Uberon: Difference between revisions
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== Connections with other AOs == | == Connections with other AOs == | ||
Uberon is connected to other AOs via bridge axiom ontologies. 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 === | === Human === | ||
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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. | 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: | |||
* http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl Alternate: [http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.obo .obo] | |||
=== Mouse === | === Mouse === |
Revision as of 19:31, 20 November 2013
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
Uberon is connected to other AOs via bridge axiom ontologies. 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:
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
- http://uberon.org - homepage
- Extensions/x-metazoan-anatomy