Uberon

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Revision as of 19:25, 20 November 2013 by Cjm (talk | contribs) (→‎EMAP)
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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:

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

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:

MA

Combination of Uberon, MA and EMAP plus bridging axioms:

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