FastAPI QuickUMLS Server

Introduction

FastAPI QuickUMLS Server is an open-source project that provides a high-throughput API server by wrapping QuickUMLS with FastAPI and leveraging multiprocessing capabilities.

Features

• High Throughput: Optimized for performance in multi-core environments.
• Multiprocessing Support: Leverages multiprocessing for concurrent handling of UMLS matching requests.
• FastAPI Framework: Built on FastAPI, known for its high performance and easy-to-use interface.
• Open Source: Free to use, modify, and distribute.

Installation

1. Clone the repository:

   git clone [email protected]:PSU3D0/fastapi-quickumls.git
   

2. Navigate to the cloned directory:

   cd fastapi-quickumls
   

3. Install dependencies:

   pip install -r requirements/local.txt
   

4. Create a directory - umls in the repo, and unzip your UMLS files here.

5. Confirm your path is valid - You should now have a umls/umls-2023AA-metathesaurus-full

6. Run docker compose build. This will take a while!

Usage

1. Start the server:

docker compose up -d

2. Access the API documentation at `http://localhost:4645/docs`.

## API Endpoints

- `GET /match`: Matches given text to UMLS concepts.
- Input: Text string for matching.
- Output: List of matched UMLS concepts.

## Configuration

- **QuickUMLS Path**: Set the QuickUMLS file path in the server configuration.
- **Maximum Workers**: Configure the number of worker processes for multiprocessing.

## Contributing

Contributions to FastAPI QuickUMLS Server are welcome! Please refer to the `CONTRIBUTING.md` file for guidelines.

## License

This project is licensed under the [MIT License](LICENSE).

## Acknowledgments

- QuickUMLS for the underlying UMLS matching functionality.
- FastAPI for the web server framework.