0000-0002-5705-5710
description: The gEAR portal is a website for visualization and analysis of multi-omic
data both in public and private domains.
example: d.a59037e8
example_extras:
- p.bfd178f5
github_request_issue: 728
homepage: https://umgear.org
license: AGPL-3.0-only
name: Gene Expression Analysis Resource
pattern: ^[dp]\.[a-z0-9]{8}$
preferred_prefix: gear
repository: https://github.com/IGS/gEAR
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://umgear.org/p?id=$1
gecko:
contact:
email: rbca.jackson@gmail.com
github: beckyjackson
name: Rebecca Jackson
orcid: 0000-0003-4871-5569
description: An ontology to represent genomics cohort attributes.
download_owl: http://purl.obolibrary.org/obo/gecko.owl
example: '0000044'
homepage: https://github.com/IHCC-cohorts/GECKO
keywords:
- genomics
- life science
- obo
- ontology
- statistics
license: CC-BY-4.0
mappings:
aberowl: GECKO
bioportal: GECKO
fairsharing: FAIRsharing.3da56b
obofoundry: gecko
ols: gecko
ontobee: GECKO
name: Genomics Cohorts Knowledge Ontology
pattern: ^\d{7}$
preferred_prefix: GECKO
rdf_uri_format: http://purl.obolibrary.org/obo/GECKO_$1
repository: https://github.com/IHCC-cohorts/GECKO
uri_format: http://purl.obolibrary.org/obo/GECKO_$1
version: '2021-01-18'
gemet:
contact:
email: helpdesk@eionet.europa.eu
github: null
name: Eionet Helpdesk
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The European Environment Information and Observation Network (Eionet)
is a partnership network of the European Environment Agency (EEA) and its 38 member
and cooperating countries. The EEA is responsible for developing Eionet and coordinating
its activities together with National Focal Points (NFPs) in the countries. This
terminology supports those efforts.
example: '627'
homepage: https://www.eionet.europa.eu/gemet/en/themes/
keywords:
- biodiversity
- ecology
- environmental science
mappings:
agroportal: GEMET
bartoc: '16'
fairsharing: FAIRsharing.9091d9
name: General Multilingual Environmental Thesaurus
pattern: ^\d+$
preferred_prefix: gemet
uri_format: https://www.eionet.europa.eu/gemet/en/concept/$1
genatlas:
description: GenAtlas is a database containing information on human genes, markers
and phenotypes.
example: HBB
homepage: http://genatlas.medecine.univ-paris5.fr/
keywords:
- disorder
- gene
- human
- life science
mappings:
biocontext: GENATLAS
fairsharing: FAIRsharing.pmg2vd
miriam: genatlas
n2t: genatlas
prefixcommons: genatlas
uniprot: DB-0027
name: Genatlas
pattern: ^\w+$
preferred_prefix: genatlas
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/genatlas:$1
publications:
- doi: 10.1016/s0764-4469(99)80021-3
pmc: null
pubmed: '9835018'
title: Genatlas database, genes and development defects.
year: 1998
- doi: 10.1006/mgme.1999.2867
pmc: null
pubmed: '10444337'
title: 'Human genes involved in chromatin remodeling in transcription initiation,
and associated diseases: An overview using the GENATLAS database.'
year: 1999
uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1
genbank:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/
keywords:
- bioinformatics
- data management
- dna
- epidemiology
- functional genomics
- genomics
- metagenomics
- transcriptomics
- virology
mappings:
biocontext: GenBank
cheminf: '000304'
edam: '2292'
fairsharing: FAIRsharing.9kahy4
go: GenBank
prefixcommons: genbank
re3data: r3d100010528
uniprot: DB-0028
name: GenBank
preferred_prefix: genbank
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/genbank:$1
publications:
- doi: 10.1186/s12859-020-3537-3
pmc: PMC7245624
pubmed: '32448124'
title: 'VADR: validation and annotation of virus sequence submissions to GenBank.'
year: 2020
- doi: 10.1093/nar/gkz956
pmc: PMC7145611
pubmed: '31665464'
title: GenBank.
year: 2020
- doi: 10.1093/nar/gky989
pmc: PMC6323954
pubmed: '30365038'
title: GenBank.
year: 2019
- doi: 10.1093/nar/gkx1094
pmc: PMC5753231
pubmed: '29140468'
title: GenBank.
year: 2018
- doi: 10.1093/nar/gkw1070
pmc: PMC5210553
pubmed: '27899564'
title: GenBank.
year: 2016
- doi: 10.1093/nar/gkv1276
pmc: PMC4702903
pubmed: '26590407'
title: GenBank.
year: 2015
- doi: 10.1093/nar/gku1216
pmc: PMC4383990
pubmed: '25414350'
title: GenBank.
year: 2014
- doi: 10.1093/nar/gkt1030
pmc: PMC3965104
pubmed: '24217914'
title: GenBank.
year: 2013
- doi: 10.1093/nar/gks1195
pmc: PMC3531190
pubmed: '23193287'
title: GenBank.
year: 2012
- doi: 10.1093/nar/gkr1202
pmc: PMC3245039
pubmed: '22144687'
title: GenBank.
year: 2011
- doi: 10.1093/nar/gkq1079
pmc: PMC3013681
pubmed: '21071399'
title: GenBank.
year: 2010
- doi: 10.1093/nar/gkn723
pmc: PMC2686462
pubmed: '18940867'
title: GenBank.
year: 2008
- doi: 10.1093/nar/gkm929
pmc: PMC2238942
pubmed: '18073190'
title: GenBank.
year: 2007
- doi: 10.1093/nar/gkl1031
pmc: PMC1781113
pubmed: '17170002'
title: Database resources of the National Center for Biotechnology Information.
year: 2006
uri_format: https://www.ncbi.nlm.nih.gov/nucleotide/$1
gendis:
comment: This resource doesn't exist on the web anymore
deprecated: true
description: Genomic Distribution of structural Superfamilies identifies and classifies
evolutionary related proteins at the superfamily level in whole genome databases.
example: '46946'
homepage: http://caps.ncbs.res.in/gendis/home.html
keywords:
- classification
- genome
mappings:
prefixcommons: gendis
name: Genomic Distribution of structural Superfamilies
preferred_prefix: gendis
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/gendis:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1
genecards:
contact:
email: marilyn.safran@weizmann.ac.il
github: null
name: Marilyn Safran
orcid: 0000-0001-5424-1393
description: The GeneCards human gene database stores gene related transcriptomic,
genetic, proteomic, functional and disease information. It uses standard nomenclature
and approved gene symbols. GeneCards presents a complete summary for each human
gene.
example: ABL1
homepage: http://www.genecards.org/
keywords:
- genetics
- genome
- life science
- transcriptomics
mappings:
biocontext: GENECARDS
fairsharing: FAIRsharing.g7jbvn
miriam: genecards
n2t: genecards
prefixcommons: genecards
re3data: r3d100012015
uniprot: DB-0030
name: GeneCards
pattern: ^[A-Za-z-0-9_]+(\@)?$
preferred_prefix: genecards
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/genecards:$1
publications:
- doi: 10.1016/s0168-9525(97)01103-7
pmc: null
pubmed: '9097728'
title: 'GeneCards: integrating information about genes, proteins and diseases.'
year: 1997
- doi: 10.1186/s12864-016-2722-2
pmc: PMC4928145
pubmed: '27357693'
title: 'VarElect: the phenotype-based variation prioritizer of the GeneCards Suite.'
year: 2016
- doi: 10.1002/cpbi.5
pmc: null
pubmed: '27322403'
title: 'The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence
Analyses.'
year: 2016
- doi: 10.1093/database/baw030
pmc: PMC4820835
pubmed: '27048349'
title: Genic insights from integrated human proteomics in GeneCards.
year: 2016
- doi: 10.1089/omi.2015.0168
pmc: PMC4799705
pubmed: '26983021'
title: 'GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation
Sequencing, RNAseq and Microarray Data.'
year: 2016
- doi: 10.1093/database/bav006
pmc: PMC4343183
pubmed: '25725062'
title: 'PathCards: multi-source consolidation of human biological pathways.'
year: 2015
- doi: 10.1093/database/baq020
pmc: PMC2938269
pubmed: '20689021'
title: 'GeneCards Version 3: the human gene integrator.'
year: 2010
- doi: 10.1093/bioinformatics/18.11.1542
pmc: null
pubmed: '12424129'
title: 'GeneCards 2002: towards a complete, object-oriented, human gene compendium.'
year: 2002
uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1
genecards.geneannot:
description: GeneAnnot provides a revised and improved annotation of Affymetrix
probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to
GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and
Ensembl mRNA sequences, while assigning sensitivity and specificity scores to
each probe-set to gene match.
example: GSTA1
homepage: http://genecards.weizmann.ac.il/geneannot/
keywords:
- gene expression
mappings:
prefixcommons: geneannot
name: 'GeneAnnot: Microarray Gene Annotation'
preferred_prefix: genecards.geneannot
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/geneannot:$1
genecards.geneloc:
description: GeneLoc presents an integrated map for each human chromosome, based
on data integrated by the GeneLoc algorithm. GeneLoc includes further links to
GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources
example: '17503'
homepage: http://genecards.weizmann.ac.il/geneloc/
keywords:
- genome
mappings:
prefixcommons: geneloc
name: Gene Location
preferred_prefix: genecards.geneloc
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/geneloc:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1
genecards.genenote:
description: GeneNote is a database of human genes and their expression profiles
in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments,
which were performed on the Affymetrix HG-U95 set A-E.
example: GC06M052656
homepage: http://genecards.weizmann.ac.il/genenote/
keywords:
- gene expression
mappings:
prefixcommons: genenote
name: Gene Normal Tissue Expression
preferred_prefix: genecards.genenote
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/genenote:$1
uri_format: http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes
genedb:
deprecated: true
description: GeneDB is a genome database for prokaryotic and eukaryotic organisms
and provides a portal through which data generated by the "Pathogen Genomics"
group at the Wellcome Trust Sanger Institute and other collaborating sequencing
centres can be accessed.
example: LinJ.20.0070
homepage: https://www.genedb.org/
keywords:
- genome
- life science
- sequence
mappings:
biocontext: GENEDB
edam: '1035'
fairsharing: FAIRsharing.j7esqq
go: GeneDB
miriam: genedb
n2t: genedb
ncbi: GeneDB
prefixcommons: genedb
re3data: r3d100010626
wikidata: P3382
name: GeneDB
pattern: ^[\w\d\.-]*$
preferred_prefix: genedb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/genedb:$1
publications:
- doi: 10.1093/nar/gkh007
pmc: PMC308742
pubmed: '14681429'
title: 'GeneDB: a resource for prokaryotic and eukaryotic organisms.'
year: 2004
uri_format: https://www.genedb.org/gene/$1
genefarm:
description: GeneFarm is a database whose purpose is to store traceable annotations
for Arabidopsis nuclear genes and gene products.
example: '4892'
homepage: http://urgi.versailles.inra.fr/Genefarm/
keywords:
- expression
- genome
- life science
- nucleotide
- sequence
mappings:
biocontext: GENEFARM
fairsharing: FAIRsharing.2mayq0
miriam: genefarm
n2t: genefarm
prefixcommons: genefarm
name: GeneFarm
pattern: ^\d+$
preferred_prefix: genefarm
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/genefarm:$1
publications:
- doi: 10.1093/nar/gki115
pmc: PMC540069
pubmed: '15608279'
title: GeneFarm, structural and functional annotation of Arabidopsis gene and
protein families by a network of experts.
year: 2005
uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1
genepio:
contact:
email: damion_dooley@sfu.ca
github: ddooley
name: Damion Dooley
orcid: 0000-0002-8844-9165
depends_on:
- chebi
- ncbitaxon
- po
- ro
- uberon
description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary
to identify, document and research foodborne pathogens and associated outbreaks.
download_owl: http://purl.obolibrary.org/obo/genepio.owl
example: 0001885
homepage: http://genepio.org/
keywords:
- epidemiology
- genomics
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: GENEPIO
biocontext: GENEPIO
fairsharing: FAIRsharing.y1mmbv
obofoundry: genepio
ols: genepio
ontobee: GENEPIO
name: Genomic Epidemiology Ontology
pattern: ^\d{7}$
preferred_prefix: GENEPIO
rdf_uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1
repository: https://github.com/GenEpiO/genepio
uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1
version: '2022-02-06'
genetree:
description: Genetree displays the maximum likelihood phylogenetic (protein) trees
representing the evolutionary history of the genes. These are constructed using
the canonical protein for every gene in Ensembl.
example: ENSGT00550000074763
homepage: http://www.ensembl.org/
keywords:
- classification
- gene
- protein
mappings:
biocontext: GENETREE
miriam: genetree
n2t: genetree
prefixcommons: genetree
uniprot: DB-0162
name: GeneTree
pattern: ^ENSGT\d+$
preferred_prefix: genetree
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/genetree:$1
publications:
- doi: 10.1093/database/bav096
pmc: PMC4761110
pubmed: '26896847'
title: Ensembl comparative genomics resources.
year: 2016
- doi: 10.1093/nar/gkj133
pmc: PMC1347495
pubmed: '16381931'
title: Ensembl 2006.
year: 2006
uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1
genewiki:
description: The Gene Wiki is project which seeks to provide detailed information
on human genes. Initial 'stub' articles are created in an automated manner, with
further information added by the community. Gene Wiki can be accessed in wikipedia
using Gene identifiers from NCBI.
example: '1017'
homepage: http://en.wikipedia.org/wiki/Gene_Wiki
keywords:
- genetics
- life science
mappings:
biocontext: GENEWIKI
fairsharing: FAIRsharing.t3snf
miriam: genewiki
n2t: genewiki
uniprot: DB-0180
name: Gene Wiki
pattern: ^\d+$
preferred_prefix: genewiki
provides: ncbigene
publications:
- doi: 10.1093/database/baw015
pmc: PMC4795929
pubmed: '26989148'
title: Wikidata as a semantic framework for the Gene Wiki initiative.
year: 2016
- doi: 10.1093/nar/gkr925
pmc: PMC3245148
pubmed: '22075991'
title: 'The Gene Wiki in 2011: community intelligence applied to human gene annotation.'
year: 2011
- doi: 10.1093/nar/gkp760
pmc: PMC2808918
pubmed: '19755503'
title: 'The Gene Wiki: community intelligence applied to human gene annotation.'
year: 2009
- doi: 10.1371/journal.pbio.0060175
pmc: PMC2443188
pubmed: '18613750'
title: A gene wiki for community annotation of gene function.
year: 2008
twitter: GeneWikiPulse
uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1
geno:
contact:
email: mhb120@gmail.com
github: mbrush
name: Matthew Brush
orcid: 0000-0002-1048-5019
description: "GENO is an OWL model of genotypes, their more fundamental sequence\
\ components, and links to related biological and experimental entities. At present\
\ many parts of the model are exploratory and set to undergo refactoring. In\
\ addition, many classes and properties have GENO URIs but are place holders for\
\ classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI,\
\ etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype\
\ associations. This will support description of asserted and inferred relationships\
\ between a genotypes, phenotypes, and environments, and the evidence/provenance\
\ behind these associations. \n\nDocumentation is under development as well, and\
\ for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"
download_json: http://purl.obolibrary.org/obo/geno.json
download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo
download_owl: http://purl.obolibrary.org/obo/geno.owl
example: '0000632'
homepage: https://github.com/monarch-initiative/GENO-ontology/
keywords:
- genomics
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: GENO
biocontext: GENO
bioportal: GENO
fairsharing: FAIRsharing.kpbna7
obofoundry: geno
ols: geno
ontobee: GENO
name: Genotype Ontology
pattern: ^\d{7}$
preferred_prefix: GENO
rdf_uri_format: http://purl.obolibrary.org/obo/GENO_$1
repository: https://github.com/monarch-initiative/GENO-ontology
uri_format: http://purl.obolibrary.org/obo/GENO_$1
version: '2023-02-21'
genpept:
description: The GenPept database is a collection of sequences based on translations
from annotated coding regions in GenBank.
example: CAA71118.1
homepage: https://www.ncbi.nlm.nih.gov/protein
mappings:
biocontext: GENPEPT
miriam: genpept
n2t: genpept
name: GenPept
pattern: ^\w{3}\d{5}(\.\d+)?$
preferred_prefix: genpept
uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept
genprop:
description: Genome properties is an annotation system whereby functional attributes
can be assigned to a genome, based on the presence of a defined set of protein
signatures within that genome.
example: GenProp0699
homepage: https://www.ebi.ac.uk/interpro/genomeproperties/
keywords:
- classification
- genome
mappings:
biocontext: GENPROP
miriam: genprop
n2t: genprop
prefixcommons: jcvi.genprop
name: Genome Properties
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^GenProp\d+$
preferred_prefix: genprop
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/jcvi.genprop:$1
uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1
geo:
banana_peel: _
description: The Gene Expression Omnibus (GEO) is a gene expression repository providing
a curated, online resource for gene expression data browsing, query and retrieval.
download_owl: http://aber-owl.net/media/ontologies/GEO/4/geo.owl
example: GDS1234
homepage: https://www.ncbi.nlm.nih.gov/geo/
keywords:
- comparative genomics
- epigenomics
- gene expression
- genome
- genomics
- life science
- omics
- ontology
- phenomics
- transcriptomics
mappings:
aberowl: GEO
biocontext: GEO
cellosaurus: GEO
edam: '1147'
fairsharing: FAIRsharing.5hc8vt
go: GEO
miriam: geo
n2t: geo
prefixcommons: geo
re3data: r3d100010283
name: NCBI Gene Expression Omnibus
pattern: ^G(PL|SM|SE|DS)\d+$
preferred_prefix: geo
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/geo:$1
publications:
- doi: 10.1093/nar/gks1193
pmc: PMC3531084
pubmed: '23193258'
title: 'NCBI GEO: archive for functional genomics data sets--update.'
year: 2012
- doi: 10.1038/nbt1206-1471
pmc: PMC2270403
pubmed: '17160034'
title: NCBI GEO standards and services for microarray data.
year: 2006
- doi: 10.1093/nar/30.1.207
pmc: PMC99122
pubmed: '11752295'
title: 'Gene Expression Omnibus: NCBI gene expression and hybridization array
data repository.'
year: 2002
- doi: 10.1038/35001676
pmc: null
pubmed: '10693778'
title: One-stop shop for microarray data.
year: 2000
- doi: 10.5281/zenodo.5706412
pmc: null
pubmed: null
title: 'MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing
Experiment - a proposal for standards in functional genomic data reporting'
year: 2012
uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1
geogeo:
banana: GEO
banana_peel: _
contact:
email: hoganwr@gmail.com
github: hoganwr
name: Bill Hogan
orcid: 0000-0002-9881-1017
description: An ontology and inventory of geopolitical entities such as nations
and their components (states, provinces, districts, counties) and the actual physical
territories over which they have jurisdiction. We thus distinguish and assign
different identifiers to the US in "The US declared war on Germany" vs. the US
in "The plane entered US airspace".
download_owl: http://purl.obolibrary.org/obo/geo.owl
example: '000000021'
homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki
keywords:
- human geography
- obo
- ontology
- physical geography
license: CC-BY-4.0
mappings:
biocontext: GEO
bioportal: GEO
fairsharing: FAIRsharing.27rndz
miriam: geogeo
obofoundry: geo
ols: geo
ontobee: GEO
name: Geographical Entity Ontology
namespace_in_lui: true
pattern: ^\d{9}$
preferred_prefix: GEOGEO
rdf_uri_format: http://purl.obolibrary.org/obo/GEO_$1
repository: https://github.com/ufbmi/geographical-entity-ontology
uri_format: http://purl.obolibrary.org/obo/GEO_$1
version: '2016-03-26'
geonames:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The GeoNames geographical database covers all countries and contains
over eleven million placenames that are available for download free of charge.
example: '3532759'
homepage: https://www.geonames.org
keywords:
- geography
- geoinformatics
mappings:
fairsharing: FAIRsharing.6dba71
re3data: r3d100010245
name: GeoNames
pattern: ^\d+$
preferred_prefix: geonames
synonyms:
- Geomames
- Geonamaes
uri_format: https://www.geonames.org/$1
geonames.feature:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: All geographical features in GeoNames are categorized into one out
of nine feature classes and further subcategorized into one out of 645 feature
codes.
example: ADM1
homepage: https://www.geonames.org/export/codes.html
name: GeoNames Feature Code
preferred_prefix: geonames.feature
uri_format: https://www.geonames.org/recent-changes/featurecode/$1/
gexo:
contact:
email: kuiper@bio.ntnu.no
github: makuintnu
name: Martin Kuiper
orcid: 0000-0002-1171-9876
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
keywords:
- life science
- ontology
mappings:
aberowl: GEXO
bioportal: GEXO
fairsharing: FAIRsharing.3e0sn4
ols: gexo
name: Gene Expression Ontology
no_own_terms: true
preferred_prefix: gexo
publications:
- doi: 10.1186/s12859-014-0386-y
pmc: PMC4279962
pubmed: '25490885'
title: Finding gene regulatory network candidates using the gene expression knowledge
base.
year: 2014
gfo:
contact:
email: heinrich.herre@imise.uni-leipzig.de
github: null
name: Heinrich Herre
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The General Formal Ontology is a top-level ontology for conceptual
modeling, which is being constantly further developed by Onto-Med. It includes
elaborations of categories like objects, processes, time and space, properties,
relations, roles, functions, facts, and situations. Moreover, we are working on
an integration with the notion of levels of reality in order to more appropriately
capture entities in the material, mental, and social areas.
download_owl: http://www.onto-med.de/ontologies/gfo.owl
example: projects_to
homepage: https://www.onto-med.de/ontologies/gfo
keywords:
- biomedical science
- life science
- ontology
mappings:
aberowl: GFO
bioportal: GFO
fairsharing: FAIRsharing.175hsz
name: General Formal Ontology
preferred_prefix: gfo
uri_format: http://www.onto-med.de/ontologies/gfo.owl#$1
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/$1
giardiadb:
description: GiardiaDB is one of the databases that can be accessed through the
EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens
of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma,
Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific
database built upon the same infrastructure, the EuPathDB portal offers an entry
point to all these resources, and the opportunity to leverage orthology for searches
across genera.
example: GL50803_102438
homepage: https://giardiadb.org/giardiadb/
keywords:
- eukaryotic
- genome
- genomics
mappings:
biocontext: GIARDIADB
fairsharing: FAIRsharing.e7skwg
miriam: giardiadb
n2t: giardiadb
prefixcommons: giardiadb
re3data: r3d100012458
name: GiardiaDB
pattern: ^\w+$
preferred_prefix: giardiadb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/giardiadb:$1
publications:
- doi: 10.1093/nar/gkn631
pmc: PMC2686445
pubmed: '18824479'
title: 'GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic
protist pathogens Giardia lamblia and Trichomonas vaginalis.'
year: 2008
twitter: EuPathDB
uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1
github:
description: GitHub is an online host of Git source code repositories.
example: biopragmatics/bioregistry
example_extras:
- biopragmatics
- cthoyt
homepage: https://github.com/
keywords:
- knowledge and information systems
- software engineering
- subject agnostic
mappings:
fairsharing: FAIRsharing.c55d5e
miriam: github
re3data: r3d100010375
name: github
pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$
preferred_prefix: github
repository: https://services.github.com/
uri_format: https://github.com/$1
github.issue:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An issue in any public repository on GitHub.
example: biopragmatics/bioregistry/424
homepage: https://github.com/
keywords:
- knowledge and information systems
- project management
- software engineering
- version control
name: GitHub Issue
preferred_prefix: github.issue
uri_format: https://bioregistry.io/resolve/github/issue/$1
github.pull:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A pull request in any public repository on GitHub.
example: biopragmatics/bioregistry/416
homepage: https://github.com/
keywords:
- knowledge and information systems
- project management
- software engineering
- version control
name: GitHub Pull Request
preferred_prefix: github.pull
uri_format: https://bioregistry.io/resolve/github/pull/$1
gitlab:
description: GitLab is The DevOps platform that empowers organizations to maximize
the overall return on software development by delivering software faster and efficiently,
while strengthening security and compliance. With GitLab, every team in your organization
can collaboratively plan, build, secure, and deploy software to drive business
outcomes faster with complete transparency, consistency and traceability.
example: morpheus.lab/morpheus
homepage: https://gitlab.com/
keywords:
- knowledge and information systems
- software engineering
- subject agnostic
mappings:
fairsharing: FAIRsharing.530e61
miriam: gitlab
name: GitLab
pattern: ^.*/.*$
preferred_prefix: gitlab
twitter: 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
glycomapsdb:
description: A database of GlycoMaps containing 2585 conformational maps.
example: '6819'
homepage: http://www.glycosciences.de/modeling/glycomapsdb/
keywords:
- small molecule
mappings:
prefixcommons: glycomapsdb
name: GlycoMapsDB
preferred_prefix: glycomapsdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/glycomapsdb:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1
glycomedb:
description: GlycomeDB is the result of a systematic data integration effort, and
provides an overview of all carbohydrate structures available in public databases,
as well as cross-links.
example: G77500AY
has_canonical: glytoucan
homepage: https://glytoucan.org/
keywords:
- life science
- molecules
- small molecules
- structure
mappings:
biocontext: GLYCOMEDB
edam: '2664'
fairsharing: FAIRsharing.k5k0yh
miriam: glycomedb
n2t: glycomedb
prefixcommons: glycomedb
re3data: r3d100011527
name: GlycomeDB
pattern: ^\w+$
preferred_prefix: glycomedb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/glycomedb:$1
publications:
- doi: 10.1093/nar/gkq1014
pmc: PMC3013643
pubmed: '21045056'
title: GlycomeDB--a unified database for carbohydrate structures.
year: 2010
- doi: 10.1093/glycob/cwp137
pmc: null
pubmed: '19759275'
title: 'Glycome-DB.org: a portal for querying across the digital world of carbohydrate
sequences.'
year: 2009
- doi: 10.1186/1471-2105-9-384
pmc: PMC2567997
pubmed: '18803830'
title: GlycomeDB - integration of open-access carbohydrate structure databases.
year: 2008
uri_format: https://glytoucan.org/Structures/Glycans/$1
glyconavi:
contact:
email: issaku@noguchi.or.jp
github: null
name: Issaku Yamada
orcid: 0000-0001-9504-189X
description: GlycoNAVI is a website for carbohydrate research. It consists of the
"GlycoNAVI Database" that provides information such as existence ratios and names
of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI
tools" such as editing of 2D structures of glycans, glycan structure viewers,
and conversion tools.
example: GN_G03681DA
example_extras:
- GN_GlyTouCan_G03681DA
homepage: https://www.noguchi.or.jp/
keywords:
- chemistry
- glycomics
- life science
- organic chemistry
mappings:
fairsharing: FAIRsharing.wvp1t7
miriam: glyconavi
name: GlycoNAVI
pattern: ^GN_[A-Za-z0-9_:]+$
preferred_prefix: glyconavi
repository: https://glyconavi.github.io/doc/
uri_format: https://glyconavi.org/hub/?id=$1
glycopost:
description: GlycoPOST is a mass spectrometry data repository for glycomics and
glycoproteomics. Users can release their "raw/processed" data via this site with
a unique identifier number for the paper publication. Submission conditions are
in accordance with the Minimum Information Required for a Glycomics Experiment
(MIRAGE) guidelines.
example: GPST000024
homepage: https://glycopost.glycosmos.org
keywords:
- glycomics
- life science
mappings:
fairsharing: FAIRsharing.2y1KMt
miriam: glycopost
name: GlycoPOST
pattern: ^GPST[0-9]{6}$
preferred_prefix: glycopost
uri_format: https://glycopost.glycosmos.org/entry/$1
glycosciencesdb:
contact:
email: thomas@luetteke-online.de
github: glycosciences
name: Thomas Lütteke
orcid: 0000-0002-7140-9933
contributor:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: A database to support glycobiology and glycomics research. Its main
focus is on 3D structures, including 3D structure models as well as references
to PDB entries that feature carbohydrates.
example: '1'
github_request_issue: 537
homepage: http://www.glycosciences.de/database/
name: Glycosciences.DB
pattern: ^\d+$
preferred_prefix: glycosciencesdb
publications:
- doi: 10.1093/nar/gky994
pmc: PMC6323918
pubmed: '30357361'
title: 'Glycosciences.DB: an annotated data collection linking glycomics and proteomics
data (2018 update).'
year: 2019
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
synonyms:
- glycosciences.db
uri_format: http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1
glygen:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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/
keywords:
- glycomics
- life science
mappings:
fairsharing: FAIRsharing.aI1J5W
uniprot: DB-0254
name: Computational and Informatics Resources for Glycoscience
preferred_prefix: glygen
publications:
- doi: cwz080
pmc: PMC7335483
pubmed: '31616925'
title: 'GlyGen: Computational and Informatics Resources for Glycoscience.'
year: null
- doi: 10.1093/glycob/cwz080
pmc: PMC7335483
pubmed: '31616925'
title: 'GlyGen: Computational and Informatics Resources for Glycoscience.'
year: 2020
twitter: gly_gen
uri_format: https://glygen.org/glycan/$1
glytoucan:
description: GlyTouCan is the single worldwide registry of glycan (carbohydrate
sugar chain) data.
example: G00054MO
homepage: https://glytoucan.org
keywords:
- glycomics
- structural biology
mappings:
biocontext: GLYTOUCAN
fairsharing: FAIRsharing.5Pze7l
miriam: glytoucan
n2t: glytoucan
re3data: r3d100012388
name: GlyTouCan
pattern: ^G[0-9]{5}[A-Z]{2}$
preferred_prefix: glytoucan
publications:
- doi: 10.1093/glycob/cwx066
pmc: PMC5881658
pubmed: '28922742'
title: 'GlyTouCan: an accessible glycan structure repository.'
year: 2017
- doi: 10.1093/nar/gkv1041
pmc: PMC4702779
pubmed: '26476458'
title: GlyTouCan 1.0--The international glycan structure repository.
year: 2015
twitter: glytoucan
uri_format: https://glytoucan.org/Structures/Glycans/$1
gmd:
description: Golm Metabolome Database (GMD) provides public access to custom mass
spectral libraries, metabolite profiling experiments as well as additional information
and tools. This collection references metabolite information, relating the biologically
active substance to metabolic pathways or signalling phenomena.
example: 68513255-fc44-4041-bc4b-4fd2fae7541d
homepage: http://gmd.mpimp-golm.mpg.de/
keywords:
- life science
- metabolomics
mappings:
biocontext: GMD
fairsharing: FAIRsharing.jykmkw
miriam: gmd
n2t: gmd
re3data: r3d100011046
name: Golm Metabolome Database
pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$
preferred_prefix: gmd
publications:
- doi: doi:10.1007/s11306-010-0198-7
pmc: PMC2874469
pubmed: '20526350'
title: Decision tree supported substructure prediction of metabolites from GC-MS
profiles
year: null
- doi: 10.1007/s11306-010-0198-7
pmc: PMC2874469
pubmed: '20526350'
title: Decision tree supported substructure prediction of metabolites from GC-MS
profiles.
