uberon.md

layout	ontology_detail
id	uberon
type	owl:Ontology
label	Uberon
title	Uberon multi-species anatomy ontology
build	checkout email_cc system method infallible svn --ignore-externals co http://svn.code.sf.net/p/obo/svn/uberon/trunk cjmungall@lbl.gov svn vcs 1
description	An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies
homepage	http://uberon.org
page	http://en.wikipedia.org/wiki/Uberon
twitter	uberanat
google_plus	+UberonOrg
wikidata_template	https://en.wikipedia.org/wiki/Template:Uberon
mailing_list	https://lists.sourceforge.net/lists/listinfo/obo-anatomy
biosharing	https://www.biosharing.org/bsg-000016
usages	user seeAlso type description examples http://bgee.org/ https://www.biosharing.org/biodbcore-000228 annotation 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. url description http://bgee.org/?page=gene&gene_id=ENSG00000244734 Uberon terms used to annotate expression of human hemoglobin subunit beta user seeAlso type description reference https://www.encodeproject.org/ https://www.biosharing.org/biodbcore-000034 annotation 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 https://doi.org/10.1093/database/bav010 user type description examples http://fantom5-collaboration.gsc.riken.jp/ annotation FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity. url description http://fantom.gsc.riken.jp/5/sstar/UBERON:0001893 FANTOM5 samples annotated to telencephalon or its parts user type description https://monarchinitiative.org/ query Querying expression and phenotype data user label type description examples https://geneontology.org/ GO Database query Querying for functional annotations relevant to a tissue url description http://amigo.geneontology.org/amigo/term/UBERON:0000955 GO annotations relevant to the uberon class for brain user label description http://phenoscape.org Phenoscape 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. url label type https://neuinfo.org/ Neuroscience Information Framework Database url label type https://scicrunch.org/ SciCrunch Database url label reference type http://single-cell.clst.riken.jp/ SCPortalen https://doi.org/10.1093/nar/gkx949 Database url label description reference type https://www.ebi.ac.uk/chembl/ ChEMBL ChEMBL uses Uberon to describe organ/tissue information in assays https://doi.org/10.1093/nar/gky1075 Database
funded_by	NIH R24OD011883 NIH R01HG004838 NIH P41HG002273 NSF DEB-0956049
canonical	uberon.owl
license	url label http://creativecommons.org/licenses/by/3.0/ CC-BY
taxon	id label NCBITaxon:33208 Metazoa
domain	anatomy
repository	https://github.com/obophenotype/uberon
tracker	https://github.com/obophenotype/uberon/issues
releases	http://purl.obolibrary.org/obo/uberon/releases/
contact	email label cjmungall@lbl.gov Chris Mungall
publications	id title http://www.ncbi.nlm.nih.gov/pubmed/22293552 Uberon, an integrative multi-species anatomy ontology id title http://www.ncbi.nlm.nih.gov/pubmed/25009735 Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
depicted_by	http://uberon.github.io/images/u-logo.jpg
exampleClass	UBERON_0002046
redirects	match url releases/ http://svn.code.sf.net/p/obo/svn/uberon/releases/ match url http://berkeleybop.org/ontologies/uberon/
dependencies	id subset go uberon/go_import.owl id subset cl uberon/cl_import.owl id subset chebi uberon/chebi_import.owl id subset pr uberon/pr_import.owl
browsers	label title url RGD Gene Ontology AmiGO 2 Browser http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=UBERON:0001062 label title url AmiGO (SUBSET) Gene Ontology AmiGO 2 Browser http://amigo.geneontology.org/amigo/term/UBERON:0001062#display-lineage-tab label title url Bgee (gene expression) Bgee gene expression queries http://bgee.org/?page=gene label title url FANTOM5 FANTOM5 Data Portal http://fantom.gsc.riken.jp/5/sstar/UBERON:0001890 label title url KnowledgeSpace INCF KnowledgeSpace Portal https://knowledge-space.org/index.php/pages/view/UBERON:0000061
products	id type title description is_canonical uberon.owl owl:Ontology Uberon core ontology true id title description page uberon/uberon-base.owl Uberon base ontology Axioms defined within Uberon and to be used in imports for other ontologies INCATools/ontology-development-kit#50 id type description title mireots_from uberon/ext.owl owl:Ontology Uberon extended Uberon edition that includes subsets of other ontologies and axioms connecting to them ncbitaxon id title description format type uberon/basic.obo Uberon basic Uberon edition that excludes external ontologies and most relations obo obo-basic-ontology id type page title description connects uberon/bridge/uberon-bridge-to-zfa.owl BridgeOntology https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies Uberon bridge to ZFA Taxonomic equivalence axioms connecting zebrafish-specific classes to generic uberon counterparts id uberon id zfa id type page title description connects uberon/bridge/uberon-bridge-to-ma.owl BridgeOntology https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies Uberon bridge to MA Taxonomic equivalence axioms connecting adult mouse specific classes to generic uberon counterparts id uberon id ma id type title description page taxon mireots_from uberon/composite-metazoan.owl MergedOntology Uberon composite metazoan ontology Extended uberon plus all metazoan ontologies https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies Metazoa ehdaa2 id type title page taxon mireots_from uberon/composite-vertebrate.owl MergedOntology Uberon composite vertebrate ontology https://github.com/obophenotype/uberon/wiki/Multi-species-composite-ontologies Metazoa ehdaa2
activity_status	active

Uberon is an integrated cross-species ontology covering anatomical structures in animals. See the Uberon website for more info, or read the Uberon paper in Genome Biology.