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mapping-commons / sssom

Simple Standard for Sharing Ontology Mappings
https://mapping-commons.github.io/sssom/
BSD 3-Clause "New" or "Revised" License
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`mapping_justification` for automated mappings #253

Open a-chahin opened 1 year ago

a-chahin commented 1 year ago

We are using a script to automate the mapping of medication data from NDC codes to RxNorm RXCUIs utilizing the "Non-Standard to Standard Relationship" mapping found in the OMOP common data model. Is semapv:MappingChaining the correct mapping justification in this case? or is there a better alternative for automated mappings?

matentzn commented 1 year ago

For the rest, here my preliminary answer I gave in https://github.com/MIT-LCP/mimic-code/pull/1418#issuecomment-1408445056

@a-chahin There are no 100% matured guidelines here. I would recommend using semapv:MappingChaining only when two already established mappings are combined. If there is a mapping justification and semantic mapping predicate for NDC->OMOP (i.e. semapv:LexicalMatching, and skos:exactMatch) and the same for OMOP->Rxnorm (which afaik there is not, because OMOP standard to non standard is "exact or broad", with no way to know which is which, and no formal justifications combined).

Its tough in your case. Depending on the mapping predicate you use for the NDC->RxNorm mapping, maybe semapv:MappingChaining is ok, but then I would make a comment in the mapping set metadata saying how the chaining exactly was applied (e.g. how you interpreted the OMOP NS-S mappings).