Skip to main content
Donate to the Python Software Foundation or Purchase a PyCharm License to Benefit the PSF! Donate Now

An automatic phenotype extractor

Project description

#ClinPhen is a free-to-use tool that automatically extracts phenotypes from clinical notes. #PIP VERSION INSTRUCTIONS ##To extract phenotypes: clinphen <path_to_clinincal_note_file>

##To see how to use other features: clinphen -h

##We also have a version that parses phenotypes from a large table of notes. You can run it with: clinphen_bulk <path_to_table_file> <path_to_output_file>

##The input file for clinphen_bulk, by default, is a 2-column table delimited by a "|" character. The first column is the patient identifier, the second is the note. It should have the following header: "MRN"|"NOTE"

##To learn more, run: clinphen_bulk -h

#STANDARD (NON-PIP) VERSION INSTRUCTIONS #Running the ClinPhen GUI on a mac:

#Running the ClinPhen GUI on a non-mac:

#Running the ClinPhen GUI on the command line: ##Open the terminal ##cd to the ClinPhen directory ##Run the following command: ./ClinPhenApp

#Running ClinPhen directly on the command line: ##Open the terminal ##cd to the ClinPhen directory ##Run the following command: ./clinphen input.txt ##Replace "input.txt" with the path to the free-text clinical note file that you want to parse. ##You can also run the command line with a custom thesaurus: ./clinphen input.txt thesaurus.txt ##Replace "thesaurus.txt" with the path to your custom thesaurus, which should be in the format: HPO_ID<tab>Synonym

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
clinphen-1.26-py2-none-any.whl (2.0 MB) Copy SHA256 hash SHA256 Wheel py2
clinphen-1.26.tar.gz (2.0 MB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page