Invalid predicates - Githubissues

Knowledge-Graph-Hub / kg-phenio

A graph for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.

BSD 3-Clause "New" or "Revised" License

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Invalid predicates #103

Open kevinschaper opened 1 year ago

kevinschaper commented 1 year ago

I'm stripping off invalid predicates in my phenio filtering in monarch-ingest, and found that I have 5128244 edges with predicates that aren't in biolink model, the categories are: 'biolink:category', 'biolink:inverseOf', 'biolink:subPropertyOf'

I'm not sure if these are edges that we want to keep and need to fix the predicates, or if these are just properties that are staying as edges in the conversion.

matentzn commented 1 year ago

What do you mean by "valid"?

category exists: https://github.com/biolink/biolink-model/blob/master/biolink-model.yaml#L507

We should:

not filter out edges with invalid predicates, but include edges with valid ones (assuming that 1 edge can have more than one predicate)
Figure out what the deal is with subPropertyOf which is probably added by KGX - and should probably be added to biolink (instead of this horrible mapping)

caufieldjh commented 1 year ago

The majority (maybe even all!) of those 'biolink:category' nodes are leftovers from category mapping in the phenio build and serve no purpose in the final graph. It's fully redundant when the categories are also present as node properties. I've added a step to remove these edges during KG-Phenio assembly but, embarrassingly, that step doesn't work correctly.