i2b2model

Python tools for working with the i2b2 data model

Edit history

• 0.1.0 - Initial commit. Parted from the i2FHIRb2 module
• 0.1.1 - Added hlevel bias and ability to explicitly set c_name in OntologyEntry
• 0.1.2 - Added more options to TableAccess to support i2b2terminology project
• 0.1.3 - Moved OntologyRoot from i2FHIRb2 to here
• 0.2.0 - Refactored for dynprops
• 0.2.1 - Include tests/scripts and tests/utils for re-use in other packages
• 0.2.2 - Moved testing tools to package base (testingutils)
• 0.2.4 - Finalize dynprops refactoring and adapt to i2FHIRb2

Requirements

1. Python 3.6 or later
2. Instance of the i2b2 database - version 1.7 or later. Note: this has only been tested on the postgres version of i2b2.

Installation

Installing the current version:

> pip install i2b2model

To install the absolute latest:

> pip install git+https://github.com/BD2KONFHIR/i2b2model

Setup

1. Select a working directory and create a configuration file:

> genconffile
db_conf generated

2. Edit the configuration file and add the appropriate parameters.

> cat db_conf
-db postgresql+psycopg2://localhost:5432/i2b2
--user i2b2
--password demouser

See the removefacts help file for details