OBO Foundry

OntoBee AberOWL OLS RGD AmiGO (SUBSET) Bgee (gene expression) FANTOM5 KnowledgeSpace Bioregistry

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

Publications

Uberon, an integrative multi-species anatomy ontology

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Funding

NIH R24-OD011883

NIH R01-HG004838

NIH P41-HG002273

NSF DEB-0956049

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/uberon-basic.obo	Uberon basic	Uberon edition that excludes external ontologies and most relations
uberon/collected-metazoan.owl	Uberon collected metazoan ontology	Uberon plus all metazoan ontologies [page]
uberon/composite-metazoan.owl	Uberon composite metazoan ontology	Uberon and all metazoan ontologies with redundant species-specific terms removed [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://doi.org/10.25504/FAIRsharing.x6d6sx
Examples: Uberon terms used to annotate expression of human hemoglobin subunit beta

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

Publications

Ontology application and use at the ENCODE DCC

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: FANTOM5 samples annotated to telencephalon or its parts

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: GO annotations relevant to the uberon class for brain

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