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When upgrading to the v1.7.13 webclient, you will notice that i2b2_config_data.js has been renamed to i2b2_config_data.json. Your old configuration will still work with this new file name, but you will need to:
There are also new optional parameters, documented below and in 1.4.2 Domain Configuration. |
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- 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.
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- The 100k patients in the large SyntheticMass Version 2 download needs an extra step to delete invalid records before import. 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.
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- 2. Set up an i2b2 project with the ACT ontology.
- Download the scripts from https://github.com/i2b2/i2b2-synthea)
- Run
create_synthea_table_<your dbServertype>.sqlin 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.
- In Postgres and Oracle, follow the additional instructions in the comments at the top of
synthea_to_i2b2_<your dbServerType>.sqlto clean up the date formatting. - Run
synthea_to_i2b2_<your dbServertype>.sqlto convert synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)- Replace references to
i2b2metadata.dboin the script. Use the database and schema where your ACT ontology tables are.
- Replace references to
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