medtext is a high-performance Python Clinical Text Analysis System.
- Python >= 3.6, <3.9
- Linux
- Java
# Set up environment
$ sudo apt-get install python3-dev build-essential default-javaThe latest medtext releases are available over pypi.
Using pip, medtext releases are available as source packages and binary wheels. It is also generally recommended installing packages in a virtual environment to avoid modifying system state:
$ git clone https://github.com/bionlplab/medtext.git
$ cd medtext
# create virtual environment
$ python -m venv medtext-venv
$ source medtext-venv/bin/activate
$ pip install -U pip setuptools wheel
# download the packages and install modules
$ pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple medtext
$ cd medtext-neg
$ pip install .
$ cd ../medtext-deid
$ pip install .
# build project
$ cd ../medtext
$ pip install .
# download all models
$ cd ..
$ bash medtext/download_all.shmedtext supports command-line interfaces for specific NLP tasks (e.g., de-identification, sentence split, or named entity recognition).
$ medtext-deid philter --repl=X -i /path/to/input.xml -o /path/to/output.xml
$ medtext-ssplit ssplit -i /path/to/input.xml -o /path/to/output.xml
$ medtext-neg-prompt neg -i /path/to/input.xml -o /path/to/output.xmlmedtext also supports the Python interactive interpreter. More details on the medtext's pipeline can be found at Pipeline.
You will find complete documentation at our Read the Docs site.
You can find information about contributing to medtext at our Contribution page.
This work is supported by the National Library of Medicine under Award No. 4R00LM013001 and the NIH Intramural Research Program, National Library of Medicine.
You can find Acknowledgment information at our Acknowledgment page.
Copyright BioNLP Lab at Weill Cornell Medicine, 2022.
Distributed under the terms of the MIT license, medtext is free and open source software.