Provenience of discharge summaries Pythonic access

This library provides integrated MIMIC-III with discharge summary provenance of data annotations and Pythonic classes.

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.dsprov

Binaries are also available on pypi.

Usage

The package includes a command line interface, which is probably most useful by dumping selected admission annotations.

Command line

# help
$ dsprov -h

# get two admission IDs (hadm_id)
$ dsprov ids -l 2

# print out two admissions
$ dsprov show -l 2

# print out admissions 139676
$ dsprov show -d 139676

# output the JSON of two admissions with indent 4
$ dsprov show -i 4 -f json -d $(dsprov ids -l 2 | awk '{print $1}' | paste -s -d, -)

API

The package can be used directly in your research to provide Python object oriented access to the annotations:

>>> from zensols.nlp import FeatureDocument
>>> from zensols.dsprov import ApplicationFactory, AdmissionMatch
>>> stash = ApplicationFactory.get_stash()
>>> am: AdmissionMatch = next(iter(stash.values()))
>>> doc: FeatureDocument = am.note_matches[0].discharge_summary.note.doc
>>> print(f'hadm: {am.hadm_id}')
>>> print(f'sentences: {len(doc.sents)}')
>>> print(f'tokens: {doc.token_len}')
>>> print(f'entities: {doc.entities}')
hadm: 120334
sentences: 46
tokens: 1039
entities: (<Admission>, <Date>, <Discharge>, <Date>, <Date of Birth>, <Sex>, ...)

Changelog

An extensive changelog is available here.

License

MIT License

Copyright (c) 2023 Paul Landes