OBO ontologies RO ids have incomplete mappings in Biolink and get rolled up to 'related_to'

[realmarcin]

We discovered this in KGX ontology transforms in KG-Microbe, but a general issue of ontology transforms (including PyOBO) based on the Biolink Model.

Examples:

ChEBI
urn:uuid:a9efa128-ffe9-42db-818e-d2d4708fe35a CHEBI:10002 biolink:related_to CHEBI:140378 RO:0000087 Graph

EC from PyOBO
urn:uuid:4254f6d3-43d9-4abf-ba1a-190ac8665fb3 EC:7.4.2.5 biolink:related_to GO:0015440 RO:0002327 Graph ec.json

One the example of ChEBI -- the RO ID comes from the ontology source. It is mapped to Biolink using the mappings in Biolink. If mappings are incomplete then the relation is rolled up to 'related_to'.

I am guessing the solutions involve improving Biolink mappings for ontology relations...