Duplicated results

[khanspers]

I'm seeing something similar to what was reported here with some results being reported twice, with different identifiers:

The query is "What genes' activity may be decreased by Imatinib Mesylate": https://ui.test.transltr.io/results?l=Imatinib%20Mesylate&i=CHEBI:31690&t=4&r=0&q=c1469eda-0209-4d12-98ad-952498685545

[sstemann]

@gaurav could you please take a look?

[gaurav]

Thanks for poking me about this one, Sarah!

C-KIT Gene

UMLS:C0920288 "C-KIT Gene" does look like it should be combined with NCBIGene:3815 "KIT". There are two ways of connecting these two concepts via UMLS:

• NCIT:C18609 "KIT Gene", which is mapped to OMIM:164920 and HGNC:6342, and
• LOINC:LP94238-0, which is mapped to HGNC:6342

We don't currently ingest NCI or LOINC, so that's probably why these are missing. I've opened an issue to look into whether we should include NCIT mappings for genes (TranslatorSRI/Babel#350). We already have a ticket to ingest LOINC mappings (TranslatorSRI/Babel#295), but even if we were to do that, I'm not sure we would include gene mappings from there. I don't think there's a quick fix here apart from ingesting those mappings.

Note that there is one UMLS identifiers already associated with that gene in NodeNorm Guppy, which is UMLS:C1416655 "KIT gene". So we could also think of this as an error on UMLS' part for not combining UMLS:C1416655 and UMLS:C0920288 into a single concept. I've sent a message to their helpdesk to see if they agree.

FWIW both UMLS IDs are coming back from SemMedDB, but I don't think there's any clever way of catching the duplication there.

ABL1 gene/protein

Similar situation: the only thing UMLS:C1439337 "Tyrosine-Protein Kinase ABL1, human" is connected to is NCIT:C17390 "Tyrosine-Protein Kinase ABL1", which is connected to OMIM:189980 and SwissPort P00519, both of which resolve to NCBIGene:25 on NodeNorm Guppy. So including NCIT mappings would fix this as well.

Overall resolution

Depends on adding NCIT mapping to genes in NodeNorm (TranslatorSRI/Babel#350), which I'll try to get into the NodeNorm November release.