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PHI-base curation

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Update all non-gene-for-gene curation sessions with new AE 'interaction_outcome' disease absent/present and control annotations #81

Closed CuzickA closed 2 years ago

CuzickA commented 3 years ago

So far I have done this for PMID:30459352 https://canto.phi-base.org/curs/cee7f6d8bab0bafd

23

CuzickA commented 3 years ago

Note this session may now need updating if we are no longer using WTpathogen WThost metagenotype as decided in PHI-Canto group meeting 28_09_2020.

Ticket to disable WTpathogen WThost metagenotype https://github.com/PHI-base/config/issues/46

PMID:30459352 https://canto.phi-base.org/curs/cee7f6d8bab0bafd session now updated 04_11_2020 #23

CuzickA commented 3 years ago

Done for https://github.com/PHI-base/curation/issues/24 Query about For now I have only added the AE disease outcome to the WT control metagenotype annotations. I'm not sure about adding it to the altered metagenotypes - to discuss.

CuzickA commented 3 years ago

Query about adding 'AE disease outcome' options 'disease present' or 'disease absent'

For #24 only added to WT control annotations as usage seems odd in some of the altered metagenotype annotations eg 'disease present' ??

For #23 added to both WT control annotations AND altered metagenotype annotations.

This needs reviewing after I have updated a few more of the sessions

_01_122021 Edit For completeness in screenshots planned for PHI-Canto supplementary figure I have decided to add 'AE disease outcome' options 'disease present' or 'disease absent' to the relevant altered metagenotype annotations for #24

CuzickA commented 3 years ago

Summary for use of AE disease interaction 1) useful in control metagenotypes 2) may not be needed in altered metagenotypes when other AEs used 'compared to control' and 'infective ability'

3) not relevant for mutualism papers

Currently added to

all metagenotype annotations for https://canto.phi-base.org/curs/cee7f6d8bab0bafd
selected metagenotype annotations for https://canto.phi-base.org/curs/8149debd202f2e6e#

CuzickA commented 3 years ago

Metagenotype control annotations added to mutualism papers but not AE interaction_outcome as not relevant

58 #57

CuzickA commented 3 years ago

34 now updated with AE disease outcome, AE compared to control

and control annotations for metagenotype

CuzickA commented 3 years ago

Cannot curate the 'empty vector controls' for the metagenotypes in this paper https://github.com/PHI-base/curation/issues/89

Also examples in this paper where it would be difficult to add the AE disease interaction Disease absent does not seem correct here, looking at host defense response when Fg protein agroinfiltrated into tobacco

CuzickA commented 3 years ago

Mostly done for #36 with a couple of queries still to resolve I have not added AE interaction_outcome to all annotations as not relevant

CuzickA commented 3 years ago

Done for #72 I have not added AE interaction_outcome to all annotations as not relevant eg for DON measurements

CuzickA commented 3 years ago

Done for https://github.com/PHI-base/curation/issues/54

CuzickA commented 2 years ago

I think this AE and the control annotations have been added where possible for all of the currently approved 29 papers. Partially curated papers will have these updates added prior to approval.

Therefore, closing ticket.