Biolink merge brings in LinkML types

[caufieldjh]

Describe the bug

See monarch-initiative/monarch-ingest#468 (comment)

Biolink imports linkml types (see https://github.com/biolink/biolink-model/blob/master/biolink-model.ttl) but these types remain in Phenio, hence they become nodes in KG-Phenio.
They don't serve any purpose here.

[matentzn]

So how will you avoid them being nodes? the moment you say:

MONDO:123 bl:category bl:Disease

That moment bl:Disease will become a node, right?

[caufieldjh]

It does, and that's a separate (but related) issue - in this case it's that all children of bl:named_thing have slots with types defined by linkml:types, so we essentially need the base version of whatever a linkml schema is, except with all the roots for namespaces in Phenio like MONDO

[matentzn]

Maybe easier for now to just extract a filter module from the linkml schema, only including the exact terms that are in there, and only configuring certain properties to be included?