Investigate Shex violations of Reactome import

[ukemi]

In the recent import of a slice of Reactome (#3), many models failed the Shex. Looking into this problem more closely suggests that there is an issue with the way cellular components are being handled in the Reactome models.

Here is an example of a Shex violation from one of the newly imported models:
R-HSA-8850843.ttl Phosphate bond hydrolysis by NTPDase proteins - imported from: Reactome http://model.geneontology.org/R-HSA-8850843 gomodel:R-HSA-8851234 [GO:0017111] BFO:0000066 [obo:go/shapes/AnatomicalEntity] gomodel:reaction_R-HSA-8851234_location_lociGO_0000139 [GO:0000139]

If I am interpreting this correctly, it is saying that there is a violation because a molrcular functions needs to occur in an anatomical entitiy, but GO:0000139 (Golgi membrane), is not an anatomical entity.

Last week when we looked at this closer we confirmed that models made by curators are passing the Shex. For example:
http://noctua.geneontology.org/editor/graph/gomodel:60ff660000001331 has a molecular function occurring in the cytosol, but running the reasoner does not violate Shex.

However, Reactome models that were imported during the last 'official' import are now violating Shex:
in http://noctua.geneontology.org/editor/graph/gomodel:R-HSA-196741, the only changes we have made to the model are in the layout. However, if you look at individuals of molecular functions that are occurring in some cellular component, they are violating the Shex, Edit Instance: gomodel:R-HSA-5223313 and Edit Instance: gomodel:R-HSA-5693319.

It seems like something has gone awry with the the Shex validation of molecular functions occurring in cellular components since the initial import since I think at that time, there were very few Shex violations. Here is the blurb about the violation:

[
{
"shape": "obo:go/shapes/TransporterActivity",
"constraints": [
{
"object": "gomodel:reaction_R-HSA-5223313_location_lociGO_0005765",
"property": "BFO:0000066",
"node_types": [
"GO:0140359"
],
"object_types": [
"GO:0005765"
],
"nobjects": 0,
"matched_range_shapes": [

        ],
        "intended-range-shapes": [
           "obo:go/shapes/AnatomicalEntity"
        ]
     }
  ]

}
]

Removing the information about where the molecular function occurs results in this individual passing the Shex.