#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_IDSynonym
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Release files for clinphen 1.27
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| File | Size | Uploaded | Provenance | |
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|---|---|---|---|---|
| clinphen-1.27-py2-none-any.whl | Python 2 | none | any | Details |
Total release size: 3.9 MB
Release files / clinphen-1.27.tar.gz
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Release files / clinphen-1.27-py2-none-any.whl
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| Size | 2.0 MB |
| Tags | Python 2 |
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