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Logical definitions for multi-species regulation terms

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



Relations Used


  • 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:

id: GO:0034053 ! modulation by symbiont of host defense-related programmed cell death
intersection_of: GO:0044419 ! interspecies interaction between organisms
intersection_of: 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. (see the documentation for a full description of the regulation phrasing.
  • Non-embedded term names e.g.
GO:0052207 ! modification of morphology or physiology of other organism via protein secreted by type III secretion system during symbiotic interaction 


GO:0015628 ! protein secretion by the type II secretion system

In this case it's not possible grammatically to embed the term. It was decided not to add an exact synonym with the parent term string embedded, but rather to manually generate the xp.

Missing Link Report

(not yet updated automatically)

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

  • 2008/01/29 plus discussion on induction, metabolism