miade
A set of tools for extracting formattable data from clinical notes stored in electronic health record systems.
Science Score: 52.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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✓Institutional organization owner
Organization uclh-criu has institutional domain (www.uclhospitals.brc.nihr.ac.uk) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary
Keywords
Repository
A set of tools for extracting formattable data from clinical notes stored in electronic health record systems.
Basic Info
- Host: GitHub
- Owner: uclh-criu
- License: other
- Language: Python
- Default Branch: master
- Homepage: https://uclh-criu.github.io/miade/
- Size: 84.8 MB
Statistics
- Stars: 6
- Watchers: 3
- Forks: 0
- Open Issues: 8
- Releases: 0
Topics
Metadata Files
README.md
A set of tools for extracting formattable data from clinical notes stored in electronic health record systems. Powered by MedCAT models.
Installing
Install MiADE
To install the stable release:
bash
pip install miade
To install the latest development version of MiADE, clone this repository and run:
bash
pip install .
Downloading models
You may also need to download these additional models to run MiADE:
spaCy - required for MedCAT
bash
python -m spacy download en_core_web_md
med7 - required for medication dosage extraction
bash
pip install https://huggingface.co/kormilitzin/en_core_med7_lg/resolve/main/en_core_med7_lg-any-py3-none-any.whl
Quickstart
Initialise MiADE with the path that you have saved your trained MedCAT models:
python
miade = NoteProcessor(Path("path/to/model/dir"))
Add annotators:
python
miade.add_annotator("problems")
miade.add_annotator("meds/allergies")
Create a note:
python
text = "Patient has penicillin allergy with rash"
note = Note(text)
Extract concepts:
```python concepts = miade.process(note)
for concept in concepts: print(concept)
{name: breaking out - eruption, id: 271807003, category: Category.REACTION, start: 204, end: 208, dosage: None, negex: False, meta: None}
{name: penicillin, id: 764146007, category: Category.ALLERGY, start: 191, end: 201, dosage: None, negex: False, meta: None}
```
Contributing
See contributing
Maintainers
| Name | Email | |-----------------|-----------------------------| | James Brandreth | j.brandreth@ucl.ac.uk | | Jennifer Jiang | jennifer.jiang.13@ucl.ac.uk |
Acknowledgement
This project wouldn't be possible without the work at Cogstack, spaCy, and med7!
Licence
This project is licensed under the Elastic License 2.0. See LICENSE for the full license text.
Owner
- Name: UCLH/UCL BRC Clinical and Research Informatics Unit
- Login: uclh-criu
- Kind: organization
- Website: https://www.uclhospitals.brc.nihr.ac.uk/clinical-research-informatics-unit
- Repositories: 4
- Profile: https://github.com/uclh-criu
We are clinicians, AI researchers, developers and analysts working together to develop a robust environment and infrastructure for the analysis of clinical data
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below"
authors:
- family-names: Brandreth
given-names: James
orchid: https://orchid.org/0000-0003-0584-0159
- family-names: Jiang
given-names: Jennifer
title: "MiADE"
version: 0.0.1
GitHub Events
Total
- Watch event: 4
- Member event: 1
- Issue comment event: 1
- Push event: 25
- Pull request event: 6
- Create event: 5
Last Year
- Watch event: 4
- Member event: 1
- Issue comment event: 1
- Push event: 25
- Pull request event: 6
- Create event: 5
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 0
- Total pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Total issue authors: 0
- Total pull request authors: 3
- Average comments per issue: 0
- Average comments per pull request: 0.25
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Issue authors: 0
- Pull request authors: 3
- Average comments per issue: 0
- Average comments per pull request: 0.25
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- anoopshah (2)
- jamesbrandreth (2)
- tomolopolis (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 19 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
pypi.org: miade
A set of tools for extracting formattable data from clinical notes stored in electronic health record systems.
- Homepage: https://github.com/uclh-criu/miade
- Documentation: https://uclh-criu.github.io/miade/
- License: BSD License
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Latest release: 1.0.7
published over 1 year ago