Metadata-Version: 2.1
Name: miade
Version: 1.0.6
Summary: A set of tools for extracting formattable data from clinical notes stored in electronic health record systems.
Author-email: Jennifer Jiang-Kells <jennifer.jiang.13@ucl.ac.uk>, James Brandreth <j.brandreth@ucl.ac.uk>
License: Elastic License 2.0
        
        URL: https://www.elastic.co/licensing/elastic-license
        
        ## Acceptance
        
        By using the software, you agree to all of the terms and conditions below.
        
        ## Copyright License
        
        The licensor grants you a non-exclusive, royalty-free, worldwide,
        non-sublicensable, non-transferable license to use, copy, distribute, make
        available, and prepare derivative works of the software, in each case subject to
        the limitations and conditions below.
        
        ## Limitations
        
        You may not provide the software to third parties as a hosted or managed
        service, where the service provides users with access to any substantial set of
        the features or functionality of the software.
        
        You may not move, change, disable, or circumvent the license key functionality
        in the software, and you may not remove or obscure any functionality in the
        software that is protected by the license key.
        
        You may not alter, remove, or obscure any licensing, copyright, or other notices
        of the licensor in the software. Any use of the licensor’s trademarks is subject
        to applicable law.
        
        ## Patents
        
        The licensor grants you a license, under any patent claims the licensor can
        license, or becomes able to license, to make, have made, use, sell, offer for
        sale, import and have imported the software, in each case subject to the
        limitations and conditions in this license. This license does not cover any
        patent claims that you cause to be infringed by modifications or additions to
        the software. If you or your company make any written claim that the software
        infringes or contributes to infringement of any patent, your patent license for
        the software granted under these terms ends immediately. If your company makes
        such a claim, your patent license ends immediately for work on behalf of your
        company.
        
        ## Notices
        
        You must ensure that anyone who gets a copy of any part of the software from you
        also gets a copy of these terms.
        
        If you modify the software, you must include in any modified copies of the
        software prominent notices stating that you have modified the software.
        
        ## No Other Rights
        
        These terms do not imply any licenses other than those expressly granted in
        these terms.
        
        ## Termination
        
        If you use the software in violation of these terms, such use is not licensed,
        and your licenses will automatically terminate. If the licensor provides you
        with a notice of your violation, and you cease all violation of this license no
        later than 30 days after you receive that notice, your licenses will be
        reinstated retroactively. However, if you violate these terms after such
        reinstatement, any additional violation of these terms will cause your licenses
        to terminate automatically and permanently.
        
        ## No Liability
        
        *As far as the law allows, the software comes as is, without any warranty or
        condition, and the licensor will not be liable to you for any damages arising
        out of these terms or the use or nature of the software, under any kind of
        legal claim.*
        
        ## Definitions
        
        The **licensor** is the entity offering these terms, and the **software** is the
        software the licensor makes available under these terms, including any portion
        of it.
        
        **you** refers to the individual or entity agreeing to these terms.
        
        **your company** is any legal entity, sole proprietorship, or other kind of
        organization that you work for, plus all organizations that have control over,
        are under the control of, or are under common control with that
        organization. **control** means ownership of substantially all the assets of an
        entity, or the power to direct its management and policies by vote, contract, or
        otherwise. Control can be direct or indirect.
        
        **your licenses** are all the licenses granted to you for the software under
        these terms.
        
        **use** means anything you do with the software requiring one of your licenses.
        
        **trademark** means trademarks, service marks, and similar rights.
        
Project-URL: Homepage, https://github.com/uclh-criu/miade
Project-URL: Documentation, https://uclh-criu.github.io/miade/
Keywords: nlp,natural-language-processing,ml,ehr,electronic-health-records,ai,health,healthcare
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENCE.md
Requires-Dist: medcat ==1.9.3
Requires-Dist: spacy <3.5.0,>=3.4.2
Requires-Dist: numpy >=1.22.0
Requires-Dist: pandas >=1.4.2
Requires-Dist: gensim >=4.3.0
Requires-Dist: typer >=0.7.0
Requires-Dist: typing >=3.7.4
Requires-Dist: pathlib >=1.0.1
Requires-Dist: pydantic >=1.10.0
Requires-Dist: negspacy >=1.0.3
Provides-Extra: dashboard
Requires-Dist: streamlit >=1.20.0 ; extra == 'dashboard'
Requires-Dist: streamlit-aggrid >=0.3.4.post3 ; extra == 'dashboard'
Requires-Dist: spacy-streamlit >=1.0.5 ; extra == 'dashboard'
Requires-Dist: seaborn >=0.12.2 ; extra == 'dashboard'
Requires-Dist: python-dotenv >=1.0.0 ; extra == 'dashboard'
Provides-Extra: dev
Requires-Dist: pytest >=7.1.3 ; extra == 'dev'
Requires-Dist: ruff >=0.5.2 ; extra == 'dev'

# <img src="assets/miade-logo.png" width="40%">

[![Build Status](https://github.com/uclh-criu/miade/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/uclh-criu/miade/actions/workflows/ci.yml?query=Tests)
![License: Elastic License 2.0](https://img.shields.io/badge/License-Elastic%202.0-blue.svg)

A set of tools for extracting formattable data from clinical notes stored in electronic health record systems. Powered by [MedCAT](https://github.com/CogStack/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](https://spacy.io/models/en) - required for MedCAT
```bash
python -m spacy download en_core_web_md
```
[med7](https://huggingface.co/kormilitzin/en_core_med7_lg) - 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](CONTRIBUTING.md)

### 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](https://cogstack.org/), [spaCy](https://spacy.io/), and [med7](https://huggingface.co/kormilitzin/en_core_med7_lg)!


## Licence

This project is licensed under the Elastic License 2.0. See [LICENSE](https://github.com/uclh-criu/miade/blob/documentation/LICENCE.md) for the full license text.
