XP:biological process xp regulation: Difference between revisions
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We first need to do testing | We first need to do testing | ||
Point OBO-Edit at this URL (or download): | |||
* [http://www.geneontology.org/scratch/ | * [http://www.geneontology.org/scratch/regulates_relations_examples/go_regtest_withPosNeg_noPF-NR.obo regulates_relations_examples/go_regtest_withPosNeg_noPF-NR.obo] | ||
The reg. terms should appear flat in OE with the reasoner off. With the reasoner on they will be placed correctly. | |||
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 | In the NR file, the stanzas look like this: | ||
<pre> | |||
[Term] | |||
id: GO:0000414 | |||
name: regulation of histone H3-K36 methylation | |||
namespace: biological_process | |||
def: "Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc] | |||
intersection_of: GO:0065007 ! biological regulation | |||
intersection_of: regulates GO:0010452 ! histone H3-K36 methylation | |||
</pre> | |||
Note the lack of an [[is_a]] to GO:0031060 ! regulation of histone methylation | |||
That's OK - the reasoner infers it dynamically | |||
Caveat on using on-the-fly reasoner mode: 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 | |||
== Tracker Items == | == Tracker Items == |
Revision as of 11:46, 8 August 2008
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
Point OBO-Edit at this URL (or download):
The reg. terms should appear flat in OE with the reasoner off. With the reasoner on they will be placed correctly.
In the NR file, the stanzas look like this:
[Term] id: GO:0000414 name: regulation of histone H3-K36 methylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc] intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010452 ! histone H3-K36 methylation
Note the lack of an is_a to GO:0031060 ! regulation of histone methylation
That's OK - the reasoner infers it dynamically
Caveat on using on-the-fly reasoner mode: 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