Leaf is a flexible tool able to work with nearly any clinical data model.
This section of leaf-scripts deals specifically with the OMOP Common Data Model.
Configuring Leaf to work with a particular database and Concept tree is often the most time-consuming aspect of Leaf installation. Using OMOP - which presents a consistent, widely-used data model - therefore offers an opportunity to create a generalizable starting point in Leaf configuration, saving time and energy in setup. (while also providing examples of how to configure Leaf programmatically!)
The scripts in this repo assume:
- You're working using SQL Server as your RDBMS.
- You have a 'vanilla' OMOP database with no renamed columns or tables.
- Your Leaf application database exists on the same server and is named
LeafDB.
While (1) and (2) should not be surprising, (3) is not the case for everyone, so before
running the setup scripts be sure to first rename modify the scripts, replacing LeafDB -> YourLocalDatabaseName.
The scripts are designed to build a basic Concept tree shaped like the following:
- Demographics 2_demographics.sql
- Encounters 3_visits.sql
- Labs 4_labs.sql
- Vitals 5_vitals.sql
Scripts are designed to be run sequentially in the order they are numbered, but this is strictly only necessary for the 0_views.sql and 1_sqlsets.sql scripts, which should be run first.
Note that we are also currently working on scripts for Conditions and Procedures.