XP:biological process xp anatomy

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XPs defining biological processes in terms of gross anatomy

Example:

 [Term]
 id: GO:0048367 ! shoot development
 intersection_of: GO:0032502 ! developmental process
 intersection_of: OBO_REL:results_in_complete_development_of PO:0009006 ! shoot

See the go/scratch/xps directory

At this time there are multiple xps for different AOs. This involves a lot of redundancy. Also, these xps can only be used contextually.

For example, if we use XP:biological_process_xp_mouse_anatomy and reason over the GO, the reasoner will infer the following link:

 GO:0043588-skin development
 --[p]-- GO:0008544-epidermis development	

Because epidermis part_of skin in mouse_anatomy and we have:

 [Term]
 id: GO:0008544 ! epidermis development
 intersection_of: GO:0032502 ! developmental process
 intersection_of: OBO_REL:results_in_complete_development_of MA:0000153 ! epidermis

However, the GO def is:

The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of a plant or animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.

i.e. it includes plants, and plants don't have skin, so the reasoner would give a True path violation because it was using contextual information globally

[edit] Generic vs specific anatomy ontologies

We need a generic AO (gAO) for use in GO.

For now there are multiples xp files on a per-species-centric AO (scAO) basis: see the go/scratch/xps dir

Also:

The cell ontology is a gAO; this has its own xp set:

Similarly for Subcellular anatomy (GO-CC is a gAO):

Uberon is a generic multi-species anatomy ontology

[edit] Ongoing research

Uberon is a multi species anatomy ontology.

Logical definitions:

Missing links discovered:

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