MIMIC III Corpus Parsing
Project description
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 --use-deprecated=legacy-resolver zensols.mimic
Binaries are also available on pypi.
Installation
- Install the package:
pip3 install zensols.mimic
- Install the database (either PostgreSQL or SQLite).
PostgreSQL
For PostgreSQL, load MIMIC-III by following the PostgreSQL instructions or
consider the PostgreSQL Docker image. The Python PostgreSQL client package
is also needed, which can be installed with pip3 install zensols.dbpg
.
SQLite Configuration
A SQLite can also be used, but it is slower an not as well tested. However, it is faster to set up and could also be useful when a database is not available. I have also created a repository to create the SQLite database file using the SQLite instructions and repository.
The following additional configuration in the --config
file is also
necessary:
[import]
sections = list: mimic_sqlite_res_imp
[mimic_sqlite_res_imp]
type = import
config_file = resource(zensols.mednlp): resources/sqlite.conf
[mimic_sqlite_conn_manager]
db_file = path: <some directory>/mimic3.sqlite3
Changelog
An extensive changelog is available here.
License
Copyright (c) 2022 Paul Landes
Project details
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