hbdb codes

Data Requirements

Download the hbdb2.sql and put it in the same directory

Environment Setup

Create a new conda environment

conda create --name hbdb_env python=3.10

Activate the conda environment

conda activate hbdb_env

Install necessary package

pip insall mysql-connector-python==9.1.0
pip install openai==1.63.0

Modify gen_scores.py and build_net.py to match your dataset format

Replace the following line in the script with your own MySQL settings:

connection = mysql.connector.connect(host='localhost', port='3306',user='root'password='XXXXXXXX')

Ensure the host, port, user, and password match your database configuration.

• host: The hostname or IP address of your MySQL server.
• port: The port number your MySQL server listens on (default is 3306).
• user: Your MySQL username.
• password: Your MySQL password (replace XXXXXXXX with the actual password).

Set your OPENAI_API_KEY in prompt.py

os.environ["OPENAI_API_KEY"] = "Your API KEY"

Build Network Steps

1. Use gpt-4o-mini to generate scores and summaries:

python gen_scores.py

2. Process the generated data:

python extract.py

3. Build the network structure in the Cytoscape format:

python build_net.py

4. Run the server to diaplay network

npm install express
node server.js

5. View the network

The URL format is http://localhost:8001/index.html?file={compound_id}_{compound_name} Take acetone for example, you can open the following URL in your browser to view its network:

http://localhost:8001/index.html?file=28_acetone

Evaluation Steps

Prepare Dataset

download BC8_BioRED_Subtask1_BioCJSON/bc8_biored_task1_train.json and put it in the same directory

Run Evaluation

python eval.py