CLARK (Clinical Annotation Research Kit),

CLARK is a natural language processing and machine learning application designed to make free-text data useful for computable phenotyping. CLARK takes free-text clinical notes as input and classifies those notes (and the associated patients) based on features (words and phrases) defined by the user. For each patient, CLARK outputs a classification (e.g., “Type 1 diabetic”), a confidence level, and significant features, essentially deriving structured “facts” from the contents of that patient’s unstructured notes. Thus far, CLARK has been applied at UNC to create computable phenotypes for diabetes, uterine fibroids, and primary ciliary dyskinesia (PCD).

CLARK was developed by NC TraCS and CoVar.

About

CLARK is a cross-platform desktop application leveraging Electron, a Python based machine learning engine and a React based user interface.

Executable and User Documentation

To download the CLARK executable without having to package it from source yourself, go to the NC TraCS website and download the CLARK zip file. (A demo dataset is also included.)

User documentation is available in the /docs folder in this repo, and can also be viewed at this link.

Development Instructions

Python setup:

Python setup requires a python3 and several dependencies found in ./server/requirements.txt. These requirements are best installed in a virtual environment

Set up a virtual environment. Ex. python3 -m virtualenv ~/.venv/clark
Activate the virtual environment. Ex. source ~/.venv/clark/bin/activate

Install the requirements

  cd server
  pip install -r requirements.txt
  cd ..

User Interface

Building the user interface requires NPM. Dependencies can be installed by calling

npm install

The user interface is transpiled and bundled using webpack

npm run build_ui

Run the application:

From a command line with the activated python environment the application can be started using

npm start

Packaging

Packaging is handled using PyInstaller to bundle the Python engine and Electron Builder to package everything together and build standalone applications and/or installers. Execution of each of these commands can be done using npm scripts.

Bundles python libraries into standalone binary
```
npm run build_server
```
Following calls to both build_server and build_ui, a standalone application can be made using
```
npm run build_standalone
```
Following calls to both build_server and build_ui, an installer can be made using
```
npm run build_installer
```

Packages are best built on the native architecture.

thommiano/clark