| Name | zensols.dsprov JSON |
| Version |
0.0.1
JSON |
| download |
| home_page | https://github.com/plandes/dsprov |
| Summary | This library provides integrated MIMIC-III with discharge summary provenance of data annotations and Pythonic classes. |
| upload_time | 2023-06-30 23:58:51 |
| maintainer | |
| docs_url | None |
| author | Paul Landes |
| requires_python | |
| license | |
| keywords |
tooling
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Provenience of discharge summaries Pythonic access
[![PyPI][pypi-badge]][pypi-link]
[![Python 3.9][python39-badge]][python39-link]
[![Python 3.10][python310-badge]][python310-link]
[![Build Status][build-badge]][build-link]
This library provides integrated MIMIC-III with discharge summary provenance of
data annotations and Pythonic classes.
## Documentation
See the [full documentation](https://plandes.github.io/dsprov/index.html).
The [API reference](https://plandes.github.io/dsprov/api.html) is also
available.
## Obtaining
The easiest way to install the command line program is via the `pip` installer:
```bash
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
```bash
# 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:
```python
>>> 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](CHANGELOG.md).
## License
[MIT License](LICENSE.md)
Copyright (c) 2023 Paul Landes
<!-- links -->
[pypi]: https://pypi.org/project/zensols.dsprov/
[pypi-link]: https://pypi.python.org/pypi/zensols.dsprov
[pypi-badge]: https://img.shields.io/pypi/v/zensols.dsprov.svg
[python39-badge]: https://img.shields.io/badge/python-3.9-blue.svg
[python39-link]: https://www.python.org/downloads/release/python-390
[python310-badge]: https://img.shields.io/badge/python-3.10-blue.svg
[python310-link]: https://www.python.org/downloads/release/python-310
[build-badge]: https://github.com/plandes/dsprov/workflows/CI/badge.svg
[build-link]: https://github.com/plandes/dsprov/actions
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"description": "# Provenience of discharge summaries Pythonic access\n\n[![PyPI][pypi-badge]][pypi-link]\n[![Python 3.9][python39-badge]][python39-link]\n[![Python 3.10][python310-badge]][python310-link]\n[![Build Status][build-badge]][build-link]\n\nThis library provides integrated MIMIC-III with discharge summary provenance of\ndata annotations and Pythonic classes.\n\n\n## Documentation\n\nSee the [full documentation](https://plandes.github.io/dsprov/index.html).\nThe [API reference](https://plandes.github.io/dsprov/api.html) is also\navailable.\n\n\n## Obtaining\n\nThe easiest way to install the command line program is via the `pip` installer:\n```bash\npip3 install --use-deprecated=legacy-resolver zensols.dsprov\n```\n\nBinaries are also available on [pypi].\n\n\n## Usage\n\nThe package includes a command line interface, which is probably most useful by\ndumping selected admission annotations.\n\n### Command line\n\n```bash\n# help\n$ dsprov -h\n\n# get two admission IDs (hadm_id)\n$ dsprov ids -l 2\n\n# print out two admissions\n$ dsprov show -l 2\n\n# print out admissions 139676\n$ dsprov show -d 139676\n\n# output the JSON of two admissions with indent 4\n$ dsprov show -i 4 -f json -d $(dsprov ids -l 2 | awk '{print $1}' | paste -s -d, -)\n```\n\n### API\n\nThe package can be used directly in your research to provide Python object\noriented access to the annotations:\n\n```python\n>>> from zensols.nlp import FeatureDocument\n>>> from zensols.dsprov import ApplicationFactory, AdmissionMatch\n>>> stash = ApplicationFactory.get_stash()\n>>> am: AdmissionMatch = next(iter(stash.values()))\n>>> doc: FeatureDocument = am.note_matches[0].discharge_summary.note.doc\n>>> print(f'hadm: {am.hadm_id}')\n>>> print(f'sentences: {len(doc.sents)}')\n>>> print(f'tokens: {doc.token_len}')\n>>> print(f'entities: {doc.entities}')\nhadm: 120334\nsentences: 46\ntokens: 1039\nentities: (<Admission>, <Date>, <Discharge>, <Date>, <Date of Birth>, <Sex>, ...)\n```\n\n\n## Changelog\n\nAn extensive changelog is available [here](CHANGELOG.md).\n\n\n## License\n\n[MIT License](LICENSE.md)\n\nCopyright (c) 2023 Paul Landes\n\n\n<!-- links -->\n[pypi]: https://pypi.org/project/zensols.dsprov/\n[pypi-link]: https://pypi.python.org/pypi/zensols.dsprov\n[pypi-badge]: https://img.shields.io/pypi/v/zensols.dsprov.svg\n[python39-badge]: https://img.shields.io/badge/python-3.9-blue.svg\n[python39-link]: https://www.python.org/downloads/release/python-390\n[python310-badge]: https://img.shields.io/badge/python-3.10-blue.svg\n[python310-link]: https://www.python.org/downloads/release/python-310\n[build-badge]: https://github.com/plandes/dsprov/workflows/CI/badge.svg\n[build-link]: https://github.com/plandes/dsprov/actions\n",
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