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An automatic phenotype extractor

Project description

#ClinPhen is freely available for academic, nonprofit, and personal use. #Licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

#ClinPhen is a 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

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