XP:biological process xp cell

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

Synopsis

Logical definitions for GO Biological Processes using OBO-Cell. These were sourced from auto-generated results, but then vetted manually.

Introduction

XPs defining biological processes in terms of cells; example:

 [Term]
 id: GO:0009994 ! oocyte differentiation
 intersection_of: GO:0030154 ! cell differentiation
 intersection_of: OBO_REL:results_in_acquisition_of_features_of CL:0000023 ! oocyte

i.e. oocyte differentiation = cell differentiation THAT results_in_acquisition_of_features_of oocyte


See the go/scratch/xps directory

This xp file has been registered in the OBO xps metadata so it is available here:


These will be examined after the NIAID cell ontology meeting (many involve immunology)

Relations used

Many relations of the results_in_X form are used. These may seem partially redundant with the BP hierarchy, but they make reasoning easier.

Examples:

  • results_in_complete_development_of
  • results_in_acquisition_of_features_of

All in ro_proposed

Results

Missing Link Report:

See also discussion on the obo-cell mail list:

Epidermal cell Example

This example works as of 2008/10/13 - although as we have an inconsistency it is hopeful this is resolved in the near future!

The cell ontology says that "epidermal cell is_a epithelial cell"

The xp definitions say that

From the above, a reasoner infers that "epidermal cell differentiation is_a epithelial cell differentiation"

Epidermal-cell-differentiation-xp.jpg

The dotted line between the two differentiation terms indicates an implied link. With the addition of this link, the direct link up to 'cell differentiation' becomes redundant, hence the zigzag line

For GO we use the reasoner in OBO-Edit:Reasoner_Repair_Mode repair mode, so we would assert the above reasoned link in GO (and remove the redundant one)

Other reports

History

See XP:Meetings

The first pass of bp_xp_cell used a relatively minimal set of relations based on has_participant. However, this set did not prove to be enough to provide necessary and sufficient conditions. We are now using a wider set from ro_proposed