Uberon multi-species anatomy ontology
An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies
G+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.
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
- ID Space
- uberon
- PURL
- http://purl.obolibrary.org/obo/uberon.owl
- License
- CC-BY
- Homepage
- http://uberon.org
- http://en.wikipedia.org/wiki/Uberon
- https://www.biosharing.org/bsg-000016
- Contact
- Chris Mungall
- Trackers
- https://github.com/obophenotype/uberon/issues
- Domain
- anatomy
- Mail List
- https://lists.sourceforge.net/lists/listinfo/obo-anatomy
- Taxon
- Metazoa
- Example
- UBERON_0002046
- Cite
- Uberon, an integrative multi-species anatomy ontology
- Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
- Funding
- NIH R24OD011883
- NIH R01HG004838
- NIH P41HG002273
- NSF DEB-0956049
- Dependencies
- go
- cl
- chebi
- pr