XP:biological process xp regulation

This page details the "standard" regulation cross-products. This is the subset of cross-products that can be trivially derived from parsing terms of the form (negative/positive) regulation of P, where P is named in GO.

When these cross-product definitions are derived, we can use a reasoner to ensure consistency within the GO.

So far this is done at periodic intervals. The first iteration fixed >1000 links in the regulation graph in GO

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

Regulation_cross-products

Methods

The following parser grammar is implemented in the OBO-Edit2 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

We can use this to derived explicit necessary and sufficient conditions for a subset of regulation terms that follow a very regular form.

The Obol grammar has more complex parsing rules: obol_biological_process_xp_self, particularly for handling multi-species regulation terms. However, this overall a much more difficult problem so we separate this out into a separate wiki project page: XP:biological_process_xp_multi_organism_process

Availability

At this time, the xp definitions are not stored in the main gene_ontology_write.obo file (although this would be ideal). Instead, a nightly process executed at Berkeley runs both the OBO-Edit2 semantic parser and the reasoner.

The results are here:

• scratch/regulates_xp_live

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

Future Plans

The current methodology of generating nightly reports and having editors look through them and manually fix the GO is clunky and time-consuming.

Current SOP

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

Implementation plan, post OboEdit2.0 release

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):

• regulates_relations_examples/go_regtest_withPosNeg_noPF-NR.obo

With the reasoner off, the regulation terms should appear "flat" in the visual displays. 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

See Also

• Regulation_cross-products