Skip to content

Latest commit

 

History

History
173 lines (172 loc) · 7.13 KB

uberon.md

File metadata and controls

173 lines (172 loc) · 7.13 KB
layout id title browsers build canonical contact dependencies depicted_by description domain funded_by homepage label license mailing_list page preferredPrefix products publications releases repository slack taxon tracker twitter usages wikidata_template activity_status
ontology_detail
uberon
Uberon multi-species anatomy ontology
title label url
Gene Ontology AmiGO 2 Browser
RGD
title label url
Gene Ontology AmiGO 2 Browser
AmiGO (SUBSET)
title label url
Bgee gene expression queries
Bgee (gene expression)
title label url
FANTOM5 Data Portal
FANTOM5
title label url
INCF KnowledgeSpace Portal
KnowledgeSpace
checkout email_cc infallible system
1
git
uberon.owl
email github label orcid
cmungall
Chris Mungall
0000-0002-6601-2165
id
bfo
id
bspo
id
chebi
id
cl
id
envo
id
go
id
nbo
id
ncbitaxon
id
omo
id
pato
id
pr
id
ro
An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies
anatomy and development
Uberon
UBERON
id title description is_canonical type
uberon.owl
Uberon
core ontology
true
owl:Ontology
id title description page
uberon/uberon-base.owl
Uberon base ontology
Axioms defined within Uberon and to be used in imports for other ontologies
id title description format type
uberon/uberon-basic.obo
Uberon basic
Uberon edition that excludes external ontologies and most relations
obo
obo-basic-ontology
id title description page taxon type
uberon/collected-metazoan.owl
Uberon collected metazoan ontology
Uberon plus all metazoan ontologies
Metazoa
MergedOntology
id title description page taxon type
uberon/composite-metazoan.owl
Uberon composite metazoan ontology
Uberon and all metazoan ontologies with redundant species-specific terms removed
Metazoa
MergedOntology
id title mireots_from page taxon type
uberon/composite-vertebrate.owl
Uberon composite vertebrate ontology
zfa
xao
fbbt
wbbt
ma
fma
emapa
ehdaa2
Vertebrata
MergedOntology
id title
Uberon, an integrative multi-species anatomy ontology
id title
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
id label
NCBITaxon:33208
Metazoa
uberanat
description examples seeAlso type user
Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee in using Uberon to annotate the site of expression, and Bgee curators one the major contributors to the ontology.
description url
Uberon terms used to annotate expression of human hemoglobin subunit beta
annotation
description publications seeAlso type user
The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The ENCODE DCC users Uberon to annotate samples
id title
Ontology application and use at the ENCODE DCC
annotation
description examples type user
FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity.
description url
FANTOM5 samples annotated to telencephalon or its parts
annotation
description type user
Querying expression and phenotype data
query
description examples type user
GO Database is used for querying for functional annotations relevant to a tissue
description url
GO annotations relevant to the uberon class for brain
query
description user
The Phenoscape project is both a major driver of and contributor to Uberon, contibuting thousands of terms. The teleost (bony fishes) component of Uberon was derived from the Teleost Anatomy Ontology, developed by the Phenoscape group. Most of the high level design of the skeletal system comes from the Vertebrate Skeletal Anatomy Ontology (VSAO), also created by the Phenoscape group. Phenoscape curators continue to extend the ontology, covering a wide variety of tetrapod structures, with an emphasis on the appendicular system.
description type user
Searchable collection of neuroscience data and ontology for neuroscience
Database
description type user
cooperative data platform to be used by diverse communities in making data more FAIR.
Database
description publications type user
SCPortalen
id title
SCPortalen: human and mouse single-cell centric database
Database
description publications type user
ChEMBL uses Uberon to describe organ/tissue information in assays
id title
ChEMBL: towards direct deposition of bioassay data
Database
active

Uberon is an integrated cross-species ontology covering anatomical structures in animals.