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Missing NAACCR Variables

Vocabulary Users
#1

Hello, I was trying to look for the OMOP concepts that are mapped to the following NAACCR fields but could not locate any. I tried to search in Athena as well. Please let me know if those are mapped or any reference where I can look for or if any work is under way? Thank you.

ALK Rearrangement​
BRAF Mutational Analysis​
CA 19-9 PreTX Lab Value​
EGFR Mutational Analysis​
NRAS Mutational Analysis​
p16​
PSA (Prostatic Specific Antigen)

Regards,
Anbu.

#2

Hi @Anbu!
NAACCR vocabulary is no longer under maintenance; the last content refresh was on 09-11-2021.
That’s why some concepts can be missed. Please welcome to Vocabulary WG and Oncology WG to discuss how to contribute better.

The important thing you should always keep in mind about NAACCR:
When you try to make proper structural mapping using the OMOPed version of NAACCR vocabulary, you should know exactly what version of the coding system is used in your data.

I tried to find NAACCR concepts related to the code of interest you mentioned - PSA (Prostatic Specific Antigen), and there are a bunch of concepts in the Athena.

#3

Thank you @Maria_Rogozhkina. Good point on the version used in the source system. Happy to be part of the WG to contribute and learn together.

Regards,
Anbu.

#4

These are all tests of somatic mutations. You can only record them if you have a value, i.e. knowledge whether or not a variation was found. If you have that, you can use the following

t