Directory Structure for the i2b2 on OMOP data package
Once you have extracted the files from the i2b2 omop data package you will notice the following directory structure in your i2b2 data directory:
Main Directory for New Data Installs (i2b2 on OMOP): YOUR_I2B2_OMOP_DATA_DIR\i2b2_omop_data\
| Directory | Description |
|---|---|
| crcdata | Contains the data installation files for the Data Repository (CRC) Cell. These CRC tables are specific to the i2b2 on OMOP project. |
| metadata | Contains the data installation files for the Ontology (ONT) Cell. These tables are also specific to the i2b2 on OMOP project. |
| workdata | Contains the data installation files for the Workplace Framework (Work) Cell. These tables are not specific to the i2b2 on OMOP project. |
In each of the above directories you will find the following:
| Directory or File | Description |
|---|---|
| \scripts\ | This directory contains all the scripts used to create the tables, stored procedures, and views |
| \omop\scripts\ | This directory contains all the scripts used to insert the sample data into the tables |
| db.properties | Properties file to define the database setup parameters (type, username, driver, etc.) |
Schema Mapping
In the classic i2b2, there are multiple database or schemas that are typically defined in the i2b2 database. Each of the schemas correlate to the appropriate data tables. However, in the i2b2 on OMOP project there is only one schema. This means all the crcdata, metadata, and workdata tables will reside in a single database or schema, which is the one for your CDM tables.
Schema for i2b2 on OMOP
| Directory Folder | Schema | Project |
|---|---|---|
| Crcdata | Your_CDM_Schema | omop |
| Metadata | Your_CDM_Schema | omop |
| Workdata | Your_CDM_Schema | omop |
Example of classic i2b2 Schema Mapping
| Directory Folder | Schema | Project |
|---|---|---|
| Crcdata | i2b2demodata | Demo |
| Hivedata | i2b2hive | |
| Imdata | i2b2imdata | |
| Metadata | i2b2metadata | Demo |
| Pmdata | i2b2pm | |
| Workdata | i2b2workdata | Demo |
