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stjude-biohackathon / KIDS23-Team3

SCCRIP (Sickle Cell Clinical Research and Intervention Program) established a longitudinal cohort at multiple sites with Sickle Cell Disease (SCD) in 2014 managed by St. Jude Clinical Hematology. A new collaborator for SCCRIP has longitudinal data for 600 SCD patients in OMOP CDM format and this effort is to convert OMOP CDM to SCCRIP format.

Home Page:https://www.stjude.org/patient-referrals/seek-treatment/taking-part-in-clinical-research/sickle-cell-clinical-research-intervention-program-sccrip.html

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VOCAB from ATHENA into OMOP CDM PostgreSQL

RaghaSrinivasan opened this issue · comments

commented

https://github.com/OHDSI/Vocabulary-v5.0/wiki/General-Structure,-Download-and-Use

Alternatively, the ETL-Synthea R package contains a function LoadVocabFromCsv which can be used for the same purpose.

March 12, 2024 - Vocabulary downloaded from ATHENA and ZIP extracted to C:\ATHENA_OHDSI_VOCAB but later renamed to C:\CDMV5VOCAB to match with CommonDataModel/PostgreSQL/VocabImport
/OMOP CDM vocabulary load - PostgreSQL.sql

Once you choose Vocabularies to download from ATHENA, you will get an email. Here is a glimpse of the instructions:

Please download and load the Standardized Vocabularies as following:

Click on <>> to download the zip file. Typical file sizes, depending on the number of vocabularies selected, are between 30 and 250 MB.
Unpack.
Reconstitute CPT-4. See below for details.
If needed, create the tables.
Load the unpacked files into the tables.

Follow special steps for CPT-4 vocabular from email -- getting UMLS Account setup takes 1-2 days for approval initially but API key is easy to get once you have UMLS Account

Scripts for importing the vocabulary csv files into your OMOP CDM vocabulary tables can be found <>. They are provided in the respective folders, e.g. Oracle/, PostgreSQL/ and SQL Server/ for supported SQL dialects. The loading scripts are inside the subfolder VocabImport/.

I had alread ycreated the OMOP CDM v5.3 table structures. Howeer, if you need to here is glimpse on how-to

https://github.com/OHDSI/CommonDataModel/tree/v5.3.1/PostgreSQL#common-data-model--postgresql

This folder contains the SQL scripts for PostgreSQL.

In order to create your instantiation of the Common Data Model, we recommend following these steps:

Create an empty schema.

Execute the script OMOP CDM postgresql ddl.txt to create the tables and fields.

Load your data into the schema.

Execute the script OMOP CDM postgresql indexes required.txt to add the minimum set of indexes and primary keys we recommend.

Execute the script OMOP CDM postgresql constraints.txt to add the constraints (foreign keys).

Note: you could also apply the constraints and/or the indexes before loading the data, but this will slow down the insertion of the data considerably.