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Missing NDC and HCPCS in OMOP and Athena


(Dennis) #1

I have a list of about 5000 NDC and HCPCS codes in a flat file which I am trying to see if those are existing in OMOP concept table. I downloaded NDC and HCPCS CDM tables from Athena and what I found was about 700 codes (NDC + HCPCS codes) are missing in the latest Athena download. That is, about 15% of the source NDC and/or HCPCS codes does not have a valid concept_code in concept table. What could be the reasons for this? If it’s of any help, here are sample 10 codes that don’t have a match in concept table.

38779227403
10106006101
J7630
49452233902
K0511
54569571300
W9092
54569296200
38779021206


(Dmytry Dymshyts) #2

@dennisrobert:

The reason is probably that they are old and obsolete, and the places we source them from don’t have them anymore. Remember: When the CMS deprecates a HCPCS code it will eradicate it from the website, so no dummy will still use it accidentally. We have been discussing this very subject here


and here

So, can you please create google document with those 700 concepts, and put the link here. And we can add the concepts then.
the format of the file:
code, description, vocabulary_id, earliest observation, latest observation


(Dennis) #3

Thanks @Dymshyts for the response. I do not have information on the description, earliest and latest observation. Will this still be useful if I share the data then?


(Dmytry Dymshyts) #4

Earliest and latest observation are the first and last occurrence of those concepts in your data.
Yes, you can share the data or just the list of the concept codes.
Actually, they are not very useful without the description, but we can try to find these descriptions elsewhere.


(Dennis) #5

@Dymshyts
Alright, here is the file
https://drive.google.com/file/d/1znF4kSO9pqNhQ2fvhvU7w8f6Re06vrwW/view?usp=sharing

Thanks again.


(Dmytry Dymshyts) #6

So I took a look on HCPCS codes,
some can be found here


so we need to scrap all this https://www.findacode.com/hcpcs-supply-codes.html in order to find some missing codes.
some can be found here:
https://seer.cancer.gov/oncologytoolbox/canmed/hcpcs/
this list we have already, so we add HCPCS concepts from here to the next HCPCS release


(Christian Reich) #7

@dennisrobert:

Thanks for the spreadsheet, but you don’t have the descriptions? And can you see in your data and give us the first and last time stamp?


(Dennis) #8

@Christian_Reich
I don’t have the corresponding NDC/HCPCS descriptions. The objective was to get it from OMOP CDM CONCEPT table. With regard to the timestamps, as I have access only to these codes and not anything else, getting first and last timestamps is also not possible. Apologies.


(Christian Reich) #9

@dennisrobert:

Understood. I thought you got data with these codes. Dima started hunting them down, but feel free to also google or use other methods. There is no magic to this.


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