Uberon

Uberon is a multi-species anatomy ontology covering metazoans (animals). It's structure is well-aligned with the development hierarchy in GO.

Uses in GO

There are two primary uses of Uberon in GO:

• Logical definitions (cross-products) - see Extensions/x-metazoan-anatomy
• Annotation Extension (col 16 annotation)

The logical definitions can be used in conjunction with annotation extensions to provide automatic "deepening" of annotations, and automatic verification.

The situation with c16 annotations is complex as individual resources may use species-specific AOs

Connections with other AOs

Human

c16 annotation for goa_human uses Uberon directly. No bridging to external AOs is required.

Chicken

c16 annotation for goa_human uses Uberon directly. No bridging to external AOs is required.

Mouse

This situation for mouse is complex. There are 3 mouse AOs:

• MA - adult (is_a / part_of)
• EMAP - embryonic staged (no is_a)
• EMAPA - embryonic "abstract" - i.e. multiple stages combined. Some is_as.

MGI c16 annotations include use of MA and EMAP. They may use EMAPA in the future.

EMAP

Note that EMAP is staged - each term represents a specific structure at a specific stage. This information is retained in the axioms linking back to Uberon

The following bridge ontology connects EMAP to Uberon:

• http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emap.owl Alternate: .obo

MA

• http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl Alternate: .obo

Combination of Uberon, MA and EMAP plus bridging axioms:

• http://purl.obolibrary.org/obo/uberon/bridge/collected-mouse-with-stages.owl

References

Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., and Haendel, M. A. (2012) Uberon, an integrative multi-species anatomy ontology Genome Biology 13, R5. http://genomebiology.com/2012/13/1/R5

See Also

• http://uberon.org - homepage
• Extensions/x-metazoan-anatomy