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Directory Structure for the i2b2
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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:
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<span style="font-size:15px;font-weight:bold">Main Directory for New Data Installs (i2b2 on OMOP):</span> <i>YOUR_I2B2_OMOP_DATA_DIR</i>\i2b2_omop_data\ |
Directory | Description |
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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. |
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Directory | Description |
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Crcdata | Contains the data installation files for the Data Repository (CRC) Cell. |
Hivedata | Contains the data installation files for the i2b2 Hive. |
Imdata | Contains the data installation files for the Identity Management (IM) Cell. |
Metadata | Contains the data installation files for the Ontology Management (ONT) Cell. |
Pmdata | Contains the data installation files for the Project Management (PM) Cell. |
Workdata | Contains the data installation files for the Workplace Framework (WORK) Cell. |
In each of the above directories you will find the following:
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Directory or File | Description |
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\scripts\ | This directory contains all the scripts used |
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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
As stated previous the main directory for your data installation is YOUR_I2B2_DATA_DIR\edu.harvard.i2b2.data\Release_1-7\NewInstall and within it are several folders contains the install scripts. These folder and the appropriate schema to which they are mapped are outlined in the following table.
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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 |
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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 |
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Crcdata | i2b2demodata | Demo |
Hivedata | i2b2hive | |
Imdata | i2b2imdata | |
Metadata | i2b2metadata | Demo |
Pmdata | i2b2pm | |
Workdata | i2b2workdata | Demo |