XP:biological process xp cell: Difference between revisions
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* [http://www.berkeleybop.org/ontologies/#bp_xp_cell downloads page] | * [http://www.berkeleybop.org/ontologies/#bp_xp_cell downloads page] | ||
* [http://www.berkeleybop.org/ontologies/obo-all/bp_xp_cell/bp_xp_cell.xp.html HTML] | * [http://www.berkeleybop.org/ontologies/obo-all/bp_xp_cell/bp_xp_cell.xp.html HTML] | ||
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All in ro_proposed | All in ro_proposed | ||
== Results == | |||
Missing Link Report: | |||
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1940574&group_id=36855&atid=440764 sf tracker] | |||
See also discussion on the obo-cell mail list: | |||
=== Epidermal cell Example === | |||
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" | |||
[[Image:epidermal-cell-differentiation-xp.jpg]] | |||
=== Other reports === | |||
* In the [http://sourceforge.net/tracker/?atid=440764&group_id=36855 GO Tracker], set the Group to be "Cell-XP" | |||
* In the [http://sourceforge.net/tracker/?group_id=76834&atid=925065 Cell Ontology tracker], set the Group to be GO-Cell-XP | |||
== History == | == History == | ||
Revision as of 12:10, 14 October 2008
Synopsis
Logical definitions for GO Biological Processes using OBO-Cell. These were sourced from auto-generated results, but then vetted manually. They may still be incomplete. The relations used may also change. osteoblast differentiation = cell differentiation THAT results_in_acquisition_of_features_of osteoblast
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
- xp obo file
- imports file - point oboedit at this
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
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"
Other reports
- In the GO Tracker, set the Group to be "Cell-XP"
- In the Cell Ontology tracker, set the Group to be GO-Cell-XP
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