XP:biological process xp anatomy
From GO Public
XPs defining biological processes in terms of gross anatomy
Example (from plant):
[Term] id: GO:0048367 ! shoot development intersection_of: GO:0032502 ! developmental process intersection_of: OBO_REL:results_in_complete_development_of PO:0009006 ! shoot
Example (from metazoa):
[Term] id: GO:0001841 ! neural tube formation intersection_of: GO:0048646 ! anatomical structure formation intersection_of: OBO_REL:results_in_formation_of UBERON:FBbt_00005554-MIAA_0000069-ZFA_0001135 ! neural tube
Gross anatomy varies considerably across organisms. The current approach is to use Uberon as much as possible for metazoan specific processes, and PO for plant specific processes.
For cellular anatomy, see XP:biological_process_xp_cellular_component and XP:biological_process_xp_cell
Contents |
Metazoa: BP xp UBERON
This has its own page, see XP:biological_process_xp_uberon
Viridiplantae: BP xp PO
For plant anatomy
See XP:biological_process_xp_plant_anatomy
Species-centric AOs
Dictyostelium
This should only have processes specific to Dictyostelium. May be some redundancy with fungi below.
Requires dicty_anatomy.obo
Fungi
This should only have processes specific to Fungi. Requires fungal_anatomy.obo (which is no longer maintained?)
Mouse
Note that this is redundant with BP xp UBERON. The eventual plan is to have this cover only mouse specific terms.
Currently this only covers adult mouse (i.e. MA not EMAP)
Mouse
Note that this is redundant with BP xp UBERON. The eventual plan is to have this cover only human specific process terms.
Requires FMA
Fly
This should be non-redundant with XP:biological_process_xp_uberon - i.e. it should in general only have process terms specific to diptera
Fly
Currently redundant with XP:biological_process_xp_uberon - The eventual plan is to have this cover only fish specific process terms.
Xenopus
none yet
Single-celled organisms
XP:biological_process_xp_cellular_component should suffice - although there may be some terms relating to colony formation etc.
Issues with single-species approach
The information below is mostly historical now that we have UBERON. It explains the need for a multi-species anatomy ontology.
Species-centric XP files must 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
