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- Download i2b2. (Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of https://www.i2b2.org/software)
- Follow the instructions in Chapter 3 of the i2b2 installation guide to create the additional i2b2 tables needed for the application server: Chapter 3. Data Installation, these sections specifically:
- 3.4 Crcdata Tables
- For 3.4.5, edit the CRC db properties file with ACT-OMOP project parameter which will be used to build the concept_dimension table from metadata tables later in the process.
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- Edit the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\db.properties file to update file to update the project properties to 'ACT_OMOP' ; db.project=ACT_OMOP
- From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data
- This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act\scripts\<db type> folder and create and load ACT-OMOP v4 Ontology metadata tables with indexes. You can now verify the new Ontology by logging Ontology by logging into the webclient.
This creates these tables;
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This will execute the create_omop_act_concept_dimension SQL script from the edu.harvard.i2b2.data\Release_1-7\NewInstall\MetadataCrcdata\scripts\act-omop\scripts\<db type> folder and loads ACT-OMOP Concept_dimension table A concept dimension table
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The concept_Dimension is populated from metadata tables. Verify create_omop_act_concept_dimension.sql to ensure it has complete metadata tables information before running the script Example: the ACT/OMOPVital_Signs information should be in the script to load the ACT/OMOPVital_Signs concept data |
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Finally set up an i2b2 OMOP project pointing pointing to the i2b2-OMOP database that you just configured.
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