A set of GO-CAMs built automatically from Reactome pathways.
geneontology / reactome-go-cams Goto Github PK
View Code? Open in Web Editor NEWA set of GO-CAMs built automatically from Reactome pathways.
A set of GO-CAMs built automatically from Reactome pathways.
I've taken a little bit of a look at this repo (reactome-go-cams), noctua-models master
, and noctua-models dev
and I think I have a better handle on what's going on. I believe that:
master
and noctua-models dev
are pretty much the same, except for ordering within the file (eyeballing and the fact that all the files are exactly the same size)dev
than master
; these are likely due to previous iterations and trials for reactome that were not wiped out in dev
, but overwrittenmaster
(i.e. automated saves to GH); while it may be due to tweaks to minerva that have happened, I have not checked to see if no people have ever modified themWhat I would propose is:
master
matching R-HSA-* are copied into reactome-go-cams and we declare that to be the source of truth (for things like resetting noctua-dev or emergencies)I'd appreciate feedback on that proposal, as well as somebody maybe double checking my thought process here.
@deustp01 URL for testing?
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.
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