PHI-base / curation

PHI-base curation

0 stars 0 forks source link

Update 'gene-for-gene' curation sessions with new GfG AE #82

Closed CuzickA closed 3 years ago

CuzickA commented 3 years ago

https://github.com/PHI-base/phipo/issues/272

https://github.com/PHI-base/curation/issues/65 DONE

CuzickA commented 3 years ago

https://github.com/PHI-base/curation/issues/19 DONE

CuzickA commented 3 years ago

https://github.com/PHI-base/curation/issues/73 DONE

CuzickA commented 3 years ago

This gene-for-gene curation session is incomplete and needs work https://canto.phi-base.org/curs/6dd9062354648dc7 https://github.com/PHI-base/curation/issues/62

CuzickA commented 3 years ago

https://github.com/PHI-base/curation/issues/22 DONE

Next check with @ValWood and Kim H-K whether we are happy with changes to these four gene-for-gene sessions.

CuzickA commented 3 years ago

New AE for Gene-for-Gene now enabled Need to update all sessions again and remove old AEs. Once this is done, curation type can be switched from PHI phenotype to Gene for gene phenotype and sessions can be reviewed with Val and Kim H-K.

65 Avr1/Sen1 DONE

73 Avrstb6/Stb6 DONE

19 Atr1/RPP1 DONE

62 Avr4/Cf4 incomplete session to review DONE

22 Tox1/Snn1 DONE

CuzickA commented 3 years ago

I believe I have removed all the old gene-for-gene AE and replaced with the new compound terms.

@jseager7 please go ahead and check if I have got them all and then switch the sessions over to the Gene-for-Gene Phenotype work flow. Thanks. PMID:31246152 PMID:29434355 PMID:20601497 PMID: 30148881 PMID:22241993

Next: Review the usage of the new compound AEs with Val and Kim H-K.

jseager7 commented 3 years ago

@CuzickA the only remaining annotations with the old gene-for-gene extensions are in the two test sessions (PMID:100900 and PMID:1). I don't think it will be a problem to leave these as they are since I'm going to be testing this change locally first. We should still be able to delete the old extensions even after the annotations are transferred to gene-for-gene phenotypes.

CuzickA commented 3 years ago

Thanks @jseager7 I forgot about the two test sessions! let me know how the local changes go

jseager7 commented 3 years ago

@CuzickA The local changes were fine, so I'll start applying the changes to the demo server first, then the main server. With regards to the old extensions that will be left over in the test sessions, I've confirmed that we can still remove them from annotations even after the annotations are transferred to the new type.

CuzickA commented 3 years ago

Currently reviewing sessions with Val and Kim H-K.

Closing ticket for now.