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Which version to download?

Vocabulary Users
#1

It seems the interface on athena.ohdsi.org for vocabularies download changed dramatically, and it now offers download of version 5.1.0 and version CDM. So which one is the latest? The version string in VOCABULARY.CSV for “None” seems to be identical in both.

Thanks in advance.

#2

Hi,
do you ask about these two options, right?
They mean the same, sorry for the ambiguity.

BR, Maria

#3

Thank you!

#4

One more question (or should I start a new topic for that?)
The unpacking of CPT4 codes overwrites downloaded CONCEPT.csv - should it do that? We followed the instructions in this automated email from Athena:

Important: All vocabularies are fully represented in the downloaded files with the exception of CPT-4: OHDSI does not have a distribution license to ship CPT-4 codes together with the descriptions. Therefore, we provide you with a utility that downloads the descriptions separately and merges them together with everything else. After unpacking, simply open a command line in the directory you unpacked all the files into and run “java -Dumls-user=xxx -Dumls-password=xxx -jar cpt4.jar 5”. Please replace “xxx” with UMLS username and password.

and the result was as follows:

Updated CPT4 records: 15640, records to update: 0
All cpt4 concepts are processed.
Writing updated data to CONCEPT.csv
CPT successfully updated.

So the CONCEPT.CSV now contains only CPT4 concepts (and the size is 2 MB from some 800 MB).

#5

Did you download ALL of the vocabularies you want? Or did you just download CPT4?

#6

Are you sure you downloaded bundle (concept.csv) with other vocabularies? And also your concept.csv (before cpr4) was not corrupted?

#7

We downloaded everything - CONCEPT.csv was ~800 MB before running the java code, and it was overwritten by the code.

#8

Yes, we did. And CONCEPT.csv before running java code was ~800 MB, but got overwritten by the code, and now contains only ~2 MB worth of CPT-4 concepts only.

#9

Thank you for the feedback - It definitely should be investigated. I will do it and let you know about the result.
As workaround I can suggest to upload concepts in 2 steps: first - everything from the original concept.scv (excluding concepts with vocabulary_id = ‘CPT4’), second - everything from the updated concept.csv (where are only cpt4 concepts). Sorry for the inconvenience.

#10

Thank you. This is exactly what we did. I just wanted to report the bug.

t