...

• 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.)In this case, download synthea_cleanup.pl to your disk, and then run "synthea_cleanup <directory-for-synthea-csv-files>" The fixed csv files will be in <directory-for-synthea-csv-files>/fixcsv.

1. Set up an i2b2 project with the ACT ontology.
2. Download the scripts from https://github.com/i2b2/i2b2-synthea
3. Run create_synthea_table_<your dbServertype>.sql in your project to create the Synthea tables.
4. Import the Synthea data you downloaded in step one into the Synthea tables in your project.
5. 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.
6. In Postgres and Oracle, follow the additional instructions in the comments at the top of synthea_to_i2b2_<your dbServerType>.sql to clean up the date formatting.
7. Run synthea_to_i2b2_<your dbServertype>.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.

...