Annotation Preview lists additional "enabled by GENEPRODUCT" in extensions

geneontology / minerva

BSD 3-Clause "New" or "Revised" License

6 stars 8 forks source link

Annotation Preview lists additional "enabled by GENEPRODUCT" in extensions #534

Open suzialeksander opened 12 months ago

suzialeksander commented 12 months ago

Some of the imported SGD YeastPathways have additional entities in the extensions. In gomodel:YeastPathways_TREDEG-YEAST-PWY, there is an annotation to ATH1 but there's a loose enabled_by(NTH1 Scer) in the extensions, and vice versa. This might have something to do with branched/cyclical pathways. Screenshot 2023-11-28 at 13 21 08

Additional oddity: ATH1 and NTH1 appear in GE, Alliance Pathway Preview. Visual Pathway Editor doesn't mention NTH1.

tagging @dustine32

dustine32 commented 12 months ago

Here's the whole model on Noctua prod: You can see each of the two enabled_by annotations (ATH1, NTH1) reflecting each other in their extensions fields.

Maybe a simple fix is to disallow enabled_by from being emitted in the GPAD export extensions column?

dustine32 commented 12 months ago

@balhoff If we wanted to remove enabled_by relations from Noctua GPAD export extensions column is this the line we'd need to take out? https://github.com/geneontology/minerva/blob/a6a9d0b84aac558fb077b3f2596bb5412710e74c/minerva-converter/src/main/resources/org/geneontology/minerva/legacy/sparql/gpad-extensions.rq#L75

Also tagging @vanaukenk @pgaudet as I feel this is executive decision-level stuff.

pgaudet commented 11 months ago

Discussion on the managers call:

There should not be 2 enablers, this violates ShEx.

Options to fix this would be

to create two separate models, one for each enabler,
or two individuals in the same model

If the model is fixed, then there will not be exported in the extensions.

Pascale

suzialeksander commented 11 months ago

note, i've manually fixed the model above. SGD is going to proceed to manually edit these models in Noctua production.

suzialeksander commented 11 months ago

For the above model, the error is

Violations
This feature is currently under development, with more user friendly error reports coming. If you have questions about the error messages you're seeing, please create a [ticket](https://github.com/geneontology/noctua).
[
   {
      "shape": "obo:go/shapes/MolecularFunction",
      "constraints": [
         {
            "property": "RO:0002333",
            "cardinality": "[0; 1]",
            "nobjects": 2
         }
      ]
   }
]