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TranslatorSRI / Babel

Babel creates cliques of equivalent identifiers across many biomedical vocabularies.
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Reassign neoplastic process from UMLS as a finding rather than a disease #111

Open gaurav opened 1 year ago

gaurav commented 1 year ago

On Slack, @colleenXu pointed out that it might make more sense for "Neoplastic process" (T191 or tree number B2.2.1.2.1.2) to be classified as a phenotypic finding rather than a disease. The code that does this is in createcompendia/diseasephenotype.py:

https://github.com/TranslatorSRI/Babel/blob/8505163b6275eded51336d21ae7e0609b2e24cbc/src/createcompendia/diseasephenotype.py#L70-L89

It would be pretty easy to reclassify B2.2.1.2.1.2 as a phenotypic feature rather than a disease, but I'm not sure about the consequences of doing so. The description of Anatomical Abnormality (T190 or A1.2.2) mentions that, "If an anatomical abnormality has a pathologic manifestation, then it will additionally be given the type 'Disease or Syndrome', e.g., "Diabetic Cataract" will be double-typed for this reason." -- so I wonder if a similar consideration is why neoplastic process is classified as a disease instead of a phenotypic feature.

colleenXu commented 1 year ago

I'm kinda confused here. How is the UMLS "neoplastic process" semantic-type related to the NCIT term Acute lymphoid leukemia in remission?

For reference, my original comment in Slack was:

Also wondering if this NCIT term should be a PhenotypicFeature / ClinicalFinding rather than a Disease: Acute lymphoid leukemia in remission https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=NCIT%3AC3586&conflate=true