XP:biological process xp anatomy

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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:0001843 ! neural tube closure
 intersection_of: GO:0060606 ! tube closure
 intersection_of: OBO_REL:results_in_formation_of UBERON:0001049 ! 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

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

NOTE: THE PRIMARY VERSION OF THIS EXTENSION FILE IS NOW AN OWL FILE IN SVN. See: Ontology_extensions#Status


This should only have processes specific to Fungi. Requires FAO.

Mouse

All mouse (adult and embryological) structures referenced in go covered in uberon

Human

All mammalian xps now in uberon

Fly

NOTE: THE PRIMARY VERSION OF THIS EXTENSION FILE IS NOW AN OWL FILE IN SVN. See: Ontology_extensions#Status

Only fly/insect specific terms in here. More general metazoan terms defined in XP:biological_process_xp_uberon

Note that this xp set currently includes definitions for many terms that are probably applicable across other insects or arthropods. E.g.

[Term]
id: GO:0007421 ! stomatogastric nervous system development
intersection_of: GO:0032502 ! developmental process
intersection_of: OBO_REL:results_in_complete_development_of FBbt:00005096 ! stomatogastric nervous system

We anticipate moving some of these to the arthropod anatomy ontology in future. For now the Dmel term can stand in as the prototypical structure.

Also many GO terms are more specific that then name would suggest:

GO:0022416 ! bristle development *** [DEF: "The process whose specific outcome is the progression of the bristle over time, from its formation to the mature structure. A bristle is an insect sensory organ."]

Worm

No nematode specific xp file yet. Subsumes into bp_xp_uberon?

Fish

Only Danio/teleost specific terms defined here. For generic metazoan terms use XP:biological_process_xp_uberon

Xenopus

none yet. Use uberon?

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