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

Vocabulary Users
#1

Hello,

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.

Thanks
Jack

#2

@Christian_Reich

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.

Thanks
Jack

#3

Hi @jchang:

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

#4

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.

Thanks
Jack

#5

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.

#6

@aostropolets

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?

Thanks
Jack

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