obophenotype
pattern for abnormal response to entity
I have many abnormal response to terms to chemical entities but also sometimes to a biological process
PATO_0000077 response to
AbnormalResponseToEntity
Maybe also children in/decreased/absent
That seems very general - we generally prefer to have these pushed into GO (response to X terms) and then simply use the abnormalBiologicalProcess pattern. Can you give some examples where that would not work?
The issue here is that GO has been pushing back lately. I'd be happy to carry on using abnormalBiologicalProcess + GO response-to-X, but GO's trying to clear out a lot of "response to" terms, and not add many new ones, I think because they want to apply more stringent criteria for what they'll count as a real, naturally occurring, distinct response process. People like me & Petra, and our ontologies, are caught in the middle :/
I don't have an example of something currently un-model-able from FYPO off the top of my head, but there are a few that might lose LDs if GO makes a "response to" term obsolete AND we don't have an alternative phenotype pattern. FYPO:0001932 "abnormal cellular response to hydroxyurea" is one.
For more info, try this GO ticket, and some of the others with the "response_to_terms" label in that issue tracker.
Ok thank you @mah11
One option would be to create a response to exposure to entity pattern. It would look convoluted, but it is actually quite easy in the end, something like:
GO:response to and 'has stimulus' some 'CHEBI:carbon' and 'has route' some 'injection'
How does GO model the relation between "response to X" processes and the X?
How does GO model the relation between "response to X" processes and the X?
I don't know, and I don't see anything obvious in https://github.com/geneontology/go-ontology/tree/master/src/design_patterns or https://github.com/geneontology/go-ontology/tree/master/docs/patterns ... best ask someone there, e.g. @pgaudet
@mah11 yes I also feel GO gets rather rid of useful terms for phenotypes, I went through our whole ontology and there were terms to previous GO terms but this have been removed from GO.
We have mostly response to chemicals/CHEBI and a few to processes (most of those are in GO). Examples:
aberrant response to N-Phenylthiourea aberrant response to SDF-1 abolished response to cheating def: "Complete resistance to cheating when mixed with cheater cells." (GO:0099139:cheating during chimeric sorocarp development is Exact synonym)
Hello,
We use for example GO:0033198 response to ATP
'response to stimulus' and ('has input' some 'ATP(4-)')
Thanks, Pascale
Update - there is a concerted effort on the equivalent Trait patterns for OBA (CC @kallia-p).
We should have w patterns:
abnormal_response_to_chemical
E = GO:'response to chemical' and has_input some CHEBI:{some chemical} Q = PATO:'process quality' var = chemical
abnormal_response_to_stress var = E = subclass of of GO:'response to stress'
Where E & Q follow the general pattern: has_part some (Q and 'characteristic of' some E) and (has_modifier some 'abnormal')
