XP:biological process xp regulation: Difference between revisions

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We first need to do testing
We first need to do testing


First load the ontology + xps from here:
Point OBO-Edit at this URL (or download):


* [http://www.geneontology.org/scratch/regulates_xp_live scratch/regulates_xp_live]
* [http://www.geneontology.org/scratch/regulates_relations_examples/go_regtest_withPosNeg_noPF-NR.obo regulates_relations_examples/go_regtest_withPosNeg_noPF-NR.obo]


Note this has many impliable links redundantly stated. Use OE1 to remove these (edit menu). Test editing.
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:

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. 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

Tracker Items

See Also