Extensions/x-multi-organism: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
 
(12 intermediate revisions by 2 users not shown)
Line 1: Line 1:
== Synopsis ==
== Synopsis ==


This XP augments [[XP:biological_process_xp_regulation]]
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:
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:
Line 10: Line 10:
It uses a small ontology of "organism roles" - parasite, symbiont etc - see the bottom of the xp obo file
It uses a small ontology of "organism roles" - parasite, symbiont etc - see the bottom of the xp obo file


== Availability ==
== URLs ==


See the [http://www.geneontology.org/scratch/xps/ go/scratch/xps] directory
* http://purl.obolibrary.org/obo/go/extensions/x-multi-organism.owl
 
* http://purl.obolibrary.org/obo/go/extensions/x-multi-organism.obo
* [http://www.geneontology.org/scratch/xps/biological_process_xp_multi_organism_process.obo xp obo file]
* [http://www.geneontology.org/scratch/xps/biological_process_xp_multi_organism_process-imports.obo imports file] - point oboedit at this


== Results ==
== Results ==
Line 37: Line 35:
id: GO:0034053 ! modulation by symbiont of host defense-related programmed cell death
id: GO:0034053 ! modulation by symbiont of host defense-related programmed cell death
intersection_of: GO:0044419 ! interspecies interaction between organisms
intersection_of: GO:0044419 ! interspecies interaction between organisms
intersection_of: OBO_REL:regulated_by obol:symbiont ! symbiont
intersection_of: regulated_by obol:symbiont ! symbiont
intersection_of: regulates GO:0012501 !  programmed cell death
intersection_of: regulates GO:0012501 !  programmed cell death
intersection_of: regulates GO:0006952 ! defense response
intersection_of: regulates GO:0006952 ! defense response
Line 45: Line 43:
* "modification" - make synonymous with "regulates" : YES. (but see also "protein modification"...)
* "modification" - make synonymous with "regulates" : YES. (but see also "protein modification"...)


* "upregulation" - narrow syn for + regulation. TODO: make consistent synonyms.
* "upregulation" - narrow syn for + regulation. TODO: make consistent synonyms. (see the [http://www.geneontology.org/GO.process.guidelines.shtml#regTerms documentation] for a full description of the regulation phrasing.
 
* Non-embedded term names e.g.
<pre>GO:0052207 ! modification of morphology or physiology of other organism via protein secreted by type III secretion system during symbiotic interaction
</pre>
and
 
<pre>
GO:0015628 ! protein secretion by the type II secretion system
</pre>
 
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 ===
=== Missing Link Report ===
Line 57: Line 66:
* [http://www.geneontology.org/scratch/regulates_xp_live/go_reglive_withPosNeg_noPF-newlinks.txt regulates missing links]
* [http://www.geneontology.org/scratch/regulates_xp_live/go_reglive_withPosNeg_noPF-newlinks.txt regulates missing links]


* [http://sourceforge.net/tracker2/index.php?func=detail&aid=2545754&group_id=36855&atid=440764 2008/01/29] plus discussion on induction, metabolism


[[Category:Regulation]]
[[Category:Regulation]]
[[Category:Cross Products]]
[[Category:Cross Products]]
[[Category:Internal Cross Products]]
[[Category:Internal Cross Products]]
[[Category:Content_PAMGO]]

Latest revision as of 14:11, 26 March 2013

Synopsis

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

URLs

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: 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 

and

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