year: 2010
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/$1
gmelin:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Gmelin database is a large database of organometallic and inorganic
compounds updated quarterly. It is based on the German publication Gmelins Handbuch
der anorganischen Chemie which was originally published by Leopold Gmelin in 1817;
the last print edition, the 8th, appeared in the 1990s.
example: '1466'
homepage: https://link.springer.com/bookseries/562
mappings:
edam: '1004'
wikidata: P1578
name: Gmelins Handbuch der anorganischen Chemie
pattern: ^[1-9][0-9]{3,6}$
preferred_prefix: gmelin
proprietary: true
references:
- https://en.wikipedia.org/wiki/Gmelin_database
gnd:
description: The Gemeinsame Normdatei (Integrated Authority File) or GND is an international
authority file for person names, subject headings and corporate bodies. It is
used mainly for documentation in libraries and increasingly also by archives and
museums. The GND is managed by the German National Library in cooperation with
various regional library networks in German-speaking Europe and other partners.
example: '117145750'
homepage: https://lobid.org/
keywords:
- culture
- knowledge and information systems
- social science
mappings:
bartoc: '430'
fairsharing: FAIRsharing.8337e2
miriam: gnd
name: Gemeinsame Normdatei
pattern: ^[0-9X\-]+$
preferred_prefix: gnd
twitter: gndnet
uri_format: https://lobid.org/gnd/$1
gno:
contact:
email: nje5@georgetown.edu
github: edwardsnj
name: Nathan Edwards
orcid: 0000-0001-5168-3196
description: An ontology for glycans based on GlyTouCan, but organized by subsumption.
download_json: http://purl.obolibrary.org/obo/gno.json
download_obo: http://purl.obolibrary.org/obo/gno.obo
download_owl: http://purl.obolibrary.org/obo/gno.owl
example: '10004892'
example_extras:
- G99373GG
homepage: https://gnome.glyomics.org/
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: GNO
bioportal: GNO
obofoundry: gno
ols: gno
ontobee: GNO
name: Glycan Naming and Subsumption Ontology
pattern: ^(\d{8}|(\w+\d+\w+))$
preferred_prefix: GNO
providers:
- code: gno.composition
description: GNOme composition browser
homepage: https://gnome.glyomics.org/CompositionBrowser.html
name: GNOme Composition Browser
uri_format: https://gnome.glyomics.org/CompositionBrowser.html?focus=$1
- code: gno.structure
description: GNOme structure browser
homepage: https://gnome.glyomics.org/StructureBrowser.html
name: GNOme Structure Viewer
uri_format: https://gnome.glyomics.org/StructureBrowser.html?focus=$1
publications:
- doi: 10.5281/zenodo.6678278
pmc: null
pubmed: null
title: GNOme - Glycan Naming and Subsumption Ontology
year: 2021
rdf_uri_format: http://purl.obolibrary.org/obo/GNO_$1
repository: https://github.com/glygen-glycan-data/GNOme
synonyms:
- gnome
uri_format: http://purl.obolibrary.org/obo/GNO_$1
version: '2022-12-20'
gnomad:
contact:
email: hrehm@mgh.harvard.edu
github: heidirehm
name: Heidi L. Rehm
orcid: 0000-0002-6025-0015
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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 (from https://gnomad.broadinstitute.org).
example: 1-55516888-G-GA
example_extras:
- M-8602-T-C
- DUP_2_5708
github_request_issue: 695
homepage: https://gnomad.broadinstitute.org
license: CC0-1.0
name: Genome Aggregation Database
preferred_prefix: gnomad
publications:
- doi: 10.1038/s41586-020-2308-7
pmc: PMC7334197
pubmed: '32461654'
title: The mutational constraint spectrum quantified from variation in 141,456
humans.
year: 2020
- doi: 10.1038/s41586-020-2287-8
pmc: PMC7334194
pubmed: '32461652'
title: A structural variation reference for medical and population genetics.
year: 2020
uri_format: https://gnomad.broadinstitute.org/variant/$1
gnpis:
contact:
email: urgi-contact@versailles.inra.fr
github: null
name: URGI Contact
orcid: 0000-0003-3001-4908
description: GnpIS is an integrative information system focused on plants and fungal
pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers,
single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g.
genomic sequences, physical maps, genome annotation and expression data) for species
of agronomical interest.
example: AY109603
homepage: https://urgi.versailles.inra.fr/gnpis/
keywords:
- life science
mappings:
biocontext: GNPIS
fairsharing: FAIRsharing.dw22y3
miriam: gnpis
n2t: gnpis
re3data: r3d100012647
name: GnpIS
pattern: ^[A-Za-z0-9]+$
preferred_prefix: gnpis
publications:
- doi: 10.1093/database/bat058
pmc: PMC3746681
pubmed: '23959375'
title: 'GnpIS: an information system to integrate genetic and genomic data from
plants and fungi.'
year: 2013
uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1
gnps.task:
contact:
email: mingxun.wang@cs.ucr.edu
github: mwang87
name: Mingxun Wang
orcid: 0000-0001-7647-6097
contributor:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: GNPS is a web-based mass spectrometry ecosystem that aims to be an
open-access knowledge base for community-wide organization and sharing of raw,
processed, or annotated fragmentation mass spectrometry data (MS/MS)
example: 4b848c342a4f4abc871bdf8a09a60807
github_request_issue: 833
homepage: https://gnps.ucsd.edu/
name: Global Natural Products Social Molecular Networking Task
pattern: ^[a-f0-9]+$
preferred_prefix: gnps.task
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1
go:
appears_in:
- agro
- chiro
- cl
- ecocore
- ecto
- envo
- maxo
- pcl
- pco
- planp
- uberon
- xpo
- zp
banana: GO
contact:
email: suzia@stanford.edu
github: suzialeksander
name: Suzi Aleksander
orcid: 0000-0001-6787-2901
depends_on:
- cl
- ncbitaxon
- ro
- uberon
description: The Gene Ontology project provides a controlled vocabulary to describe
gene and gene product attributes in any organism.
download_json: http://purl.obolibrary.org/obo/go.json
download_obo: http://purl.obolibrary.org/obo/go.obo
download_owl: http://purl.obolibrary.org/obo/go.owl
example: '0032571'
homepage: http://geneontology.org/
keywords:
- gene
- life science
- obo
- ontology
license: CC-BY-4.0
logo: https://obofoundry.org/images/go_logo.png
mappings:
aberowl: GO
agroportal: GO
bartoc: '572'
biocontext: GO
bioportal: GO
edam: '1176'
fairsharing: FAIRsharing.6xq0ee
go: GO
hl7: 2.16.840.1.113883.6.128
miriam: go
n2t: go
ncbi: GO
obofoundry: go
ols: go
ontobee: GO
prefixcommons: go
re3data: r3d100014165
uniprot: DB-0037
wikidata: P686
mastodon: go@genomic.social
name: Gene Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: GO
providers:
- 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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/go:$1
- code: go_site
description: A non-PURL link through the GO site
homepage: http://www.geneontology.org
name: GO Site Link
uri_format: http://www.geneontology.org/GO:$1
- code: jax
description: The JAX endpoint for exploring GO
homepage: http://www.informatics.jax.org
name: Jackson Laboratories
uri_format: http://www.informatics.jax.org/vocab/gene_ontology/GO:$1
- code: miriam_obo_legacy
description: An old URI style for MIRIAM + GO
homepage: https://identifiers.org/
name: MIRIAM OBO Legacy
uri_format: http://identifiers.org/obo.go/GO:$1
- code: nextprot
description: The neXtProt endpoint for exploring GO
homepage: https://www.nextprot.org/
name: neXtProt GO Browser
uri_format: https://www.nextprot.org/term/GO:$1
- 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
publications:
- doi: 10.1093/nar/gkaa1113
pmc: PMC7779012
pubmed: '33290552'
title: 'The Gene Ontology resource: enriching a GOld mine.'
year: 2021
- doi: 10.1093/nar/gky1055
pmc: PMC6323945
pubmed: '30395331'
title: 'The Gene Ontology Resource: 20 years and still GOing strong.'
year: 2019
- doi: 10.1093/nar/gku1179
pmc: PMC4383973
pubmed: '25428369'
title: 'Gene Ontology Consortium: going forward.'
year: 2014
- doi: 10.1186/1471-2164-14-513
pmc: PMC3733925
pubmed: '23895341'
title: 'Dovetailing biology and chemistry: integrating the Gene Ontology with
the ChEBI chemical ontology.'
year: 2013
- doi: 10.1093/nar/gks1050
pmc: PMC3531070
pubmed: '23161678'
title: Gene Ontology annotations and resources.
year: 2012
- doi: 10.1093/nar/gkr1028
pmc: PMC3245151
pubmed: '22102568'
title: 'The Gene Ontology: enhancements for 2011.'
year: 2011
- doi: 10.1093/nar/gkp1018
pmc: PMC2808930
pubmed: '19920128'
title: 'The Gene Ontology in 2010: extensions and refinements.'
year: 2009
- doi: 10.1093/nar/gkh036
pmc: PMC308770
pubmed: '14681407'
title: The Gene Ontology (GO) database and informatics resource.
year: 2004
- doi: 10.1038/75556
pmc: PMC3037419
pubmed: '10802651'
title: 'Gene ontology: tool for the unification of biology. The Gene Ontology
Consortium.'
year: 2000
rdf_uri_format: http://purl.obolibrary.org/obo/GO_$1
repository: https://github.com/geneontology/go-ontology
synonyms:
- gobp
- gobpid
- gocc
- goccid
- gomf
- gomfid
twitter: news4go
uri_format: http://amigo.geneontology.org/amigo/term/GO:$1
version: '2023-04-01'
go.gpi:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
contributor_extras:
- email: null
github: sierra-moxon
name: Sierra Moxon
orcid: 0000-0002-8719-7760
description: This describes the metadata schema for the Gene Product Information
(GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier
space refer to the columns in GPI files.
example: db-object-id
homepage: http://geneontology.org/docs/gene-product-information-gpi-format/#db-object-id
mappings:
biolink: gpi
name: Gene Product Information Schema
preferred_prefix: go.gpi
uri_format: http://geneontology.org/docs/gene-product-information-gpi-format/#$1
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: http://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/README.md#goref$1
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/$1
go.rule:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: GO Rules are a way of documenting the set of filters and reports that
should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore,
some are code in the GAF parsing software, ontobio.
example: '0000004'
homepage: https://github.com/geneontology/go-site/tree/master/metadata/rules
name: Gene Ontology Rules
part_of: go
pattern: ^\d{7}$
preferred_prefix: GORULE
uri_format: https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md
goa:
description: The GOA (Gene Ontology Annotation) project provides high-quality Gene
Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB)
and International Protein Index (IPI). This involves electronic annotation and
the integration of high-quality manual GO annotation from all GO Consortium model
organism groups and specialist groups.
example: P12345
homepage: https://www.ebi.ac.uk/GOA/
keywords:
- biology
- gene
- life science
- ontology
- protein
mappings:
biocontext: GOA
fairsharing: FAIRsharing.7zffgc
miriam: goa
n2t: goa
ncbi: GOA
prefixcommons: goa
name: Gene Ontology Annotation Database
pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z,
0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$
preferred_prefix: goa
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/goa:$1
provides: uniprot
publications:
- doi: 10.1093/nar/gku1113
pmc: PMC4383930
pubmed: '25378336'
title: 'The GOA database: gene Ontology annotation updates for 2015.'
year: 2014
- doi: 10.1093/nar/gkn803
pmc: PMC2686469
pubmed: '18957448'
title: The GOA database in 2009--an integrated Gene Ontology Annotation resource.
year: 2008
uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1
goche:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Represent chemical entities having particular CHEBI roles
download_owl: https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl
example: '25512'
homepage: https://github.com/geneontology/go-ontology
keywords:
- ontology
name: GO Chemicals
pattern: ^\d+$
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
uri_format: https://biopragmatics.github.io/providers/goche/$1
goeco:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A GO annotation is a statement about the function of a particular gene.
Each annotation includes an evidence code to indicate how the annotation to a
particular term is supported.
example: IPI
homepage: http://geneontology.org/docs/guide-go-evidence-codes/
name: GO Evidence Code
preferred_prefix: goeco
gold:
description: 'The Genomes OnLine Database (GOLD) catalogues genome and metagenome
sequencing projects from around the world, along with their associated metadata.
Information in GOLD is organized into four levels: Study, Biosample/Organism,
Sequencing Project and Analysis Project.'
example: Gs0000008
homepage: https://gold.jgi.doe.gov/
keywords:
- genome
- genomics
- metabolomics
- metagenomics
- ontology and terminology
- phylogenetics
mappings:
fairsharing: FAIRsharing.5q1p14
miriam: gold
prefixcommons: gold
re3data: r3d100010808
name: Genomes Online Database
pattern: ^[A-Z][a-z][0-9]+$
preferred_prefix: gold
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/gold:$1
publications:
- doi: 10.1093/nar/gkaa983
pmc: PMC7778979
pubmed: '33152092'
title: 'Genomes OnLine Database (GOLD) v.8: overview and updates.'
year: 2021
- doi: 10.1093/nar/gky977
pmc: PMC6323969
pubmed: '30357420'
title: 'Genomes OnLine database (GOLD) v.7: updates and new features.'
year: 2019
- doi: 10.1093/nar/gkp848
pmc: PMC2808860
pubmed: '19914934'
title: 'The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic
projects and their associated metadata.'
year: 2009
- doi: 10.1093/nar/gkm884
pmc: PMC2238992
pubmed: '17981842'
title: 'The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic
projects and their associated metadata.'
year: 2007
- doi: '11125068'
pmc: PMC29859
pubmed: '11125068'
title: 'Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.'
year: null
- doi: 10.1093/nar/29.1.126
pmc: PMC29859
pubmed: '11125068'
title: 'Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.'
year: 2001
- doi: 10.1093/bioinformatics/15.9.773
pmc: null
pubmed: '10498782'
title: 'Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing
genome projects world-wide.'
year: 1999
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=$1
gold.meta:
description: "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has\
\ been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold,\
\ and this namespace is kept here for support to already existing citations, new\
\ ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine\
\ Database)is a resource for centralized monitoring of genome and metagenome projects\
\ worldwide. It stores information on complete and ongoing projects, along with\
\ their associated metadata. This collection references metadata associated with\
\ samples."
example: Gm00047
has_canonical: gold
homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
mappings:
biocontext: GOLD.META
miriam: gold.meta
n2t: gold.meta
name: GOLD metadata
pattern: ^Gm\d+$
preferred_prefix: gold.meta
uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1
goldbook:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The Compendium is popularly referred to as the "Gold Book", in recognition
of the contribution of the late Victor Gold, who initiated work on the first edition.
It is one of the series of IUPAC "Colour Books" on chemical nomenclature, terminology,
symbols and units (see the list of source documents), and collects together terminology
definitions from IUPAC recommendations already published in Pure and Applied Chemistry
and in the other Colour Books.
Terminology definitions published by IUPAC are drafted by international committees
of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC''s
Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In
this edition of the Compendium these IUPAC-approved definitions are supplemented
with some definitions from ISO and from the International Vocabulary of Basic
and General Terms in Metrology; both these sources are recognised by IUPAC as
authoritative. The result is a collection of nearly 7000 terms, with authoritative
definitions, spanning the whole range of chemistry.'
example: G02681
homepage: https://goldbook.iupac.org
license: CC BY 4.0-NC-ND
mappings:
bartoc: '1884'
wikidata: P4732
name: IUPAC Gold Book Compendium of Chemical Terminology
pattern: ^[A-Z]{1,2}\d{5}$
preferred_prefix: goldbook
rdf_uri_format: http://dx.doi.org/10.1351/goldbook.$1
uri_format: https://goldbook.iupac.org/terms/view/$1
google.book:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Search the world's most comprehensive index of full-text books.
example: qafeQTWIWmcC
github_request_issue: 511
homepage: https://books.google.com
mappings:
wikidata: P675
name: Google Books
preferred_prefix: google.book
uri_format: https://books.google.com/books?id=$1
google.patent:
contributor_extras:
- email: benjamin_gyori@hms.harvard.edu
github: bgyori
name: Benjamin M. Gyori
orcid: 0000-0001-9439-5346
description: Google Patents covers the entire collection of granted patents and
published patent applications from the USPTO, EPO, and WIPO. US patent documents
date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using
patent number, inventor, classification, and filing date.
example: US4145692
example_extras:
- USRE38117E1
homepage: https://www.google.com/patents/
mappings:
biocontext: GOOGLE.PATENT
cellosaurus: Patent
miriam: google.patent
n2t: google.patent
name: Google Patents
pattern: ^[A-Z]{2,4}\d+([A-Z])?([0-9])?$
preferred_prefix: google.patent
synonyms:
- patent
uri_format: https://www.google.com/patents/$1
google.scholar:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'Google Scholar provides a simple way to broadly search for scholarly
literature. You can search across many disciplines and sources: articles, theses,
books, abstracts and court opinions, from academic publishers, professional societies,
online repositories, universities and other web sites.'
example: PjrpzUIAAAAJ
homepage: https://scholar.google.com/
mappings:
biolink: GSID
name: Google Scholar Researcher
preferred_prefix: google.scholar
gorel:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Documentation of GO that provides a description of some of the commonly
used relationships and conventions in GO.
download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl
example: '0002005'
homepage: http://geneontology.org/docs/ontology-relations/
keywords:
- ontology
mappings:
biolink: GOREL
go: GOREL
name: GO Relations
pattern: ^\d{7}$
preferred_prefix: gorel
providers:
- code: obo.legacy
description: Legacy OBO PURLs
homepage: http://purl.obolibrary.org/obo/gorel.owl
name: Legacy OBO
uri_format: http://purl.obolibrary.org/obo/GOREL_$1
gpcrdb:
contact:
email: david.gloriam@sund.ku.dk
github: null
name: David Gloriam
orcid: 0000-0002-4299-7561
description: The G protein-coupled receptor database (GPCRDB) collects, large amounts
of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding
constants, mutations and oligomers, and derived data such as multiple sequence
alignments and homology models.
example: RL3R1_HUMAN
homepage: http://www.gpcrdb.org/
keywords:
- life science
- molecular biology
- protein
- small molecule
mappings:
biocontext: GPCRDB
fairsharing: FAIRsharing.e4n3an
miriam: gpcrdb
n2t: gpcrdb
prefixcommons: gpcrdb
uniprot: DB-0038
name: G protein-coupled receptor database
pattern: ^\w+$
preferred_prefix: gpcrdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/gpcrdb:$1
publications:
- doi: 10.1093/nar/26.1.275
pmc: PMC147194
pubmed: '9399852'
title: 'GPCRDB: an information system for G protein-coupled receptors.'
year: 1998
- doi: 10.1093/nar/gkaa1080
pmc: PMC7778909
pubmed: '33270898'
title: 'GPCRdb in 2021: integrating GPCR sequence, structure and function.'
year: 2021
- doi: 10.1093/nar/gkx1109
pmc: PMC5753179
pubmed: '29155946'
title: 'GPCRdb in 2018: adding GPCR structure models and ligands.'
year: 2018
- doi: 10.1111/bph.13509
pmc: PMC4919580
pubmed: '27155948'
title: 'GPCRdb: the G protein-coupled receptor database - an introduction.'
year: 2016
- doi: 10.1093/nar/gkv1178
pmc: PMC4702843
pubmed: '26582914'
title: 'GPCRdb: an information system for G protein-coupled receptors.'
year: 2015
- doi: 10.1093/nar/gkt1255
pmc: PMC3965068
pubmed: '24304901'
title: 'GPCRDB: an information system for G protein-coupled receptors.'
year: 2013
- doi: 10.1093/nar/gkq1009
pmc: PMC3013641
pubmed: '21045054'
title: 'GPCRDB: information system for G protein-coupled receptors.'
year: 2010
- doi: 10.1093/nar/gkg103
pmc: PMC165550
pubmed: '12520006'
title: GPCRDB information system for G protein-coupled receptors.
year: 2003
- doi: 10.1093/nar/29.1.346
pmc: PMC29816
pubmed: '11125133'
title: 'Collecting and harvesting biological data: the GPCRDB and NucleaRDB information
systems.'
year: 2001
twitter: gpcrdb
uri_format: https://gpcrdb.org/protein/$1
gpcrnava:
description: The GPCR NaVa database describes sequence variants within the family
of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological
functions and are the targets for most of today's medicines. The acronym NaVa
stands for Natural Variant, which means any (non-artificial) variant that occurs
in humans.
example: '1150'
homepage: http://nava.liacs.nl/
keywords:
- pathway
- protein
mappings:
prefixcommons: gnd
name: GPCR Natural Variants database
preferred_prefix: gpcrnava
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/gnd:$1
uri_format: http://nava.liacs.nl/cgi-bin/nava.py?id=$1
gpmdb:
description: The Global Proteome Machine Database was constructed to utilize the
information obtained by GPM servers to aid in the difficult process of validating
peptide MS/MS spectra as well as protein coverage patterns.
example: GPM32310002988
homepage: http://gpmdb.thegpm.org/
keywords:
- bioinformatics
- proteomics
mappings:
biocontext: GPMDB
fairsharing: FAIRsharing.fhcmwq
miriam: gpmdb
n2t: gpmdb
name: Global Proteome Machine Database
pattern: ^GPM\d+$
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
publications:
- doi: 10.1021/pr049882h
pmc: null
pubmed: '15595733'
title: Open source system for analyzing, validating, and storing protein identification
data.
year: 2004
twitter: GPMDB
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=$1
gramene.growthstage:
banana: GRO
contact:
email: po-discuss@plantontology.org
github: null
name: Plant Ontology Administrators
orcid: null
deprecated: true
description: Gramene is a comparative genome mapping database for grasses and crop
plants. It combines a semi-automatically generated database of cereal genomic
and expressed sequence tag sequences, genetic maps, map relations, quantitative
trait loci (QTL), and publications, with a curated database of mutants (genes
and alleles), molecular markers, and proteins. This collection refers to growth
stage ontology information in Gramene.
example: '0007133'
homepage: http://www.gramene.org/plant_ontology/
keywords:
- anatomy
- obo
- ontology
mappings:
biocontext: GRAMENE.GROWTHSTAGE
bioportal: GRO-CPGA
miriam: gro
n2t: gramene.growthstage
obofoundry: gro
prefixcommons: gramene.po
name: Gramene Growth Stage Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: GRO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/gramene.po:$1
rdf_uri_format: http://purl.obolibrary.org/obo/GRO_$1
synonyms:
- cpga
- gro-cpga
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=$1
gramene.taxonomy:
banana: GR_tax
banana_peel: ':'
description: Gramene is a comparative genome mapping database for grasses and crop
plants. It combines a semi-automatically generated database of cereal genomic
and expressed sequence tag sequences, genetic maps, map relations, quantitative
trait loci (QTL), and publications, with a curated database of mutants (genes
and alleles), molecular markers, and proteins. This datatype refers to taxonomic
information in Gramene.
example: 013681
homepage: http://www.gramene.org/
mappings:
biocontext: GRAMENE.TAXONOMY
miriam: gramene.taxonomy
n2t: gramene.taxonomy
name: Gramene Taxonomy
pattern: ^\d+$
preferred_prefix: gramene.taxonomy
uri_format: https://archive.gramene.org/db/ontology/search?id=GR_tax:$1
grassbase:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: GrassBase provides an interactive guide to nomenclature for the whole
grass family. It provides lists of over 60,000 names for any given genus, geographical
region or genus within a geographical region, helps find the accepted name, synonyms
and distribution for any given name, and gives a desription for each species.
example: imp10873
github_request_issue: 218
homepage: https://www.kew.org/data/grasses-syn/index.htm
mappings:
wikidata: P1832
name: GrassBase
pattern: ^(imp|gen)\d{5}$
preferred_prefix: grassbase
uri_format: https://www.kew.org/data/grasses-db/www/$1
greengenes:
contact:
email: GLAndersen@lbl.gov
github: null
name: Gary L Andersen
orcid: 0000-0002-1618-9827
description: A 16S rRNA gene database which provides chimera screening, standard
alignment, and taxonomic classification using multiple published taxonomies.
example: '100000'
homepage: http://greengenes.lbl.gov/
keywords:
- genetics
- life science
- rna
mappings:
biocontext: GREENGENES
fairsharing: FAIRsharing.bpxgb6
miriam: greengenes
n2t: greengenes
ncbi: Greengenes
prefixcommons: greengenes
re3data: r3d100010549
name: 16S rRNA gene database
pattern: ^\d+$
preferred_prefix: greengenes
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/greengenes:$1
publications:
- doi: 10.1128/aem.03006-05
pmc: PMC1489311
pubmed: '16820507'
title: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible
with ARB.
year: 2006
uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1
grid:
description: International coverage of the world's leading research organisations,
indexing 92% of funding allocated globally.
example: grid.225360.0
homepage: https://www.grid.ac/
keywords:
- data management
mappings:
biocontext: GRID
fairsharing: FAIRsharing.0pUMYW
miriam: grid
n2t: grid
name: Global Research Identifier Database
pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$
preferred_prefix: grid
twitter: grid_ac
uri_format: https://www.grid.ac/institutes/$1
grin:
description: GRIN provides National Genetic Resources Program (NGRP) personnel and
germplasm users continuous access to databases for the maintenance of passport,
characterization, evaluation, inventory, and distribution data important for the
effective management and utilization of national germplasm collections.
example: '159787'
homepage: http://www.ars-grin.gov/
keywords:
- life science
mappings:
fairsharing: FAIRsharing.3axym7
prefixcommons: grin
name: Germplasm Resources Information Network
preferred_prefix: grin
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/grin:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1
grin.taxonomy:
description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants
provides information on scientific and common names, classification, distribution,
references, and economic impact.
example: '19333'
homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en
mappings:
biocontext: GRIN.TAXONOMY
go: GRIN
miriam: grin.taxonomy
n2t: grin.taxonomy
ncbi: GRIN
wikidata: P1421
name: GRIN URL
pattern: ^\d+$
preferred_prefix: grin.taxonomy
uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1
gro:
contact:
email: vlee@ebi.ac.uk
github: null
name: Vivian Lee
orcid: null
deprecated: true
description: The Gene Regulation Ontology (GRO) is a conceptual model for the domain
of gene regulation. It covers processes that are linked to the regulation of gene
expression as well as physical entities that are involved in these processes (such
as genes and transcription factors) in terms of ontology classes and semantic
relations between classes.
download_owl: http://aber-owl.net/media/ontologies/GRO/5/gro.owl
example: Lipid
homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html
keywords:
- ontology
mappings:
aberowl: GRO
bioportal: GRO
name: Gene Regulation Ontology
preferred_prefix: gro
uri_format: http://www.bootstrep.eu/ontology/GRO#$1
grsdb:
description: GRSDB is a database of G-quadruplexes and contains information on composition
and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped
in the eukaryotic pre-mRNA sequences, including those that are alternatively processed
(alternatively spliced or alternatively polyadenylated). The data stored in the
GRSDB is based on computational analysis of NCBI Entrez Gene entries and their
corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.
example: '10142'
homepage: http://bioinformatics.ramapo.edu/GRSDB2/
keywords:
- dna
- rna
mappings:
biocontext: GRSDB
miriam: grsdb
n2t: grsdb
prefixcommons: grsdb
name: G-Rich Sequences Database
pattern: ^\d+$
preferred_prefix: grsdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/grsdb:$1
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=$1
gsso:
appears_in:
- ontoavida
- scdo
banana: GSSO
contact:
email: kronkcj@mail.uc.edu
github: Superraptor
name: Clair Kronk
orcid: 0000-0001-8397-8810
description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary
ontology connecting terms from biology, medicine, psychology, sociology, and gender
studies, aiming to bridge gaps between linguistic variations inside and outside
of the health care environment. A large focus of the ontology is its consideration
of LGBTQIA+ terminology.
download_json: http://purl.obolibrary.org/obo/gsso.json
download_obo: http://purl.obolibrary.org/obo/gsso.obo
download_owl: http://purl.obolibrary.org/obo/gsso.owl
example: 002368
homepage: https://gsso.research.cchmc.org/
keywords:
- obo
- ontology
license: Apache 2.0 License
mappings:
aberowl: GSSO
bioportal: GSSO
miriam: gsso
obofoundry: gsso
ols: gsso
ontobee: GSSO
name: Gender, Sex, and Sexual Orientation Ontology
namespace_in_lui: true
pattern: ^\d{6}$
preferred_prefix: GSSO
rdf_uri_format: http://purl.obolibrary.org/obo/GSSO_$1
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/$1
gudmap:
description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is
a consortium of laboratories working to provide the scientific and medical community
with tools to facilitate research on the GenitoUrinary (GU) tract.
example: Q-2958
homepage: http://www.gudmap.org/
keywords:
- cell biology
- developmental biology
- genomics
- molecular biology
mappings:
biocontext: GUDMAP
fairsharing: FAIRsharing.910c39
miriam: gudmap
n2t: gudmap
re3data: r3d100012193
name: Genitourinary Development Molecular Anatomy Project
pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$
preferred_prefix: gudmap
publications:
- doi: 10.1242/dev.063594
pmc: PMC3188593
pubmed: '21652655'
title: The GUDMAP database--an online resource for genitourinary research.
year: 2011
- doi: 10.1681/asn.2007101078
pmc: null
pubmed: '18287559'
title: 'GUDMAP: the genitourinary developmental molecular anatomy project.'
year: 2008
twitter: 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/$1
gwascentral.study:
description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype
information) is a database of summary level findings from genetic association
studies, both large and small. It gathers datasets from public domain projects,
and accepts direct data submission. It is based upon Marker information encompassing
SNP and variant information from public databases, to which allele and genotype
frequency data, and genetic association findings are additionally added. A Study
(most generic level) contains one or more Experiments, one or more Sample Panels
of test subjects, and one or more Phenotypes. This collection references a GWAS
Central Study.
example: HGVST1828
homepage: https://www.gwascentral.org/studies
keywords:
- gene
- genome
mappings:
biocontext: GWASCENTRAL.STUDY
miriam: gwascentral.study
n2t: gwascentral.study
prefixcommons: hgvbase
name: GWAS Central Study
pattern: ^HGVST\d+$
preferred_prefix: gwascentral.study
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hgvbase:$1
uri_format: https://www.gwascentral.org/study/$1
gxa.expt:
description: The Gene Expression Atlas (GXA) is a semantically enriched database
of meta-analysis based summary statistics over a curated subset of ArrayExpress
Archive, servicing queries for condition-specific gene expression patterns as
well as broader exploratory searches for biologically interesting genes/samples.
