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 1 Metazoa: BP xp UBERON 2 Viridiplantae: BP xp PO 3 Species-centric AOs 3.1 Dictyostelium 3.2 Fungi 3.3 Mouse 3.4 Mouse 3.5 Fly 3.6 Fly 3.7 Xenopus 3.8 Single-celled organisms 3.9 Issues with single-species approach

Metazoa: BP xp UBERON

• biological_process_xp_uber_anatomy.obo

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

• go/scratch/xps/biological_process_xp_dicty_anatomy.obo

This should only have processes specific to Dictyostelium. May be some redundancy with fungi below.

Requires dicty_anatomy.obo

Fungi

• go/scratch/xps/biological_process_xp_fungal_anatomy.obo

This should only have processes specific to Fungi. Requires fungal_anatomy.obo (which is no longer maintained?)

Mouse

• XP:biological_process_xp_mouse_anatomy

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

• XP:biological_process_xp_human_anatomy

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

• go/scratch/xps/biological_process_xp_fly_anatomy.obo

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

• go/scratch/xps/biological_process_xp_zebrafish_anatomy.obo

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