Open dougli1sqrd opened 4 years ago
The question would seem to be whether or not this is an intermediate production for the annotation production. If so, I'd say they go on the pile in /products/annotation; if not, some new top-level directory in /products, TBD.
If it is this--https://github.com/biolink/ontobio/issues/341#issuecomment-499292690--but for all files, I would be tempted not to load any more into the Makefile, but to add it as a separately optimizable step that is making a distinct product.
This is an earlier version of what would be added to the pipeline
sh 'materialize.py --log target/groups/mgi/mgi-inferences.log infer --ontology target/go-ontology.json --target target/groups/mgi/mgi.inferred.gaf --gaf target/groups/mgi/mgi.gaf'
sh 'materialize.py --log target/groups/pombase/pombase-inferences.log infer --ontology target/go-ontology.json --target target/groups/pombase/pombase.inferred.gaf --gaf target/groups/pombase/pombase.gaf'
sh 'materialize.py --log target/groups/wb/wb-inferences.log infer --ontology target/go-ontology.json --target target/groups/wb/wb.inferred.gaf --gaf target/groups/wb/wb.gaf'<br class="Apple-interchange-newline">
The way we'd want to do this moving forward would have changed. Adding here as the branch that this work was on as an experiment will be removed.
@kltm I'd like to propose to put this in a current project - this would address
https://github.com/geneontology/go-ontology/issues/19721 and generally, allow curators to sop making double annotations.
Thanks, Pascale
@pgaudet It depends on how you might want to look at this. IIRC, this might be a bigger ask as it was not as far along as we thought when work stopped on it. It has been a few years(!) since this was in the fire, so my memory is a little hazy. Either way, depending on priorities, this might be something that @dustine32 could help us out with in March. @pgaudet , how about if we touch bases on this on Monday?
@pgaudet - I could have sworn we had a GO rule for this? I can't find it
We shouldn't be implementing this if there is no clearly documented rule
Sure I can make a rule, I didn't know that this is how we wanted to implemented this.
It would be nice to distinguish between an annontation rule (what is allowed and not allowed) versus post-processing we do on annotation, like interontology links and asserting has part annotations.
(@kltm I put the other ticket in the pipeline QC and maintenance - up to you where these go)
@pgaudet Is it a separate issue or related to this?
Noting creation of GORULE:0000062 for this https://github.com/geneontology/go-site/pull/1810
@dustine32 @pgaudet Okay, I think I have a handle on this. I think the things that need to be done are:
I think this may be out of scope for the "cleanup" project, so bumping over to QC for the time being.
In Issue https://github.com/biolink/ontobio/issues/341 we made a script for producing
enables o has_part -> enables
annotations in ontobio. We ran the results in a specialized jenkins job and posted the results to skyhook. Details in the ticket link above.These should be run in the pipeline on all sources.
The script returns a log and inferred annotations in this way.
We need: