Extensions/x-multi-organism

Synopsis

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

• xp obo file
• imports file - point oboedit at this

Results

Relations Used

• regulates,positively_regulates,negatively_regulates
• regulated_by
• regulates_process_in

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

• newlinks.txt

(not yet updated automatically)

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

• regulates missing links