XP:biological process xp cell
NOTE: THE PRIMARY VERSION OF THIS EXTENSION FILE IS NOW AN OWL FILE IN SVN. See: Ontology_extensions#Status
Logical definitions for GO Biological Processes using OBO-Cell. These were sourced from auto-generated results, but then vetted manually.
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)
Many relations of the results_in_X form are used. These may seem partially redundant with the BP hierarchy, but they make reasoning easier.
All in ro_proposed
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
- epidermal cell differentiation is a differentiation process that results_in_the_acquisition_of_features_of an epidermal cell
- epithelial cell differentiation is a differentiation process that results_in_the_acquisition_of_features_of an epithelial cell
From the above, a reasoner infers that "epidermal cell differentiation is_a epithelial cell differentiation"
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)
- In the GO Tracker, set the Group to be "Cell-XP"
- In the Cell Ontology tracker, set the Group to be GO-Cell-XP
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