Reactome ChatBot

The Reactome ChatBot is an interactive tool that provides information about biological entities and processes using natural language processing techniques. It leverages the Reactome database to retrieve relevant information based on user queries.

Installation

Prerequisites

• Python 3.x
• Poetry (for dependency management)

Installation Steps

Clone the repository:

   git clone https://github.com/your_username/reactome_chatbot.git

Navigate to the project directory:

cd reactome_chatbot

Install dependencies using Poetry:

poetry install

Usage

usage: chat.py [-h] [--openai-key OPENAI_KEY] [--query QUERY] [--verbose]

Reactome ChatBot

optional arguments: -h, --help show this help message and exit --openai-key OPENAI_KEY API key for OpenAI --query QUERY Query string to run --verbose Enable verbose mode

Generating Embeddings

Dependencies

Reactome Dockerized Graph database form DockerHub: https://hub.docker.com/r/reactome/graphdb

To generate embeddings using the embedding generator script, use the following command:

poetry run python bin/embedding_generator.py --openai-key=<your-key>

This command will generate embeddings using the specified OpenAI API key.

Running the ChatBot

Interactively

To run the ChatBot interactively, execute the following command:

poetry run python bin/chat.py

This will start the ChatBot in interactive mode, allowing users to input queries and receive responses in real-time.

Providing Queries Non-interactively

You can also provide queries non-interactively by passing them as command-line arguments.

For example:

poetry run python bin/chat.py --query "What is TP53 involved in?"

This will execute the ChatBot with the provided query and print the response.

Configuration

Environment Variables

You can set environment variables for the ChatBot and other components:

OPENAI_API_KEY: API key for the ChatBot (required)

export OPENAI_API_KEY=your_openai_api_key

You can also use a .env file to set the environment variable for the chatbot.

To Run the UI run the following command

poetry run chainlit run bin/app.py -w

Contributing

Contributions to the Reactome ChatBot project are welcome! If you encounter any issues or have suggestions for improvements, feel free to open an issue or submit a pull request.