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Missing concepts in CPT4 vocabulary in OMOP vocabulary v5.0 31-AUG-23


I downloaded OMOP standard vocabularies on 1/5/2024 with version v5.0 31-AUG-23. However, following OMOP concepts are missing in CPT4 vocabulary in the new OMOP vocabulary download.

  • 2101937 Initial evaluation for condition (HEP C)(EPI, DSP)
  • 2110284 Fetal non-stress test
  • 2213559 Interpretation or explanation of results of psychiatric, other medical examinations and procedures, or other accumulated data to family or other responsible persons, or advising them how to assist patient
  • 2313621 Breath hydrogen or methane test (eg, for detection of lactase deficiency, fructose intolerance, bacterial overgrowth, or oro-cecal gastrointestinal transit)

I can find these concepts in the CONCEPT_CPT4.csv file, but not in the CONCEPT.csv, in the 1/5/2024 download.

The cpt4.jar ran successfully with no errors.

The previous OMOP vocabulary I downloaded was on 5/2/2023 with version v5.0 23-JAN-23. The above four concepts were presented.

Please advise how to fix it.



I am sorry for tagging you if you are not the right person to ask. If so, can you please let me know where I can find help for this issue.


Hi @jchang:

It’s there in Athena. Must be something with running the jar. Let me pass this on to somebody.

Thanks @Christian_Reich

I unpack the downloaded vocabulary zip file again, but couldn’t find those concept in the CONCEPT.csv file, this is before running the jar file.


They won’t be there before you run the cpt4.jar since this is the program that adds them. Even though you ran it with no issues before, I’ll suggest re-running it. UMLS API can be erratic sometimes.


Thank you, Anna. I did notice there were some failures in updating the concepts, including the above-mentioned 4 cpt code concepts.

I just re-ran the cpt4.jar, but saw the similar failures in the log file. Should I keep running it? is there an alternative approach?