This collection references experiments.
example: E-MTAB-2037
homepage: https://www.ebi.ac.uk/gxa/
mappings:
biocontext: GXA.EXPT
miriam: gxa.expt
n2t: gxa.expt
name: GXA Expt
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^[AEP]-\w{4}-\d+$
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/$1
gxa.gene:
description: The Gene Expression Atlas (GXA) is a semantically enriched database
of meta-analysis based summary statistics over a curated subset of ArrayExpress
Archive, servicing queries for condition-specific gene expression patterns as
well as broader exploratory searches for biologically interesting genes/samples.
This collection references genes.
example: AT4G01080
homepage: https://www.ebi.ac.uk/gxa/
mappings:
biocontext: GXA.GENE
miriam: gxa.gene
n2t: gxa.gene
name: GXA Gene
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^\w+$
preferred_prefix: gxa.gene
uri_format: https://www.ebi.ac.uk/gxa/genes/$1
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
keywords:
- obo
- ontology
mappings:
biocontext: HABRONATTUS
obofoundry: habronattus
name: Habronattus courtship
preferred_prefix: HABRONATTUS
rdf_uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1
uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1
hagr.genage:
description: GenAge is a database of human and model organism genes related to longevity
and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.
example: '0001'
homepage: http://genomics.senescence.info/genes/
keywords:
- aging
- genes
- longevity
mappings:
prefixcommons: genage
name: The Ageing Gene Database
preferred_prefix: hagr.genage
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/genage:$1
publications:
- doi: 10.1093/nar/gks1155
pmc: PMC3531213
pubmed: '23193293'
title: 'Human Ageing Genomic Resources: integrated databases and tools for the
biology and genetics of ageing.'
year: 2012
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://genomics.senescence.info/genes/details.php?id=$1
hagr.gendr:
description: 'GenDR is a database of genes associated with dietary restriction (DR).
GenDR includes two datasets: 1) genes inferred from experiments in model organisms
in which genetic manipulations cancel out or disrupt the life-extending effects
of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray
DR studies in mammals'
example: '2'
homepage: http://genomics.senescence.info/diet/
keywords:
- aging
- dietary restriction
- genes
- longevity
mappings:
prefixcommons: gendr
name: The Dietary Restriction Gene Database
preferred_prefix: hagr.gendr
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/gendr:$1
publications:
- doi: 10.1371/journal.pgen.1002834
pmc: PMC3415404
pubmed: '22912585'
title: Dissecting the gene network of dietary restriction to identify evolutionarily
conserved pathways and new functional genes.
year: 2012
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://genomics.senescence.info/diet/details.php?id=$1
hamap:
contact:
email: alan.bridge@isb-sib.ch
github: null
name: Alan Bridge
orcid: 0000-0003-2148-9135
description: HAMAP is a system that identifies and semi-automatically annotates
proteins that are part of well-conserved and orthologous microbial families or
subfamilies. These are used to build rules which are used to propagate annotations
to member bacterial, archaeal and plastid-encoded protein entries.
example: MF_01400
homepage: https://hamap.expasy.org/
keywords:
- life science
- protein
mappings:
biocontext: HAMAP
edam: '2766'
fairsharing: FAIRsharing.63m4ss
go: HAMAP
miriam: hamap
n2t: hamap
prefixcommons: hamap
uniprot: DB-0041
name: High-quality Automated and Manual Annotation of microbial Proteomes
pattern: ^MF_\d+$
preferred_prefix: hamap
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hamap:$1
publications:
- doi: 10.1093/nar/gku1002
pmc: PMC4383873
pubmed: '25348399'
title: 'HAMAP in 2015: updates to the protein family classification and annotation
system.'
year: 2014
- doi: 10.1093/nar/gks1157
pmc: PMC3531088
pubmed: '23193261'
title: HAMAP in 2013, new developments in the protein family classification and
annotation system.
year: 2012
uri_format: https://hamap.expasy.org/unirule/$1
hancestro:
contact:
email: danielle.welter@uni.lu
github: daniwelter
name: Danielle Welter
orcid: 0000-0003-1058-2668
description: Human ancestry ontology for the NHGRI GWAS Catalog
download_owl: http://purl.obolibrary.org/obo/hancestro.owl
example: 0290
homepage: https://github.com/EBISPOT/ancestro
keywords:
- demographics
- human genetics
- obo
- ontology
- population genetics
license: CC-BY-4.0
mappings:
aberowl: HANCESTRO
biolink: HANCESTRO
bioportal: HANCESTRO
fairsharing: FAIRsharing.rja8qp
obofoundry: hancestro
ols: hancestro
ontobee: HANCESTRO
name: Human Ancestry Ontology
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^\d{4}$
preferred_prefix: HANCESTRO
providers:
- code: legacy
description: Legacy URI
homepage: http://www.ebi.ac.uk/ancestro
name: Legacy
uri_format: http://www.ebi.ac.uk/ancestro/ancestro_$1
publications:
- doi: 10.1186/s13059-018-1396-2
pmc: PMC5815218
pubmed: '29448949'
title: A standardized framework for representation of ancestry data in genomics
studies, with application to the NHGRI-EBI GWAS Catalog.
year: 2018
rdf_uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1
repository: https://github.com/EBISPOT/ancestro
uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1
version: '2023-02-16'
hao:
contact:
email: diapriid@gmail.com
github: mjy
name: Matt Yoder
orcid: 0000-0002-5640-5491
description: A structured controlled vocabulary of the anatomy of the Hymenoptera
(bees, wasps, and ants)
download_obo: http://purl.obolibrary.org/obo/hao.obo
download_owl: http://purl.obolibrary.org/obo/hao.owl
example: 0000187
homepage: http://hymao.org
keywords:
- anatomy
- life science
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: HAO
biocontext: HAO
bioportal: HAO
fairsharing: FAIRsharing.kj3m5n
obofoundry: hao
ols: hao
ontobee: HAO
name: Hymenoptera Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: HAO
publications:
- doi: 10.1371/journal.pone.0015991
pmc: PMC3012123
pubmed: '21209921'
title: A gross anatomy ontology for hymenoptera.
year: 2010
rdf_uri_format: http://purl.obolibrary.org/obo/HAO_$1
repository: https://github.com/hymao/hao
uri_format: http://purl.obolibrary.org/obo/HAO_$1
version: '2021-03-05'
hathitrust:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Hathitrust is a partnership of academic and research institutions,
offering a collection of millions of titles digitized from libraries around the
world.
example: 008893080
github_request_issue: 510
homepage: https://www.hathitrust.org
name: Hathi Trust Digital Library
pattern: ^\d+$
preferred_prefix: hathitrust
uri_format: https://catalog.hathitrust.org/Record/$1
hba:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
human brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo
example: '4005'
example_extras:
- '265504410'
homepage: https://human.brain-map.org
keywords:
- ontology
name: Human Brain Atlas
pattern: ^\d+$
preferred_prefix: HBA
uri_format: https://biopragmatics.github.io/providers/hba/$1
hbvar:
description: This is a relational database of information about hemoglobin variants
and mutations that cause thalassemia.
example: '2526'
homepage: http://globin.cse.psu.edu/globin/hbvar
keywords:
- protein
mappings:
prefixcommons: hbvar
name: A Database of Human Hemoglobin Variants and Thalassemias
preferred_prefix: hbvar
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hbvar:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1
hc.din:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A Drug Identification Number (DIN) is a computer-generated eight digit
number assigned by Health Canada to a drug product prior to being marketed in
Canada. It uniquely identifies all drug products sold in a dosage form in Canada
and is located on the label of prescription and over-the-counter drug products
that have been evaluated and authorized for sale in Canada.
example: 02069237
homepage: https://www.canada.ca/en/health-canada/services/drugs-health-products/drug-products/fact-sheets/drug-identification-number.html
mappings:
hl7: 2.16.840.1.113883.5.1105
name: Health Canada Drug Identification Number
pattern: ^\d{8}$
preferred_prefix: hc.din
references:
- http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/index-eng.php
hc.npn:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Licensed Natural Health Products Database contains information
about natural health products that have been issued a product licence by Health
Canada.
example: '18125'
homepage: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/search-rechercheReq.do?lang=eng
mappings:
hl7: 2.16.840.1.113883.5.1107
name: Health Canada Natural Product Number
pattern: ^\d+$
preferred_prefix: hc.npn
references:
- https://www.canada.ca/en/health-canada/services/drugs-health-products/natural-non-prescription/applications-submissions/product-licensing/licensed-natural-health-products-database.html
uri_format: http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1
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/2023-04-18/hcao.owl
homepage: https://www.humancellatlas.org
keywords:
- ontology
mappings:
ols: hcao
name: Human Cell Atlas Ontology
no_own_terms: true
preferred_prefix: hcao
hcpcs:
contact:
email: Cynthia.Hake@cms.hhs.gov
github: null
name: Cynthia Hake
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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
keywords:
- biomedical science
- business administration
- ontology
mappings:
aberowl: HCPCS
biolink: HCPCS
bioportal: HCPCS
fairsharing: FAIRsharing.x81wz8
name: Healthcare Common Procedure Coding System
preferred_prefix: hcpcs
uri_format: http://purl.bioontology.org/ontology/HCPCS/$1
hcvdb:
description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr),
a collection of computer-annotated sequences based on reference genomes.mainly
dedicated to HCV protein sequences, 3D structures and functional analyses.
example: M58335
homepage: http://euhcvdb.ibcp.fr/euHCVdb/
keywords:
- gene
mappings:
biocontext: HCVDB
miriam: hcvdb
n2t: hcvdb
prefixcommons: hcv
name: Hepatitis C Virus Database Project
pattern: ^M\d{5}$
preferred_prefix: hcvdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hcv:$1
uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1
hdr:
description: The Homeodomain Resource is a curated collection of sequence, structure,
interaction, genomic and functional information on the homeodomain family. It
contains sets of curated homeodomain sequences from fully sequenced genomes, including
experimentally derived homeodomain structures, homeodomain protein-protein interactions,
homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic
disorders.
example: '63'
homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/
keywords:
- genome
mappings:
biocontext: HDR
miriam: hdr
n2t: hdr
prefixcommons: hdr
name: Homeodomain Research
pattern: ^\d+$
preferred_prefix: hdr
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hdr:$1
uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1
hepro:
contact:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
contributor:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
description: HEPRO is an ontology of informational entities and processes related
to health procedures and health activities.
download_json: https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.json
download_owl: https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.owl
example: '0000001'
github_request_issue: 810
homepage: https://openlhs.github.io/HEPRO/
keywords:
- ontology
license: CC-BY-4.0
name: Health Procedure Ontology
owners:
- name: Université de Sherbrooke
partnered: false
ror: 00kybxq39
wikidata: null
pattern: ^\d{7}$
preferred_prefix: HEPRO
repository: https://github.com/OpenLHS/HEPRO
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://purl.obolibrary.org/obo/HEPRO_$1
hesa:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An identifier for institutions in the United Kingdom, used in GRID
and ROR.
example: '0154'
homepage: https://www.hesa.ac.uk
keywords:
- bibliometrics
- institution
name: UK Higher Education Statistics Agency
pattern: ^\d+$
preferred_prefix: hesa
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
edam: '3265'
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=$1
hgnc:
contact:
email: elspeth@genenames.org
github: null
name: Elspeth Bruford
orcid: 0000-0002-8380-5247
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
name and symbol (short-form abbreviation) for each known human gene. All approved
symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers
refer to records in the HGNC symbol database.
download_owl: http://aber-owl.net/media/ontologies/HGNC/1/hgnc.owl
example: '16793'
homepage: http://www.genenames.org
keywords:
- classification
- gene
- life science
- ontology
mappings:
aberowl: HGNC
biocontext: HGNC
bioportal: HGNC
cellosaurus: HGNC
edam: '2298'
fairsharing: FAIRsharing.amcv1e
go: HGNC
hl7: 2.16.840.1.113883.6.281
miriam: hgnc
n2t: hgnc
ncbi: HGNC
prefixcommons: hgnc
uniprot: DB-0042
wikidata: P354
name: HUGO Gene Nomenclature Committee
pattern: ^\d{1,5}$
preferred_prefix: hgnc
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hgnc:$1
- 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
- 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
publications:
- doi: 10.1093/nar/gkaa980
pmc: PMC7779007
pubmed: '33152070'
title: 'Genenames.org: the HGNC and VGNC resources in 2021.'
year: 2021
- doi: 10.1093/nar/gky930
pmc: PMC6324057
pubmed: '30304474'
title: 'Genenames.org: the HGNC and VGNC resources in 2019.'
year: 2019
- doi: 10.1159/000131404
pmc: null
pubmed: '295268'
title: International system for human gene nomenclature (1979) ISGN (1979).
year: 1979
uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1
hgnc.genefamily:
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
name and symbol (short-form abbreviation) for each known human gene. All approved
symbols are stored in the HGNC database, and each symbol is unique. In addition,
HGNC also provides a unique numerical ID to identify gene families, providing
a display of curated hierarchical relationships between families.
example: '2029'
has_canonical: hgnc.genegroup
homepage: http://www.genenames.org
mappings:
biocontext: HGNC.GENEFAMILY
miriam: hgnc.genefamily
n2t: hgnc.genefamily
name: HGNC gene family
pattern: ^\d+$
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/$1
hgnc.symbol:
description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene
name and symbol (short-form abbreviation) for each known human gene. All approved
symbols are stored in the HGNC database, and each symbol is unique. This collection
refers to records using the HGNC symbol.
example: DAPK1
homepage: https://www.genenames.org/
mappings:
biocontext: HGNC.SYMBOL
miriam: hgnc.symbol
n2t: hgnc.symbol
wikidata: P353
name: HGNC gene symbol
pattern: ^[A-Za-z-0-9_]+(\@)?$
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: oncomx
description: Mutation profiles for a gene
homepage: https://oncomx.org
name: OncoMX
uri_format: https://oncomx.org/searchview/?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
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: https://www.hipsci.org
mappings:
cellosaurus: HipSci
name: Human Induced Pluripotent Stem Cells Initiative
preferred_prefix: hipsci
uri_format: https://www.hipsci.org/lines/#/lines/$1
hivreagentprogram:
description: Cell line collections
example: ARP-1513
homepage: https://www.hivreagentprogram.org/
mappings:
cellosaurus: HIVReagentProgram
name: NIH HIV Reagent Program
preferred_prefix: hivreagentprogram
uri_format: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx
hl7.v2codesystem:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A registry of code systems (each are small vocabularies themselves)
used by HL7 international, related to FHIR.
example: 0778
homepage: https://terminology.hl7.org/codesystems-v2.html
name: HL7 V2 Code Systems
pattern: ^\d+$
preferred_prefix: hl7.v2codesystem
uri_format: http://terminology.hl7.org/CodeSystem/v2-$1
hl7.v3codesystem:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A registry of code systems (each are small vocabularies themselves)
used by HL7 international, related to FHIR.
example: AcknowledgementCondition
homepage: https://terminology.hl7.org/codesystems-v2.html
name: HL7 V2 Code Systems
pattern: ^\w+$
preferred_prefix: hl7.v3codesystem
uri_format: https://terminology.hl7.org/CodeSystem-v3-$1
hmdb:
description: The Human Metabolome Database (HMDB) is a database containing detailed
information about small molecule metabolites found in the human body.It contains
or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.
example: HMDB00001
homepage: http://www.hmdb.ca/
keywords:
- biochemistry
- bioinformatics
- chemical
- human
- life science
- metabolite
- metabolomics
- molecular biology
- omics
- phenomics
- proteomics
mappings:
biocontext: HMDB
cheminf: 000408
edam: '2622'
fairsharing: FAIRsharing.sye5js
miriam: hmdb
n2t: hmdb
prefixcommons: hmdb
re3data: r3d100011285
wikidata: P2057
name: Human Metabolome Database
pattern: ^HMDB\d+$
preferred_prefix: hmdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hmdb:$1
publications:
- doi: 10.1093/nar/gkab1062
pmc: PMC8728138
pubmed: '34986597'
title: 'HMDB 5.0: the Human Metabolome Database for 2022.'
year: 2022
- doi: 10.1093/nar/gkx1089
pmc: PMC5753273
pubmed: '29140435'
title: 'HMDB 4.0: the human metabolome database for 2018.'
year: 2018
- doi: 10.1093/nar/gks1065
pmc: PMC3531200
pubmed: '23161693'
title: HMDB 3.0--The Human Metabolome Database in 2013.
year: 2012
- doi: 10.1093/nar/gkn810
pmc: PMC1899095
pubmed: '17202168'
title: 'HMDB: a knowledgebase for the human metabolome'
year: null
- doi: 10.1093/nar/gkl923
pmc: PMC1899095
pubmed: '17202168'
title: 'HMDB: the Human Metabolome Database.'
year: 2007
synonyms:
- HMDB
twitter: WishartLab
uri_format: http://www.hmdb.ca/metabolites/$1
hms.lincs.antibody:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Database contains all publicly available HMS LINCS datasets and information
for each dataset about experimental reagents (small molecule perturbagens, cells,
antibodies, and proteins) and experimental and data analysis protocols.
example: '80001'
homepage: https://lincs.hms.harvard.edu/db/antibodies/
name: HMS Library of Integrated Network-based Cellular Signatures Antibodies
pattern: ^8\d{4}$
preferred_prefix: hms.lincs.antibody
uri_format: https://lincs.hms.harvard.edu/db/antibodies/$1
hms.lincs.cell:
comment: this is NOT the same as lincs.cell. On https://lincs.hms.harvard.edu/db/cells/?search=MCF-10A&extra_form_shown=&dataset_types=,
you can see there's a mapping to the other resource.
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Database contains all publicly available HMS LINCS datasets and information
for each dataset about experimental reagents (small molecule perturbagens, cells,
antibodies, and proteins) and experimental and data analysis protocols.
example: '50583'
homepage: https://lincs.hms.harvard.edu/db/cell/
name: HMS LINCS Cell
pattern: ^5\d{4}$
preferred_prefix: hms.lincs.cell
references:
- https://github.com/identifiers-org/identifiers-org.github.io/issues/223
uri_format: https://lincs.hms.harvard.edu/db/cells/$1
hms.lincs.compound:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Database contains all publicly available HMS LINCS datasets and information
for each dataset about experimental reagents (small molecule perturbagens, cells,
antibodies, and proteins) and experimental and data analysis protocols.
example: 10001-101
example_extras:
- 11996-999
homepage: https://lincs.hms.harvard.edu/db/sm/
name: HMS LINCS Compound
pattern: ^1\d{4}-\d{3}$
preferred_prefix: hms.lincs.compound
synonyms:
- HMS-LINCS
- hmsl_id
uri_format: https://lincs.hms.harvard.edu/db/sm/$1
hms.lincs.dataset:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
example: '20003'
homepage: https://lincs.hms.harvard.edu/db/datasets/
name: HMS Library of Integrated Network-based Cellular Signatures Datasets
pattern: ^2\d{4}$
preferred_prefix: hms.lincs.dataset
uri_format: https://lincs.hms.harvard.edu/db/datasets/$1
hog:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Documentation of HOGS (Homologous Organs Groups). Contains links to
HOGs download, HOGs onthology, HOGs creation, composition, etc.
download_obo: ftp://ftp.bgee.org/general/ontologies/HOG.obo
example: '0000255'
homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships
keywords:
- ontology
name: Homologous Organ Groups
pattern: ^\d{7}$
preferred_prefix: hog
uri_format: https://biopragmatics.github.io/providers/hog/$1
hogenom:
description: HOGENOM is a database of homologous genes from fully sequenced organisms
(bacteria, archeae and eukarya). This collection references phylogenetic trees
which can be retrieved using either UniProt accession numbers, or HOGENOM tree
family identifier.
example: HBG284870
homepage: http://pbil.univ-lyon1.fr/databases/hogenom/
keywords:
- classification
- life science
- phylogenetics
- phylogeny
- sequence
mappings:
biocontext: HOGENOM
fairsharing: FAIRsharing.qe8tz8
miriam: hogenom
n2t: hogenom
prefixcommons: hogenom
uniprot: DB-0044
name: Database of Complete Genome Homologous Genes Families
pattern: ^\w+$
preferred_prefix: hogenom
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hogenom:$1
publications:
- doi: 10.1186/1471-2105-10-s6-s3
pmc: PMC2697650
pubmed: '19534752'
title: Databases of homologous gene families for comparative genomics.
year: 2009
- doi: 10.1101/gr.10.3.379
pmc: PMC311423
pubmed: '10720578'
title: 'HOBACGEN: database system for comparative genomics in bacteria.'
year: 2000
uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1
hoip:
contact:
email: yuki.yamagata@riken.jp
github: yuki-yamagata
name: Yuki Yamagata
orcid: 0000-0002-9673-1283
contributor:
email: j.harry.caufield@gmail.com
github: caufieldjh
name: Harry Caufield
orcid: 0000-0001-5705-7831
description: An ontology of processes triggered by homeostatic imbalance, with a
focus on COVID-19 infectious processes.
download_owl: https://github.com/yuki-yamagata/hoip/raw/master/hoip_0308.owl
example: 0040379
github_request_issue: 668
homepage: https://knowledge.brc.riken.jp/bioresource/ontology/HOIP
keywords:
- ontology
license: CC-BY-4.0
mappings:
aberowl: HOIP
bioportal: HOIP
name: Homeostasis imbalance process ontology
pattern: ^\d{7}$
preferred_prefix: hoip
repository: https://github.com/yuki-yamagata/hoip
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://purl.bioontology.org/ontology/HOIP/HOIP_$1
hom:
contact:
email: bgee@sib.swiss
github: fbastian
name: Frederic Bastian
orcid: 0000-0002-9415-5104
description: This ontology represents concepts related to homology, as well as other
concepts used to describe similarity and non-homology.
download_owl: http://purl.obolibrary.org/obo/hom.owl
example: 0000049
homepage: https://github.com/BgeeDB/homology-ontology
keywords:
- anatomy
- life science
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: HOM
biocontext: HOM
bioportal: HOM
fairsharing: FAIRsharing.efv7gw
obofoundry: hom
ols: hom
ontobee: HOM
name: Homology Ontology
pattern: ^\d{7}$
preferred_prefix: HOM
publications:
- doi: 10.1016/j.tig.2009.12.012
pmc: null
pubmed: '20116127'
title: An ontology to clarify homology-related concepts.
year: 2010
rdf_uri_format: http://purl.obolibrary.org/obo/HOM_$1
repository: https://github.com/BgeeDB/homology-ontology
uri_format: http://purl.obolibrary.org/obo/HOM_$1
version: '2015-01-07'
homd.seq:
description: The Human Oral Microbiome Database (HOMD) provides a site-specific
comprehensive database for the more than 600 prokaryote species that are present
in the human oral cavity. It contains genomic information based on a curated 16S
rRNA gene-based provisional naming scheme, and taxonomic information. This datatype
contains genomic sequence information.
example: SEQF1003
homepage: http://www.homd.org/index.php
keywords:
- genome
- microbial
mappings:
biocontext: HOMD.SEQ
miriam: homd.seq
n2t: homd.seq
prefixcommons: homd.seq
name: HOMD Sequence Metainformation
pattern: ^SEQF\d+$
preferred_prefix: homd.seq
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/homd.seq:$1
publications:
- doi: 10.1093/database/baq013
pmc: PMC2911848
pubmed: '20624719'
title: 'The Human Oral Microbiome Database: a web accessible resource for investigating
oral microbe taxonomic and genomic information.'
year: 2010
uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1
homd.taxon:
description: The Human Oral Microbiome Database (HOMD) provides a site-specific
comprehensive database for the more than 600 prokaryote species that are present
in the human oral cavity. It contains genomic information based on a curated 16S
rRNA gene-based provisional naming scheme, and taxonomic information. This datatype
contains taxonomic information.
example: '811'
homepage: http://www.homd.org/index.php
keywords:
- microbial
- taxonomy
mappings:
biocontext: HOMD.TAXON
miriam: homd.taxon
n2t: homd.taxon
ncbi: HOMD
prefixcommons: homd.taxon
name: Human Oral Microbiome Database
pattern: ^\d+$
preferred_prefix: homd.taxon
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/homd.taxon:$1
publications:
- doi: 10.1093/database/baq013
pmc: PMC2911848
pubmed: '20624719'
title: 'The Human Oral Microbiome Database: a web accessible resource for investigating
oral microbe taxonomic and genomic information.'
year: 2010
uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1
homologene:
description: HomoloGene is a system for automated detection of homologs among the
annotated genes of several completely sequenced eukaryotic genomes.
example: '1000'
homepage: https://www.ncbi.nlm.nih.gov/homologene/
keywords:
- gene
- genome
- life science
mappings:
biocontext: HOMOLOGENE
fairsharing: FAIRsharing.mzc066
miriam: homologene
n2t: homologene
prefixcommons: homologene
wikidata: P593
name: HomoloGene
pattern: ^\d+$
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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/homologene:$1
publications:
- doi: 10.1093/nar/gkq1172
pmc: PMC3013733
pubmed: '21097890'
title: Database resources of the National Center for Biotechnology Information.
year: 2010
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=$1
hoso:
contact:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
contributor:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
description: HOSO is an ontology of informational entities and processes related
to healthcare organizations and services.
example: '0000001'
github_request_issue: 813
homepage: https://openlhs.github.io/HOSO/
license: CC-BY-4.0
name: Healthcare Organizations and Services Ontology
pattern: ^\d{7}$
preferred_prefix: hoso
repository: https://github.com/OpenLHS/HOSO
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
hovergen:
contact:
email: duret@biomserv.univ-lyon1.fr
github: null
name: Laurent Duret
orcid: 0000-0003-2836-3463
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
keywords:
- dna
- gene
- life science
- protein
mappings:
biocontext: HOVERGEN
fairsharing: FAIRsharing.dg1f0e
miriam: hovergen
n2t: hovergen
prefixcommons: hovergen
name: Homologous Vertebrate Genes Database
pattern: ^HBG\d+$
preferred_prefix: hovergen
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hovergen:$1
publications:
- doi: 10.1093/bioinformatics/bti325
pmc: null
pubmed: '15713731'
title: 'Tree pattern matching in phylogenetic trees: automatic search for orthologs
or paralogs in homologous gene sequence databases.'
year: 2005
uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN
hp:
appears_in:
- chiro
- maxo
- scdo
banana: HP
contact:
email: dr.sebastian.koehler@gmail.com
github: drseb
name: Sebastian Koehler
orcid: 0000-0002-5316-1399
description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary
of phenotypic abnormalities encountered in human disease. Each term in the HPO
describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently
being developed using the medical literature, Orphanet, DECIPHER, and OMIM.
download_json: http://purl.obolibrary.org/obo/hp.json
download_obo: http://purl.obolibrary.org/obo/hp.obo
download_owl: http://purl.obolibrary.org/obo/hp.owl
example: '0011140'
homepage: http://www.human-phenotype-ontology.org/
keywords:
- biomedical science
- genetics
- obo
- ontology
- phenomics
- preclinical studies
license: hpo
logo: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png
mappings:
aberowl: HP_O
bartoc: '1937'
biocontext: HPO
bioportal: HP_O
fairsharing: FAIRsharing.kbtt7f
hl7: 2.16.840.1.113883.6.339
miriam: hp
n2t: hp
obofoundry: hp
ols: hp
ontobee: HP
wikidata: P3841
mastodon: hpo@masto.ai
name: Human Phenotype Ontology
namespace_in_lui: true
pattern: ^\d{7}$
preferred_prefix: HP
publications:
- doi: 10.1093/nar/gky1105
pmc: PMC6324074
pubmed: '30476213'
title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
year: 2019
- doi: 10.1093/nar/gkw1039
pmc: PMC5210535
pubmed: '27899602'
title: The Human Phenotype Ontology in 2017.
year: 2016
- doi: 10.1016/j.ajhg.2015.05.020
pmc: PMC4572507
pubmed: '26119816'
title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare
Disease.'
year: 2015
- doi: 10.1093/nar/gkt1026
pmc: PMC3965098
pubmed: '24217912'
title: 'The Human Phenotype Ontology project: linking molecular biology and disease
through phenotype data.'
year: 2013
- doi: 10.1111/j.1399-0004.2010.01436.x
pmc: null
pubmed: '20412080'
title: The human phenotype ontology.
year: 2010
- doi: 10.1016/j.ajhg.2008.09.017
pmc: PMC2668030
pubmed: '18950739'
title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human
hereditary disease.'
year: 2008
rdf_uri_format: http://purl.obolibrary.org/obo/HP_$1
repository: https://github.com/obophenotype/human-phenotype-ontology
synonyms:
- hpo
twitter: hp_ontology
uri_format: https://hpo.jax.org/app/browse/term/HP:$1
version: '2023-04-05'
hpa:
contact:
email: mathias.uhlen@scilifelab.se
github: null
name: Mathias Uhlen
orcid: 0000-0002-4858-8056
description: The Human Protein Atlas (HPA) is a publicly available database with
high-resolution images showing the spatial distribution of proteins in different
normal and cancer human cell lines. Primary access to this collection is through
Ensembl Gene identifiers.
example: ENSG00000026508
homepage: http://www.proteinatlas.org/
keywords:
- biomedical science
- protein
- proteomics
- structure
- systems biology
- transcriptomics
mappings:
biocontext: HPA
fairsharing: FAIRsharing.j0t0pe
go: HPA
miriam: hpa
n2t: hpa
prefixcommons: hpa
re3data: r3d100010931
uniprot: DB-0046
name: Human Protein Atlas tissue profile information
pattern: ^ENSG\d{11}$
preferred_prefix: hpa
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hpa:$1
publications:
- doi: 10.1126/science.aan2507
pmc: null
pubmed: '28818916'
title: A pathology atlas of the human cancer transcriptome.
year: 2017
- doi: eaal3321
pmc: null
pubmed: '28495876'
title: A subcellular map of the human proteome.
year: null
- doi: 10.1126/science.aal3321
pmc: null
pubmed: '28495876'
title: A subcellular map of the human proteome.
year: 2017
- doi: 10.15252/msb.20155865
pmc: PMC4848759
pubmed: '27044256'
title: Transcriptomics resources of human tissues and organs.
year: 2016
- doi: 10.1126/science.1260419
pmc: null
pubmed: '25613900'
title: Proteomics. Tissue-based map of the human proteome.
year: 2015
- doi: 10.1038/nbt1210-1248
pmc: null
pubmed: '21139605'
title: Towards a knowledge-based Human Protein Atlas.
