PCORnet Common Data Model in i2b2
|Copyright:||Copyright (c) 2014 Univeristy of Kansas Medical Center|
- CDM spec exported as HTML
- script to extract "parseable" spreadsheet from HTML
- script to convert CDM parseable spreadsheet to I2B2 terms (in CSV format)
- design notes and doctests
- see Usage below
- utility I/O module
- dependencies; see below
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."
$ 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...
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