SARS-CoV2 is listed as a blank entry in the browse species list

[vanaukenk]

Creating the ticket here since this is where the issue is visible, although the work may need to be done elsewhere.

The Browse species menu has a blank entry that, when clicked, shows three SARS-COV2-containing models.

We need to update the Browse species menu to list the proper species name for SARS-COV2.

[tmushayahama]

@ukemi @vanaukenk @lpalbou lets go through some landing page tickets sometime if tagged high priority. I just saw this old ticket now.

[vanaukenk]

This is still unresolved on the Noctua and Noctua-dev landing pages, but I'm not sure what needs to be done to fix this. We need input from @kltm @balhoff @cmungall

[vanaukenk]

[kltm]

First step here is to understand where the data is coming from. It this a list from minerva? An external source?

[vanaukenk]

@tmushayahama - what is the source of the species data for the browsing functionality on the Noctua landing page?

[tmushayahama]

@vanaukenk @kltm it is coming from minerva search taxa api specifically http://barista-dev.berkeleybop.org/search/taxa . More specifically it is a sparql query to get distinct model level metadata (annotation) for taxon. Code is here https://github.com/geneontology/minerva/blob/735ab0fc14af3b219567ca68521671a13d44b14f/minerva-server/src/main/java/org/geneontology/minerva/server/handler/TaxonHandler.java#L64

@balhoff will have more info on this

[vanaukenk]

@balhoff @cmungall Do you know if there's additional work that needs to be done here? Thx.

[kltm]

[adjusted comment to add a little more clarity] @vanaukenk I believe the work here would be to 1) check that the upstream data is correct 2) check that minerva is interpreting it correctly and 3) check that sparql query is correct (pretty likely). This data would be coming in through ontology/import, @balhoff would probably be the best trace that at the moment. (I would note that incidentally that NEO (noctua-amigo) does not seem to have this information either and they share some of the same sources.) That said, I'm a little unclear about the expectations in the interface given some of the trouble we've had around the sars-cov2 annotation. it might be good to understand what the correct answer here is and work backwards.

[balhoff]

The PR by @cmungall was supposed to have included NCBITaxon:2697049 in the taxslim, which is imported into go-gaf and go-lego. However I don't see it in the latest release. I'm looking into it.

[vanaukenk]

This appears to be fixed on production. Thx.

[tmushayahama]

@vanaukenk @balhoff I don't think it is fixed, just checked the production. Now the models are not present (0 results). Also on a separate note, no organism should have 0 results as the Sparql query is "Give all unique species in models" i.e. at least one model @balhoff can you check the /taxa endpoint https://github.com/geneontology/minerva/blob/7a068ed41dc9a95652e25cba73c60ead9a214e23/minerva-server/src/main/java/org/geneontology/minerva/server/handler/TaxonHandler.java#L64

[pgaudet]

My understanding from discussions with @kltm is that the SARS-CoV2 is not in NEO anymore? Can someone confirm whether this is the case?

[kltm]

@pgaudet sars-cov2 is not currently being added to NEO. See https://github.com/geneontology/neo/issues/85

[vanaukenk]

This is fixed.