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Why can't I find CPT concepts in my CONCEPTS table?

Vocabulary Users
#1

I’ve spent a frustrating morning trying to figure out why I don’t have any CPT concepts in the CONCEPTS table. So I came to the OHDSI forums and I find tantalizing clues. It seems that I missed a step by not running the CPT4.jar file. But when I find the cpt4.jar file in my downloads folder, I can’t get it to run by double-clicking it and I find I need to run it from a batch file, but that doesn’t work either. Then I find the file has been updated and I should download the new one, but I can’t find it on GitHub.

So I thought that maybe with the help of people who know what they’re doing, we could have a thread which answers all of these questions for those of us who are new to this. Things like:

  1. What is wrong with the CONCEPT.CSV file that requires correction?
  2. Where can I find the latest version of cpt4.jar?
  3. What exactly does cpt4.jar do?
  4. How exactly (with details) do you run the cpt4.jar file?
  5. Why doesn’t someone just correct the CONCEPT.CSV file and repost it?
  6. Is it possible for someone to just extract the CPT records from the corrected CONCEPT.CSV file (maybe call it CPT_CONCEPT.CSV) and post those so they could just be appended to existing concepts tables?

I’ve created 6 OMOP instances and appending the missing data would be preferable to deleting and reloading a complete concepts table.

Thanks for any insights.

–Roger Carlson

#2

@roger.carlson:

Sorry to hear your frustration. It’s actually straightforward:

Our license agreement does not allow us to distribute the descriptions of CPT4 codes. Only the codes themselves. The National Library of Medicine (with the UMLS), the CMS and the AMA are the only organizations who can do that. You need to have a license from any of those institutions. The easiest license to get is the one through the UMLS, and they will make you agree with the license. After that, you can manually retrieve every CPT4 description (not a good idea) or make it easy on yourself and run the cpt4.jar tool, which will fetch the descriptions for you. Sorry about that, but there is nothing we can do.We had many conversations with the AMA about it.

In your download zip file.

See above.

As written in the email with the download link and the readme file. You can run the bat file, or you copy into the command the line “java -Dumls-user=xxx -Dumls-password=xxx -jar cpt4.jar 5”, You need to put your UMLS login and password in.

See above. We would violate our license.

See above. We would violate our license.

Yeah. Don’t do it. Run the jar and your concept file will be perfect.

#3

Thanks, Christian. That helps a lot.

#4

Do I actually need the concept_name to use the cpt codes in the concept table. IOW, if I loaded the CONCEPT_CPT.CSV into the concepts table, shouldn’t I be able to use that for mapping even without the concept name?

#5

@roger.carlson:
concept_name column cannot be null in concept table. If you try to load CONCEPT_CPT.CSV directly into the concept table, an error will be thrown – with my own experience.

#6

@roger.carlson we are having issues with executing the jar file using our credentials and UMLS support has not responded to requests. Any thoughts?

Vocab Constraints Issue - Help required
#7

I ran that jar file with my company UMLS credentials a few days ago. Everything worked correctly.

#8

@s_wood_villagemd It could be a number of things. Your UMLS login/password may be incorrect. Or you may not be running the jar file correctly. How are you running it?

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