ClinPhen
ClinPhen is a fast, high-accuracy tool that automatically converts clinical notes into a prioritized list of patient phenotypes.
PIP Installation
ClinPhen can be downloaded through pip.
On the terminal, run:
pip install clinphen
Then, you can use ClinPhen to extract phenotypes from any free-text clinical note by running:
clinphen /path/to/clinical/note/file
Learn how to toggle different features of ClinPhen with:
clinphen --help
Source code
All source code is available in a git repository.
Manuscript
Cole A. Deisseroth, Johannes Birgmeier, Ethan E. Bodle, Jennefer Kohler, Dena Matalon, Yelena Nazarenko, Casie A. Genetti, Catherine A. Brownstein, Klaus Schmitz-Abe, Kelly Schoch, Heidi Cope, Rebecca Signer, Undiagnosed Diseases Network, Julian A. Martinez-Agosto, Vandana Shashi, Alan H. Beggs, Matthew T. Wheeler, Jonathan A. Bernstein, Gill Bejerano.
ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis.
How to cite
Deisseroth CA, Birgmeier J, Bodle EE, Kohler JN, Matalon DR, Nazarenko Y, Genetti CA, Brownstein CA, Schmitz-Abe K, Schoch K, Cope H, Signer R; Undiagnosed Diseases Network, Martinez-Agosto JA, Shashi V, Beggs AH, Wheeler MT, Bernstein JA, and Bejerano G (2018). ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis. Genetics in Medicine, 2018. DOI: 10.1038/s41436-018-0381-1
PMID: 30514889
ClinPhen is freely available for academic, nonprofit, and personal use.
Licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. Please email 
for commercial licensing inquiries.