Uberon

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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.

This page outlines the aspects of Uberon relevant for GO. For more details, the uberon website and paper provide a better guide.

Note that much of what is outlined here is also applicable to CL

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.

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

Connections with other AOs

For more details see:

http://geneontology.org/meeting/ontology/uberon-and-cl-in-go-2013.pptx

Uberon is connected to other AOs via bridge axiom ontologies. collector ontologies imports triads of uberon + ssAO + bridge.

See the Uberon paper for details.

Note that use of a bridge ontology results in an ontology with a lot of redundancy - for example:

  • uberon:nervous-system
    • ma:nervous-system
    • emeapa:nervous-system
    • wbbt:nervous-system
    • zfa:nervous-system


This can lead to complex lattices.

For the purposes of making logical definitions in GO, we can make use of

* http://purl.obolibrary.org/obo/uberon/composite-metazoan.owl

This merges in generic classes from ssAOs and leaves genuinely-species specific classes as leaf nodes.

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.

C elegans

WBbt will be used.

Note that whilst uberon is scoped to metazoan, most detail is in vertebrates. There is not much overlap between WBbt and Uberon - just high level terms like "nervous system". There is slightly more overlap between WBbt and CL.

Bridge to uberon:

Bridge to CL:

Drosophila

FBbt will be used for c16 annotation(?).

Note that whilst uberon is scoped to metazoan, most detail is in vertebrates. There is not much overlap between FBbt and Uberon - just high level terms like "nervous system", plus functional grouping classes like "eye" (Uberon is closely aligned with GO here - GO has an eye development grouping, under which is camera-type eye and compound eye). There is slightly more overlap between FBbt and CL - e.g. neuron, interneuron, ...

Note that for logical definitions, uberon is used for most development terms, except when the term was clearly added to support Dmel annotation and the structure is not found in vertebrates (as a general rule).

Bridge to uberon:

Bridge to CL:

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