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response to other organism #12975
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@dosumis: this seems to have been done - close? |
I think it should be response is_a single-org process, part-of a
multi-org process
…On 14 Feb 2017, at 8:02, Melanie Courtot wrote:
@dosumis: this seems to have been done - close?
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#12975 (comment)
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@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 ? |
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) |
@dosumis P2G checks that a term is either a subclass of multi-organism process or a descendant via part_of. |
@cmungall can this be merged and closed ? Thanks, Pascale |
This is done, ie 'response to other organism' (GO:0051707) is a subclass of multi-organism process. |
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 |
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 ? |
close? |
Not yet. |
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 |
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.
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