year: 2010
- doi: 10.1002/path.2440
pmc: null
pubmed: '18853439'
title: The Human Protein Atlas--a tool for pathology.
year: 2008
- doi: 10.1074/mcp.r800013-mcp200
pmc: null
pubmed: '18669619'
title: A genecentric Human Protein Atlas for expression profiles based on antibodies.
year: 2008
- doi: 10.1074/mcp.m500279-mcp200
pmc: null
pubmed: '16127175'
title: A human protein atlas for normal and cancer tissues based on antibody proteomics.
year: 2005
twitter: ProteinAtlas
uri_format: http://www.proteinatlas.org/$1
hpath:
description: An ontology of histopathological morphologies used by pathologists
to classify/categorise animal lesions observed histologically during regulatory
toxicology studies. The ontology was developed using real data from over 6000
regulatory toxicology studies donated by 13 companies spanning nine species.
download_owl: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo
example: '2000191'
homepage: https://github.com/Novartis/hpath
keywords:
- microbiology
- ontology
- taxonomy
mappings:
fairsharing: FAIRsharing.kj336a
ols: hpath
name: Histopathology Ontology
pattern: ^\d+$
preferred_prefix: hpath
repository: https://github.com/Novartis/hpath
synonyms:
- MC
uri_format: http://purl.obolibrary.org/obo/MC_$1
version: '2019-07-05'
hpm.peptide:
description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
result from the draft map of the human proteome project. The project was based
on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
mass spectrometry. The HPM contains direct evidence of translation of a number
of protein products derived from human genes, based on peptide identifications
of multiple organs/tissues and cell types from individuals with clinically defined
healthy tissues. The HPM portal provides data on individual proteins, as well
as on individual peptide spectra. This collection references individual peptides
through spectra.
example: '9606117'
homepage: http://www.humanproteomemap.org/index.php
mappings:
biocontext: HPM.PEPTIDE
miriam: hpm.peptide
n2t: hpm.peptide
name: Human Proteome Map Peptide
pattern: ^\d+$
preferred_prefix: hpm.peptide
uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1
hpm.protein:
description: The Human Proteome Map (HPM) portal integrates the peptide sequencing
result from the draft map of the human proteome project. The project was based
on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform
mass spectrometry. The HPM contains direct evidence of translation of a number
of protein products derived from human genes, based on peptide identifications
of multiple organs/tissues and cell types from individuals with clinically defined
healthy tissues. The HPM portal provides data on individual proteins, as well
as on individual peptide spectra. This collection references proteins.
example: '1968'
homepage: http://www.humanproteomemap.org/index.php
mappings:
biocontext: HPM.PROTEIN
miriam: hpm.protein
n2t: hpm.protein
ncbi: HPM
name: Human Proteome Map
pattern: ^\d+$
preferred_prefix: hpm.protein
uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1
hprd:
contact:
email: pandey@jhmi.edu
github: null
name: Akhilesh Pandey
orcid: 0000-0001-9943-6127
description: The Human Protein Reference Database (HPRD) represents a centralized
platform to visually depict and integrate information pertaining to domain architecture,
post-translational modifications, interaction networks and disease association
for each protein in the human proteome.
example: '00001'
homepage: http://www.hprd.org/
keywords:
- protein
- structure
mappings:
biocontext: HPRD
fairsharing: FAIRsharing.y2qws7
miriam: hprd
n2t: hprd
prefixcommons: hprd
re3data: r3d100010978
name: Human Protein Reference Database
pattern: ^\d+$
preferred_prefix: hprd
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hprd:$1
publications:
- doi: 10.1093/nar/gkn892
pmc: PMC2686490
pubmed: '18988627'
title: Human Protein Reference Database--2009 update.
year: 2008
uri_format: http://www.hprd.org/protein/$1
hpscreg:
contact:
email: stefanie.seltmann@ibmt.fraunhofer.de
github: null
name: Stefanie Seltmann
orcid: 0000-0002-8411-3226
description: hPSCreg is a freely accessible global registry for human pluripotent
stem cell lines (hPSC-lines).
example: BCRTi001-A
homepage: https://hpscreg.eu/
keywords:
- biomedical science
- life science
mappings:
cellosaurus: hPSCreg
fairsharing: FAIRsharing.7C0aVE
miriam: hpscreg
n2t: hpscreg
re3data: r3d100012863
name: Human Pluripotent Stem Cell Registry
pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$
preferred_prefix: hpscreg
publications:
- doi: s1873-5061(20)30188-4
pmc: null
pubmed: '32707486'
title: 'Access to stem cell data and registration of pluripotent cell lines: The
Human Pluripotent Stem Cell Registry (hPSCreg).'
year: null
- doi: 10.1016/j.scr.2020.101887
pmc: null
pubmed: '32707486'
title: 'Access to stem cell data and registration of pluripotent cell lines: The
Human Pluripotent Stem Cell Registry (hPSCreg).'
year: 2020
- doi: s2213-6711(20)30235-6
pmc: PMC7419703
pubmed: '32679065'
title: A Manually Curated Database on Clinical Studies Involving Cell Products
Derived from Human Pluripotent Stem Cells.
year: null
- doi: 10.1016/j.stemcr.2020.06.014
pmc: PMC7419703
pubmed: '32679065'
title: A Manually Curated Database on Clinical Studies Involving Cell Products
Derived from Human Pluripotent Stem Cells.
year: 2020
- doi: s1873-5061(19)30169-2
pmc: null
pubmed: '31450190'
title: 'A pathway for attesting ethical provenance of cell lines: Lessons from
the European human pluripotent stem cell registry (hPSC(reg)).'
year: null
- doi: 10.1016/j.scr.2019.101539
pmc: null
pubmed: '31450190'
title: 'A pathway for attesting ethical provenance of cell lines: Lessons from
the European human pluripotent stem cell registry (hPSC'
year: 2019
- doi: s2213-6711(17)30531-3
pmc: PMC5768986
pubmed: '29320760'
title: A Standard Nomenclature for Referencing and Authentication of Pluripotent
Stem Cells.
year: null
- doi: 10.1016/j.stemcr.2017.12.002
pmc: PMC5768986
pubmed: '29320760'
title: A Standard Nomenclature for Referencing and Authentication of Pluripotent
Stem Cells.
year: 2018
- doi: 10.1093/nar/gkv963
pmc: PMC4702942
pubmed: '26400179'
title: hPSCreg--the human pluripotent stem cell registry.
year: 2015
uri_format: https://hpscreg.eu/cell-line/$1
hsapdv:
appears_in:
- scdo
contact:
email: frederic.bastian@unil.ch
github: fbastian
name: Frédéric Bastian
orcid: 0000-0002-9415-5104
description: Life cycle stages for Human
download_obo: http://purl.obolibrary.org/obo/hsapdv.obo
download_owl: http://purl.obolibrary.org/obo/hsapdv.owl
example: 0000194
homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv
keywords:
- anatomy
- developmental biology
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: HSAPDV
biocontext: HSAPDV
biolink: HsapDv
bioportal: HSAPDV
fairsharing: FAIRsharing.c6vhm3
obofoundry: hsapdv
ols: hsapdv
ontobee: HsapDv
name: Human Developmental Stages
pattern: ^\d{7}$
preferred_prefix: HsapDv
rdf_uri_format: http://purl.obolibrary.org/obo/HsapDv_$1
repository: https://github.com/obophenotype/developmental-stage-ontologies
synonyms:
- HsapDv
uri_format: http://purl.obolibrary.org/obo/HsapDv_$1
version: '2020-03-10'
hsdb:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Hazardous Substances Data Bank (HSDB) is a toxicology database
that focuses on the toxicology of potentially hazardous chemicals. It provides
information on human exposure, industrial hygiene, emergency handling procedures,
environmental fate, regulatory requirements, nanomaterials, and related areas.
example: '5621'
homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb
mappings:
wikidata: P2062
name: Hazardous Substances Data Bank
pattern: ^\d+$
preferred_prefix: hsdb
uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1
hso:
contact:
email: fernanda.dorea@sva.se
github: nandadorea
name: Fernanda Dorea
orcid: 0000-0001-8638-8525
depends_on:
- bfo
- ncbitaxon
- obi
- ro
- uberon
description: The health Surveillance Ontology (HSO) focuses on "surveillance system
level data", that is, data outputs from surveillance activities, such as number
of samples collected, cases observed, etc. It aims to support One-Health surveillance,
covering animal health, public health and food safety surveillance.
download_owl: http://purl.obolibrary.org/obo/hso.owl
example: '0000062'
homepage: https://w3id.org/hso
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: HSO
bioportal: HSO
obofoundry: hso
ols: hso
ontobee: HSO
name: Health Surveillance Ontology
pattern: ^\d{7}$
preferred_prefix: HSO
providers:
- code: hso.legacy
description: An incorrect encoding of OBO purls
homepage: http://purl.obolibrary.org/obo/hso
name: HSO Hash
uri_format: http://purl.obolibrary.org/obo/hso.owl#HSO_$1
rdf_uri_format: http://purl.obolibrary.org/obo/HSO_$1
repository: https://github.com/SVA-SE/HSO
uri_format: http://purl.obolibrary.org/obo/HSO_$1
version: '2021-12-13'
hssp:
description: HSSP (homology-derived structures of proteins) is a derived database
merging structural (2-D and 3-D) and sequence information (1-D). For each protein
of known 3D structure from the Protein Data Bank, the database has a file with
all sequence homologues, properly aligned to the PDB protein.
example: 102l
homepage: http://swift.cmbi.kun.nl/swift/hssp/
keywords:
- clustering
- protein
- sequence
mappings:
biocontext: HSSP
miriam: hssp
n2t: hssp
ncbi: HSSP
prefixcommons: hssp
name: Database of homology-derived secondary structure of proteins
pattern: ^\w{4}$
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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/hssp:$1
publications:
- doi: 10.1093/nar/24.1.201
pmc: PMC145595
pubmed: '8594579'
title: The HSSP database of protein structure-sequence alignments.
year: 1996
- doi: null
pmc: PMC308328
pubmed: '7937066'
title: The HSSP database of protein structure-sequence alignments.
year: 1994
uri_format: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2
htn:
contact:
email: aellenhicks@gmail.com
github: aellenhicks
name: Amanda Hicks
orcid: 0000-0002-1795-5570
description: An ontology for representing clinical data about hypertension, intended
to support classification of patients according to various diagnostic guidelines
download_owl: http://purl.obolibrary.org/obo/htn.owl
example: '00000014'
homepage: https://github.com/aellenhicks/htn_owl
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: HTN
bioportal: HTN
obofoundry: htn
ols: htn
ontobee: HTN
name: Hypertension Ontology
pattern: ^\d{8}$
preferred_prefix: HTN
rdf_uri_format: http://purl.obolibrary.org/obo/HTN_$1
repository: https://github.com/aellenhicks/htn_owl
uri_format: http://purl.obolibrary.org/obo/HTN_$1
huge:
description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results
from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa
cDNA sequencing project.
example: KIAA0001
homepage: http://www.kazusa.or.jp/huge/
keywords:
- computational biology
- dna
- life science
- protein
- structure
mappings:
biocontext: HUGE
fairsharing: FAIRsharing.zx2ztd
miriam: huge
n2t: huge
prefixcommons: huge
uniprot: DB-0049
name: Human Unidentified Gene-Encoded
pattern: ^KIAA\d{4}$
preferred_prefix: huge
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/huge:$1
publications:
- doi: 10.1093/nar/gkh035
pmc: PMC308769
pubmed: '14681467'
title: 'HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi
and ROUGE.'
year: 2004
uri_format: https://www.kazusa.or.jp/huge/gfpage/$1
iao:
appears_in:
- agro
- clyh
- duo
- ecocore
- ecto
- fovt
- labo
- maxo
- pco
- psdo
- xpo
contact:
email: jiezheng@pennmedicine.upenn.edu
github: zhengj2007
name: Jie Zheng
orcid: 0000-0002-2999-0103
description: An ontology of information entities, originally driven by work by the
Ontology of Biomedical Investigation (OBI) digital entity and realizable information
entity branch.
download_obo: http://purl.obolibrary.org/obo/iao.obo
download_owl: http://purl.obolibrary.org/obo/iao.owl
example: '0000030'
homepage: https://github.com/information-artifact-ontology/IAO/
keywords:
- biomedical science
- data management
- knowledge and information systems
- obo
- ontology
- subject agnostic
license: CC-BY-4.0
logo: https://avatars0.githubusercontent.com/u/13591168?v=3&s=200
mappings:
aberowl: IAO
biocontext: IAO
bioportal: IAO
fairsharing: FAIRsharing.gq1xtx
go: IAO
miriam: iao
n2t: iao
obofoundry: iao
ols: iao
ontobee: IAO
name: Information Artifact Ontology
pattern: ^\d{7}$
preferred_prefix: IAO
providers:
- code: legacy
description: A URI from the semanticweb.og
homepage: http://www.semanticweb.org
name: Legacy URI
uri_format: http://www.semanticweb.org/ontologies/2011/9/Ontology1317751904226.owl#IAO_$1
publications:
- doi: 10.3233/978-1-61499-101-4-68
pmc: null
pubmed: '22874154'
title: An information artifact ontology perspective on data collections and associated
representational artifacts.
year: 2012
rdf_uri_format: http://purl.obolibrary.org/obo/IAO_$1
repository: https://github.com/information-artifact-ontology/IAO
uri_format: http://purl.obolibrary.org/obo/IAO_$1
version: '2022-11-07'
icd10:
contact:
email: info@who.int
github: null
name: World Health Organization
orcid: null
contributor_extras:
- email: null
github: joeflack4
name: Joe Flack
orcid: 0000-0002-2906-7319
- email: nicolas.matentzoglu@gmail.com
github: matentzn
name: Nicolas Matentzoglu
orcid: 0000-0002-7356-1779
- email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The 10th revision of the International Classification of Diseases
(ICD) issued by the World Health Organization (WHO). ICD is formally named ''The
International Statistical Classification of Diseases and Related Health Problems''.
It contains codes for diseases, signs and symptoms, abnormal findings, complaints,
social circumstances, and external causes of injury or diseases.
Note that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification)
issued by the U.S. National Center for Health Statistics for use in the United
States.'
example: C34
example_decoys:
- G00X
- C34.90
- C4A.8
- C91.Z
- C91.Z0
example_extras:
- V20
- G00
- A01.1
- XVIII
- R25-R29
- R25
- R25.3
homepage: https://icd.who.int/browse10
keywords:
- biomedical science
- classification
- disease
- epidemiology
- global health
- health science
- ontology
- taxonomy
mappings:
aberowl: ICD10
bartoc: '447'
biocontext: ICD
biolink: ICD10
bioportal: ICD10
edam: '2611'
fairsharing: FAIRsharing.nj16g
hl7: 2.16.840.1.113883.6.3
miriam: icd
n2t: icd
prefixcommons: icd
wikidata: P494
name: International Classification of Diseases, 10th Revision
pattern: ^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\.[0-9]))?))$
preferred_prefix: icd10
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/icd:$1
- code: icd10_2008
description: The 2008 revision of ICD-10
homepage: https://icd.who.int/browse10/2008/en#
name: ICD-10 Version 2008
uri_format: https://icd.who.int/browse10/2008/en#/$1
- code: icd10_2010
description: The 2010 revision of ICD-10
homepage: https://icd.who.int/browse10/2010/en#
name: ICD-10 Version 2010
uri_format: https://icd.who.int/browse10/2010/en#/$1
- code: icd10_2014
description: The 2014 revision of ICD-10
homepage: https://icd.who.int/browse10/2014/en#
name: ICD-10 Version 2014
uri_format: https://icd.who.int/browse10/2014/en#/$1
- code: icd10_2015
description: The 2015 revision of ICD-10
homepage: https://icd.who.int/browse10/2015/en#
name: ICD-10 Version 2015
uri_format: https://icd.who.int/browse10/2015/en#/$1
- code: icd10_2016
description: The 2016 revision of ICD-10
homepage: https://icd.who.int/browse10/2016/en#
name: ICD-10 Version 2016
uri_format: https://icd.who.int/browse10/2016/en#/$1
- code: icdcodelookup
description: This site is dedicated exclusively to helping you look up ICD-10
codes, quickly access the codes you use most, and become more comfortable with
the new code set in general.
homepage: https://icdcodelookup.com/icd-10/codes
name: ICD Code Lookup
uri_format: https://icdcodelookup.com/icd-10/codes/$1
synonyms:
- ICD
- ICD-10
- ICD10
- ICD10WHO
uri_format: https://icd.who.int/browse10/2019/en#/$1
icd10cm:
contact:
email: pbrooks@hcfa.gov
github: null
name: Patricia Brooks
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: ICD-10-CM is the official system of assigning codes to diagnoses and
procedures associated with hospital utilization in the United States issued by
the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid
Services (CMS).
example: F45.21
example_decoys:
- C000
- c00
- C00-D499
- C00-99
- C34.90000
example_extras:
- C00-D49
- U49
- C34
- C34.90
- C4A.8
- C91.Z
- C91.Z0
- T37.0X1A
homepage: https://www.icd10data.com/ICD10CM
keywords:
- biomedical science
- health science
- medicine
- ontology
mappings:
aberowl: ICD10CM
bioportal: ICD10CM
fairsharing: FAIRsharing.hpvbxb
hl7: 2.16.840.1.113883.6.90
wikidata: P4229
name: International Classification of Diseases, 10th Revision, Clinical Modification
pattern: ^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$
preferred_prefix: icd10cm
providers:
- code: bioportal.purl
description: PURL from BioPortal
homepage: http://purl.bioontology.org/ontology/ICD10CM
name: BioPortal PURL
uri_format: http://purl.bioontology.org/ontology/ICD10CM/$1
synonyms:
- ICD10CM
uri_format: https://icd.codes/icd10cm/$1
icd10pcs:
contact:
email: patricia.brooks2@cms.hhs.gov
github: null
name: Pat Brooks
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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
keywords:
- biomedical science
- epidemiology
- health science
- ontology
mappings:
aberowl: ICD10PCS
bioportal: ICD10PCS
fairsharing: FAIRsharing.85k1jm
hl7: 2.16.840.1.113883.6.4
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=$1
icd11:
comment: The codes, such as RA00.0, need their own namespace.
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Diagnostic tool for epidemiology, health management and clinical purposes,
maintained by the World Health Organization (WHO). It provides a system of diagnostic
codes for classifying diseases, including nuanced classifications of a wide variety
of signs, symptoms, abnormal findings, complaints, social circumstances, and external
causes of injury or disease.
example: '402558626'
homepage: https://icd.who.int/
keywords:
- biomedical science
- epidemiology
- global health
- health science
mappings:
fairsharing: FAIRsharing.97805c
hl7: 2.16.840.1.113883.6.347
wikidata: P7807
name: International Classification of Diseases, 11th Revision
pattern: ^[1-9]\d*$
preferred_prefix: icd11
synonyms:
- ICD-11
uri_format: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1
icd9:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The International Classification of Diseases (ICD) is designed to promote
international comparability in the collection, processing, classification, and
presentation of mortality statistics.
example: '277.9'
homepage: https://www.cdc.gov/nchs/icd/icd9.htm
mappings:
biolink: ICD9
hl7: 2.16.840.1.113883.6.42
wikidata: P493
name: International Classification of Diseases, 9th Revision
pattern: ^(\d\d\d|V\d\d|E[8-9]\d\d)(\.\d{1,2})?$
preferred_prefix: icd9
synonyms:
- ICD9
- ICD9_2005
- MTHICD9_2006
uri_format: http://www.icd9data.com/getICD9Code.ashx?icd9=$1
icd9cm:
contact:
email: pbrooks@hcfa.gov
github: null
name: Patricia Brooks
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: ICD-9-CM is the official system of assigning codes to diagnoses and
procedures associated with hospital utilization in the United States.
example: '784'
homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm
keywords:
- biomedical science
- epidemiology
- health science
- medicine
- ontology
- preclinical studies
mappings:
aberowl: ICD9CM
bioportal: ICD9CM
fairsharing: FAIRsharing.10zsxb
hl7: 2.16.840.1.113883.6.2
wikidata: P1692
name: International Classification of Diseases, 9th Revision, Clinical Modification
pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$
preferred_prefix: icd9cm
synonyms:
- IC9CM
- ICD9CM
- ICD9CM_2005
- ICD9CM_2006
- ICDCM_2005
uri_format: http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1
icdc:
contact:
email: annika.jahnke-bornemann@uni-hamburg.de
github: null
name: Annika Jahnke-Bornemann
orcid: 0000-0001-7815-151X
description: The Integrated Canine Data Commons is one of several repositories within
the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure
that provides secure access to a large, comprehensive, and expanding collection
of cancer research data. The ICDC was established to further research on human
cancers by enabling comparative analysis with canine cancer.
example: 000009
homepage: https://caninecommons.cancer.gov/#/
keywords:
- atmospheric science
- earth science
- meteorology
- oceanography
- remote sensing
- social science
mappings:
fairsharing: FAIRsharing.d95034
miriam: icdc
name: Integrated Canine Data Commons
pattern: ^\d{6}$
preferred_prefix: icdc
twitter: ICDC_Hamburg
uri_format: https://caninecommons.cancer.gov/#/study/$1
icdo:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The International Classification of Diseases for Oncology (ICD-O) is
a domain-specific extension of the International Statistical Classification of
Diseases and Related Health Problems for tumor diseases
download_owl: http://aber-owl.net/media/ontologies/ICDO/12/icdo.owl
example: 9861/3
homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/
keywords:
- ontology
mappings:
aberowl: ICDO
bartoc: '445'
hl7: 2.16.840.1.113883.6.43
prefixcommons: icdo
wikidata: P563
name: International Classification of Diseases for Oncology
pattern: ^[8-9]\d{3}(/[0-3])?$
preferred_prefix: icdo
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/icdo:$1
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=$1
iceberg.cime:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: ICEs have also been reported capable to mobilize other genetic elements,
such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable
elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles
for the spread of antiobiotic resistances and virulence factors. However, unlike
ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack
the machinery of other conjugative elements.
example: '6'
homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100
keywords:
- biology
- genomics
name: ICEberg cis-integrative and mobilizable element
part_of: iceberg
pattern: ^\d+$
preferred_prefix: iceberg.cime
publications:
- doi: 10.1093/nar/gky1123
pmc: PMC6323972
pubmed: '30407568'
title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative
elements.'
year: 2019
- doi: 10.1093/nar/gkr846
pmc: PMC3244999
pubmed: '22009673'
title: 'ICEberg: a web-based resource for integrative and conjugative elements
found in Bacteria.'
year: 2011
uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME
iceberg.element:
description: ICEberg (Integrative and conjugative elements) is a database of integrative
and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
elements that can integrate into and excise from a host chromosome, and can carry
likely virulence determinants, antibiotic-resistant factors and/or genes coding
for other beneficial traits. It contains details of ICEs found in representatives
bacterial species, and which are organised as families. This collection references
ICE elements.
example: '100'
homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100
mappings:
biocontext: ICEBERG.ELEMENT
miriam: iceberg.element
n2t: iceberg.element
name: ICEberg integrative and conjugative element
part_of: iceberg
pattern: ^\d+$
preferred_prefix: iceberg.element
publications:
- doi: 10.1093/nar/gky1123
pmc: PMC6323972
pubmed: '30407568'
title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative
elements.'
year: 2019
- doi: 10.1093/nar/gkr846
pmc: PMC3244999
pubmed: '22009673'
title: 'ICEberg: a web-based resource for integrative and conjugative elements
found in Bacteria.'
year: 2011
synonyms:
- iceberg.ice
uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1
iceberg.family:
description: ICEberg (Integrative and conjugative elements) is a database of integrative
and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible
elements that can integrate into and excise from a host chromosome, and can carry
likely virulence determinants, antibiotic-resistant factors and/or genes coding
for other beneficial traits. It contains details of ICEs found in representatives
bacterial species, and which are organised as families. This collection references
ICE families.
example: '1'
homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php
mappings:
biocontext: ICEBERG.FAMILY
miriam: iceberg.family
n2t: iceberg.family
name: ICEberg family
part_of: iceberg
pattern: ^\d+$
preferred_prefix: iceberg.family
publications:
- doi: 10.1093/nar/gky1123
pmc: PMC6323972
pubmed: '30407568'
title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative
elements.'
year: 2019
- doi: 10.1093/nar/gkr846
pmc: PMC3244999
pubmed: '22009673'
title: 'ICEberg: a web-based resource for integrative and conjugative elements
found in Bacteria.'
year: 2011
uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1
iceberg.ime:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: ICEs have also been reported capable to mobilize other genetic elements,
such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable
elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles
for the spread of antiobiotic resistances and virulence factors. However, unlike
ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack
the machinery of other conjugative elements.
example: '1'
homepage: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100
keywords:
- biology
- genomics
name: ICEberg integrative and mobilizable element
part_of: iceberg
pattern: ^\d+$
preferred_prefix: iceberg.ime
publications:
- doi: 10.1093/nar/gky1123
pmc: PMC6323972
pubmed: '30407568'
title: 'ICEberg 2.0: an updated database of bacterial integrative and conjugative
elements.'
year: 2019
- doi: 10.1093/nar/gkr846
pmc: PMC3244999
pubmed: '22009673'
title: 'ICEberg: a web-based resource for integrative and conjugative elements
found in Bacteria.'
year: 2011
uri_format: https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME
iceo:
contact:
email: liumeng94@sjtu.edu.cn
github: Lemon-Liu
name: Meng LIU
orcid: 0000-0003-3781-6962
description: A biological ontology to standardize and integrate Integrative and
Conjugative Element (ICE) information and to support computer-assisted reasoning.
download_owl: http://purl.obolibrary.org/obo/iceo.owl
example: '0000712_1'
example_extras:
- '0000712'
homepage: https://github.com/ontoice/ICEO
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: ICEO
bioportal: ICEO
obofoundry: iceo
ols: iceo
ontobee: ICEO
name: Integrative and Conjugative Element Ontology
pattern: ^\d{7}(_\d)?$
preferred_prefix: ICEO
publications:
- doi: 10.1038/s41597-021-01112-5
pmc: PMC8776819
pubmed: '35058462'
title: ICEO, a biological ontology for representing and analyzing bacterial integrative
and conjugative elements.
year: 2022
rdf_uri_format: http://purl.obolibrary.org/obo/ICEO_$1
repository: https://github.com/ontoice/ICEO
uri_format: http://purl.obolibrary.org/obo/ICEO_$1
version: '2.1'
icepo:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The Ion Channel Electrophysiology Ontology supports the capture of
voltage-gated ion channel electrophysiological data from the literature in a structured
manner and thus enables other applications such as querying and reasoning tools. '
download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo
example: '0000002'
homepage: https://download.nextprot.org/pub/current_release/controlled_vocabularies/
keywords:
- ontology
name: Ion Channel Electrophysiology Ontology
pattern: ^\d{7}$
preferred_prefix: icepo
publications:
- doi: null
pmc: PMC4823818
pubmed: null
title: 'ICEPO: the ion channel electrophysiology ontology'
year: null
twitter: neXtProt_news
uri_format: https://biopragmatics.github.io/providers/icepo/$1
icf:
comment: This might be possible to roll directly into ICD11
contact:
email: info@who.int
github: null
name: The World Health Organization
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The International Classification of Functioning, Disability and Health,
known more commonly as ICF, is a classification of health and health-related domains.
