search

geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
BSD 3-Clause "New" or "Revised" License
31 stars 10 forks source link

Add report in 'direct_annot_to_list_of_terms' and 'reg_ann_to_list_of_terms' to include a group with ECO_0000204 #4963

Open pgaudet opened 5 months ago

pgaudet commented 5 months ago

We would like to add another report in the GH actions triggered by the labels direct_ann_to_list_of_terms and reg_ann_to_list_of_terms

to also include TAS and NAS? We end up missing Reactome (TAS) annotations. (and we might was well fix NAS annotations.)

Thanks, Pascale

@deustp01

kltm commented 5 months ago

[@pgaudet I directly edited yours above to clarify]

kltm commented 5 months ago

Let me clarify this a little: currently, the GOlr query uses evidence_subset_closure:ECO:0000006 directly--there is no "evidence list" being used. Is there another term that you wish to be used instead of ECO:0000006 ("experimental evidence) as the single ECO term closure used? Otherwise, it would require some rewriting, and I'd want to ticket it as a project (i.e. not a trivial change).

pgaudet commented 4 months ago

Ha ! Makes sense. Could we have another report in the list of reports, to children of author statement http://purl.obolibrary.org/obo/ECO_0000204?

kltm commented 3 months ago

@mugitty I think this may be what @pgaudet was outlining?

mugitty commented 3 months ago

@kltm, @pgaudet confirmed that this was the feature request

pgaudet commented 3 weeks ago

@kltm can this be implemented?

pgaudet commented 3 weeks ago

@cmungall

pgaudet commented 1 week ago

Please include this in the 'normal' EXP report if possible, or generate another report 'GOIDs__author-statement'

kltm commented 1 week ago

Clarifying for my own use, we want to have a union of results with (new) ECO:0000204 and (current) ECO:0000006.

kltm commented 1 week ago

@pgaudet PR at https://github.com/geneontology/go-annotation/pull/5290 . I think it's good to merge; if you have a moment for testing, could you merge it in and give it a spin?