uberon.md

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 http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=UBERON:0001062 title label url Gene Ontology AmiGO 2 Browser AmiGO (SUBSET) http://amigo.geneontology.org/amigo/term/UBERON:0001062#display-lineage-tab title label url Bgee gene expression queries Bgee (gene expression) http://bgee.org/?page=gene title label url FANTOM5 Data Portal FANTOM5 http://fantom.gsc.riken.jp/5/sstar/UBERON:0001890 title label url INCF KnowledgeSpace Portal KnowledgeSpace https://knowledge-space.org/index.php/pages/view/UBERON:0000061	checkout email_cc infallible system git clone https://github.com/obophenotype/uberon.git cjmungall@lbl.gov 1 git	uberon.owl	email github label orcid cjmungall@lbl.gov 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	https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/uberon-logos/uberon_logo_black-banner.png	An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies	anatomy and development	id title https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=R24OD011883&arg_ProgOfficeCode=205 NIH R24-OD011883 id title https://grantome.com/grant/NIH/R01-HG004838 NIH R01-HG004838 id title https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=P41HG002273&arg_ProgOfficeCode=55 NIH P41-HG002273 id title https://www.nsf.gov/awardsearch/showAward?AWD_ID=0956049 NSF DEB-0956049	http://uberon.org	Uberon	label url CC BY 3.0 http://creativecommons.org/licenses/by/3.0/	https://lists.sourceforge.net/lists/listinfo/obo-anatomy	http://en.wikipedia.org/wiki/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 INCATools/ontology-development-kit#50 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 https://obophenotype.github.io/uberon/combined_multispecies/ 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 https://obophenotype.github.io/uberon/combined_multispecies/ 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 https://obophenotype.github.io/uberon/combined_multispecies/ Vertebrata MergedOntology	id title https://www.ncbi.nlm.nih.gov/pubmed/22293552 Uberon, an integrative multi-species anatomy ontology id title https://www.ncbi.nlm.nih.gov/pubmed/25009735 Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon	http://purl.obolibrary.org/obo/uberon/releases/	https://github.com/obophenotype/uberon	https://obo-communitygroup.slack.com/archives/C01CR698CF2	id label NCBITaxon:33208 Metazoa	https://github.com/obophenotype/uberon/issues	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 http://bgee.org/?page=gene&gene_id=ENSG00000244734 https://doi.org/10.25504/FAIRsharing.x6d6sx annotation http://bgee.org/ 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 https://www.ncbi.nlm.nih.gov/pubmed/25776021 Ontology application and use at the ENCODE DCC https://doi.org/10.25504/FAIRsharing.v0hbjs annotation https://www.encodeproject.org/ 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 http://fantom.gsc.riken.jp/5/sstar/UBERON:0001893 annotation http://fantom5-collaboration.gsc.riken.jp/ description type user Querying expression and phenotype data query https://monarchinitiative.org/ 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 http://amigo.geneontology.org/amigo/term/UBERON:0000955 query https://geneontology.org/ 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. http://phenoscape.org description type user Searchable collection of neuroscience data and ontology for neuroscience Database https://neuinfo.org/ description type user cooperative data platform to be used by diverse communities in making data more FAIR. Database https://scicrunch.org/ description publications type user SCPortalen id title https://www.ncbi.nlm.nih.gov/pubmed/29045713 SCPortalen: human and mouse single-cell centric database Database http://single-cell.clst.riken.jp/ description publications type user ChEMBL uses Uberon to describe organ/tissue information in assays id title https://www.ncbi.nlm.nih.gov/pubmed/30398643 ChEMBL: towards direct deposition of bioassay data Database https://www.ebi.ac.uk/chembl/	https://en.wikipedia.org/wiki/Template:Uberon	active

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