i2b2-synthea

06-2022

0. Set up an i2b2 project with the ACT ontology.

Option A. Download the Synthea-i2b2 63k sample and load this into your i2b2 project.

Option B. Load a Synthea dataset and convert into i2b2 format.

1. Download SyntheticMass Data, Version 2 (24 May, 2017)

• All data sets (1k, COVID 10k, COVID 100k) have been verified to work EXCEPT the 100k patients in the large SyntheticMass Version 2 download. This version needs an extra step to delete invalid records before import. (Details coming soon.)

2. Run create_synthea_table_[dbtype].sql in your project to create the Synthea tables, for your database platform.
3. Import the Synthea data you downloaded in step one into the Synthea tables in your project.
4. Load the i2b2-to-SNOMED table in this repository into your project. https://www.nlm.nih.gov/healthit/snomedct/us_edition.html
   • Click on the "Download SNOMED-CT to ICD-10-CM Mapping Resources" link to download. (You will need a UMLS account.)
   • Unzip the file
   • Import the TSV file into a table called SNOMED_to_ICD10 in your database.
5. In Postgres and Oracle, follow the additional instructions in the comments at the top of synthea_to_i2b2_[dbtype].sql to clean up the date formatting.
6. Run synthea_to_i2b2_[dbtype].sql to convert synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)
   • In MSSQL, replace references to i2b2metadata.dbo in the script. Use the database and schema where your ACT ontology tables are.