pdfQL

• Biohackathon Belgium Team 9
• Track 3 (Automatic Curation of Oligogenic Disease Evidence from PDFs)

Installation

UV

# Create virtual environment
uv venv

# Activate environment
source .venv/bin/activate         # Linux/macOS
.venv\Scripts\activate           # Windows

# Install package in development mode
uv pip install -e .[llm]

Conda

# Create conda environment with Python 3.12
conda create -n pdfql python=3.12 -y

# Activate environment
conda activate pdfql

# Install package in development mode
pip install -e .[llm]

Run

pdfql PDF [OUTPUT]

It will fetch the information from PDF file and store the result into database pdfql.db.

Special case

import tsv into database

pdfql [--database=FILE] --import TSV

force update information in database

pdfql --force-fetch PDF

choose LLM model

pdfql --model=NAME --model-param=K=V,...

Current supports:

• empty develop/debug use
• To be continue

Authors

• Yu-Ting Wei
• Kaan Cetindag
• Ta-Shun Su