Add more Biolink category checks

Knowledge-Graph-Hub / universalizer

The KG-Hub Universalizer provides functions for knowledge graph cleanup and identifier normalization.

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

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Add more Biolink category checks #5

Closed caufieldjh closed 1 year ago

caufieldjh commented 1 year ago

At present, Biolink categories are only:

Checked to ensure they aren't OntologyClass
Assigned on a node-by-node basis through SSSOM maps

It would be preferable to do additional category verification by getting categories with OAK (see what KGX does too)

This should be optional from the CLI.

Gotta output a list of "unmappable" nodes in order to catch those OAK may not know about.

matentzn commented 1 year ago

Yeah, I think this is a very good idea.

caufieldjh commented 1 year ago

Also need to check for existence of conflicting category assignments. A node can have multiple categories, but not if any of them are the wrong type (like OntologyClass) or incompatible as per Biolink.

There may be category assignments represented as relations, and that's mostly just noise in a property graph, but it's preferable to convert them to categories and remove the redundant relations.