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A new option is now available for loading Synthea data files into i2b2. Synthetic patient data generated by Synthea is hosted on SyntheticMass..The Synthea sample files have been converted to i2b2-ACT format. The zipped data files can be downloaded from https://github.com/i2b2/i2b2-synthea
Synthea Load Process:
- Create db Schema with name labeled synthea
- Load Synthea data from the sample data files provided
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- Download
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- 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.)
- Set up an i2b2 project with the ACT ontology.
- Run
create_synthea_table_
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<your dbServertype>.sql
in your project to create the Synthea tables.- Import the Synthea data you downloaded in step one into the Synthea tables in your project.
- 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.
- 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.
- Replace references to
ACT Version-4 Ontology data load
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