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Adding CPT-4 vocabulary for OHDSI on AWS

vocabularies
cdm
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(David Pritchard) #1

Greetings all. I’ve set up an OHDSI on AWS environment as described at https://github.com/OHDSI/OHDSIonAWS, however, I am unable to see any CPT-4 codes when searching for codes in ATLAS.

In order to try and add the CPT-4 codes, I have downloaded the OMOP v5 vocabulary from https://athena.ohdsi.org/ and ran CPT4.jar to add the CPT-4 codes to the CONCEPT.csv file, and then imported the resulting vocabulary into a schema in Redshift. However, I’m not sure how to make ATLAS aware of the new vocabulary entries. Is there a particular table that I should add them to?


(Chris Knoll) #2

You don’t need to do anything. Just putting them into the CDM’s concept table will make them come back like any other concept.


(David Pritchard) #3

Maybe the issue is that I can’t see the the new data source in ATLAS in the first place. In Redshift, I have the the following schema, of which I want to access the tables in the p0025_v5 schema from ATLAS.

mycdm=# \dn
         List of schemas
          name          | owner
------------------------+--------
 cmsdesynpuf100k        | master
 cmsdesynpuf100kresults | master
 cmsdesynpuf1k          | master
 cmsdesynpuf1kresults   | master
 p0024                  | master
 p0024_v5               | master
 public                 | rdsdb
 synthea100k            | master
 synthea100kresults     | master
 synthea1k              | master
 synthea1kresults       | master
(11 rows)

But in ATLAS, I only see the following tables when clicking on the “Data Sources” tab.
22%20PM


(Chris Knoll) #4

When you created your new source (ie: the new schema) you added a record for it in the WebAPI’s source table?


(David Pritchard) #5

I haven’t added a record for it in the WebAPI’s source table. Are these the instructions for doing so? https://github.com/OHDSI/WebAPI/wiki/CDM-Configuration


(Chris Knoll) #6

Yes.


(David Pritchard) #7

Many thanks for your input.


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