Extensions/x-multi-organism: Difference between revisions

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== Synopsis ==
== Synopsis ==
Logical definitions for multi-species regulation terms


This XP augments [[XP:biological_process_xp_regulation]]
This XP augments [[XP:biological_process_xp_regulation]]

Revision as of 22:17, 4 July 2008

Synopsis

Logical definitions for multi-species regulation terms

This XP augments XP:biological_process_xp_regulation

It "catches" some of the MOPs that do not conform to the strict "+/- regulation of PROCESS" grammar. The obol grammar is still incomplete, and there will be certain patterns that are not caught:

  • regulation of qualities, such as levels of RNA in host
  • non-conforming terms

It uses a small ontology of "organism roles" - parasite, symbiont etc - see the bottom of the xp obo file

Availability

See the go/scratch/xps directory

Results

Relations Used

Issues

  • other organism
  • defense-related qualifier

We should probably use a nested cross-product here. For now we're just adding two regulates link as part of the necessary and sufficient conditions:

[Term]
id: GO:0034053 ! modulation by symbiont of host defense-related programmed cell death
intersection_of: GO:0044419 ! interspecies interaction between organisms
intersection_of: OBO_REL:regulated_by obol:symbiont ! symbiont
intersection_of: regulates GO:0012501 !  programmed cell death
intersection_of: regulates GO:0006952 ! defense response
intersection_of: regulates_process_in obol:host ! host
  • "modification" - make synonymous with "regulates" : YES. (but see also "protein modification"...)
  • "upregulation" - narrow syn for + regulation. TODO: make consistent synonyms.

Missing Link Report

(not yet updated automatically)

This has some false positives. It is also redundant with the report generated here: