This library provides integrated MIMIC-III with discharge summary provenance of data annotations and Pythonic classes.
Project description
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
Copyright (c) 2023 Paul Landes
Project details
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