eGFR (Estimated glomerular filtration rate) mapped to Biomarker EGFR

[barveaditya]

Hello,

It looks like the lab test for eGFR (note the capitalisation - expanded to Estimated glomerular filtration rate) is mapped to Epidermal Growth Factor Receptor (EGFR; concept_id 3040084) in the lab names file (https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/OPTUM_PANTHER/Vocab%20Updates/JNJ_OPTUM_EHR_LABNAM.txt) as well as the NLPM file (https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/OPTUM_PANTHER/Vocab%20Updates/JNJ_OPTUM_EHR_NLPM.txt). This presents a problem of overwriting, and all eGFR tests need a separate one.

There also is a problem that multiple different Estimated glomerular filtration rates exist (mdrd, mayo, african-american, non-african-american), and while the non-african-american is mapped maybe correctly (concept: 3049187) in the NLPM file, all the other ones are mapped to the wrong one as above. Additionally, they also need to be correctly moved to the Labs section. We can hopefully resolve these concept_ids.

Regards Aditya

[clairblacketer]

Thank you @barveaditya! This is very helpful. We have a refresh of this ETL coming up and I will be sure to put it on the roadmap.

[bradanton]

Hi @clairblacketer, I have checked our local vocab and it looks good. I guess we can reload .txt files on Git as well, what do you think?

[clairblacketer]

Hi @bradanton yes, let's reload those files

[bradanton]

@clairblacketer https://github.com/OHDSI/ETL-LambdaBuilder/pull/114