As the functioning and disability of an individual occurs in a context, ICF also
includes a list of environmental factors. ICF is the WHO framework for measuring
health and disability at both individual and population levels.
download_owl: http://aber-owl.net/media/ontologies/ICF/3/icf.owl
example: '326705068'
homepage: https://icd.who.int/dev11/l-icf/en
keywords:
- biomedical science
- health science
- medicine
- ontology
- primary health care
mappings:
aberowl: ICF
bioportal: ICF
fairsharing: FAIRsharing.7rngj0
hl7: 2.16.840.1.113883.6.254
name: International Classification of Functioning, Disability and Health
pattern: ^\d+$
preferred_prefix: icf
uri_format: http://id.who.int/icd/entity/$1
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=$1
ico:
appears_in:
- scdo
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: The Informed Consent Ontology (ICO) is an ontology for the informed
consent and informed consent process in the medical field.
download_owl: http://purl.obolibrary.org/obo/ico.owl
example: '0000066'
homepage: https://github.com/ICO-ontology/ICO
keywords:
- biomedical science
- clinical studies
- health science
- medicine
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: ICO
biocontext: ICO
bioportal: ICO
fairsharing: FAIRsharing.b9znd5
obofoundry: ico
ols: ico
ontobee: ICO
name: Informed Consent Ontology
pattern: ^\d{7}$
preferred_prefix: ICO
rdf_uri_format: http://purl.obolibrary.org/obo/ICO_$1
repository: https://github.com/ICO-ontology/ICO
uri_format: http://purl.obolibrary.org/obo/ICO_$1
version: 1.0.187
ideal:
description: IDEAL provides a collection of knowledge on experimentally verified
intrinsically disordered proteins. It contains manual annotations by curators
on intrinsically disordered regions, interaction regions to other molecules, post-translational
modification sites, references and structural domain assignments.
example: IID00001
homepage: https://www.ideal-db.org
keywords:
- biology
mappings:
biocontext: IDEAL
fairsharing: FAIRsharing.h3y42f
miriam: ideal
n2t: ideal
uniprot: DB-0251
name: Intrinsically Disordered proteins with Extensive Annotations and Literature
pattern: ^IID\d+$
preferred_prefix: ideal
publications:
- doi: 10.1093/nar/gkt1010
pmc: PMC3965115
pubmed: '24178034'
title: IDEAL in 2014 illustrates interaction networks composed of intrinsically
disordered proteins and their binding partners.
year: 2013
uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1
ido:
appears_in:
- scdo
contact:
email: Lindsay.Cowell@utsouthwestern.edu
github: lgcowell
name: Lindsay Cowell
orcid: 0000-0003-1617-8244
description: Infectious Disease Ontology holds entities relevant to both biomedical
and clinical aspects of most infectious diseases.
download_owl: http://purl.obolibrary.org/obo/ido.owl
example: '0000504'
homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology
keywords:
- biomedical science
- molecular infection biology
- obo
- ontology
- preclinical studies
license: CC-BY-3.0
mappings:
aberowl: IDO
biocontext: IDO
bioportal: IDO
fairsharing: FAIRsharing.aae3v6
miriam: ido
n2t: ido
obofoundry: ido
ols: ido
ontobee: IDO
name: Infectious Disease Ontology
pattern: ^[0-9]+$
preferred_prefix: IDO
providers:
- code: obo.1
description: This incorrect encoding was found inside IDO-COVID-19
homepage: http://purl.obolibrary.org
name: Nonstandard OBO PURL
uri_format: http://purl.obolibrary.org/obo/ido.owl/IDO_$1
publications:
- doi: 10.1186/s13326-021-00245-1
pmc: PMC8286442
pubmed: '34275487'
title: The Infectious Disease Ontology in the age of COVID-19.
year: 2021
rdf_uri_format: http://purl.obolibrary.org/obo/IDO_$1
repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology
uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1
version: '2017-11-03'
idocovid19:
contact:
email: johnbeverley2021@u.northwestern.edu
github: johnbeve
name: John Beverly
orcid: 0000-0002-1118-1738
description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension
of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology
(VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal
Ontology as its starting point, and covers epidemiology, classification, pathogenesis,
and treatment of terms used to represent infection by the SARS-CoV-2 virus strain,
and the associated COVID-19 disease.
download_owl: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19
example: 0001191
homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
keywords:
- ontology
mappings:
aberowl: IDO-COVID-19
bioportal: IDO-COVID-19
ols: idocovid19
name: The COVID-19 Infectious Disease Ontology
pattern: ^\d{7}$
preferred_prefix: idocovid19
providers:
- code: obo1
description: This variation uses incorrect usage of dashes instead of underscores
homepage: http://purl.obolibrary.org
name: Incorrect OBO PURL variation 1
uri_format: http://purl.obolibrary.org/obo/IDO-COVID-19_$1
repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19
uri_format: http://purl.obolibrary.org/obo/COVIDO_$1
version: '2020-07-21'
idoden:
contact:
email: elvira@imbb.forth.gr
github: null
name: Elvira Mitraka
orcid: 0000-0003-0719-3485
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An ontology for dengue fever.
download_owl: http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl
example: '0003463'
homepage: https://bioportal.bioontology.org/ontologies/IDODEN
keywords:
- medicine
- ontology
mappings:
aberowl: IDODEN
bioportal: IDODEN
fairsharing: FAIRsharing.askzq4
name: Dengue Fever Ontology
pattern: ^\d{7}$
preferred_prefix: idoden
references:
- https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479
uri_format: http://purl.bioontology.org/ontology/IDODEN_$1
idog:
contact:
email: baoym@big.ac.cn
github: null
name: Yiming Bao
orcid: 0000-0002-9922-9723
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Provides the worldwide dog research community a variety of data services
including access to genes, genomes, SNPs, breed/disease Traits, gene expression
experiments, dog-guman homology, and literatur. In addition, iDog provides online
tools for performing genomic data visualization and analyses.
example: '4'
homepage: https://ngdc.cncb.ac.cn/idog/
license: CC-BY-4.0
mappings:
re3data: r3d100012176
name: Integrated Resource for Domestic Dog
pattern: ^\d+$
preferred_prefix: idog
publications:
- doi: 10.1093/nar/gky1041
pmc: PMC6323916
pubmed: '30371881'
title: 'iDog: an integrated resource for domestic dogs and wild canids'
year: 2019
references:
- https://github.com/biopragmatics/bioregistry/pull/725
uri_format: https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1
idomal:
appears_in:
- scdo
contact:
email: topalis@imbb.forth.gr
github: null
name: Pantelis Topalis
orcid: 0000-0002-1635-4810
deprecated: true
description: An application ontology to cover all aspects of malaria as well as
the intervention attempts to control it.
download_obo: http://purl.obolibrary.org/obo/idomal.obo
download_owl: http://purl.obolibrary.org/obo/idomal.owl
example: '0002350'
example_extras:
- '50000015'
homepage: https://www.vectorbase.org/ontology-browser
keywords:
- biomedical science
- life science
- molecular infection biology
- obo
- ontology
license: CC0-1.0
mappings:
aberowl: IDOMAL
biocontext: IDOMAL
bioportal: IDOMAL
fairsharing: FAIRsharing.2q8c28
obofoundry: idomal
ols: idomal
ontobee: IDOMAL
name: Malaria Ontology
pattern: ^(5?)\d{7}$
preferred_prefix: IDOMAL
publications:
- doi: 10.1186/2041-1480-4-16
pmc: PMC3848731
pubmed: '24034841'
title: 'IDOMAL: the malaria ontology revisited.'
year: 2013
- doi: 10.1186/1475-2875-9-230
pmc: PMC2925367
pubmed: '20698959'
title: 'IDOMAL: an ontology for malaria.'
year: 2010
rdf_uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1
repository: https://github.com/VEuPathDB-ontology/IDOMAL
twitter: VectorBase
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#$1
idpo:
contact:
email: f.quaglia@ibiom.cnr.it
github: federicaquaglia
name: Federica Quaglia
orcid: 0000-0002-0341-4888
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions
and functions directly associated with their disordered state. GO is used to describe
functional aspects of an IDP/IDR.
example: '00056'
homepage: https://www.disprot.org/ontology
keywords:
- protein structure
- proteins
- structural biochemistry
- structural bioinformatics
name: Intrinsically Disordered Proteins Ontology
pattern: ^\d{5}$
preferred_prefix: idpo
uri_format: https://www.disprot.org/idpo/IDPO:$1
idr:
contact:
email: j.a.moore@dundee.ac.uk
github: null
name: Josh Moore
orcid: 0000-0003-4028-811X
description: Image Data Resource (IDR) is an online, public data repository that
seeks to store, integrate and serve image datasets from published scientific studies.
We have collected and are continuing to receive existing and newly created “reference
image" datasets that are valuable resources for a broad community of users, either
because they will be frequently accessed and cited or because they can serve as
a basis for re-analysis and the development of new computational tools.
example: '0001'
homepage: https://idr.openmicroscopy.org
keywords:
- biomedical science
- botany
- life science
mappings:
fairsharing: FAIRsharing.6wf1zw
miriam: idr
re3data: r3d100012435
name: Image Data Resource
pattern: ^[0-9]{4}$
preferred_prefix: idr
publications:
- doi: 10.1038/nmeth.4326
pmc: PMC5536224
pubmed: '28775673'
title: 'The Image Data Resource: A Bioimage Data Integration and Publication Platform.'
year: 2017
twitter: openmicroscopy
uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1
iedb:
description: The Immune Epitope Database (IEDB) is a freely available resource funded
by NIAID. It catalogs experimental data on antibody and T cell epitopes studied
in humans, non-human primates, and other animal species in the context of infectious
disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools
to assist in the prediction and analysis of epitopes.
example: '1038233'
homepage: https://www.lji.org/
keywords:
- bioinformatics
- immunology
- life science
- protein
- small molecule
mappings:
fairsharing: FAIRsharing.c886cd
miriam: iedb
prefixcommons: tied
re3data: r3d100012702
name: Immune Epitope Database
pattern: ^[0-9]+$
preferred_prefix: iedb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/tied:$1
publications:
- doi: 10.1093/nar/gku938
pmc: PMC4384014
pubmed: '25300482'
title: The immune epitope database (IEDB) 3.0.
year: 2014
- doi: 10.1111/j.1365-2567.2012.03611.x
pmc: PMC3461392
pubmed: '22681406'
title: 'The immune epitope database: a historical retrospective of the first decade.'
year: 2012
- doi: 10.1093/nar/gkp1004
pmc: PMC2808938
pubmed: '19906713'
title: The immune epitope database 2.0.
year: 2009
- doi: null
pmc: null
pubmed: '16312048'
title: 'The immune epitope database and analysis resource: from vision to blueprint.'
year: 2004
uri_format: https://www.iedb.org/reference/$1
ietf.language:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Shorthand representations of languages and their subtypes
example: en-GB
example_extras:
- en
- ar-SA
- aaf
homepage: http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry
mappings:
wikidata: P305
name: Internet Engineering Task Force Language Tag
pattern: ^\w{2,3}(-\w+)?$
preferred_prefix: ietf.language
synonyms:
- bcp47
iev:
deprecated: true
description: The Event Ontology is an ontology of pathways. It classifies pathways,
sub-pathways and other biological phenomena to form a DAG structure.
example: '0000000'
homepage: http://www.inoh.org
keywords:
- obo
- ontology
- pathway
- structure
mappings:
biocontext: IEV
obofoundry: iev
prefixcommons: iev
name: Event (INOH pathway ontology)
pattern: ^\d{7}$
preferred_prefix: IEV
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/iev:$1
rdf_uri_format: http://purl.obolibrary.org/obo/IEV_$1
uri_format: http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$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=$1
igsn:
description: IGSN is a globally unique and persistent identifier for material samples
and specimens. IGSNs are obtained from IGSN e.V. Agents.
example: AU124
homepage: http://www.geosamples.org/
keywords:
- subject agnostic
mappings:
fairsharing: FAIRsharing.c7f365
miriam: igsn
n2t: igsn
name: International Geo Sample Number
pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$
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/
keywords:
- comparative genomics
- genomics
mappings:
cellosaurus: IGSR
fairsharing: FAIRsharing.4Vs9VM
re3data: r3d100010180
name: International Genome Sample Resource
preferred_prefix: igsr
publications:
- doi: 10.1093/nar/gkz836
pmc: PMC6943028
pubmed: '31584097'
title: The International Genome Sample Resource (IGSR) collection of open human
genomic variation resources.
year: 2020
- doi: 10.1038/nature15393
pmc: PMC4750478
pubmed: '26432245'
title: A global reference for human genetic variation.
year: 2015
twitter: 1000genomes
uri_format: https://www.internationalgenome.org/data-portal/sample/$1
ihw:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The International Histocompatibility Working Group provides a comprehensive
inventory of HLA reference genes to support worldwide research in immunogenetics.
We also offer selected cell lines and DNA from our substantial DNA Bank of more
than 1,000 cell lines from selected families, as well as individuals with diverse
ethnicity and immunologic characteristics.
example: IHW09326
homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html
mappings:
cellosaurus: IHW
name: International Histocompatibility Workshop cell lines
pattern: ^IHW\d+$
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
keywords:
- transcriptomics
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=$1
imdrf:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The International Medical Device Regulators Forum (IMDRF) is a forum
of voluntary medical device regulators from around the world who have come together
to build on the strong foundational work of the Global Harmonization Task Force
on Medical Devices (GHTF), and to accelerate international medical device regulatory
harmonization and convergence.
homepage: http://www.imdrf.org/
name: International Medical Device Regulators Forum
no_own_terms: true
preferred_prefix: imdrf
references:
- https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes
imex:
banana: IM
banana_peel: '-'
description: The International Molecular Exchange (IMEx) is a consortium of molecular
interaction databases which collaborate to share manual curation efforts and provide
accessibility to multiple information sources.
example: 19210-3
example_extras:
- '19210'
homepage: https://www.imexconsortium.org/
keywords:
- interaction
- molecule
mappings:
biocontext: IMEX
miriam: imex
n2t: imex
prefixcommons: imex
re3data: r3d100010669
name: International Molecular Exchange
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^\d+(-\d+)?$
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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/imex:$1
- code: intact.search
description: Search page on IntAct
homepage: https://www.ebi.ac.uk/intact
name: IntAct Search
uri_format: https://www.ebi.ac.uk/intact/search?query=IM-$1
publications:
- doi: 10.1002/pmic.200700286
pmc: null
pubmed: '17893861'
title: 'Submit your interaction data the IMEx way: a step by step guide to trouble-free
deposition.'
year: 2007
uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1
img.gene:
description: The integrated microbial genomes (IMG) system is a data management,
analysis and annotation platform for all publicly available genomes. IMG contains
both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
with all other publicly available genomes from all three domains of life, together
with a large number of plasmids and viruses. This datatype refers to gene information.
example: '638309541'
homepage: http://img.jgi.doe.gov/
keywords:
- gene
- genome
mappings:
biocontext: IMG.GENE
miriam: img.gene
n2t: img.gene
prefixcommons: img.gene
name: Integrated Microbial Genomes Gene
pattern: ^\d+$
preferred_prefix: img.gene
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/img.gene:$1
publications:
- doi: 10.1093/nar/gkm846
pmc: PMC2238897
pubmed: '17933782'
title: 'The integrated microbial genomes (IMG) system in 2007: data content and
analysis tool extensions.'
year: 2007
uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1
img.taxon:
description: The integrated microbial genomes (IMG) system is a data management,
analysis and annotation platform for all publicly available genomes. IMG contains
both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated
with all other publicly available genomes from all three domains of life, together
with a large number of plasmids and viruses. This datatype refers to taxon information.
example: '648028003'
homepage: http://img.jgi.doe.gov/
keywords:
- genome
- taxonomy
mappings:
biocontext: IMG.TAXON
miriam: img.taxon
n2t: img.taxon
prefixcommons: img.taxon
name: Integrated Microbial Genomes Taxon
pattern: ^\d+$
preferred_prefix: img.taxon
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/img.taxon:$1
publications:
- doi: 10.1093/nar/gkm846
pmc: PMC2238897
pubmed: '17933782'
title: 'The integrated microbial genomes (IMG) system in 2007: data content and
analysis tool extensions.'
year: 2007
uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1
imgt.hla:
contact:
email: steven.marsh@ucl.ac.uk
github: null
name: Steven G. E. Marsh
orcid: 0000-0003-2855-4120
description: IMGT, the international ImMunoGeneTics project, is a collection of
high-quality integrated databases specialising in Immunoglobulins, T cell receptors
and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA
is a database for sequences of the human MHC, referred to as HLA. It includes
all the official sequences for the WHO Nomenclature Committee For Factors of the
HLA System. This collection references allele information through the WHO nomenclature.
example: A*01:01:01:01
homepage: https://www.ebi.ac.uk/imgt/hla/allele.html
keywords:
- biomedical science
- dna
- immunogenetics
- immunology
- protein
- rna
mappings:
biocontext: IMGT.HLA
cellosaurus: IPD-IMGT/HLA
edam: '2773'
fairsharing: FAIRsharing.e28v7g
go: IMGT_HLA
miriam: imgt.hla
n2t: imgt.hla
ncbi: IMGT/HLA
prefixcommons: imgthla
re3data: r3d100010804
name: IMGT/HLA human major histocompatibility complex sequence database
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^[A-Z0-9*:]+$
preferred_prefix: imgt.hla
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/imgthla:$1
publications:
- doi: 10.1093/nar/gkz950
pmc: PMC7145640
pubmed: '31667505'
title: IPD-IMGT/HLA Database.
year: 2020
- doi: 10.1093/nar/gku1161
pmc: PMC4383959
pubmed: '25414341'
title: 'The IPD and IMGT/HLA database: allele variant databases.'
year: 2014
- doi: 10.1093/nar/gkn662
pmc: PMC2686596
pubmed: '18838392'
title: The IMGT/HLA database.
year: 2008
- doi: 10.1007/978-1-60327-118-9_3
pmc: null
pubmed: '18449991'
title: The IMGT/HLA database.
year: 2007
- doi: 10.1002/humu.20406
pmc: null
pubmed: '16944494'
title: The IMGT/HLA and IPD databases.
year: 2006
- doi: 10.1093/nar/gkj088
pmc: PMC1347451
pubmed: '16381979'
title: IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell
receptor nucleotide sequences.
year: 2006
- doi: 10.1093/nar/gkg070
pmc: PMC165517
pubmed: '12520010'
title: 'IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility
complex.'
year: 2003
- doi: 10.1093/nar/29.1.210
pmc: PMC29780
pubmed: '11125094'
title: IMGT/HLA Database--a sequence database for the human major histocompatibility
complex.
year: 2001
- doi: 10.1034/j.1399-0039.2000.550314.x
pmc: null
pubmed: '10777106'
title: IMGT/HLA database--a sequence database for the human major histocompatibility
complex.
year: 2000
synonyms:
- IPD-IMGT/HLA
uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1
imgt.ligm:
description: IMGT, the international ImMunoGeneTics project, is a collection of
high-quality integrated databases specialising in Immunoglobulins, T cell receptors
and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM
is a comprehensive database of fully annotated sequences of Immunoglobulins and
T cell receptors from human and other vertebrates.
example: M94112
homepage: http://www.imgt.org/
keywords:
- dna
mappings:
biocontext: IMGT.LIGM
go: IMGT_LIGM
miriam: imgt.ligm
n2t: imgt.ligm
ncbi: IMGT/LIGM
prefixcommons: imgt.ligm
name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors
pattern: ^M\d+$
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']
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/imgt.ligm:$1
publications:
- doi: 10.1093/nar/gkj088
pmc: PMC1347451
pubmed: '16381979'
title: IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell
receptor nucleotide sequences.
year: 2006
uri_format: http://www.imgt.org/ligmdb/view?id=$1
imgt.primerdb:
description: The IMGT/PRIMER-DB database provides standardized information on oligonucleotides
or primers of the immunoglobulins (IG) and T cell receptors (TR).
example: IPP900099
homepage: http://imgt.org/IMGTPrimerDB/
keywords:
- dna
mappings:
prefixcommons: imgt.primerdb
re3data: r3d100012535
name: IMGT/PRIMER-DB
preferred_prefix: imgt.primerdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/imgt.primerdb:$1
uri_format: http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList
imotdb:
comment: This resource doesn't exist on the web anymore
deprecated: true
description: The interacting motif database or iMOTdb , lists interacting motifs
thatare identified for all structural entries in the PDB. The conserved patterns
or finger prints are identified for individual structural entries and also grouped
together for reporting the common motifs shared among all superfamily members.
example: '53784'
homepage: http://caps.ncbs.res.in/imotdb/
keywords:
- interaction
- protein
mappings:
prefixcommons: imotdb
name: Database of Spatially Interacting Motifs in Proteins
preferred_prefix: imotdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/imotdb:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1
imr:
contact:
email: curator@inoh.org
github: null
name: INOH curators
orcid: null
deprecated: true
description: MoleculeRole Ontology is an ontology for proteins/chemicals. It is
used to annotate protein family names, generic/concrete protein names and chemical
names in the INOH pathway data.
example: '0000001'
homepage: http://www.inoh.org
keywords:
- obo
- ontology
- protein
- small molecule
mappings:
biocontext: IMR
obofoundry: imr
prefixcommons: imr
name: Molecule role (INOH Protein name/family name ontology)
pattern: ^\d{7}$
preferred_prefix: IMR
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/imr:$1
rdf_uri_format: http://purl.obolibrary.org/obo/IMR_$1
uri_format: http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1
inaturalist.observation:
contributor:
email: null
github: oolonek
name: Pierre-Marie Allard
orcid: 0000-0003-3389-2191
description: The identifier for an observation in iNaturalist
example: '36010371'
github_request_issue: 517
homepage: https://www.inaturalist.org/observations
mappings:
wikidata: P5683
name: iNaturalist Observation
pattern: ^[1-9]\d*$
preferred_prefix: inaturalist.observation
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://www.inaturalist.org/observations/$1
inaturalist.place:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Identifier for a place in iNaturalist
example: '7207'
homepage: https://www.inaturalist.org/places
mappings:
wikidata: P7471
name: iNaturalist Place
pattern: ^[1-9]\d*$
preferred_prefix: inaturalist.place
uri_format: https://www.inaturalist.org/places/$1
inaturalist.taxon:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Identifier for a species in iNaturalist
example: '21723'
homepage: https://www.inaturalist.org/taxa
mappings:
wikidata: P3151
name: iNaturalist Taxonomy
pattern: ^[1-9]\d{0,6}$
preferred_prefix: inaturalist.taxon
uri_format: https://www.inaturalist.org/taxa/$1
inaturalist.user:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Identifier for a user in iNaturalist
example: '1426686'
homepage: https://www.inaturalist.org/users
keywords:
- person
name: iNaturalist User
pattern: ^[1-9]\d*$
preferred_prefix: inaturalist.user
uri_format: https://www.inaturalist.org/users/$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/
keywords:
- cheminformatics
- chemistry
- knowledge and information systems
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
publications:
- doi: 10.1186/s13321-021-00517-z
pmc: PMC8147039
pubmed: '34030732'
title: 'InChI version 1.06: now more than 99.99% reliable.'
year: 2021
- doi: 10.1186/s13321-015-0068-4
pmc: PMC4486400
pubmed: '26136848'
title: InChI, the IUPAC International Chemical Identifier.
year: 2015
- doi: 10.1007/s10822-015-9854-3
pmc: null
pubmed: '26081259'
title: Many InChIs and quite some feat.
year: 2015
twitter: inchi_trust
uri_format: http://www.chemspider.com/$1
inchikey:
description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383)
is an identifier for chemical substances, and is derived solely from a structural
representation of that substance. Since these can be quite unwieldly, particularly
for web use, the InChIKey was developed. These are of a fixed length (25 character)
and were created as a condensed, more web friendly, digital representation of
the InChI.
example: RYYVLZVUVIJVGH-UHFFFAOYSA-N
homepage: http://www.chemspider.com/
mappings:
biocontext: INCHIKEY
miriam: inchikey
n2t: inchikey
wikidata: P235
name: InChIKey
pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])$
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
keywords:
- biomedical science
mappings:
fairsharing: FAIRsharing.9gqfpm
name: The International Harmonization of Nomenclature and Diagnostic criteria
preferred_prefix: inhand
proprietary: true
publications:
- doi: 10.1177/0192623309353423
pmc: null
pubmed: '20032296'
title: Proliferative and nonproliferative lesions of the rat and mouse respiratory
tract.
year: 2009
inn:
comment: can not find a place to resolve to
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
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
innatedb:
description: InnateDB has been developed to facilitate systems level investigations
of the mammalian (human, mouse and bovine) innate immune response. Its goal is
to provide a manually-curated knowledgebase of the genes, proteins, and particularly,
the interactions and signaling responses involved in mammalian innate immunity.
InnateDB incorporates information of the whole human, mouse and bovine interactomes
by integrating interaction and pathway information from several of the major publicly
available databases but aims to capture an improved coverage of the innate immunity
interactome through manual curation.
example: '20021'
homepage: http://www.innatedb.ca/
keywords:
- gene
- immunology
- interaction
- life science
- pathway
- protein
mappings:
fairsharing: FAIRsharing.rb2drw
prefixcommons: innatedb
re3data: r3d100010676
name: A Knowledge Resource for Innate Immunity Interactions and Pathways
preferred_prefix: innatedb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/innatedb:$1
publications:
- doi: 10.1093/nar/gks1147
pmc: PMC3531080
pubmed: '23180781'
title: 'InnateDB: systems biology of innate immunity and beyond--recent updates
and continuing curation.'
year: 2012
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
twitter: innatedb
uri_format: http://www.innatedb.ca/getGeneCard.do?id=$1
ino:
contact:
email: yongqunh@med.umich.edu
github: yongqunh
name: Yongqun Oliver He
orcid: 0000-0001-9189-9661
description: he Interaction Network Ontology (INO) is an ontology in the domain
of interactions and interaction networks. INO represents general and species-neutral
types of interactions and interaction networks, and their related elements and
relations. INO is a community-driven ontology, aligns with BFO, and is developed
by following the OBO Foundry principles.
download_owl: http://purl.obolibrary.org/obo/ino.owl
example: '0000003'
homepage: https://github.com/INO-ontology/ino
keywords:
- life science
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: INO
biolink: INO
bioportal: INO
fairsharing: FAIRsharing.mm72as
obofoundry: ino
ols: ino
ontobee: INO
name: Interaction Network Ontology
pattern: ^\d{7}$
preferred_prefix: INO
publications:
- doi: 10.1186/s13040-016-0118-0
pmc: PMC5168857
pubmed: '28031747'
title: The Interaction Network Ontology-supported modeling and mining of complex
interactions represented with multiple keywords in biomedical literature.
year: 2016
- doi: 10.1186/2041-1480-6-2
pmc: PMC4362819
pubmed: '25785184'
title: Development and application of an interaction network ontology for literature
mining of vaccine-associated gene-gene interactions.
year: 2015
- doi: 10.1186/2041-1480-2-s2-s8
pmc: PMC3102897
pubmed: '21624163'
title: Mining of vaccine-associated IFN-γ gene interaction networks using the
Vaccine Ontology.
year: 2011
rdf_uri_format: http://purl.obolibrary.org/obo/INO_$1
repository: https://github.com/INO-ontology/ino
uri_format: http://purl.obolibrary.org/obo/INO_$1
version: 1.1.13
insdc:
description: The International Nucleotide Sequence Database Collaboration (INSDC)
consists of a joint effort to collect and disseminate databases containing DNA
and RNA sequences.
example: X58356
homepage: https://www.ncbi.nlm.nih.gov/Genbank/
keywords:
- dna
mappings:
biocontext: INSDC
miriam: insdc
n2t: insdc
prefixcommons: insdc
name: Nucleotide Sequence Database
pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4,6}\d{8,10}|[A-J][A-Z]{2}\d{5})(\.\d+)?$
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: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/insdc:$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
publications:
- doi: 10.1093/nar/18.6.1517
pmc: PMC330520
pubmed: '2326192'
title: Recent changes in the GenBank On-line Service.
year: 1990
- doi: 10.1093/nar/gkl986
pmc: PMC1781245
pubmed: '17202161'
title: GenBank.
year: 2007
- doi: 10.1093/nar/gkl913
pmc: PMC1897316
pubmed: '17148479'
title: EMBL Nucleotide Sequence Database in 2006.
year: 2006
- doi: 10.1126/science.298.5597.1333b
pmc: null
pubmed: '12436968'
title: Nucleotide sequence database policies.
year: 2002
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/$1
insdc.gca:
description: The genome assembly database contains detailed information about genome
assemblies for eukaryota, bacteria and archaea. The scope of the genome collections
database does not extend to viruses, viroids and bacteriophage.
example: GCA_000155495.1
has_canonical: ncbi.assembly
homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database
mappings:
biocontext: INSDC.GCA
miriam: insdc.gca
n2t: insdc.gca
name: Genome assembly database
pattern: ^GC[AF]_[0-9]{9}\.[0-9]+$
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/$1
insdc.run:
comment: 'https://www.insdc.org/ is the authoritative source for INSDC. However,
confusingly, they don''t mention runs in this table. I think we should ask them
to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html
Runs | (E\|D\|S)RR[0-9]{6,} | ERR123456 -- | -- | --'
contributor:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
description: An experimental run, served thrugh the ENA
example: ERR436051
github_request_issue: 131
has_canonical: ena.embl
homepage: https://www.insdc.org/
name: International Nucleotide Sequence Database Collaboration (INSDC) Run
pattern: ^(E|D|S)RR[0-9]{6,}$
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/$1
insdc.sra:
description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the
next generation of sequencing platforms Data submitted to SRA. It is organized
using a metadata model consisting of six objects: study, sample, experiment, run,
analysis and submission. The SRA study contains high-level information including
goals of the study and literature references, and may be linked to the INSDC BioProject
database.'
example: SRX000007
homepage: https://www.ncbi.nlm.nih.gov/sra
keywords:
- biology
- epidemiology
- genomics
- virology
mappings:
biocontext: INSDC.SRA
fairsharing: FAIRsharing.g7t2hv
miriam: insdc.sra
n2t: insdc.sra
re3data: r3d100010775
name: Sequence Read Archive
pattern: ^[SED]R[APRSXZ]\d+$
preferred_prefix: insdc.sra
providers:
- 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
- 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
publications:
- doi: 10.1186/s13742-015-0064-7
pmc: PMC4425880
pubmed: '25960871'
title: Investigation into the annotation of protocol sequencing steps in the sequence
read archive.
year: 2015
- doi: 10.1093/nar/gkr854
pmc: PMC3245110
pubmed: '22009675'
title: 'The Sequence Read Archive: explosive growth of sequencing data.'
year: 2011
- doi: 10.1093/nar/gkm1000
pmc: PMC2238880
pubmed: '18045790'
title: Database resources of the National Center for Biotechnology Information.
year: 2007
uri_format: https://www.ncbi.nlm.nih.gov/sra/$1
intact:
contact:
email: orchard@ebi.ac.uk
github: null
name: Sandra Orchard
orcid: 0000-0002-8878-3972
description: IntAct provides a freely available, open source database system and
analysis tools for protein interaction data.
example: EBI-2307691
homepage: https://www.ebi.ac.uk/intact/
keywords:
- biology
- interaction
- protein
mappings:
biocontext: INTACT
fairsharing: FAIRsharing.d05nwx
go: IntAct
miriam: intact
n2t: intact
prefixcommons: intact
re3data: r3d100010671
uniprot: DB-0051
name: IntAct protein interaction database
owners:
- name: European Bioinformatics Institute
partnered: false
ror: 02catss52
wikidata: null
pattern: ^EBI\-[0-9]+$
preferred_prefix: intact
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/intact:$1
publications:
- doi: 10.1093/nar/gkt1115
pmc: PMC3965093
pubmed: '24234451'
title: The MIntAct project--IntAct as a common curation platform for 11 molecular
interaction databases.
year: 2013
- doi: 10.1038/nmeth.1637
pmc: PMC3246345
pubmed: '21716279'
title: 'PSICQUIC and PSISCORE: accessing and scoring molecular interactions.'
year: 2011
- doi: 10.1093/nar/gkp878
pmc: PMC2808934
pubmed: '19850723'
title: The IntAct molecular interaction database in 2010.
year: 2009
- doi: 10.1186/1741-7007-5-44
pmc: PMC2189715
pubmed: '17925023'
title: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular
interactions.
year: 2007
- doi: 10.1093/nar/gkh052
pmc: PMC308786
pubmed: '14681455'
title: 'IntAct: an open source molecular interaction database.'
year: 2004
twitter: intact_project
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/search?query=$1
interfil:
description: The Intermediate Filament Database functions as a continuously updated
review of the intermediate filament field and it is hoped that users will contribute
to the development and expansion of the database on a regular basis. Contributions
may include novel variants, new patients with previously discovered sequence and
allelic variants.
example: NM_006262
homepage: http://www.interfil.org
keywords:
- genome
mappings:
prefixcommons: interfil
name: Human Intermediate Filament Database
preferred_prefix: interfil
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/interfil:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.interfil.org/details.php?id=$1
interlex:
description: 'InterLex is a dynamic lexicon, initially built on the foundation of
NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed
to help improve the way that biomedical scientists communicate about their data,
so that information systems can find data more easily and provide more powerful
means of integrating data across distributed resources and datasets. InterLex
allows for the association of data fields and data values to common data elements
and terminologies enabling the crowdsourcing of data-terminology mappings within
and across communities. InterLex provides a stable layer on top of the many other
existing terminologies, lexicons, ontologies, and common data element collections
and provides a set of inter-lexical and inter-data-lexical mappings. '
example: 0101963
homepage: https://www.fdilab.org
keywords:
- anatomy
- biomedical science
- neurobiology
mappings:
fairsharing: FAIRsharing.67sssf
miriam: ilx
wikidata: P696
name: InterLex
pattern: ^[0-9]+$
preferred_prefix: interlex
publications:
- doi: 10.3389/fninf.2013.00018
pmc: PMC3757470
pubmed: '24009581'
title: 'NeuroLex.org: an online framework for neuroscience knowledge.'
year: 2013
references:
- https://github.com/AllenInstitute/nomenclature
synonyms:
- ILX
uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1
interpro:
contact:
email: interhelp@ebi.ac.uk
github: null
name: InterPro Help
orcid: null
description: InterPro is a database of protein families, domains and functional
sites in which identifiable features found in known proteins can be applied to
unknown protein sequences.
example: IPR016380
homepage: http://www.ebi.ac.uk/interpro/index.html
keywords:
- bioinformatics
- biology
- domain
- obo
- ontology
- protein
mappings:
biocontext: IPR
biolink: interpro
edam: '1133'
fairsharing: FAIRsharing.pda11d
go: InterPro
miriam: interpro
n2t: interpro
ncbi: InterPro
obofoundry: ipr
prefixcommons: interpro
re3data: r3d100010798
uniprot: DB-0052
wikidata: P2926
name: InterPro
pattern: ^IPR\d{6}$
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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/interpro:$1
publications:
- doi: 10.1093/nar/gkaa977
pmc: PMC7778928
pubmed: '33156333'
title: 'The InterPro protein families and domains database: 20 years on.'
year: 2021
- doi: 10.1093/nar/gky1100
pmc: PMC6323941
pubmed: '30398656'
title: 'InterPro in 2019: improving coverage, classification and access to protein
sequence annotations.'
year: 2019
- doi: 10.1093/nar/gki106
pmc: PMC540060
pubmed: '15608177'
title: InterPro, progress and status in 2005.
year: 2005
rdf_uri_format: http://purl.obolibrary.org/obo/IPR_$1
repository: https://proteinswebteam.github.io/interpro-blog/
synonyms:
- IP
- IPR
- InterPro
twitter: InterProDB
uri_format: https://www.ebi.ac.uk/interpro/entry/$1
iobc:
contact:
email: kushida@biosciencedbc.jp
github: kushidatatsuya
name: Tatsuya Kushida
orcid: 0000-0002-0784-4113
description: 'Interlinking Ontology for Biological Concepts (IOBC) contains approximately
80,000 biological concepts such as biological phenomena, diseases, molecular functions,
gene products, chemicals, and medical cares, and approximately 20,000 related
concepts such as earth science and environmental science. The concepts are structured
by thirty-five relations such as has function, has role, has quality, and precedes.
