NN failures: JAK genes

[cbizon]

Query: What genes are downed by Ruxolitinib?

PK: ab417e9e-cac8-45c8-a114-4f4d4514c038

We get results for JAK1, JAK2, and JAK3, but also at least "Janus Kinase 1" and "Janus Kinase 2".

It looks like the UMLS identifiers (e.g. UMLS:C0169661) are not merging with the other gene/protein ids.

[gaurav]

I've confirmed that UMLS:C0169661 "Janus kinase 2" is being included by the protein module, not the leftover UMLS module. It really should be combined with UniProtKB:A8K910 "A8K910_HUMAN Tyrosine-protein kinase (trembl)" and UniProtKB:O60674 "JAK2_HUMAN Tyrosine-protein kinase JAK2 (sprot)" (which is not currently the case: https://nodenorm.ci.transltr.io/1.5/get_normalized_nodes?curie=NCBIGene%3A3717&curie=UMLS%3AC0169661&conflate=true&drug_chemical_conflate=false&description=false). I think this is another case of proteins and chemicals not being properly combined (TranslatorSRI/Babel#310), so diagnosing and fixing that issue should fix this as well. Assigning to Guppy.

[gaurav]

FWIW we do combine UMLS:C1527617 "JAK2 protein, human" with the other protein identifiers, but not UMLS:C0169661 "Janus kinase 2", which we have both as its own clique as a protein as well as in a ChemicalEntity clique with MESH:D053614 "Janus Kinase 2". So even once we close TranslatorSRI/Babel#310, there will be a bit left over as to why MESH:D053614 isn't being merged with the other JAX2 proteins.

[gaurav]

Pushing the chemical/protein issue to Hammerhead.

[sstemann]

this is still a problem in Hammerhead

https://ui.test.transltr.io/results?l=Ruxolitinib%20Phosphate&i=CHEBI:66917&t=4&r=0&q=6f79bab3-c6b8-43d7-a4b6-8a27e167ba82