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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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response to fungus descendants #18072

Open ValWood opened 4 years ago

ValWood commented 4 years ago

GO:0009610 response to symbiotic fungus

descendents: GO:0019732    antifungal humoral response is_a
GO:0009817    defense response to fungus, incompatible interaction is_a
GO:1900150    regulation of defense response to fungus regulates
GO:0061760    antifungal innate immune response is_a

GO:0070947    neutrophil mediated killing of fungus

We should not have taxon specific versions of these terms?

vanaukenk commented 4 years ago

@ValWood - was this ticket meant for the ontology tracker?

pgaudet commented 4 years ago

Right - it may be clearer to annotate 'innate immune response' part of 'response to fungus', etc.

Pascale

ValWood commented 4 years ago

I think "response to x" as an extension would work. Then we would not need to repeat every term for every clade...

ValWood commented 4 years ago

~Real life example

I have just done

GO:0038187 | pattern recognition receptor activity | IMP | B | part_of cell surface pattern recognition receptor signaling pathway , part_of response to fungus

@CuzickA had done GO:1900150 | regulation of defense response to fungus

which is also correct, but if you go down these "defense response to " branches you do not see the important terms about mechanism.

If we did keep these we would require a lot of pre-composition to enable people to locate them

for example I would be requesting cell surface pattern recognition receptor signaling pathway involved in defense response to fungus

If you are searching "top down" it's too tempting to go down the branch related to your pathogen species of interest...