i2b2-synthea

Work in progress

ONLY WORKS IN MSSQL AT PRESENT (9-15-21)

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.)

3. Set up an i2b2 project with the ACT ontology.
4. Run create_synthea_table_sqlserver.sql in your project to create the Synthea tables.
5. Import the Synthea data you downloaded in step one into the Synthea tables in your project.
6. 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.
7. Run synthea_to_i2b2_sqlserver.sql to convert synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)
   • Replace references to i2b2metadata.dbo in the script. Use the database and schema where your ACT ontology tables are.