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Mapping of records - Retrieving standard concept


(Selva Muthu Kumaran Sathappan) #1

Hello Everyone,

I am a new joinee here. Recently joined a public health institute after my graduation. I am currently doing manual mapping between our terms and Athena standard terms. My question is how can I get a single record as a result through Athena search. For example, I have a query term “Basophils” under “measurment” domain, “Lab Test” class and “LOINC” vocabulary. Inspite of multiple filters, I get multiple records as output. Is there anyway how can I find that one matching record as output? As I am from a non medical/non health care background, it is quite time consuming for me do this for all the records and the accuracy of my mapping is also not high. Do you have any suggestions/approach on how can I get these kind of tasks done with high accuracy and efficiency?

Or how can I find that one corresponding accurate standard concept from multiple results? Is there any reading that I should be doing?

Just FYI, our input/terms sheet only has these lab test name and lab test result code if that can help

As I am from a tech background, need some guidance on this area. Neither my team is experienced in this. Thanks for your time


(Anna Ostropolets) #2

I can feel your pain. Manual mapping has never been enjoyable or efficient enough. Long story short: you can use Usagi or Metamap.
The latter might give you better results but requires an additional transformation of UMLS codes to OMOP concept codes; USAGI is pretty intuitive and will give you OMOP concept_ids right away.