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Create a GO-CAM -> TSV file for end user consumption #2008
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Also tagging @pgaudet |
Noting for @balhoff, technically, not having the SPARQL endpoint or store involved (i.e. a file-to-file transformation) would likely be easier to reuse and recreate. (Dealing with the endpoint complicates things and the blazegraph is--or should be--a moving target right now.) |
@cmungall what are the desired columns? Something like this (using noted property path)?
Taking this model as an example: http:https://noctua.geneontology.org/editor/graph/gomodel:645d887900000758? For hormone activity enabled by BGLAP, would we only include the |
And for the BGLAP model mentioned above:
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@balhoff Curious: would end users be wanting URIs or CURIEs? Guess it depends on the audience? |
@kltm just an information example for now. We can do curies in the end. But I want to check that I'm pulling out the right stuff. |
I think having a pipe separate list for this should be fine (it should always be a tree structure and hence the list can always be interpreted as a chain) It may turn out that this is overkill and there is not so much information in nested part-ofs. Looking at that model, one of the paths is clearly wrong (unless neurotransmitters can think). But as a first pass, having this be transparent is a great way for us to easily spot check some of these |
@cmungall specifying the order of transitive part-ofs might require a different approach; I'm using SPARQL right now, nice and simple but property paths don't capture that. If we're okay with interpreting as a bag of relevant terms then we can use the property paths. |
With some BP and CC aggregation (unordered):
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Create a GO-CAM -> TSV file for end user consumption.
This could fill the ecological niche of our previous SIF effort.
TBD:
Tagging @dustine32 @balhoff
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