Amy Glen

Can you post the query(ies) used to produce the above nodes? I suspect that the query asked for `biolink:ChemicalEntity`; our system currently overrides `Node.categories` with the specific category(ies) the query...

it looks like, during canonicalization of KG2, one of the concepts equivalent to UniProtKB:P45983 has a category of ChemicalEntity, which explains why that concept cluster is being returned. maybe it's...

noted - definitely worth considering excluding deprecated nodes from canonicalization. although, apparently 68% of the nodes in KG2pre are marked as `deprecated=true`, so if we fully excluded those nodes, I...

yup, looks like the KEGG node is the problem as @edeutsch explained above in the case of rheumatoid arthritis - just ran this query on KG2.7.5pre neo4j: ``` match (n)...

though I just looked into a second example (MONDO:0005550 - 'infectious disease'), and in this case it seems that a REACT node is the problem: ``` match (n) where n.id...

but a little more surveying seems to suggest KEGG is the bigger problem - some other examples of KEGG nodes incorrectly labeled as Pathways in KG2pre are: * KEGG:04930 -...

this is still an issue in RTX-KG2pre; for instance, this node in KG2.8.2pre named 'Melanoma' has a category of Pathway: ``` { "id": "KEGG:05218", "name": "Melanoma", "full_name": "Melanoma", "category": "biolink:Pathway",...