Each concept has both of English and Japanese labels. For further information
including the developmental method, see papers in the PUBLICATIONS PAGE. The license
for this ontology is specified in the Creative Commons Attribution-NonCommercial
4.0 International. If you use data from this ontology, please be sure attribute
this ontology as follows: "Interlinking Ontology for Biological Concepts © National
Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International".'
download_owl: http://aber-owl.net/media/ontologies/IOBC/25/iobc.owl
example: '200906038218908385'
example_extras:
- AC21_cat
- AC21
- OWLClass_00000000000000000321
homepage: https://github.com/kushidat/IOBC
keywords:
- ontology
license: CC-BY-NC-4.0
mappings:
aberowl: IOBC
bioportal: IOBC
name: Interlinking Ontology for Biological Concepts
preferred_prefix: iobc
publications:
- doi: 10.1007/s00354-019-00074-y
pmc: null
pubmed: null
title: Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking
Ontology for Biological Concepts
year: 2019
repository: https://github.com/kushidat/IOBC
uri_format: http://purl.jp/bio/4/id/$1
ipi:
deprecated: true
description: IPI provides a top level guide to the main databases that describe
the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross
references between the primary data sources, it provides minimally redundant but
complete sets of proteins for featured species, and it maintains stable and unique
identifiers.
example: IPI00000001
homepage: http://www.ebi.ac.uk/IPI
keywords:
- protein
mappings:
biocontext: IPI
prefixcommons: ipi
name: International Protein Index
preferred_prefix: ipi
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ipi:$1
publications:
- doi: 10.1002/pmic.200300721
pmc: null
pubmed: '15221759'
title: 'The International Protein Index: an integrated database for proteomics
experiments.'
year: 2004
uri_format: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default
irct:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'Iranian Registry of Clinical Trials. This is a Primary Registry in
the WHO Registry Network set up with the help from the Ministry of Health and
Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS).
(from homepage)
Note that the website uses a different identifier then the one reported in this
semantic space.'
example: IRCT20080904001199N7
homepage: https://en.irct.ir/
name: Iranian Registry of Clinical Trials
pattern: ^IRCT\d+N\d+$
preferred_prefix: irct
references:
- https://en.irct.ir/trial/65035
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/
keywords:
- gene
- protein
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
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ird.segment:$1
publications:
- doi: 10.1093/nar/gkm905
pmc: PMC2238987
pubmed: '17965094'
title: 'BioHealthBase: informatics support in the elucidation of influenza virus
host pathogen interactions and virulence.'
year: 2007
uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1
irefweb:
description: 'iRefWeb is an interface to a relational database containing the latest
build of the interaction Reference Index (iRefIndex) which integrates protein
interaction data from ten different interaction databases: BioGRID, BIND, CORUM,
DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates
interactions with the PubMed record from which they are derived.'
example: '617102'
homepage: http://wodaklab.org/iRefWeb/
keywords:
- interaction
- life science
- protein
mappings:
biocontext: IREFWEB
fairsharing: FAIRsharing.t31wcb
miriam: irefweb
n2t: irefweb
prefixcommons: irefweb
re3data: r3d100012725
name: iRefWeb
pattern: ^\d+$
preferred_prefix: irefweb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/irefweb:$1
publications:
- doi: 10.1093/database/baq023
pmc: PMC2963317
pubmed: '20940177'
title: 'iRefWeb: interactive analysis of consolidated protein interaction data
and their supporting evidence.'
year: 2010
twitter: wodaklab
uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1
iresite:
description: The IRESite database presents information about experimentally studied
IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract
the eukaryotic ribosomal translation initiation complex and thus promote translation
initiation independently of the presence of the commonly utilized 5'-terminal
7mG cap structure.
example: '322'
homepage: http://www.iresite.org
keywords:
- life science
- regulation
- rna
mappings:
fairsharing: FAIRsharing.kd39j4
prefixcommons: iresite
name: Database of experimentally verified IRES structures
preferred_prefix: iresite
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/iresite:$1
publications:
- doi: 10.1093/nar/gkp981
pmc: PMC2808886
pubmed: '19917642'
title: IRESite--a tool for the examination of viral and cellular internal ribosome
entry sites.
year: 2009
- doi: 10.1093/nar/gkj081
pmc: PMC1347444
pubmed: '16381829'
title: 'IRESite: the database of experimentally verified IRES structures (www.iresite.org).'
year: 2006
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1
iro:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
example: 0000008
name: Insect Resistance Ontology
pattern: ^\d{7}$
preferred_prefix: iro
uri_format: https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1
isbn:
description: The International Standard Book Number (ISBN) is for identifying printed
books.
example: '9781584885658'
homepage: http://isbndb.com/
keywords:
- bibliography
mappings:
biocontext: ISBN-13
biolink: isbn
edam: '2634'
go: ISBN
miriam: isbn
n2t: isbn
prefixcommons: isbn
name: International Standard Book Number
pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[
-]?(\d|X)$
preferred_prefix: isbn
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/isbn:$1
- code: worldcat
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
ised:
description: ISED catalogues the influenza sequence and epitope information obtained
in countries worldwide and currently hosts a total of 49368 influenza A and 4761
influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences
collected in 42 countries, and a total of 545 amantadine-resistant influenza virus
sequences collected in Korea.
example: AY209920
homepage: http://influenza.korea.ac.kr
keywords:
- protein
mappings:
prefixcommons: ised
name: Influenza Sequence and Epitope Database
preferred_prefix: ised
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ised:$1
isfinder:
description: ISfinder is a database of bacterial insertion sequences (IS). It assigns
IS nomenclature and acts as a repository for ISs. Each IS is annotated with information
such as the open reading frame DNA sequence, the sequence of the ends of the element
and target sites, its origin and distribution together with a bibliography, where
available.
example: ISA1083-2
homepage: http://www-is.biotoul.fr/i
keywords:
- gene
- life science
- sequence
mappings:
biocontext: ISFINDER
fairsharing: FAIRsharing.xhpc3h
miriam: isfinder
n2t: isfinder
ncbi: ISFinder
prefixcommons: isfinder
name: Insertion sequence elements database
pattern: ^IS\w+(\-\d)?$
preferred_prefix: isfinder
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/isfinder:$1
publications:
- doi: 10.1093/nar/gkj014
pmc: PMC1347377
pubmed: '16381877'
title: 'ISfinder: the reference centre for bacterial insertion sequences.'
year: 2006
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/$1
iso.3166:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: An identifier for a country in numeric format per ISO 3166-1
example: '554'
homepage: https://www.iso.org/iso-3166-country-codes.html
mappings:
wikidata: P299
name: ISO 3166-1 Country Code
pattern: ^\d+$
preferred_prefix: iso.3166
iso15926:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The primary purpose of ISO 15926 is to provide a foundation ontology
to support the integration and sharing of data related to the lifecycle of a process
plant in such a way that it is consistent, unambiguous, and minimizing the number
of ways something could be expressed. Further purpose of ISO 15926-14 is to meet
needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient
reasoning and that capture lifecycle information. A specific purpose is to demonstrate
lifecycle modelling through a representation of the lifecycle model of ISO/IEC
81346-1. Another specific purpose is to exemplify how this standard can be used
to develop industrial ontologies through various real-world use cases from industry.
(from https://nfdi4cat.org/services/ontologie-sammlung/)
download_rdf: https://github.com/uwasystemhealth/modular_ontologies/raw/master/LIS-14.ttl
example: activityBoundOf
homepage: https://15926.org/home/
name: ISO 15926-14
preferred_prefix: iso15926
uri_format: http://standards.iso.org/iso/15926/part14/$1
isrctn:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The ISRCTN registry is a primary clinical trial registry recognised
by WHO and ICMJE that accepts all clinical research studies (whether proposed,
ongoing or completed), providing content validation and curation and the unique
identification number necessary for publication. All study records in the database
are freely accessible and searchable. (from homepage)
example: ISRCTN10175490
homepage: https://www.isrctn.com/
name: International Traditional Medicine Clinical Trial Registry
pattern: ^ISRCTN\d+$
preferred_prefix: isrctn
providers:
- code: doi
description: DOI resolution of ISRCTN
homepage: https://doi.org/10.1186
name: DOI
uri_format: https://doi.org/10.1186/$1
uri_format: https://www.isrctn.com/$1
issn:
description: The International Standard Serial Number (ISSN) is a unique eight-digit
number used to identify a print or electronic periodical publication, rather than
individual articles or books.
example: 0745-4570
homepage: https://portal.issn.org
mappings:
biocontext: ISSN
biolink: issn
go: ISSN
miriam: issn
n2t: issn
name: International Standard Serial Number
pattern: ^\d{4}-\d{3}[\dX]$
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/$1
itis:
contact:
email: itiswebmaster@itis.gov
github: null
name: Gerald Guala
orcid: 0000-0002-4972-3782
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Information system with taxonomic data on plants, animals, fungi, and
microbes of North America and the world.
example: '589462'
homepage: https://www.itis.gov/
keywords:
- biodiversity
- life science
- taxonomy
mappings:
bartoc: '17791'
fairsharing: FAIRsharing.t19hpa
re3data: r3d100011213
wikidata: P815
name: Integrated Taxonomic Information System
pattern: ^\d+$
preferred_prefix: itis
uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1
itmctr:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The International Traditional Medicine Clinical Trial Registry (ITMCTR)
is a non-profit online register of clinical trials being conducted in the field
of traditional medicine. It isoperated by the China Academy of Chinese Medical
Sciences and The China Center For Evidence Based Traditional Chinese Medicine.
It is recognized as a Primary Registry of WHO, and contributes data to the WHO
ICTRP. (from website)
example: ITMCTR2023000002
homepage: http://itmctr.ccebtcm.org.cn
logo: http://itmctr.ccebtcm.org.cn/Content/images/ny_logo.png
name: International Traditional Medicine Clinical Trial Registry
pattern: ^ITMCTR\d+$
preferred_prefix: itmctr
ito:
banana: ITO
banana_peel: _
contact:
email: matthias.samwald@meduniwien.ac.at
github: null
name: Matthias Samwald
orcid: 0000-0002-4855-2571
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.
download_owl: http://aber-owl.net/media/ontologies/ITO/17/ito.owl
example: '01625'
homepage: https://bioportal.bioontology.org/
keywords:
- artificial intelligence
- ontology
mappings:
aberowl: ITO
bioportal: ITO
fairsharing: FAIRsharing.89e853
miriam: ito
name: Intelligence Task Ontology
pattern: ^\d+$
preferred_prefix: ito
publications:
- doi: 10.1038/s41597-022-01435-x
pmc: PMC9205953
pubmed: '35715466'
title: A curated, ontology-based, large-scale knowledge graph of artificial intelligence
tasks and benchmarks.
year: 2022
- doi: 10.5281/zenodo.5561989
pmc: null
pubmed: null
title: Intelligence Task Ontology and Knowledge Graph (ITO)
year: 2022
- doi: 10.48550/arxiv.2110.01434
pmc: null
pubmed: null
title: A curated, ontology-based, large-scale knowledge graph of artificial intelligence
tasks and benchmarks
year: 2021
uri_format: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:$1
iuphar.family:
description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
properties of identified mammalian sodium, calcium and potassium channels, as
well as the related cyclic nucleotide-modulated ion channels and the recently
described transient receptor potential channels. It includes information on nomenclature
systems, and on inter and intra-species molecular structure variation. This collection
references families of receptors or subunits.
example: '78'
homepage: http://www.guidetopharmacology.org/
keywords:
- protein
mappings:
biocontext: IUPHAR.FAMILY
miriam: iuphar.family
n2t: iuphar.family
prefixcommons: iuphar.family
name: IUPHAR family
pattern: ^\d+$
preferred_prefix: iuphar.family
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/iuphar.family:$1
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=$1
iuphar.receptor:
description: The IUPHAR Compendium details the molecular, biophysical and pharmacological
properties of identified mammalian sodium, calcium and potassium channels, as
well as the related cyclic nucleotide-modulated ion channels and transient receptor
potential channels. It includes information on nomenclature systems, and on inter
and intra-species molecular structure variation. This collection references individual
receptors or subunits.
example: '101'
homepage: http://www.guidetopharmacology.org/targets.jsp
mappings:
biocontext: IUPHAR.RECEPTOR
go: IUPHAR_RECEPTOR
miriam: iuphar.receptor
n2t: iuphar.receptor
uniprot: DB-0182
wikidata: P5458
name: Guide to Pharmacology Target
pattern: ^\d+$
preferred_prefix: iuphar.receptor
publications:
- doi: 10.1093/nar/gkab1010
pmc: PMC8689838
pubmed: '34718737'
title: 'The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for
COVID-19, malaria and antibacterials.'
year: 2022
- doi: 10.1111/j.1476-5381.2012.02141.x
pmc: PMC3575771
pubmed: '23003568'
title: GuideToPharmacology.org--an update.
year: 2012
synonyms:
- IUPHAR_GPCR
- IUPHARobj
uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1
ivdb:
description: IVDB hosts complete genome sequences of influenza A virus generated
by BGI and curates all other published influenza virus sequences after expert
annotations. IVDB provides a series of tools and viewers for analyzing the viral
genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.
example: E13035
homepage: http://influenza.psych.ac.cn/
keywords:
- dna
- gene
- genome
mappings:
prefixcommons: ivdb
name: Influenza Virus Database
preferred_prefix: ivdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ivdb:$1
uri_format: http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1
jax:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Information about the C57BL/6J. Includes genetic background and disease
data.
example: '004435'
homepage: https://www.jax.org/strain
keywords:
- life science
mappings:
biocontext: JAX
fairsharing: FAIRsharing.5701h1
name: Jackson Laboratories Strain
pattern: ^\d{6}$
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/$1
jcm:
description: The Japan Collection of Microorganisms (JCM) collects, catalogues,
and distributes cultured microbial strains, restricted to those classified in
Risk Group 1 or 2.
example: '17254'
homepage: http://www.jcm.riken.go.jp/
keywords:
- life science
- microbial
- taxonomy
mappings:
biocontext: JCM
fairsharing: FAIRsharing.h2wrt2
miriam: jcm
n2t: jcm
ncbi: JCM
prefixcommons: jcm
name: Japan Collection of Microorganisms
pattern: ^\d+$
preferred_prefix: jcm
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/jcm:$1
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=$1
jcsd:
description: The Japan Chemical Substance Dictionary is an organic compound dictionary
database prepared by the Japan Science and Technology Agency (JST).
example: J55.713G
homepage: http://jglobal.jst.go.jp/en/
keywords:
- chemical
- structure
mappings:
biocontext: JCSD
miriam: jcsd
n2t: jcsd
prefixcommons: jcsd
name: Japan Chemical Substance Dictionary
pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$
preferred_prefix: jcsd
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/jcsd:$1
uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1
jgi.proposal:
contact:
email: sewilson@lbl.gov
github: null
name: Steven E. Wilson
orcid: 0000-0002-8489-208X
contributor:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
contributor_extras:
- email: aclum@lbl.gov
github: aclum
name: Alicia Clum
orcid: 0000-0002-5004-3362
description: Identifiers for proposals/projects at the Joint Genome Institute
example: '502930'
github_request_issue: 853
homepage: https://genome.jgi.doe.gov/portal/
name: Joint Genome Institute Proposals
pattern: ^\d+$
preferred_prefix: jgi.proposal
publications:
- doi: 10.1128/msystems.00804-20
pmc: PMC8269246
pubmed: '34006627'
title: DOE JGI Metagenome Workflow
year: 2021
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1
jrct:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: This system submits an implementation plan to the Minister of Health,
Labor and Welfare for clinical research conducted at medical institutions, etc.
based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring
Safety of Regenerative Medicine, etc.' It is a system for performing notification
procedures such as In addition, based on the clinical research practice standards
stipulated in the same law, we disclose information that the World Health Organization
(WHO) requires to be disclosed, information that ensures the transparency of the
research process, and information that contributes to the selection of participation
in clinical research by the public. (translated from website)
example: jRCTs041220087
homepage: https://jrct.niph.go.jp
name: Japan Registry of Clinical Trials
pattern: ^jRCT\w?\d+$
preferred_prefix: jrct
providers:
- code: ''
description: ''
homepage: ''
name: ''
uri_format: https://jrct.niph.go.jp/latest-detail/$1
uri_format: https://jrct.niph.go.jp/en-latest-detail/$1
jstor:
description: JSTOR (Journal Storage) is a digital library containing digital versions
of historical academic journals, as well as books, pamphlets and current issues
of journals. Some public domain content is free to access, while other articles
require registration.
example: '3075966'
homepage: http://www.jstor.org/
mappings:
biocontext: JSTOR
go: JSTOR
miriam: jstor
n2t: jstor
name: Digital archive of scholarly articles
pattern: ^\d+$
preferred_prefix: jstor
uri_format: http://www.jstor.org/stable/$1
jws:
description: JWS Online is a repository of curated biochemical pathway models, and
additionally provides the ability to run simulations of these models in a web
browser.
example: achcar11
homepage: http://jjj.biochem.sun.ac.za/models/
keywords:
- model
- pathway
mappings:
biocontext: JWS
miriam: jws
n2t: jws
prefixcommons: jws
name: JWS Online
pattern: ^\w+$
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/
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/jws:$1
publications:
- doi: 10.1093/bioinformatics/bth200
pmc: null
pubmed: '15072998'
title: Web-based kinetic modelling using JWS Online.
year: 2004
uri_format: https://jjj.bio.vu.nl/models/$1
kaggle:
description: Kaggle is a platform for sharing data, performing reproducible analyses,
interactive data analysis tutorials, and machine learning competitions.
example: nasa/kepler-exoplanet-search-results
homepage: https://kaggle.com
mappings:
miriam: kaggle
n2t: kaggle
re3data: r3d100012705
name: Kaggle
pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$
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=$1
kcris:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'The Clinical Research Information Service (CRIS) is a non-profit online
registration system for clinical trials (researches) to be conducted in Korea.
It has been established at the Korea Disease Control and Prevention Agency (KDCA)
with support from the Ministry of Health and Welfare (MOHW). It joined the WHO
International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary
Registry. (from about page)
Note that the web page that resolves this trial does not correspond to the semantic
space'
example: KCT0008394
homepage: https://cris.nih.go.kr
name: Korean Clinical Research Information Service
pattern: ^KCT\d+$
preferred_prefix: kcris
references:
- https://cris.nih.go.kr/cris/search/detailSearchEn.do?seq=23973
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
biolink: KEGG
cheminf: 000409
go: KEGG
miriam: kegg
n2t: kegg
uniprot: DB-0053
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
publications:
- doi: 10.1093/nar/gkw1092
pmc: PMC5210567
pubmed: '27899662'
title: 'KEGG: new perspectives on genomes, pathways, diseases and drugs.'
year: 2016
synonyms:
- KEGG
uri_format: http://www.kegg.jp/entry/$1
kegg.brite:
description: KEGG BRITE is a collection of hierarchical classifications (see new
hierarchies and last updates) representing our knowledge on various aspects of
biological systems. In contrast to KEGG PATHWAY, which is limited to molecular
interactions and reactions, KEGG BRITE incorporates many different types of relationships.
example: ko00071
homepage: http://www.genome.jp/kegg/brite.html
keywords:
- classification
- ontology
- pathway
mappings:
biolink: KEGG.BRITE
prefixcommons: kegg.brite
name: KEGG BRITE
part_of: kegg
preferred_prefix: kegg.brite
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.brite:$1
uri_format: http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1
kegg.compound:
description: KEGG compound contains our knowledge on the universe of chemical substances
that are relevant to life.
example: C12345
homepage: https://www.genome.jp/kegg/ligand.html
keywords:
- small molecule
mappings:
biocontext: KEGG.COMPOUND
edam: '2605'
miriam: kegg.compound
n2t: kegg.compound
prefixcommons: kegg.compound
wikidata: P665
name: KEGG Compound
part_of: kegg
pattern: ^C\d+$
preferred_prefix: kegg.compound
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.compound:$1
publications:
- doi: 10.1002/0471250953.bi0112s38
pmc: null
pubmed: '22700311'
title: Using the KEGG database resource.
year: 2012
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/
keywords:
- classification
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
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.disease:$1
uri_format: http://www.kegg.jp/entry/$1
kegg.drug:
description: KEGG DRUG contains chemical structures of drugs and additional information
such as therapeutic categories and target molecules.
example: D00123
homepage: https://www.genome.jp/kegg/drug/
keywords:
- small molecule
mappings:
biocontext: KEGG.DRUG
edam: '2609'
miriam: kegg.drug
n2t: kegg.drug
prefixcommons: kegg.drug
wikidata: P665
name: KEGG Drug
part_of: kegg
pattern: ^D\d+$
preferred_prefix: kegg.drug
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.drug:$1
publications:
- doi: 10.1093/nar/gkj102
pmc: PMC1347464
pubmed: '16381885'
title: 'From genomics to chemical genomics: new developments in KEGG.'
year: 2006
synonyms:
- KEGG DRUG
- KEGG.DRUG
uri_format: https://www.kegg.jp/entry/$1
kegg.environ:
deprecated: true
description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential
oils, and other health-promoting substances, which are mostly natural products
of plants. It will contain environmental substances and other health-damagine
substances as well. Each KEGG ENVIRON entry is identified by the E number and
is associated with the chemical component, efficacy information, and source species
information whenever applicable.
example: ev:E00032
homepage: http://www.genome.jp/kegg/drug/environ.html
mappings:
biocontext: KEGG.ENVIRON
miriam: kegg.environ
n2t: kegg.environ
name: KEGG Environ
part_of: kegg
pattern: ^(ev\:)?E\d+$
preferred_prefix: kegg.environ
synonyms:
- KEGG.EDRUG
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:$1
kegg.genes:
description: KEGG GENES is a collection of gene catalogs for all complete genomes
and some partial genomes, generated from publicly available resources.
example: bsu:BSU01340
homepage: http://www.genome.jp/kegg/genes.html
keywords:
- dna
- gene
- protein
mappings:
biocontext: KEGG.GENES
biolink: KEGG.GENES
miriam: kegg.genes
n2t: kegg.genes
prefixcommons: kegg.gene
wikidata: P665
name: KEGG Genes
part_of: kegg
pattern: ^\w+:[\w\d\.-]*$
preferred_prefix: kegg.genes
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.gene:$1
publications:
- doi: 10.1093/nar/gkj102
pmc: PMC1347464
pubmed: '16381885'
title: 'From genomics to chemical genomics: new developments in KEGG.'
year: 2006
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
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.genome:$1
publications:
- doi: 10.1093/nar/gkr988
pmc: PMC3245020
pubmed: '22080510'
title: KEGG for integration and interpretation of large-scale molecular data sets.
year: 2011
synonyms:
- kegg_genome
- kegg_genomes
uri_format: http://www.kegg.jp/entry/$1
kegg.glycan:
description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of
experimentally determined glycan structures. It contains all unique structures
taken from CarbBank, structures entered from recent publications, and structures
present in KEGG pathways.
example: G00123
homepage: https://www.genome.jp/kegg/glycan/
keywords:
- small molecule
mappings:
biocontext: KEGG.GLYCAN
edam: '2613'
miriam: kegg.glycan
n2t: kegg.glycan
prefixcommons: kegg.glycan
name: KEGG Glycan
part_of: kegg
pattern: ^G\d+$
preferred_prefix: kegg.glycan
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.glycan:$1
publications:
- doi: 10.1093/glycob/cwj010
pmc: null
pubmed: '16014746'
title: KEGG as a glycome informatics resource.
year: 2005
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:$1
kegg.metagenome:
description: The KEGG Metagenome Database collection information on environmental
samples (ecosystems) of genome sequences for multiple species.
example: T30002
homepage: http://www.genome.jp/kegg/catalog/org_list3.html
keywords:
- genome
mappings:
biocontext: KEGG.METAGENOME
miriam: kegg.metagenome
n2t: kegg.metagenome
prefixcommons: kegg.metagenome
name: KEGG Metagenome
part_of: kegg
pattern: ^T3\d+$
preferred_prefix: kegg.metagenome
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.metagenome:$1
publications:
- doi: 10.1093/nar/gkr988
pmc: PMC3245020
pubmed: '22080510'
title: KEGG for integration and interpretation of large-scale molecular data sets.
year: 2011
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/$1
kegg.orthology:
description: KEGG Orthology (KO) consists of manually defined, generalised ortholog
groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all
organisms.
example: K00001
homepage: http://www.genome.jp/kegg/ko.html
keywords:
- classification
- pathway
mappings:
biocontext: KEGG.ORTHOLOGY
miriam: kegg.orthology
n2t: kegg.orthology
prefixcommons: kegg.orthology
name: KEGG Orthology
part_of: kegg
pattern: ^K\d+$
preferred_prefix: kegg.orthology
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.orthology:$1
uri_format: http://www.kegg.jp/entry/$1
kegg.pathway:
description: KEGG PATHWAY is a collection of manually drawn pathway maps representing
our knowledge on the molecular interaction and reaction networks.
example: rsk00410
homepage: https://www.genome.jp/kegg/pathway.html
keywords:
- pathway
mappings:
biocontext: KEGG.PATHWAY
biolink: KEGG.PATHWAY
edam: '2343'
go: KEGG_PATHWAY
miriam: kegg.pathway
n2t: kegg.pathway
prefixcommons: kegg.pathway
wikidata: P665
name: KEGG Pathways Database
part_of: kegg
pattern: ^\w{2,4}\d{5}$
preferred_prefix: kegg.pathway
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.pathway:$1
publications:
- doi: 10.1002/0471250953.bi0112s38
pmc: null
pubmed: '22700311'
title: Using the KEGG database resource.
year: 2012
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/
keywords:
- enzyme
- pathway
mappings:
biocontext: KEGG.REACTION
edam: '2608'
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
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/kegg.reaction:$1
publications:
- doi: 10.1002/0471250953.bi0112s38
pmc: null
pubmed: '22700311'
title: Using the KEGG database resource.
year: 2012
rdf_uri_format: http://www.kegg.jp/entry/$1
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=$1.pdf
labo:
contact:
email: paul.fabry@usherbrooke.ca
github: pfabry
name: Paul Fabry
orcid: 0000-0002-3336-2476
depends_on:
- iao
- obi
- ogms
- omiabis
- omrse
- opmi
description: LABO is an ontology of informational entities formalizing clinical
laboratory tests prescriptions and reporting documents.
download_owl: http://purl.obolibrary.org/obo/labo.owl
example: '0000124'
homepage: https://github.com/OpenLHS/LABO
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: LABO
bioportal: LABO
obofoundry: labo
ols: labo
ontobee: LABO
name: clinical LABoratory Ontology
pattern: ^\d{7}$
preferred_prefix: LABO
publications:
- doi: 10.5281/zenodo.6522019
pmc: null
pubmed: null
title: 'LABO: An ontology for laboratory test prescription and reporting'
year: 2019
rdf_uri_format: http://purl.obolibrary.org/obo/LABO_$1
repository: https://github.com/OpenLHS/LABO
uri_format: http://purl.obolibrary.org/obo/LABO_$1
version: '2021-06-08'
langual:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: 'Langual stands for "langua alimentaria" or "language of food". it
is an automated method for describing, capturing and retrieving data about food.
the work on langual was started in the late 1970''s by the center for food safety
and applied nutrition (cfsan) of the united states food and drug administration
as an ongoing co-operative effort of specialists in food technology, information
science and nutrition. the thesaurus provides a standardized language for describing
foods, specifically for classifying food products for information retrieval. langual
is based on the concept that: - any food (or food product) can be systematically
described by a combination of characteristics - these characteristics can be categorized
into viewpoints and coded for computer processing - the resulting viewpoint/characteristic
codes can be used to retrieve data about the food from external databases'
example: B2067
github_request_issue: 507
homepage: https://www.langual.org
name: Langua aLimentaria Thesaurus
pattern: ^B\d+$
preferred_prefix: langual
uri_format: https://www.langual.org/langual_thesaurus.asp?termid=$1
lbctr:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Lebanese Clinical Trials Registry is an online register of clinical
trials being undertaken in Lebanon. It includes trials that target humans from
the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures,
preventive measures, lifestyle, devices, treatment and rehabilitation strategies
and complementary therapies. (from homepage)
example: LBCTR2023015204
homepage: https://lbctr.moph.gov.lb/
name: Lebanon Clinical Trials Registry
pattern: ^LBCTR\d+$
preferred_prefix: lbctr
references:
- https://lbctr.moph.gov.lb/Trials/Details/5204
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
keywords:
- animal breeding
- animal husbandry
- genetics
- genomics
- ontology
mappings:
aberowl: LBO
agroportal: LBO
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
uri_format: http://purl.obolibrary.org/obo/LBO_$1
leafsnap:
description: identifier for a tree species of the United States and Canada on the
Leafsnap electronic field guide
example: Amelanchier laevis
homepage: http://leafsnap.com/
mappings:
wikidata: P10538
name: Leafsnap
preferred_prefix: leafsnap
uri_format: http://leafsnap.com/species/$1/
lei:
description: Established by the Financial Stability Board in June 2014, the Global
Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation
and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen
by the LEI Regulatory Oversight Committee, representing public authorities from
around the globe that have come together to jointly drive forward transparency
within the global financial markets. GLEIF is a supra-national not-for-profit
organization headquartered in Basel, Switzerland.
example: HWUPKR0MPOU8FGXBT394
homepage: https://www.gleif.org/
mappings:
miriam: lei
n2t: lei
name: Global LEI Index
pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$
preferred_prefix: lei
uri_format: https://www.gleif.org/lei/$1
lepao:
contact:
email: lagonzalezmo@unal.edu.co
github: luis-gonzalez-m
name: Luis A. Gonzalez-Montana
orcid: 0000-0002-9136-9932
depends_on:
- aism
- bfo
- bspo
- caro
- pato
- ro
- uberon
description: The Lepidoptera Anatomy Ontology contains terms used for describing
the anatomy and phenotype of moths and butterflies in biodiversity research.
download_obo: http://purl.obolibrary.org/obo/lepao.obo
download_owl: http://purl.obolibrary.org/obo/lepao.owl
example: '0000005'
homepage: https://github.com/insect-morphology/lepao
keywords:
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: LEPAO
bioportal: LEPAO
obofoundry: lepao
ols: lepao
ontobee: LEPAO
name: Lepidoptera Anatomy Ontology
pattern: ^\d{7}$
preferred_prefix: LEPAO
rdf_uri_format: http://purl.obolibrary.org/obo/LEPAO_$1
repository: https://github.com/insect-morphology/lepao
uri_format: http://purl.obolibrary.org/obo/LEPAO_$1
version: '2023-02-18'
lgai.cede:
description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset
with molecular instance level annotations (i.e. atom-bond level position annotations
within an image) for molecular structure images. This dataset was designed to
encourage research on detection-based pipelines for Optical Chemical Structure
Recognition (OCSR).
example: LGCEDe-S-000002244
homepage: https://www.lgresearch.ai
mappings:
miriam: lgai.cede
name: LG Chemical Entity Detection Dataset (LGCEDe)
pattern: ^LGCEDe-S-\d{9}$
preferred_prefix: lgai.cede
uri_format: https://s3.us-east-2.amazonaws.com/lg.cede/$1
lgic:
comment: Website is gone
deprecated: true
description: The Ligand-Gated Ion Channel database provides nucleic and proteic
sequences of the subunits of ligand-gated ion channels. These transmembrane proteins
can exist under different conformations, at least one of which forms a pore through
the membrane connecting two neighbouring compartments. The database can be used
to generate multiple sequence alignments from selected subunits, and gives the
atomic coordinates of subunits, or portion of subunits, where available.
example: 5HT3Arano
homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
keywords:
- gene
- protein
- sequence
mappings:
biocontext: LGIC
miriam: lgic
n2t: lgic
prefixcommons: lgicdb
name: Ligand-Gated Ion Channel database
pattern: ^\w+$
preferred_prefix: lgic
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/lgicdb:$1
publications:
- doi: 10.1093/nar/27.1.340
pmc: PMC148177
pubmed: '9847222'
title: The Ligand Gated Ion Channel Database.
year: 1999
uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php
licebase:
contact:
email: Inge.Jonassen@uib.no
github: null
name: Inge Jonassen
orcid: 0000-0003-4110-0748
description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major
pathogens of salmon, significantly impacting upon the global salmon farming industry.
