Annotation Preview lists additional "enabled by GENEPRODUCT" in extensions

[suzialeksander]

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.

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

tagging @dustine32

[dustine32]

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]

@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]

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]

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

[suzialeksander]

For the above model, the error is

Violations
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[
   {
      "shape": "obo:go/shapes/MolecularFunction",
      "constraints": [
         {
            "property": "RO:0002333",
            "cardinality": "[0; 1]",
            "nobjects": 2
         }
      ]
   }
]