Comments (14)
@ukemi @vanaukenk @lpalbou lets go through some landing page tickets sometime if tagged high priority. I just saw this old ticket now.
from noctua-landing-page.
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
from noctua-landing-page.
from noctua-landing-page.
First step here is to understand where the data is coming from. It this a list from minerva? An external source?
from noctua-landing-page.
@tmushayahama - what is the source of the species data for the browsing functionality on the Noctua landing page?
from noctua-landing-page.
@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
from noctua-landing-page.
@balhoff @cmungall
Do you know if there's additional work that needs to be done here? Thx.
from noctua-landing-page.
[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.
from noctua-landing-page.
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.
from noctua-landing-page.
This appears to be fixed on production. Thx.
from noctua-landing-page.
@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
from noctua-landing-page.
My understanding from discussions with @kltm is that the SARS-CoV2 is not in NEO anymore? Can someone confirm whether this is the case?
from noctua-landing-page.
@pgaudet sars-cov2 is not currently being added to NEO. See geneontology/neo#85
from noctua-landing-page.
This is fixed.
from noctua-landing-page.
Related Issues (20)
- Getting all annotations to an obsolete term in a single search HOT 1
- Browse by Species field is wrong size HOT 1
- Standardize Organism filter
- Add option or default to search over 'regulates' for 'Filter by Term' for models
- Add reference input helper popup
- add ability to filter on model id from the landing page HOT 14
- add expand/collapse option to landing page to quickly scan annotations in models HOT 1
- Figure out a way to limit what groups are listed on the landing page HOT 2
- Model state not displaying on landing page for a particular model HOT 5
- Add columns and icons for 'errors' and 'unsaved' model-level metadata HOT 1
- Consider adding an 'announcements' banner HOT 4
- Organisms on the autocomplete not displaying HOT 3
- Protein-containing complex (GO:0032991) and children no longer available in term search autocomplete HOT 2
- New bug in mousing over form and graph icons HOT 1
- Add Pathway Editor icon to the Open In menu on the Noctua landing page HOT 1
- Blank entries at the top of the list for Organism filter HOT 13
- Save functionality under the Model Info section is not working HOT 1
- "exact term" is no longer default
- Enable searching on obsolete terms HOT 5
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