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TranslatorSRI / NodeNormalization

Service that produces Translator compliant nodes given a curie
MIT License
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support for LOINC curies #214

Open gglusman opened 1 year ago

gglusman commented 1 year ago

Our Multiomics Wellness KG uses LOINC curies. Evan tells me the LOINC namespace isn't currently supported. What needs to be done to support it? Thanks, -- Gwênlyn

gaurav commented 1 year ago

I think there's three main things we'll need to add LOINC CURIEs to NodeNorm/NameRes:

  1. Figuring out which Biolink types to classify these CURIEs as. I think these are the classification types for LOINC identifiers, so we might need to map all of them to Biolink types, although it looks like most of them might be ClinicalFinding (which we could record as a ClinicalMeasurement), biolink:Procedure and biolink:AdministrativeEntity.
  2. Figuring out if LOINC identifiers should be cliqued with existing identifiers. The main overlap is between LOINC (e.g. LOINC:8480-6 "systolic blood pressure"), UMLS terms (e.g. UMLS:C0871470 "Systolic Pressure") and EFO (e.g. EFO:0006335 "systolic blood pressure"). UMLS has some LOINC identifiers for some concepts, but not for this one, and EFO has mappings to NCIt, SNOMEDCT and MedDRA. I'd like to find resources that comprehensively map LOINC to identifiers that can be mapped to EFO and UMLS before we add LOINC.
  3. Based on section 10 of the LOINC license, it looks like we should be able to incorporate LOINC IDs in NodeNorm as long as we credit them properly (which we should be able to do once we have EPC in NodeNorm, https://github.com/TranslatorSRI/NodeNormalization/issues/218).

@cbizon I'm tagging you into this conversation in case you have any insights on EFO-LOINC mappings or if you have any other thoughts on adding LOINC to Babel.