XP:biological process xp anatomy
From GO Public
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:
