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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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GO:0009814 defense response, incompatible interaction #18742

Closed ValWood closed 4 years ago

ValWood commented 4 years ago

Is defined Definition A response of a plant to a pathogenic agent that prevents the occurrence or spread of disease.

but has non-plant annotations: non_plant.txt

pgaudet commented 4 years ago

There are C. elegans annotations to this term

@vanaukenk Should we extend the definition ? or is this a different process?

ValWood commented 4 years ago

I don't think we should include this term. It isn't describing a process really... See https://github.com/geneontology/go-ontology/issues/18738

Refers to the outcome of the process (i.e whether disease is observed). If disease is not observed the interaction is "incompatible" This isn't about the process per se. A particular interaction can be compatible or incompatible for a particular pathogen genotype/host genotype combination.

@vanaukenk do you know which process this was trying to capture? i would not move it to the broader non-plant term because "incompatible interaction" doesn't really belongs in GO does it?

@pgaudet there is already a broader parent. I think they should all go. I should have put this ticket on the annotation tracker ?

vanaukenk commented 4 years ago

@ValWood I think the C. elegans annotations to this term are in error. I'll raise a dispute in Protein2GO.

ValWood commented 4 years ago

You might want to mention not moving up to an "incompatible interaction parent" and point to the ticket. Otherwise it will need to be reannotated again.

vanaukenk commented 4 years ago

@ValWood Agreed. I suspect this was just a term selection error (the word 'incompatible' doesn't appear in either of the references).

vanaukenk commented 4 years ago

@ValWood

I created annotation disputes for annotations from both references that have C. elegans annotations to this term:

https://www.ncbi.nlm.nih.gov/pubmed/20600277 https://www.ncbi.nlm.nih.gov/pubmed/27184844

vanaukenk commented 4 years ago

@pgarmiri has deleted the C. elegans (and one mouse) annotations to this term and the dispute resolved in Protein2GO.

ValWood commented 4 years ago

@pgaudet

Action we could merge this up to GO:0045087 innate immune response and nothing would be wrong, or lost .

"incompatible interaction" only means that the specific combination of pathogen and host do not cause disease.

ValWood commented 4 years ago

actually closing this one as "duplicate of" https://github.com/geneontology/go-ontology/issues/18738