OHDSI Home | Forums | Wiki | Github

CPT4 Concept Name Missing

Vocabulary Users
#1

Hi,

I have downloaded vocabulary. Ran the cpt.bat file with username and password for UMLS. It ran successfully, It showed “CPT successfully updated.” However concept names are blank in majority of records why? Please advise.

Thanks,
Amy.

#2

Hello,
do you check CONCEPT.csv file, right?

BR, Maria

#3

Yes. Total record count of CPT4 codes is 15446. Out of them, only 1660 records having concept_name, The rest records have blank concept_name.

#4

I can’t reproduce this behavior ;(
Could you send me several not processed concept_ids, please?
How many concepts are in the “original” concept.csv?
It looks like the fixed bug - also I recommend to recreate your vocabulary bundle and repeat cpt4 running.

BR, Maria

#5

Here are a few concept_id for missing concept_name in CPT4 Vocabulary_Id
2102972, 2102973, 2102974, 2102975, 2102912, 2102913, 2102914 , 2102915

Original Concept file size is 703,967 KB;
After ran cpt.bat the concept file size become 705,027 KB

Thanks,
Amy

#6

Actually, we have some additional logic for invalid concepts - but in your case they are valid so I can explain it by the behavior of the external UMLS-service.

Did you get a chance to create a new bundle and check the result after cpt4.jar?

BR, Maria

#7

Hi,

I didn’t run cpt4.jar. I ran cpt.bat come with the download. Did you also fix bugs in cpt.bat?

Thanks,
Amy

#8

Hi,

Please let me know if cpt.bat also fixed, I will give it a try again. Somehow I can’t run cpt4.jar.

Thanks,
Amy

#9

@amy_chuang: The bat file just runs the jar file just like in the download email you got. Run it from the command line and send the resulting output to the support team. You need a UMLS license, and you have to put the login/password into the command line or bat file.

#10

@Christian_Reich and @maria.pozhidaeva

We created/downloaded a new bundle. After ran cpt4.jar (with UMLS login and password like I did before)
It successfully processed. Screen shot attached.

CPT4jarprocress.PNG919×320 83.1 KB

We import data from concept.csv file (file list attached)

OMOP Vocabulary File List.PNG809×461 48.5 KB

Although we didn’t use concept_cpt4.csv, we notice concept names in that file are all blank.
After data imported from concept.csv, here are the results:
Total of 13891 cpt4 codes have no concept_name; only 1749 cpt4 codes have concept name

Thought?

#11

Hello,
I guess it depends on the UMLS - sometimes the service doesn’t work due to maintenance.
I can advice you to try later - anyway I also will check the behavior.

BR, Maria

#12

But we already tried twice. and both process at the end indicated as 'CPT successfully updated"

#13

Can you look into the file “not-processed-concepts.out”? It will tell you what it couldn’t fetch. My hunch is they are all in there, because somehow the connection to the UMLS doesn’t work.

#14

There are 23 concept_id in the file - it matches the result message (Not process CPT4: 23)

#15

@Christian_Reich,
Would you please advise us what is the next step to obtain concept name for cpt4 codes? As mentioned earlier that we have downloaded twice, and followed the instruction provided, each time, at the end it said successfully processed. However majority of concept names are blank.

Thanks,
Amy

t