OHDSI Home | Forums | Wiki | Github

Athena 5.4 not compatible?

Implementers
#1

I do not believe Athena is compatible with the 5.4 common data model, please correct me if I am wrong.

I spent many hours trying to resolve the CONCEPTS_RELATIONSHIPS.csv file and why it was so awkwardly spaced with both tabs and spaces?

I was trying to manually import, because I do not have an API key yet. Please let me know if I should wait for the API Key to run the .jar file.

#2

CONCEPT_RELATIONSHIP has not changed since V5.0, @Yang. Both tabs and spaces?

#3

Edit! fixed again. The OHDSI community is amazing.

As a side question, do I need to run the .jar file and get the api key? I would like to set atlas up ASAP so the 3 business days thing is an inconvenience. Concepts and the rest of the vocabulary and tables are being uploaded with no problems.

(i am going to answer this myself: probably yes. Concepts_ancestors is pulling a foreign key constraint because “Key (ancestor_concept_id)=(724965) is not present in table “concept”.” Going on Athena, 724965 is a CPT4 thing which I have not downloaded yet. )

So I am going to assume that I wait for the API Key, propagate concepts.csv with cpt4 data using the .sh script, then this should work smoothly?

#4

Yes, need to run cpt4.jar and then truncate and reload the concept table.

t