Re-structure pathogen growth in host terms

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Pathogen-Host Interaction Phenotype Ontology

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Re-structure pathogen growth in host terms #310

Closed ValWood closed 3 years ago

ValWood commented 3 years ago

pathogen growth present within host seemed to be a leaf node.

I expected descendants

PHIPO:0000368 | increased pathogen growth within host

PHIPO:0000365 | decreased pathogen growth within host

CuzickA commented 3 years ago

I think the difficulty here is the split between 'normal' and 'abnormal' vs 'presence' and 'absence'.

ValWood commented 3 years ago

Should we have "normal phenotypes " for growth though? How would we define 'normal'? this will be too variable...

CuzickA commented 3 years ago

Maybe it would be better to re-group these under present and absent

CuzickA commented 3 years ago

@jseager7 have the following terms been used in any sessions please?

PHIPO:0000033 abnormal pathogen growth on host surface PHIPO:0000175 normal pathogen growth on host surface PHIPO:0000364 abnormal pathogen growth within host PHIPO:0000354 normal pathogen growth within host

jseager7 commented 3 years ago

PHIPO:0000033 'abnormal pathogen growth on host surface'
- (no sessions)
PHIPO:0000175 'normal pathogen growth on host surface'
- (no sessions)
PHIPO:0000364 'abnormal pathogen growth within host'
- (no sessions)
PHIPO:0000354 'normal pathogen growth within host'
- PMID:16517760 _mutualism papercould change to growth present
- PMID:17041146 _mutualism papercould change to growth present
- PMID:22241993 _inverse GfG papercould change to growth present
- PMID:28715477 _bacteria-mouse papercould change to growth present

CuzickA commented 3 years ago

What do you think @ValWood, shall I restructure under present/absent, obsolete the top 3 unused terms above and merge normal pathogen growth within host into PHIPO:0000954 pathogen growth present within host

ValWood commented 3 years ago

Sounds good!

CuzickA commented 3 years ago

Merge PHIPO:0000354 normal pathogen growth within host into PHIPO:0000954 pathogen growth present within host 1f79915

moved terms under present/absent renamed PHIPO:0000954 pathogen growth present within host -> presence of pathogen growth within host PHIPO:0000363 absent pathogen growth within host -> absence of pathogen growth within host a718a41

obsolete PHIPO:0000364 abnormal pathogen growth within host 419cec3

Now looks like this

CuzickA commented 3 years ago

rename PHIPO:0000350 pathogen growth absent on host surface -> absence of pathogen growth on host surface PHIPO:0000349 pathogen growth present on host surface -> presence of pathogen growth on host surface re-grouped terms under absence/presence a995085

obsolete 19d59b3 PHIPO:0000033 abnormal pathogen growth on host surface PHIPO:0000175 normal pathogen growth on host surface

Will keep ticket open until check that merge term above loads correctly in PHI-Canto