Lice control is primarily accomplished through chemotherapeutants, though emerging
resistance necessitates the development of new treatment methods (biological agents,
prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing
genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome
browser, and access to related high-thoughput genomics data. LiceBase also mines
and stores data from related genome sequencing and functional genomics projects.
example: EMLSAT00000003403
homepage: https://licebase.org
keywords:
- life science
mappings:
biocontext: LICEBASE
fairsharing: FAIRsharing.c7w81a
miriam: licebase
n2t: licebase
re3data: r3d100013547
name: LiceBase
pattern: ^[A-Za-z0-9\-\/]+$
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=$1
ligandexpo:
contact:
email: jwest@rcsb.rutgers.edu
github: null
name: John Westbrook
orcid: 0000-0002-6686-5475
description: Ligand Expo is a data resource for finding information about small
molecules bound to proteins and nucleic acids.
example: ABC
homepage: http://ligand-depot.rutgers.edu/index.html
keywords:
- chemical
- interaction
- life science
- nucleic acid
- protein
- structure
mappings:
biocontext: LIGANDEXPO
fairsharing: FAIRsharing.2ma4gq
miriam: ligandexpo
n2t: ligandexpo
prefixcommons: ligandexpo
name: Ligand Expo
pattern: ^(\w){3}$
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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ligandexpo:$1
publications:
- doi: 10.1093/bioinformatics/bth214
pmc: null
pubmed: '15059838'
title: 'Ligand Depot: a data warehouse for ligands bound to macromolecules.'
year: 2004
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
linkml:
comment: 'Closes #508'
contact:
email: cjmungall@lbl.gov
github: cmungall
name: Chris Mungall
orcid: 0000-0002-6601-2165
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Linkml is a flexible modeling language that allows you to author schemas
in yaml that describe the structure of your data. additionally, it is a framework
for working with and validating data in a variety of formats (json, rdf, tsv),
with generators for compiling linkml schemas to other frameworks.
example: SchemaDefinition
github_request_issue: 512
homepage: https://linkml.io/linkml-model/docs/SchemaDefinition/
keywords:
- data integration
- ontology and terminology
mappings:
biolink: linkml
fairsharing: FAIRsharing.cb7086
name: LinkML
preferred_prefix: linkml
publications:
- doi: 10.5281/zenodo.5598314
pmc: null
pubmed: null
title: 'linkml/linkml-model: v1.5.0rc2'
year: 2023
repository: https://github.com/linkml/
twitter: linkml_data
uri_format: https://w3id.org/linkml/$1
lipidbank:
description: LipidBank is an open, publicly free database of natural lipids including
fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
example: BBA0001
homepage: http://lipidbank.jp/index.html
keywords:
- life science
- lipid
- molecule
- structure
mappings:
biocontext: LIPIDBANK
edam: '2665'
fairsharing: FAIRsharing.bdn9br
miriam: lipidbank
n2t: lipidbank
prefixcommons: lipidbank
name: LipidBank
pattern: ^\w+\d+$
preferred_prefix: lipidbank
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/lipidbank:$1
publications:
- doi: null
pmc: null
pubmed: '12058481'
title: '[LIPIDBANK for Web, the newly developed lipid database].'
year: 2002
uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1
lipidmaps:
description: The LIPID MAPS Lipid Classification System is comprised of eight lipid
categories, each with its own subclassification hierarchy. All lipids in the LIPID
MAPS Structure Database (LMSD) have been classified using this system and have
been assigned LIPID MAPS ID's which reflects their position in the classification
hierarchy.
example: LMPR0102010012
homepage: http://www.lipidmaps.org
keywords:
- biomedical science
- endocrinology
- life science
- lipid
- structure
- systems biology
- taxonomy
mappings:
biocontext: LIPIDMAPS
cheminf: '000564'
edam: '2625'
fairsharing: FAIRsharing.cpneh8
miriam: lipidmaps
n2t: lipidmaps
prefixcommons: lipidmaps
re3data: r3d100012315
wikidata: P2063
name: LIPID MAPS
pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$
preferred_prefix: lipidmaps
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/lipidmaps:$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/lipidmaps/$1
publications:
- doi: 10.1194/jlr.r800095-jlr200
pmc: PMC2674711
pubmed: '19098281'
title: Update of the LIPID MAPS comprehensive classification system for lipids.
year: 2008
- doi: 10.1093/nar/gkm324
pmc: PMC1933166
pubmed: '17584797'
title: LIPID MAPS online tools for lipid research.
year: 2007
- doi: 10.1093/nar/gkl838
pmc: PMC1669719
pubmed: '17098933'
title: 'LMSD: LIPID MAPS structure database.'
year: 2006
- doi: 10.1194/jlr.e400004-jlr200
pmc: null
pubmed: '15722563'
title: A comprehensive classification system for lipids.
year: 2005
synonyms:
- LIPID MAPS
- LIPID_MAPS_class
- LIPID_MAPS_instance
twitter: lipidmaps
uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1
lipro:
contact:
email: bakerc@unb.ca
github: null
name: Christopher Baker
orcid: 0000-0003-4004-6479
deprecated: true
description: An ontology representation of the LIPIDMAPS nomenclature classification.
download_owl: http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl
keywords:
- obo
- ontology
mappings:
aberowl: LIPRO
biocontext: LIPRO
bioportal: LIPRO
obofoundry: lipro
name: Lipid Ontology
preferred_prefix: LIPRO
rdf_uri_format: http://purl.obolibrary.org/obo/LIPRO_$1
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
keywords:
- life science
mappings:
fairsharing: FAIRsharing.84c1a7
name: LNCipedia
preferred_prefix: lncipedia
publications:
- doi: 10.1093/nar/gkv295
pmc: PMC4417186
pubmed: '25829178'
title: 'An update on LNCipedia: a database for annotated human lncRNA sequences.'
year: 2015
- doi: 10.1093/nar/gku1060
pmc: PMC4383901
pubmed: '25378313'
title: 'An update on LNCipedia: a database for annotated human lncRNA sequences.'
year: 2014
- doi: 10.1093/nar/gks915
pmc: PMC3531107
pubmed: '23042674'
title: 'LNCipedia: a database for annotated human lncRNA transcript sequences
and structures.'
year: 2012
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
keywords:
- obo
- ontology
mappings:
biocontext: LOGGERHEAD
obofoundry: loggerhead
name: Loggerhead nesting
preferred_prefix: LOGGERHEAD
rdf_uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1
uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1
loinc:
contact:
email: loinc@regenstrief.org
github: null
name: LOINC Support
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The international standard for identifying health measurements, observations,
and documents.
example: LL379-9
homepage: https://loinc.org/
keywords:
- biomedical science
- life science
- ontology
- preclinical studies
mappings:
aberowl: LOINC
bartoc: '1897'
biolink: LOINC
bioportal: LOINC
fairsharing: FAIRsharing.2mk2zb
hl7: 2.16.840.1.113883.6.1
wikidata: P4338
name: Logical Observation Identifiers Names and Codes
pattern: ^(\d|\w)+-\d$
preferred_prefix: loinc
publications:
- doi: 10.1016/s1386-5056(98)00089-6
pmc: null
pubmed: '9749897'
title: Combining laboratory data sets from multiple institutions using the logical
observation identifier names and codes (LOINC).
year: 1998
- doi: 10.1093/jamia/ocu012
pmc: PMC5566197
pubmed: '25656513'
title: Supporting interoperability of genetic data with LOINC.
year: 2015
- doi: 10.1016/j.jbi.2012.01.005
pmc: PMC3376691
pubmed: '22285984'
title: Enabling international adoption of LOINC through translation.
year: 2012
rdf_uri_format: http://loinc.org/rdf/$1
synonyms:
- LNC
twitter: LOINC
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
loqate:
description: The data presented here is a result of systematically tracking the
localization and abundance of 5330 yeast proteins at single-cell resolution under
three different stress conditions (DTT, H2O2 and nitrogen starvation) using the
GFP-tagged yeast library
example: '1001'
homepage: http://www.weizmann.ac.il/molgen/loqate/
mappings:
prefixcommons: loqate
name: The localization and quantitation atlas of the yeast proteome
preferred_prefix: loqate
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/loqate:$1
publications:
- doi: 10.1093/nar/gkt933
pmc: PMC3965041
pubmed: '24150937'
title: LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new
tool for multiparametric dissection of single-protein behavior in response to
biological perturbations in yeast.
year: 2013
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://www.weizmann.ac.il/molgen/loqate/gene/view/$1
lotus:
comment: IDs are actually leading to the structural part of LOTUS only, which might
change in the future. Will adapt the regexp in case.
contact:
email: adriano.rutz@ik.me
github: adafede
name: Adriano Rutz
orcid: 0000-0003-0443-9902
contributor:
email: adriano.rutz@ik.me
github: adafede
name: Adriano Rutz
orcid: 0000-0003-0443-9902
description: LOTUS, actually, represents the most exhaustive resource of documented
structure-organism pairs. Within the frame of current computational approaches
in Natural Produts’s research and related fields, these documented structure-organism
pairs should allow a more complete understanding of organisms and their chemistry.
example: LTS0004651
github_request_issue: 222
homepage: https://lotus.naturalproducts.net
keywords:
- chemistry
- drugs
- metabolites
logo: https://upload.wikimedia.org/wikipedia/commons/6/64/Lotus_initiative_logo.svg
name: LOTUS Initiative for Open Natural Products Research
pattern: ^LTS\d{7}$
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/$1
lpt:
contact:
email: caripark@iastate.edu
github: caripark
name: Carissa Park
orcid: 0000-0002-2346-5201
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary
for the description of traits (measurable or observable characteristics) pertaining
to products produced by or obtained from the body of an agricultural animal or
bird maintained for use and profit.
download_obo: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo
download_owl: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl
example: '0000156'
homepage: https://github.com/AnimalGenome/livestock-product-trait-ontology
keywords:
- animal husbandry
- ontology
mappings:
aberowl: LPT
agroportal: LPT
biocontext: LPT
bioportal: LPT
fairsharing: FAIRsharing.g78mbm
name: Livestock Product Trait Ontology
pattern: ^\d+$
preferred_prefix: lpt
repository: https://github.com/AnimalGenome/livestock-product-trait-ontology
uri_format: http://purl.obolibrary.org/obo/LPT_$1
lrg:
banana: LRG
banana_peel: _
description: A Locus Reference Genomic (LRG) is a manually curated record that contains
stable genomic, transcript and protein reference sequences for reporting clinically
relevant sequence variants. All LRGs are generated and maintained by the NCBI
and EMBL-EBI.
example: '1'
homepage: http://www.lrg-sequence.org/
mappings:
biocontext: LRG
hl7: 2.16.840.1.113883.6.283
miriam: lrg
n2t: lrg
name: Locus Reference Genomic
pattern: ^\d+$
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: http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml
lspci:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Internal identifiers form the LSP for ChEBML compound classes (e.g.,
combining various salts and ions)
example: '1'
homepage: https://labsyspharm.github.io/lspci/
keywords:
- chemistry
- drugs
- metabolites
name: Laboratory of Systems Pharmacology Compound
pattern: ^\d+$
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=$1
ma:
banana: MA
contact:
email: Terry.Hayamizu@jax.org
github: tfhayamizu
name: Terry Hayamizu
orcid: 0000-0002-0956-8634
description: A structured controlled vocabulary of the adult anatomy of the mouse
(Mus)
download_obo: http://purl.obolibrary.org/obo/ma.obo
download_owl: http://purl.obolibrary.org/obo/ma.owl
example: '0002502'
homepage: https://github.com/obophenotype/mouse-anatomy-ontology
keywords:
- anatomy
- mouse
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: MA
biocontext: MA
bioportal: MA
fairsharing: FAIRsharing.pdwqcr
go: MA
miriam: ma
n2t: ma
obofoundry: ma
ols: ma
ontobee: MA
prefixcommons: ma
name: Mouse adult gross anatomy
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: MA
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/ma:$1
publications:
- doi: 10.1186/gb-2005-6-3-r29
pmc: PMC1088948
pubmed: '15774030'
title: 'The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating
data.'
year: 2005
rdf_uri_format: http://purl.obolibrary.org/obo/MA_$1
repository: https://github.com/obophenotype/mouse-anatomy-ontology
uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1
version: '2017-02-07'
macie:
description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database
of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction
describing the chemical compounds involved, as well as the species name in which
the reaction occurs. The individual reaction stages for each overall reaction
are listed with mechanisms, alternative mechanisms, and amino acids involved.
example: M0001
homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html
keywords:
- enzyme
- life science
- pathway
mappings:
biocontext: MACIE
edam: '2641'
fairsharing: FAIRsharing.7xkx69
miriam: macie
n2t: macie
prefixcommons: macie
name: Mechanism, Annotation and Classification in Enzymes
pattern: ^M\d{4}$
preferred_prefix: macie
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/macie:$1
publications:
- doi: 10.1093/nar/gkl774
pmc: PMC1634735
pubmed: '17082206'
title: 'MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools
for searching catalytic mechanisms.'
year: 2006
- doi: 10.1093/bioinformatics/bti693
pmc: PMC2748267
pubmed: '16188925'
title: 'MACiE: a database of enzyme reaction mechanisms.'
year: 2005
uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1
maizegdb.locus:
description: MaizeGDB is the maize research community's central repository for genetics
and genomics information.
example: '25011'
homepage: http://www.maizegdb.org/
keywords:
- dna
- genetics
- genome
- genomics
- life science
mappings:
biocontext: MAIZEGDB.LOCUS
fairsharing: FAIRsharing.aq280w
go: MaizeGDB_Locus
miriam: maizegdb.locus
n2t: maizegdb.locus
ncbi: MaizeGDB
prefixcommons: maizegdb
re3data: r3d100010795
uniprot: DB-0058
name: MaizeGDB Locus
pattern: ^\d+$
preferred_prefix: maizegdb.locus
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/maizegdb:$1
publications:
- doi: 10.3389/fpls.2019.01050
pmc: PMC6724615
pubmed: '31555312'
title: 'MaizeDIG: Maize Database of Images and Genomes.'
year: 2019
- doi: 10.1093/nar/gky1046
pmc: PMC6323944
pubmed: '30407532'
title: 'MaizeGDB 2018: the maize multi-genome genetics and genomics database.'
year: 2019
- doi: 10.1007/978-1-4939-3167-5_9
pmc: null
pubmed: '26519406'
title: 'MaizeGDB: The Maize Genetics and Genomics Database.'
year: 2016
- doi: 10.1093/nar/gkv1007
pmc: PMC4702771
pubmed: '26432828'
title: 'MaizeGDB update: new tools, data and interface for the maize model organism
database.'
year: 2015
- doi: 10.1155/2008/496957
pmc: PMC2518694
pubmed: '18769488'
title: 'MaizeGDB: The maize model organism database for basic, translational,
and applied research.'
year: 2008
- doi: 10.1093/nar/gkl1048
pmc: PMC1899092
pubmed: '17202174'
title: MaizeGDB's new data types, resources and activities.
year: 2007
synonyms:
- MaizeGDB
uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1
mamo:
banana: MAMO
banana_peel: _
contact:
email: n.lenovere@gmail.com
github: null
name: Nicolas Le Novere
orcid: 0000-0002-6309-7327
deprecated: true
description: The Mathematical Modelling Ontology (MAMO) is a classification of the
types of mathematical models used mostly in the life sciences, their variables,
relationships and other relevant features.
download_owl: http://purl.obolibrary.org/obo/mamo.owl
example: '0000026'
homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/
keywords:
- computational biology
- mathematics
- obo
- ontology
- systems biology
license: Artistic License 2.0
mappings:
aberowl: MAMO
biocontext: MAMO
bioportal: MAMO
fairsharing: FAIRsharing.kbz5jh
miriam: mamo
n2t: mamo
obofoundry: mamo
ols: mamo
ontobee: MAMO
name: Mathematical modeling ontology
pattern: ^\d{7}$
preferred_prefix: MAMO
rdf_uri_format: http://purl.obolibrary.org/obo/MAMO_$1
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'
mampol:
description: The Mammalia Polymorphism Database is a secondary database designed
to provide a collection of all the existing polymorphic sequences in the MammaliaOnline
query interfaces facilitate data interrogation by different polymorphism parameter
values and keyword queries (based on SQL searches).
example: MAMpol005339
homepage: http://mampol.uab.es
keywords:
- dna
mappings:
prefixcommons: mampol
name: Mammalia Polymorphism Database
preferred_prefix: mampol
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/mampol:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1
mao:
contact:
email: julie@igbmc.u-strasbg.fr
github: null
name: Julie Thompson
orcid: null
deprecated: true
description: An ontology for data retrieval and exchange in the fields of multiple
DNA/RNA alignment, protein sequence and protein structure alignment.
example: MAO:0000061
homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html
keywords:
- alignment
- obo
- ontology
- sequence
mappings:
biocontext: MAO
obofoundry: mao
prefixcommons: mao
name: Multiple alignment
preferred_prefix: MAO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/mao:$1
rdf_uri_format: http://purl.obolibrary.org/obo/MAO_$1
uri_format: http://purl.obolibrary.org/obo/MAO_$1
massbank:
contact:
email: tobias.schulze@ufz.de
github: tsufz
name: Tobias Schulze
orcid: 0000-0002-9744-8914
description: MassBank is a federated database of reference spectra from different
instruments, including high-resolution mass spectra of small metabolites (<3000
Da).
example: MSBNK-IPB_Halle-PB000166
homepage: http://www.massbank.jp
keywords:
- chemistry
- life science
- physics
mappings:
biocontext: MASSBANK
fairsharing: FAIRsharing.dk451a
miriam: massbank
n2t: massbank
wikidata: P6689
name: MassBank
pattern: ^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$
preferred_prefix: massbank
providers:
- code: massbankeu
description: MassBank in Europe
homepage: https://massbank.eu/
name: MassBank in Europe
uri_format: https://massbank.eu/MassBank/RecordDisplay?id=$1
publications:
- doi: 10.1002/jms.1777
pmc: null
pubmed: '20623627'
title: 'MassBank: a public repository for sharing mass spectral data for life
sciences.'
year: 2010
repository: https://github.com/MassBank
uri_format: https://massbank.jp/RecordDisplay?id=$1
massive:
contact:
email: miw023@ucsd.edu
github: null
name: Mingxun Wang
orcid: 0000-0001-7647-6097
description: MassIVE is a community resource developed by the NIH-funded Center
for Computational Mass Spectrometry to promote the global, free exchange of mass
spectrometry data.
example: MSV000082131
homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
keywords:
- functional genomics
- metabolomics
- metaproteomics
- omics
- phenomics
- proteomics
mappings:
biocontext: MASSIVE
fairsharing: FAIRsharing.LYsiMd
miriam: massive
n2t: massive
uniprot: DB-0241
name: MassIVE
pattern: ^MSV\d+$
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
publications:
- doi: 10.1038/s41592-020-0955-0
pmc: PMC7541731
pubmed: '32929271'
title: 'MassIVE.quant: a community resource of quantitative mass spectrometry-based
proteomics datasets.'
year: 2020
- doi: 10.1093/nar/gkz984
pmc: PMC7145525
pubmed: '31686107'
title: 'The ProteomeXchange consortium in 2020: enabling ''big data'' approaches
in proteomics.'
year: 2020
- doi: 10.1016/j.cels.2018.08.004
pmc: PMC6279426
pubmed: '30172843'
title: Assembling the Community-Scale Discoverable Human Proteome.
year: 2018
- doi: 10.1093/nar/gkw936
pmc: PMC5210636
pubmed: '27924013'
title: 'The ProteomeXchange consortium in 2017: supporting the cultural change
in proteomics public data deposition.'
year: 2016
- doi: 10.1038/nbt.3597
pmc: PMC5321674
pubmed: '27504778'
title: Sharing and community curation of mass spectrometry data with Global Natural
Products Social Molecular Networking.
year: 2016
repository: https://ccms-ucsd.github.io/MassIVEDocumentation
uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1
mat:
contact:
email: j.bard@ed.ac.uk
github: null
name: Jonathan Bard
orcid: null
deprecated: true
description: Minimal set of terms for anatomy
download_obo: http://aber-owl.net/media/ontologies/MAT/3/mat.obo
example: '0000000'
keywords:
- obo
- ontology
mappings:
aberowl: MAT
biocontext: MAT
bioportal: MAT
obofoundry: mat
name: Minimal Anatomical Terminology
pattern: ^\d{7}$
preferred_prefix: MAT
rdf_uri_format: http://purl.obolibrary.org/obo/MAT_$1
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/
keywords:
- biology
- interaction
- protein
- small molecule
mappings:
fairsharing: FAIRsharing.91yrz6
prefixcommons: matrixdb
re3data: r3d100010672
name: MatrixDB
preferred_prefix: matrixdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/matrixdb:$1
publications:
- doi: 10.1093/nar/gky1035
pmc: PMC6324007
pubmed: '30371822'
title: 'MatrixDB: integration of new data with a focus on glycosaminoglycan interactions.'
year: 2019
- doi: 10.1093/nar/gku1091
pmc: PMC4383919
pubmed: '25378329'
title: 'MatrixDB, the extracellular matrix interaction database: updated content,
a new navigator and expanded functionalities.'
year: 2014
- doi: 10.1093/nar/gkq830
pmc: PMC3013758
pubmed: '20852260'
title: MatrixDB, the extracellular matrix interaction database.
year: 2010
- doi: 10.1093/bioinformatics/btp025
pmc: PMC2647840
pubmed: '19147664'
title: MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate
interactions.
year: 2009
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=$1&class=Association
maxo:
appears_in:
- ecto
contact:
email: Leigh.Carmody@jax.org
github: LCCarmody
name: Leigh Carmody
orcid: 0000-0001-7941-2961
depends_on:
- chebi
- foodon
- go
- hp
- iao
- nbo
- obi
- ro
- uberon
description: An ontology to represent medically relevant actions, procedures, therapies,
interventions, and recommendations.
download_json: http://purl.obolibrary.org/obo/maxo.json
download_obo: http://purl.obolibrary.org/obo/maxo.obo
download_owl: http://purl.obolibrary.org/obo/maxo.owl
example: 0000008
homepage: https://github.com/monarch-initiative/MAxO
keywords:
- obo
- ontology
license: CC-BY-4.0
logo: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png
mappings:
aberowl: MAXO
biolink: MAXO
bioportal: MAXO
obofoundry: maxo
ols: maxo
ontobee: MAXO
name: Medical Action Ontology
pattern: ^\d{7}$
preferred_prefix: MAXO
rdf_uri_format: http://purl.obolibrary.org/obo/MAXO_$1
repository: https://github.com/monarch-initiative/MAxO
twitter: MonarchInit
uri_format: http://purl.obolibrary.org/obo/MAXO_$1
version: '2023-04-18'
mba:
contact:
email: chinhda@alleninstitute.org
github: null
name: Allen Institute for Brain Science
orcid: null
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: A controlled vocabulary to support the study of transcription in the
mouse brain
download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo
example: '688'
homepage: https://mouse.brain-map.org
keywords:
- ontology
mappings:
bioportal: ABA-AMB
name: Mouse Brain Atlas
pattern: ^\d+$
preferred_prefix: MBA
uri_format: https://biopragmatics.github.io/providers/mba/$1
mcc:
contact:
email: usha@molecularconnections.com
github: null
name: Usha Mahadevan
orcid: null
deprecated: true
description: Ontologies provide a common platform of controlled vocabulary for researchers
who need to share information across a particular domain, inclusive of machine-interpretable
definitions of basic concepts in the domain and relations among them. The need
for ontologies that provide a systematic arrangement of available data and allow
cross talk across various related domains is gaining momentum. In this backdrop,
we have developed a comprehensive ontology on primary and established cell lines-both
normal and pathologic. It covers around 400 cell lines. This ontology has been
built to include the major domains in the field of biology like anatomy, bio-molecules,
chemicals and drugs, pathological conditions and genetic variations around the
cell lines. An extensive network of relations has been built across these concepts
to enable different combinations of queries. The ontology covers all cell lines
from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.
example: ThoracicArtery
homepage: http://www.molecularconnections.com
keywords:
- ontology
mappings:
bioportal: MCCL
name: Cell Line Ontology [derivative]
preferred_prefix: mcc
uri_format: http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1
mco:
contact:
email: citlalli.mejiaalmonte@gmail.com
github: citmejia
name: Citlalli Mejía-Almonte
orcid: 0000-0002-0142-5591
depends_on:
- bfo
- chebi
- cl
- clo
- micro
- ncbitaxon
- ncit
- obi
- omit
- omp
- pato
- peco
- uberon
- zeco
description: Microbial Conditions Ontology is an ontology...
download_obo: http://purl.obolibrary.org/obo/mco.obo
download_owl: http://purl.obolibrary.org/obo/mco.owl
example: 0000858
homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
keywords:
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: MCO
bioportal: MCO
obofoundry: mco
ols: mco
ontobee: MCO
name: Microbial Conditions Ontology
pattern: ^\d+$
preferred_prefix: MCO
rdf_uri_format: http://purl.obolibrary.org/obo/MCO_$1
repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology
uri_format: http://purl.obolibrary.org/obo/MCO_$1
version: '2019-05-15'
mdm:
contact:
email: bernd.mueller@zbmed.de
github: null
name: Bernd Müller
orcid: 0000-0003-3062-8192
description: The MDM (Medical Data Models) Portal is a meta-data registry for creating,
analysing, sharing and reusing medical forms. Electronic forms are central in
numerous processes involving data, including the collection of data through electronic
health records (EHRs), Electronic Data Capture (EDC), and as case report forms
(CRFs) for clinical trials. The MDM Portal provides medical forms in numerous
export formats, facilitating the sharing and reuse of medical data models and
exchange between information systems.
download_owl: http://aber-owl.net/media/ontologies/MDM/4/mdm.owl
example: '4776'
homepage: https://medical-data-models.org/
keywords:
- biomedical science
- medicine
- ontology
- translational medicine
mappings:
aberowl: MDM
biocontext: MDM
bioportal: MDM
fairsharing: FAIRsharing.wnk2eq
miriam: mdm
n2t: mdm
re3data: r3d100013816
name: Medical Data Models
pattern: ^\d+$
preferred_prefix: mdm
publications:
- doi: 10.1093/database/bav121
pmc: PMC4750548
pubmed: '26868052'
title: 'Portal of medical data models: information infrastructure for medical
research and healthcare.'
year: 2016
uri_format: https://medical-data-models.org/forms/$1
meddra:
contact:
email: mssohelp@meddra.org
github: null
name: MedDRA MSSO
orcid: null
description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed
by the International Council for Harmonisation of Technical Requirements for Registration
of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology
to facilitate sharing of regulatory information internationally for medical products
used by humans. It is used within regulatory processes, safety monitoring, as
well as for marketing activities. Products covered by the scope of MedDRA include
pharmaceuticals, biologics, vaccines and drug-device combination products. The
MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level
Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into
Lowest Level Terms (LLT).
example: '10015919'
homepage: http://bioportal.bioontology.org/ontologies/MEDDRA
keywords:
- biomedical science
- medicine
- ontology
- preclinical studies
mappings:
aberowl: MEDDRA
bartoc: '1237'
biocontext: MEDDRA
bioportal: MEDDRA
fairsharing: FAIRsharing.ad3137
hl7: 2.16.840.1.113883.6.163
miriam: meddra
n2t: meddra
wikidata: P3201
name: Medical Dictionary for Regulatory Activities Terminology
pattern: ^\d+$
preferred_prefix: meddra
publications:
- doi: 10.1016/s1386-5056(00)00062-9
pmc: null
pubmed: '10961570'
title: The use of a medical dictionary for regulatory activities terminology (MedDRA)
in prescription-event monitoring in Japan (J-PEM).
year: 2000
- doi: 10.2165/00002018-199920020-00002
pmc: null
pubmed: '10082069'
title: The medical dictionary for regulatory activities (MedDRA).
year: 1999
rdf_uri_format: http://purl.bioontology.org/ontology/MDRFRE/$1
synonyms:
- MEDRA
- MeDRA
- MedDRA
- Medical Dictionary for Regulatory Activities
uri_format: http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1
medgen:
description: MedGen is a portal for information about conditions and phenotypes
related to Medical Genetics. Terms from multiple sources are aggregated into concepts,
each of which is assigned a unique identifier and a preferred name and symbol.
