Overview

PCORnet Common Data Model in i2b2

Author: Dan Connolly
Contact: http://informatics.kumc.edu/
Copyright: Copyright (c) 2014 Univeristy of Kansas Medical Center
License:MIT

The Greater Plains Collaborative, a PCORI CDRN, uses i2b2 as its core technology. PCORnet is developing a PCORNet Common Data Model (CDM). This is an effort to represent the CDM as i2b2 terminology.

Contents

pcornet-cdm-spec.html
CDM spec exported as HTML
grokdm.py
script to extract "parseable" spreadsheet from HTML
dmtoterms.py
script to convert CDM parseable spreadsheet to I2B2 terms (in CSV format)
dmtoterms.rst
design notes and doctests
Makefile
see Usage below
laio.py
utility I/O module
requirements.txt
dependencies; see below

Note

pcornet-cdm-spec.html is included here under the terms from section 2.1 "License and Use" of the draft: "The PCORnet data model is freely available for use. An open-source license will be selected by PCORI and included in the next release of the data model."

Dependencies

Install requirements:

$ virtualenv ~/pyenv/grok-spec
New python executable in /home/dconnolly/pyenv/grok-spec/bin/python
Installing Setuptools...
Installing Pip... ...done.
$ . ~/pyenv/grok-spec/bin/activate
(grok-spec)$ pip install -r requirements.txt
...
Successfully installed xlrd docutils
Cleaning up...

Usage

To run the tests, format the design document, and build the terms:

(grok-spec)$ make
python -m doctest dmtoterms.rst
python -m doctest dmtoterms.py
rst2html.py dmtoterms.rst dmtoterms.html
rst2html.py README.rst README.html
python dmtoterms.py pcori_terms.csv