XP:biological process xp regulation
There is far more detail on this page; however, some of it is historical:
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. Just like for SO. (add link to SO xp docs here)
We first need to do testing
First load the ontology + xps from here:
Note this has many impliable links redundantly stated. Use OE1 to remove these (edit menu). Test editing.
Caveat: we can always move the main file to repair mode for the regulation xps, but what about when external xps come along? This may prove too big a burden on the reasoner. but we will be somewhat committed to repair mode