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Sessions with 'Unknown' expression levels #70

Closed jseager7 closed 4 years ago

jseager7 commented 4 years ago

Required for https://github.com/pombase/canto/issues/2215

@ValWood @CuzickA Here is a list of curation sessions on the main PHI-Canto server that use the 'Unknown' expression level.

I was wrong before when I claimed there were no sessions using this expression level: I must have been getting confused with a search I did for experimental conditions. You may want to check these sessions before we commit to disabling the 'Unknown' expression type.

Alayne mentioned that the genotypes in the following sessions could be good test cases for the new expression types mentioned in issue #68.

CuzickA commented 4 years ago

79c56f92435923ab https://github.com/PHI-base/curation/issues/42

It looks like there is an error in the pathogen genotype (deletion and overexpression??) image

I have corrected this to

image

_Note: have also now corrected genotype name from MGG08054 to chia1delta (autocomplete had removed this earlier) image

Therefore removing the use of 'unknown' expression level from this session.

CuzickA commented 4 years ago

https://canto.phi-base.org/curs/cc6cf06675cc6e13 https://github.com/PHI-base/curation/issues/66

Looked again at paper and below 'unknown' should be 'not assayed' image

Now updated to this (conditions still need updating when PHI-ECO loaded) image

__Just noticed host alleles also use 'unknown' assume this should be 'overexpression' as Y2Hexpt. image

image

CuzickA commented 4 years ago

https://github.com/PHI-base/curation/issues/57

changed 'unknown' to 'not assayed'

image image

CuzickA commented 4 years ago

For https://canto.phi-base.org/curs/87e386b652573063 #55 changed pathogen 'unknown' expr to either 'overexpression' as in Fig 2 or 'not assayed' image

Now looks like image

CuzickA commented 4 years ago

For https://canto.phi-base.org/curs/59484877a87d5786 #65 image

changing pathogen genotypes 'unknown' expr to 'not assayed' now looks like this image

CuzickA commented 4 years ago

For https://canto.phi-base.org/curs/a16f44010111a5c4 #54 image

changed pathogen genotypes 'unknown' exp to 'not assayed' image

CuzickA commented 4 years ago

For https://canto.phi-base.org/curs/dc027c00e7ceab6f #60 image

changed pathogen and host genotypes from 'unknown' expr to 'overexpression' image

CuzickA commented 4 years ago

For http://canto.phi-base.org/curs/f41d30e250b8f9b0 #19

Unused metagenotypes (also unused pathogen and host genotype) with 'unknown' expr level. image Genotypes now deleted.

CuzickA commented 4 years ago

For http://canto.phi-base.org/curs/3b2c44b436098af1 #18 image Allele name still needs some attention when checking. I have changed unknown expr to not assayed.

CuzickA commented 4 years ago

For http://canto.phi-base.org/curs/bd02fdb6831712ca #22

image

changed 'unknown' expr to 'not assayed'

CuzickA commented 4 years ago

For https://canto.phi-base.org/curs/b06680e815f64df0 #53 image Changed 'unknown' expr to 'not assayed'

CuzickA commented 4 years ago

Hi @jseager7 I think I have removed 'unknown' expression types from the genotypes in the above sessions. Please could you re-run your search on a new JSON output to check that I haven't missed any uses of 'unknown' expression. If they have all successfully been removed please go ahead and disable the 'unknown' expression type.

Tagging @martin2urban FYI the JSON output files you previously sent MC for both 'approved' and 'all' sessions will contain 'unknown' expression type in some of the genotypes prior to my corrections. This may not be a problem but I thought I would draw your attention to it.

jseager7 commented 4 years ago

@CuzickA Many thanks for all your hard work on this. I've checked the export, and there's just one reference to 'Unknown' expression remaining: it's in PMID:30610168 (session 79c56f92435923ab), annotated on the MGG_08054+ allele.

image

CuzickA commented 4 years ago

Thanks @jseager7 I have now deleted the above unused genotype.

jseager7 commented 4 years ago

Thanks. I've double checked the export and there are no more uses of Unknown expression. Closing now.