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PHI-base / phipo

Pathogen-Host Interaction Phenotype Ontology
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useful synonym #157

Closed ValWood closed 4 years ago

ValWood commented 4 years ago

PHIPO:0000992 | increased expression of a host gene product involved in pathogen interaction

add synonym

increased expression of a host defense related marker gene (maybe this would be a better primary term name? More understandable for the community - we should aim to craft the term names to match the pathogen community syntax/experiments)

CuzickA commented 4 years ago

I like the above suggestion for a primary term name but I think it needs to include 'pathogen'. There may be examples of host only genotypes where a defence pathway is activated and similar marker genes are used as a read out of this.

ValWood commented 4 years ago

But if the defense pathway is activated it must be in response to a pathogen , no?

This will be in the pathogen host interaction branch and the def should already state that this is in response to pathogen. It can then be refined more if we ever need such a term (but this seems unlikely because we are annotating pathogens?)

If you still think it is needed we can discuss further but making the terms names more closely match authors usage will be helpful.

CuzickA commented 4 years ago

But if the defense pathway is activated it must be in response to a pathogen , no?

There are host mutations that can constitutively activate eg cell death pathway without the presence of the pathogen. They are very sickly plants!

ValWood commented 4 years ago

Ah OK.

CuzickA commented 4 years ago

@ValWood I could change primary term label to one of the below or similar? increased expression of a host defense related marker gene involved in pathogen interaction increased expression of a host defense related marker gene induced by pathogen

ValWood commented 4 years ago

I think increased expression of a host defense related marker gene involved in pathogen interaction is OK becasue the PHI will be covered in def and/or parentage

CuzickA commented 4 years ago

changed term label to increased expression of a host defense related marker gene involved in pathogen interaction

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