The core content of the record may include names, identifiers used by other databases,
mode of inheritance, clinical features, and map location of the loci affecting
the disorder.
example: '760050'
homepage: https://www.ncbi.nlm.nih.gov/medgen/
mappings:
biocontext: MedGen
biolink: medgen
miriam: medgen
n2t: medgen
ncbi: MedGen
name: Human Medical Genetics
pattern: ^[CN]*\d{4,7}$
preferred_prefix: medgen
uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1
medlineplus:
contact:
email: custserv@nlm.nih.gov
github: null
name: NLM Customer Service
orcid: null
description: MedlinePlus is the National Institutes of Health's Web site for patients
and their families and friends. Produced by the National Library of Medicine,
it provides information about diseases, conditions, and wellness issues using
non-technical terms and language.
example: 002804
homepage: http://www.nlm.nih.gov/medlineplus/
keywords:
- biomedical science
- health science
- medicine
- ontology
mappings:
aberowl: MEDLINEPLUS
biocontext: MEDLINEPLUS
bioportal: MEDLINEPLUS
fairsharing: FAIRsharing.bf8dsb
hl7: 2.16.840.1.113883.6.173
miriam: medlineplus
n2t: medlineplus
name: MedlinePlus Health Topics
pattern: ^\d+$
preferred_prefix: medlineplus
providers:
- code: medlineplus.fp
description: First-party version of medline plus.
homepage: https://medlineplus.gov
name: MedLine Plus home page
uri_format: https://medlineplus.gov/ency/article/$1.htm
uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm
merops.clan:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: The MEROPS database is an information resource for peptidases (also
termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
them.
example: IA
homepage: https://www.ebi.ac.uk/merops
name: MEROPS Clan
part_of: merops
preferred_prefix: merops.clan
publications:
- doi: 10.1093/nar/gkx1134
pmc: PMC5753285
pubmed: '29145643'
title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors
in 2017 and a comparison with peptidases in the PANTHER database.
year: 2018
references:
- https://github.com/biopragmatics/bioregistry/issues/439
uri_format: https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1
merops.entry:
description: The MEROPS database is an information resource for peptidases (also
termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
them. This collections references inhibitors.
example: I31.952
example_extras:
- S01.001
homepage: http://merops.sanger.ac.uk/index.htm
keywords:
- biomedical science
- enzyme
- life science
- protein
- structure
mappings:
biocontext: MEROPS.INHIBITOR
edam: '2629'
fairsharing: FAIRsharing.2s4n8r
go: MEROPS
miriam: merops.inhibitor
n2t: merops.inhibitor
prefixcommons: merops
name: MEROPS Entry
pattern: ^[SCTAGMNUI]\d{2}\.([AB]\d{2}|\d{3})$
preferred_prefix: merops.entry
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/merops:$1
publications:
- doi: 10.1093/nar/27.1.325
pmc: PMC148173
pubmed: '9847218'
title: 'MEROPS: the peptidase database.'
year: 1999
- doi: 10.1042/bj2900205
pmc: PMC1132403
pubmed: '8439290'
title: Evolutionary families of peptidases.
year: 1993
- doi: 10.1093/nar/gkx1134
pmc: PMC5753285
pubmed: '29145643'
title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors
in 2017 and a comparison with peptidases in the PANTHER database.
year: 2018
- doi: 10.1093/nar/gkv1118
pmc: PMC4702814
pubmed: '26527717'
title: Twenty years of the MEROPS database of proteolytic enzymes, their substrates
and inhibitors.
year: 2015
- doi: 10.1016/j.biochi.2015.10.003
pmc: PMC4756867
pubmed: '26455268'
title: Peptidase specificity from the substrate cleavage collection in the MEROPS
database and a tool to measure cleavage site conservation.
year: 2015
- doi: 10.1093/nar/gkr987
pmc: PMC3245014
pubmed: '22086950'
title: 'MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.'
year: 2011
- doi: 10.1093/nar/gkm954
pmc: PMC2238837
pubmed: '17991683'
title: 'MEROPS: the peptidase database.'
year: 2007
references:
- https://github.com/biopragmatics/bioregistry/issues/439
synonyms:
- merops.inhibitor
uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1
merops.family:
description: The MEROPS database is an information resource for peptidases (also
termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit
them. These are hierarchically classified and assigned to a Family on the basis
of statistically significant similarities in amino acid sequence. Families thought
to be homologous are grouped together in a Clan. This collection references peptidase
families.
example: S1
homepage: http://merops.sanger.ac.uk/index.htm
mappings:
biocontext: MEROPS.FAMILY
miriam: merops.family
n2t: merops.family
name: MEROPS Family
part_of: merops
pattern: ^[SCTAGMNU]\d+$
preferred_prefix: merops.family
publications:
- doi: 10.1093/nar/gkx1134
pmc: PMC5753285
pubmed: '29145643'
title: The MEROPS database of proteolytic enzymes, their substrates and inhibitors
in 2017 and a comparison with peptidases in the PANTHER database.
year: 2018
references:
- https://github.com/biopragmatics/bioregistry/issues/439
uri_format: https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1
mesh:
contact:
email: custserv@nlm.nih.gov
github: null
name: NLM Customer Service
orcid: null
description: MeSH (Medical Subject Headings) is the National Library of Medicine's
controlled vocabulary thesaurus. It consists of sets of terms naming descriptors
in a hierarchical structure that permits searching at various levels of specificity.
This thesaurus is used by NLM for indexing articles from biomedical journals,
cataloguing of books, documents, etc.
example: C063233
example_extras:
- D000001
homepage: http://id.nlm.nih.gov/mesh/
keywords:
- bioinformatics
- biomedical science
- classification
- life science
- metascience
- ontology
- topics
license: CC0-1.0
mappings:
aberowl: MESH
bartoc: '391'
biocontext: MESH
biolink: MESH
bioportal: MESH
cellosaurus: MeSH
edam: '1177'
fairsharing: FAIRsharing.qnkw45
go: MeSH
hl7: 2.16.840.1.113883.6.177
miriam: mesh
n2t: mesh
prefixcommons: mesh
wikidata: P486
name: Medical Subject Headings
pattern: ^(C|D)\d{6,9}$
preferred_prefix: mesh
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/mesh:$1
publications:
- doi: null
pmc: PMC197951
pubmed: '13982385'
title: Medical subject headings.
year: 1963
rdf_uri_format: http://id.nlm.nih.gov/mesh/$1
synonyms:
- MESH
- MESHA
- MESHC
- MESHCS
- MESHD
- MESHPP
- MESH_DESCRIPTOR_UI
- MESH_SUPPLEMENTAL_RECORD_UI
- MSH
- MSH2010_2010_02_22
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
provides: mesh
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
provides: mesh
uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded
mesh.vocab:
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
description: Medical Subject Headings vocabulary is the set of predicates used in
the MeSH RDF dump
example: term
homepage: https://hhs.github.io/meshrdf/
name: Medical Subject Headings Vocabulary
part_of: mesh
preferred_prefix: mesh.vocab
references:
- https://id.nlm.nih.gov/mesh/query
repository: https://github.com/HHS/meshrdf
uri_format: http://id.nlm.nih.gov/mesh/vocab#$1
metabolights:
description: MetaboLights is a database for Metabolomics experiments and derived
information. The database is cross-species, cross-technique and covers metabolite
structures and their reference spectra as well as their biological roles, locations
and concentrations, and experimental data from metabolic experiments. This collection
references individual metabolomics studies.
example: MTBLS1
homepage: https://www.ebi.ac.uk/metabolights/
mappings:
biocontext: METABOLIGHTS
cellosaurus: MetaboLights
miriam: metabolights
n2t: metabolights
re3data: r3d100011556
wikidata: P3890
name: MetaboLights Compound
pattern: ^MTBLS\d+$
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/$1
metacyc.compound:
description: MetaCyc is a curated database of experimentally elucidated metabolic
pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different
organisms. MetaCyc contains pathways involved in both primary and secondary metabolism,
as well as associated metabolites, reactions, enzymes, and genes. The goal of
MetaCyc is to catalog the universe of metabolism by storing a representative sample
of each experimentally elucidated pathway.
example: CPD-10330
homepage: https://metacyc.org
keywords:
- life science
- metabolomics
- systems biology
mappings:
biocontext: METACYC.COMPOUND
biolink: MetaCyc
fairsharing: FAIRsharing.yytevr
go: MetaCyc
miriam: metacyc.compound
n2t: metacyc.compound
re3data: r3d100011294
name: Metabolic Encyclopedia of metabolic and other pathways
pattern: ^[A-Za-z0-9+_.%-:]+$
preferred_prefix: metacyc.compound
publications:
- doi: 10.1093/nar/gkv1164
pmc: PMC4702838
pubmed: '26527732'
title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection
of pathway/genome databases.
year: 2015
- doi: 10.1093/nar/gkt1103
pmc: PMC3964957
pubmed: '24225315'
title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection
of Pathway/Genome Databases.
year: 2013
- doi: 10.1093/nar/gkr1014
pmc: PMC3245006
pubmed: '22102576'
title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection
of pathway/genome databases.
year: 2011
synonyms:
- MetaCyc
twitter: BioCyc
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/$1
metatlas:
contact:
email: mihail.anton@chalmers.se
github: mihai-sysbio
name: Mihail Anton
orcid: 0000-0002-7753-9042
contributor:
email: mihail.anton@chalmers.se
github: mihai-sysbio
name: Mihail Anton
orcid: 0000-0002-7753-9042
description: A resource for exploring metabolism, starting with a set of of community-curated
genome-scale metabolic models of human and model organisms, enriched with pathway
maps and other tools for easy browsing and analysis.
example: MAM01234c
example_decoys:
- MAR11851c
example_extras:
- MAR11851
github_request_issue: 495
homepage: https://metabolicatlas.org
keywords:
- chemistry
- metabolites
- reactions
mappings:
miriam: metatlas
name: Metabolic Atlas
pattern: ^(MAM\d{5}\w)|(MAR\d{5})$
preferred_prefix: metatlas
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
metatlas.metabolite:
contact:
email: mihail.anton@chalmers.se
github: mihai-sysbio
name: Mihail Anton
orcid: 0000-0002-7753-9042
contributor:
email: mihail.anton@chalmers.se
github: mihai-sysbio
name: Mihail Anton
orcid: 0000-0002-7753-9042
description: A subspace of Metabolic Atlas for compartment-specific records for
metabolites.
example: MAM01234c
github_request_issue: 495
homepage: https://metabolicatlas.org
keywords:
- chemistry
- metabolites
name: Metabolic Atlas Metabolite
part_of: metatlas
pattern: ^MAM\d{5}\w$
preferred_prefix: metatlas.metabolite
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
metatlas.reaction:
contact:
email: mihail.anton@chalmers.se
github: mihai-sysbio
name: Mihail Anton
orcid: 0000-0002-7753-9042
contributor:
email: mihail.anton@chalmers.se
github: mihai-sysbio
name: Mihail Anton
orcid: 0000-0002-7753-9042
description: A subspace of Metabolic Atlas for reactions.
example: MAR11851
github_request_issue: 495
homepage: https://metabolicatlas.org
keywords:
- chemistry
- reactions
name: Metabolic Atlas Reaction
part_of: metatlas
pattern: ^MAR\d{5}$
preferred_prefix: metatlas.reaction
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: https://metabolicatlas.org/identifier/MetabolicAtlas/$1
metlin:
description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a
repository of metabolite information as well as tandem mass spectrometry data,
providing public access to its comprehensive MS and MS/MS metabolite data. An
annotated list of known metabolites and their mass, chemical formula, and structure
are available, with each metabolite linked to external resources for further reference
and inquiry.
example: '1455'
homepage: http://masspec.scripps.edu/
mappings:
biocontext: METLIN
miriam: metlin
n2t: metlin
re3data: r3d100012311
name: Metabolite and Tandem Mass Spectrometry Database
pattern: ^\d{4}$
preferred_prefix: metlin
uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1
metnetdb:
description: The MetNet database (MetNetDB) contains information on networks of
metabolic and regulatory and interactions in Arabidopsis. Types of interactions
in MetNetDB include transcription, translation, protein modification, assembly,
allosteric regulation, translocation from one subcellular compartment to another.
example: '377369'
homepage: http://www.metnetdb.org/MetNet_db.htm
keywords:
- dna
- interaction
- pathway
- protein
- regulation
- rna
- small molecule
mappings:
prefixcommons: metnetdb
name: Metabolic Network Exchange Database
preferred_prefix: metnetdb
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/metnetdb:$1
reviewer:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
uri_format: http://metnetonline.org/browse_pathway2.php?pthID=$1
mex:
description: A public place to process, interpret and share GC/MS metabolomics datasets.
example: '36'
homepage: https://www.metabolome-express.org/
mappings:
biocontext: MEX
miriam: mex
n2t: mex
name: Metabolome Express
pattern: ^\d+$
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=$1
mf:
contact:
email: janna.hastings@gmail.com
github: jannahastings
name: Janna Hastings
orcid: 0000-0002-3469-4923
description: The Mental Functioning Ontology is an overarching ontology for all
aspects of mental functioning.
download_owl: http://purl.obolibrary.org/obo/mf.owl
example: 0000091
homepage: https://github.com/jannahastings/mental-functioning-ontology
keywords:
- biomedical science
- cognitive neuroscience
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: MF
biocontext: MF
bioportal: MF
fairsharing: FAIRsharing.4gm9gt
obofoundry: mf
ols: mf
ontobee: MF
name: Mental Functioning Ontology
pattern: ^\d{7}$
preferred_prefix: MF
rdf_uri_format: http://purl.obolibrary.org/obo/MF_$1
repository: https://github.com/jannahastings/mental-functioning-ontology
uri_format: http://purl.obolibrary.org/obo/MF_$1
version: '2022-07-19'
mfmo:
contact:
email: druzinsk@uic.edu
github: RDruzinsky
name: Robert Druzinsky
orcid: 0000-0002-1572-1316
depends_on:
- uberon
description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the
muscles of the head and neck that participate in feeding, swallowing, and other
oral-pharyngeal behaviors.
download_owl: http://purl.obolibrary.org/obo/mfmo.owl
example: 0000208
homepage: https://github.com/rdruzinsky/feedontology
keywords:
- anatomy
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: MFMO
biocontext: MFMO
bioportal: MFMO
fairsharing: FAIRsharing.669cnk
obofoundry: mfmo
ols: mfmo
ontobee: MFMO
name: Mammalian Feeding Muscle Ontology
pattern: ^\d{7}$
preferred_prefix: MFMO
providers:
- code: conflated
description: A conflated URL with parts.
homepage: http://purl.obolibrary.org
name: OBO PURL Parts
uri_format: http://purl.obolibrary.org/obo/mfmo.owl#MFMO_$1
rdf_uri_format: http://purl.obolibrary.org/obo/MFMO_$1
repository: https://github.com/RDruzinsky/feedontology
uri_format: http://purl.obolibrary.org/obo/MFMO_$1
version: '2013-11-16'
mfo:
contact:
email: henrich@embl.de
github: ThorstenHen
name: Thorsten Henrich
orcid: 0000-0002-1548-3290
deprecated: true
description: A structured controlled vocabulary of the anatomy and development of
the Japanese medaka fish, Oryzias latipes.
download_obo: http://aber-owl.net/media/ontologies/MFO/14/mfo.obo
download_owl: http://purl.obolibrary.org/obo/mfo.owl
example: MFO_0000001
homepage: http://ani.embl.de:8080/mepd/
keywords:
- anatomy
- development
- fish
- obo
- ontology
mappings:
aberowl: MFO
biocontext: MFO
bioportal: MFO
obofoundry: mfo
prefixcommons: mfo
name: Medaka fish anatomy and development
preferred_prefix: MFO
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/mfo:$1
rdf_uri_format: http://purl.obolibrary.org/obo/MFO_$1
uri_format: http://purl.obolibrary.org/obo/MFO_$1
mfoem:
contact:
email: janna.hastings@gmail.com
github: jannahastings
name: Janna Hastings
orcid: 0000-0002-3469-4923
description: An ontology of affective phenomena such as emotions, moods, appraisals
and subjective feelings.
download_owl: http://purl.obolibrary.org/obo/mfoem.owl
example: '000204'
homepage: https://github.com/jannahastings/emotion-ontology
keywords:
- biomedical science
- obo
- ontology
license: CC-BY-3.0
mappings:
aberowl: MFOEM
biocontext: MFOEM
bioportal: MFOEM
fairsharing: FAIRsharing.dx30m8
obofoundry: mfoem
ols: mfoem
ontobee: MFOEM
name: Emotion Ontology
pattern: ^\d{6}$
preferred_prefix: MFOEM
publications:
- doi: 10.1186/2041-1480-5-38
pmc: PMC4417517
pubmed: '25937879'
title: Evaluating the Emotion Ontology through use in the self-reporting of emotional
responses at an academic conference.
year: 2014
rdf_uri_format: http://purl.obolibrary.org/obo/MFOEM_$1
repository: https://github.com/jannahastings/emotion-ontology
uri_format: http://purl.obolibrary.org/obo/MFOEM_$1
version: '2022-07-19'
mfomd:
contact:
email: janna.hastings@gmail.com
github: jannahastings
name: Janna Hastings
orcid: 0000-0002-3469-4923
description: The Mental Disease Ontology is developed to facilitate representation
for all aspects of mental disease. It is an extension of the Ontology for General
Medical Science (OGMS) and Mental Functioning Ontology (MF).
download_owl: http://purl.obolibrary.org/obo/mfomd.owl
example: '0000046'
homepage: https://github.com/jannahastings/mental-functioning-ontology
keywords:
- obo
- ontology
- psychiatry
license: CC-BY-3.0
mappings:
aberowl: MFOMD
biocontext: MFOMD
bioportal: MFOMD
fairsharing: FAIRsharing.q053vb
obofoundry: mfomd
ols: mfomd
ontobee: MFOMD
name: Mental Disease Ontology
pattern: ^\d{7}$
preferred_prefix: MFOMD
rdf_uri_format: http://purl.obolibrary.org/obo/MFOMD_$1
repository: https://github.com/jannahastings/mental-functioning-ontology
uri_format: http://purl.obolibrary.org/obo/MFOMD_$1
version: '2020-04-26'
mge:
banana: mge
deprecated: true
description: ACLAME is a database dedicated to the collection and classification
of mobile genetic elements (MGEs) from various sources, comprising all known phage
genomes, plasmids and transposons.
example: '2'
homepage: http://aclame.ulb.ac.be/
keywords:
- gene
- genome
- life science
mappings:
biocontext: ACLAME
edam: '2631'
fairsharing: FAIRsharing.5tfcy8
miriam: mge
n2t: mge
prefixcommons: aclame
name: Aclame
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: mge
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/aclame:$1
publications:
- doi: 10.1093/nar/gkp938
pmc: PMC2808911
pubmed: '19933762'
title: 'ACLAME: a CLAssification of Mobile genetic Elements, update 2010.'
year: 2009
- doi: 10.1093/nar/gkh084
pmc: PMC308818
pubmed: '14681355'
title: 'ACLAME: a CLAssification of Mobile genetic Elements.'
year: 2004
synonyms:
- aclame
uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1
mgi:
banana: MGI
description: The Mouse Genome Database (MGD) project includes data on gene characterization,
nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes,
allelic variants and mutants, and strain data.
example: '6017782'
homepage: http://www.informatics.jax.org/
keywords:
- expression
- life science
- ontology and terminology
- phenotype
- sequence
mappings:
biocontext: MGI
cellosaurus: MGI
edam: '3274'
fairsharing: FAIRsharing.fcwyhz
go: MGI
miriam: mgi
n2t: mgi
ncbi: MGI
prefixcommons: mgi
re3data: r3d100010266
uniprot: DB-0060
wikidata: P671
name: Mouse Genome Informatics
namespace_in_lui: true
pattern: ^\d+$
preferred_prefix: MGI
providers:
- 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
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/mgi:$1
- code: mgi.marker
description: MGI Marker
homepage: http://www.informatics.jax.org/marker
name: MGI Marker
uri_format: http://www.informatics.jax.org/marker/MGI:$1
publications:
- doi: 10.1126/science.8091224
pmc: null
pubmed: '8091224'
title: A database for mouse development.
year: 1994
- doi: 10.1093/nar/gky1056
pmc: PMC6323923
pubmed: '30407599'
title: Mouse Genome Database (MGD) 2019.
year: 2019
- doi: 10.1093/nar/gky922
pmc: PMC6324054
pubmed: '30335138'
title: 'The mouse Gene Expression Database (GXD): 2019 update.'
year: 2019
- doi: 10.1093/ilar/ilx013
pmc: PMC5886341
pubmed: '28838066'
title: 'Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological
Knowledgebase for the Laboratory Mouse.'
year: 2017
- doi: 10.1007/978-1-4939-6427-7_3
pmc: null
pubmed: '27933520'
title: 'Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic,
and Biological Data in Support of Primary and Translational Research.'
year: 2017
- doi: 10.1093/nar/gkw1040
pmc: PMC5210536
pubmed: '27899570'
title: 'Mouse Genome Database (MGD)-2017: community knowledge resource for the
laboratory mouse.'
year: 2016
- doi: 10.1093/nar/gkt1225
pmc: PMC3964950
pubmed: '24285300'
title: 'The Mouse Genome Database: integration of and access to knowledge about
the laboratory mouse.'
year: 2013
- doi: 10.1093/nar/gks1115
pmc: PMC3531104
pubmed: '23175610'
title: 'The mouse genome database: genotypes, phenotypes, and models of human
disease.'
year: 2012
- doi: 10.1093/nar/gkr974
pmc: PMC3245042
pubmed: '22075990'
title: 'The Mouse Genome Database (MGD): comprehensive resource for genetics and
genomics of the laboratory mouse.'
year: 2011
- doi: 10.1093/nar/gki113
pmc: PMC540067
pubmed: '15608240'
title: 'The Mouse Genome Database (MGD): from genes to mice--a community resource
for mouse biology.'
year: 2005
synonyms:
- MGD
- MGI
twitter: mgi_mouse
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/$1
mi:
banana: MI
contact:
email: luana.licata@gmail.com
github: luanalicata
name: Luana Licata
orcid: 0000-0001-5084-9000
description: The Molecular Interactions (MI) ontology forms a structured controlled
vocabulary for the annotation of experiments concerned with protein-protein interactions.
MI is developed by the HUPO Proteomics Standards Initiative.
download_obo: http://purl.obolibrary.org/obo/mi.obo
download_owl: http://purl.obolibrary.org/obo/mi.owl
example: 0058
homepage: https://github.com/HUPO-PSI/psi-mi-CV
keywords:
- interaction
- life science
- molecule
- obo
- ontology
license: CC-BY-4.0
mappings:
aberowl: MI
biocontext: PSIMI
biolink: MI
bioportal: MI
fairsharing: FAIRsharing.8qzmtr
go: PSI-MI
miriam: mi
n2t: psimi
obofoundry: mi
ols: mi
ontobee: MI
prefixcommons: psi.mi
name: Molecular Interactions Controlled Vocabulary
namespace_in_lui: true
pattern: ^\d{4}$
preferred_prefix: MI
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/psi.mi:$1
publications:
- doi: 10.1038/nbt926
pmc: null
pubmed: '14755292'
title: The HUPO PSI's molecular interaction format--a community standard for the
representation of protein interaction data.
year: 2004
rdf_uri_format: http://purl.obolibrary.org/obo/MI_$1
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:$1
miaa:
comment: same as MAT
contributor:
email: cthoyt@gmail.com
github: cthoyt
name: Charles Tapley Hoyt
orcid: 0000-0003-4423-4370
deprecated: true
name: Minimal Information About Anatomy ontology
preferred_prefix: miaa
references:
- https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf
miapa:
contact:
email: hilmar.lapp@duke.edu
github: hlapp
name: Hilmar Lapp
orcid: 0000-0001-9107-0714
description: 'The MIAPA ontology is intended to be an application ontology for the
purpose of semantic annotation of phylogenetic data according to the requirements
and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA)
metadata reporting standard. The ontology leverages (imports) primarily from the
CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and
SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds
some assertions of its own, as well as some classes and individuals that may eventually
get pushed down into one of the respective source ontologies.
This ontology is maintained at http://github.com/miapa/miapa, and requests for
changes or additions should be filed at the issue tracker there. The discussion
list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be
found at the project''s main page at http://evoio.org/wiki/MIAPA.'
download_owl: http://purl.obolibrary.org/obo/miapa.owl
example: '0000010'
homepage: http://www.evoio.org/wiki/MIAPA
keywords:
- life science
- obo
- ontology
- phylogenetics
- phylogeny
license: CC0-1.0
mappings:
aberowl: MIAPA
biocontext: MIAPA
bioportal: MIAPA
fairsharing: FAIRsharing.ca48xs
obofoundry: miapa
ols: miapa
ontobee: MIAPA
name: Minimum Anformation About a Phylogenetic Analysis Ontology
pattern: ^\d{7}$
preferred_prefix: MIAPA
publications:
- doi: 10.1089/omi.2006.10.231
pmc: PMC3167193
pubmed: '16901231'
title: 'Taking the first steps towards a standard for reporting on phylogenies:
Minimum Information About a Phylogenetic Analysis (MIAPA).'
year: 2006
rdf_uri_format: http://purl.obolibrary.org/obo/MIAPA_$1
repository: https://github.com/evoinfo/miapa
uri_format: http://purl.obolibrary.org/obo/MIAPA_$1
micro:
appears_in:
- mco
contact:
email: carrine.blank@umontana.edu
github: carrineblank
name: Carrine Blank
orcid: 0000-0002-2100-6351
description: An ontology of prokaryotic phenotypic and metabolic characters
download_owl: http://purl.obolibrary.org/obo/micro.owl
example: 0002999
homepage: https://github.com/carrineblank/MicrO
keywords:
- bioinformatics
- microbiology
- obo
- ontology
license: CC BY 2.0
mappings:
aberowl: MICRO
biocontext: MICRO
fairsharing: FAIRsharing.brhpb0
obofoundry: micro
ols: micro
ontobee: MICRO
name: Ontology of Prokaryotic Phenotypic and Metabolic Characters
pattern: ^\d{7}$
preferred_prefix: MICRO
publications:
- doi: 10.1186/s13326-016-0060-6
pmc: PMC4830071
pubmed: '27076900'
title: 'MicrO: an ontology of phenotypic and metabolic characters, assays, and
culture media found in prokaryotic taxonomic descriptions.'
year: 2016
rdf_uri_format: http://purl.obolibrary.org/obo/MICRO_$1
repository: https://github.com/carrineblank/MicrO
uri_format: http://purl.obolibrary.org/obo/MICRO_$1
version: 1.5.1
microscope:
description: MicroScope is an integrative resource that supports systematic and
efficient revision of microbial genome annotation, data management and comparative
analysis.
example: '5601141'
homepage: http://www.genoscope.cns.fr/agc/microscope
keywords:
- comparative genomics
- life science
mappings:
biocontext: MICROSCOPE
fairsharing: FAIRsharing.3t5qc3
miriam: microscope
n2t: microscope
re3data: r3d100012928
name: MicroScope
pattern: ^\d+$
preferred_prefix: microscope
publications:
- doi: 10.1093/nar/gks1194
pmc: PMC3531135
pubmed: '23193269'
title: MicroScope--an integrated microbial resource for the curation and comparative
analysis of genomic and metabolic data.
year: 2012
uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1
microsporidia:
description: MicrosporidiaDB is one of the databases that can be accessed through
the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic
pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium,
Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported
by a taxon-specific database built upon the same infrastructure, the EuPathDB
portal offers an entry point to all these resources, and the opportunity to leverage
orthology for searches across genera.
example: ECU03_0820i
homepage: http://microsporidiadb.org/micro/
keywords:
- eukaryotic
- genome
mappings:
biocontext: MICROSPORIDIA
miriam: microsporidia
n2t: microsporidia
prefixcommons: microsporidia
name: MicrosporidiaDB
pattern: ^\w+$
preferred_prefix: microsporidia
providers:
- code: bio2rdf
description: Bio2RDF is an open-source project that uses Semantic Web technologies
to build and provide the largest network of Linked Data for the Life Sciences.
Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
Data from a diverse set of heterogeneously formatted sources obtained from multiple
data providers.
homepage: https://bio2rdf.org
name: Bio2RDF
uri_format: http://bio2rdf.org/microsporidia:$1
publications:
- doi: 10.1093/nar/gkp941
pmc: PMC2808945
pubmed: '19914931'
title: 'EuPathDB: a portal to eukaryotic pathogen databases.'
year: 2009
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/$1
mimodb:
description: MimoDB is a database collecting peptides that have been selected from
random peptide libraries based on their ability to bind small compounds, nucleic
acids, proteins, cells, tissues and organs. It also stores other information such
as the corresponding target, template, library, and structures. As of March 2016,
this database was renamed Biopanning Data Bank.
example: '1'
homepage: http://immunet.cn/bdb/
keywords:
- interaction
- life science
- protein
mappings:
biocontext: MIMODB
fairsharing: FAIRsharing.bv0zjz
miriam: mimodb
n2t: mimodb
prefixcommons: mimodb
name: MimoDB
pattern: ^\d+$
preferred_prefix: mimodb
providers:
- code: bi