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response to other organism #12975

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dosumis opened this issue Jan 31, 2017 · 13 comments
Closed

response to other organism #12975

dosumis opened this issue Jan 31, 2017 · 13 comments

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@dosumis
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dosumis commented Jan 31, 2017

Alice (@zebrafishembryo ) notes that 'response to other organism' (GO:0051707) is no longer a subclass of multi-organism process. This is causing problems for annotators as the need to be able to record the taxon of the 'other' organism in these cases, but this is only allowed for multi-organism processes.

The change may have come from me (although I haven't manage to track it down).

The might potentially be justified by saying that it covers the process in the responding organism only, but I wouldn't want to be dogmatic about this.

So, I propose to change back - but this leaves at least one class as a child of both single an multi-organism process: viral induced premature senescence (GO:0090401)

There is (currently) no axiom declaring disjointness between single and multi-organism processes, so this will not cause the build to fail. But the disjointness probably should be declared.

After discussion with Alice (@zebrafishembryo) I came up with a possible fix:

Rename -> viral-induction of premature senescence
Add logical def: 'modulation by virus of host process' and 'positively regulates' some 'cellular senescence'

But on reflection, I'm not sure this works as it may be an endogenous response to viral infection, rather than something the virus has evolved to induce:

definition "A cellular senescence process associated with the dismantling of a cell as a response to viral infection."^^xsd:string

Not sure of solution.

@dosumis
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dosumis commented Jan 31, 2017

  • Add back classification of 'response to other organism' under 'multi-organism process' @dosumis

@ukemi ukemi added this to Ontology meeting TBD in ontology weekly meetings Feb 7, 2017
@ukemi ukemi moved this from Ontology meeting TBD to Ontology Call February 9, 2017 in ontology weekly meetings Feb 7, 2017
@ukemi ukemi moved this from Ontology Call February 9, 2017 to In progress in ontology weekly meetings Feb 14, 2017
@ukemi ukemi moved this from In progress to Ontology call February 16th 2017 in ontology weekly meetings Feb 14, 2017
@mcourtot
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@dosumis: this seems to have been done - close?

@cmungall
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cmungall commented Feb 14, 2017 via email

@dosumis
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dosumis commented Feb 14, 2017

@tonysawfordebi Is it necessary that a term be a subclassOf multi-organism process in order to specify a second taxon in protein2GO, or can it be a descendant via part_of ?

@mcourtot
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was looking at "killing by virus of host cell during superinfection exclusion" which is a subclass of "response to virus", itself a subclass of "response to other organism". It is defined as "The viral-killing of a host cell by a pre-existing virus in response to a subsequent infection of the host cell by second virus." - if we keep this classification then response to other organism would have to remain a multi-organism process (though I like Chris' proposal better, just pointing out if we go this route there may be a bit of clean-up associated)

@tonysawfordebi
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@dosumis P2G checks that a term is either a subclass of multi-organism process or a descendant via part_of.

@pgaudet
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pgaudet commented Nov 23, 2017

@cmungall can this be merged and closed ? Thanks, Pascale

@pgaudet
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pgaudet commented May 31, 2018

This is done, ie 'response to other organism' (GO:0051707) is a subclass of multi-organism process.

@pgaudet pgaudet closed this as completed May 31, 2018
@pgaudet pgaudet reopened this Jun 4, 2018
@pgaudet
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pgaudet commented Jun 4, 2018

Oups I didn't check correctly - the relation between 'response to other organism' (GO:0051707) is_a subclass of multi-organism process.

Chnaged relation @cmungall suggested: part-of a multi-org process (I cannot find single-organism process).

Thanks, Pascale

@pgaudet
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pgaudet commented Jun 4, 2018

  • When I change 'response to other organism' (GO:0051707) from is_a to part_of subclass of multi-organism process, we loose 'bearer of some multi-organismal process quality'.
  • If we have bearer of some multi-organismal process quality, then automatically we get 'is_a' multiorganism process.

So I dont think we can make part_of based on the current design patterns.

@cmungall @ukemi I propose to keep is_a and close this; ok ?

@ValWood
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ValWood commented Dec 3, 2019

close?

@pgaudet
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pgaudet commented Dec 3, 2019

Not yet.

@pgaudet pgaudet removed this from Ontology meeting TBD in ontology weekly meetings Jan 20, 2020
@pgaudet
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pgaudet commented Feb 10, 2020

I changed the parent class for 'response to other organism' to 'interspecies interactions between organisms.

This should fix the rule violation, for example here

http://snapshot.geneontology.org/reports/goa_dog-report.html#gorule-0000015

WARNING - Violates GO Rule: GORULE:0000015: Dual species taxon check -- UniProtKB E2R560 HYAL2 GO:0009615 GO_REF:0000024 ISS UniProtKB:Q12891 P Hyaluronidase HYAL2 protein taxon:9615|taxon:11746 20120222 UniProt

Thanks, Pascale

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