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.

uberon

Products

uberon.owl Uberon core ontology
uberon/uberon-base.owl Uberon base ontology Axioms defined within Uberon and to be used in imports for other ontologies [page]
uberon/ext.owl Uberon edition that includes subsets of other ontologies and axioms connecting to them Uberon extended
uberon/basic.obo Uberon basic Uberon edition that excludes external ontologies and most relations
uberon/bridge/uberon-bridge-to-zfa.owl Uberon bridge to ZFA Taxonomic equivalence axioms connecting zebrafish-specific classes to generic uberon counterparts [page]
uberon/bridge/uberon-bridge-to-ma.owl Uberon bridge to MA Taxonomic equivalence axioms connecting adult mouse specific classes to generic uberon counterparts [page]
uberon/composite-metazoan.owl Uberon composite metazoan ontology Extended uberon plus all metazoan ontologies [page]
uberon/composite-vertebrate.owl Uberon composite vertebrate ontology [page]

Usages

User
http://bgee.org/
Description
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.
Type
annotation
See also
https://www.biosharing.org/biodbcore-000228
Examples
User
https://www.encodeproject.org/
Description
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
Type
annotation
See also
https://www.biosharing.org/biodbcore-000034
Publications
User
http://fantom5-collaboration.gsc.riken.jp/
Description
FANTOM5 is using Uberon and CL to annotate samples allowing for transcriptome analyses with cell-type and tissue-level specificity.
Type
annotation
Examples
User
https://monarchinitiative.org/
Description
Querying expression and phenotype data
Type
query
User
https://geneontology.org/
Description
GO Database is used for querying for functional annotations relevant to a tissue
Type
query
Examples
User
http://phenoscape.org
Description
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.
User
https://neuinfo.org/
Description
Searchable collection of neuroscience data and ontology for neuroscience
Type
Database
User
https://scicrunch.org/
Description
cooperative data platform to be used by diverse communities in making data more FAIR.
Type
Database
User
http://single-cell.clst.riken.jp/
Description
SCPortalen
Type
Database
Publications
User
https://www.ebi.ac.uk/chembl/
Description
ChEMBL uses Uberon to describe organ/tissue information in assays
Type
Database
Publications

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