zensols.mimic 0.1.1

MIMIC III Corpus Parsing

MIMIC III Corpus Parsing

A utility library for parsing the MIMIC-III corpus. This uses spaCy and extends the zensols.mednlp to parse the MIMIC-III medical note dataset, which include:

• Re-groups pseudo tokens as a single token.
• Modifies the spaCy tokenizer to deal with pseudo tokens--specifically not break on syntax used in the pseudo tokens.

Documentation

See the full documentation. The API reference is also available.

Obtaining

The easiest way to install the command line program is via the pip installer:

pip3 install zensols.mimic

Binaries are also available on pypi.

Installation

1. Install the package: pip3 install zensols.mimic
2. Install the database (either Postgres, which is tested, or SQLite). For Postgres, load MIMIC-III by following the Postgres instructions. An SQLite database file can also be used, but it has not been tested and it might need more configuration (resource library) work. Refer to the SQLite instructions to create the file if you chose to try this method.

Changelog

An extensive changelog is available here.

License

MIT License

Copyright (c) 2022 Paul Landes