Pheknowlator knowledge graph in OBO format about pheknowlator HOT 4 CLOSED

Update

@ablack3 take a look at the R Library called rdflib, it looks to parallel the library that I recommend in Python RDFLib and should provide you with the functionality you need.

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Hey @ablack3 - thanks so much for the suggestion. We will definitely look into creating a version of the output in OBO. I think that there are a few other formats that we provide that will still be useful for you (e.g. any of the identifier edge list text files).

In the meantime, I want to share a tutorial I created that provides examples in Python using NetworkX and RDFLib using the Vaccine Ontology from the Open Biomedical Ontology Foundry and one of the PheKnowLator builds.

Jupyter Notebook: RDF_Graph_Processing_Example.ipynb

Looking forward to going over this tomorrow!

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@bill-baumgartner - Do you know of an easy way to convert an OWL graph into an OBO graph? I suspect that this will be painful given that @ablack3 was unable to do this using ROBOT on only the merged ontology subset (meaning that the errors raised are from the original ontologies and are likely to vary by ontology).

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@ablack3 - closing this for now. Please re-open if you still need this output type.

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