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TranslatorSRI / NodeNormalization

Service that produces Translator compliant nodes given a curie
MIT License
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Interleukin - 2 not working on node normalizer or arax synonyms #151

Open Genomewide opened 1 year ago

Genomewide commented 1 year ago

I think I found a normalization bug. Node normalizer returns nothing for either of these curies (FMA:84051 or LOINC:MTHU015779) for interleukin-2:

From the smart API:

curl -X 'GET' \
  'https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=LOINC%3AMTHU015779&conflate=true' \
  -H 'accept: application/json'

They are also disconnected on the ARAX synonyms search (if that is run on something different).

For FMA:84051 biolink:Protein Interleukin-2 is a named thing. This is different on the arax 'synonyms' than if you search for 'interleukin 2' which returns biolink:NamedThing and LOINC:MTHU015779?

So, the terms are unconnected and should be. An Screen Shot 2022-10-10 at 1 34 14 PM Screen Shot 2022-10-10 at 1 31 53 PM Screen Shot 2022-10-10 at 1 31 30 PM d you can only get to the ARAX FMA information is by searching with the FMA CURIE.

gaurav commented 1 year ago

Thanks for reporting this issue!

The development NodeNorm is out of sync with the production NameRes, since we're testing a new release, but the production NodeNorm (https://nodenorm.transltr.io/1.3/get_normalized_nodes?curie=LOINC%3AMTHU015779&conflate=true) doesn't have LOINC:MTHU015779. However, I'm not sure where LOINC:MTHU015779 is coming from -- if you search the production NameRes for interleukin 2, you get a bunch of results including PUBCHEM.COMPOUND:130168 and NCBIGene:3558 (https://name-lookup.transltr.io/lookup?string=interleukin%202&offset=0&limit=10). Both of those identifiers refer to the small molecule and gene form of interleukin-2 respectively (https://nodenorm.transltr.io/1.3/get_normalized_nodes?curie=PUBCHEM.COMPOUND%3A130168&curie=NCBIGene%3A3558&conflate=false).

So, I think the big questions is: where is ARAX's synonym search getting LOINC:MTHU015779, and how can we stop it? I had a look at the RTX repository, and it looks to me like it generates synonyms by itself. I've opened an issue with ARAX (https://github.com/RTXteam/RTX/issues/1920) and will follow up once I hear back from them.