XP:biological process xp regulation: Difference between revisions

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Manage the XPs directly in the main .obo file
Manage the XPs directly in the main .obo file
=== Alternate plan ===
This plan is designed to allow us to press ahead with OE1 (see [[OBO-Edit:Why_xps_wont_work_for_GO_in_OE1]]).
We will take the less conservative step of abandoning [[OBO-Edit:Reasoner Repair Mode|Repair Mode]] and going with reasoner constantly-on mode FOR EDITORS ONLY. The reasoner will be run in batch mode to make the public version of the ontology.


== Tracker Items ==
== Tracker Items ==

Revision as of 13:30, 24 June 2008

There is far more detail on this page; however, some of it is historical:

Regulation_cross-products

The following rule is implemented in the OE2 semantic parser:

  • negative regulation of P -> biological_regulation THAT negatively_regulates P
  • regulation of P -> biological_regulation THAT regulates P
  • positive regulation of P -> biological_regulation THAT positively_regulates P

The Obol grammar has more complex parsing rules: obol_biological_process_xp_self. See XP:biological_process_xp_multi_organism_process for example

Location:

This directory is updated NIGHTLY

See the README. In particular the newlinks report. This report will become obsolete once the regulation xps are in the main ontology.

Implementation

Short term:

convert to XPs in batch using OE2 semantic parser - editors check the above report and fix missing links

Medium term (post OE2):

Manage the XPs directly in the main .obo file

Alternate plan

This plan is designed to allow us to press ahead with OE1 (see OBO-Edit:Why_xps_wont_work_for_GO_in_OE1).

We will take the less conservative step of abandoning Repair Mode and going with reasoner constantly-on mode FOR EDITORS ONLY. The reasoner will be run in batch mode to make the public version of the ontology.

Tracker Items

See Also