Skip to content

Latest commit

 

History

History
35 lines (25 loc) · 1.51 KB

README.md

File metadata and controls

35 lines (25 loc) · 1.51 KB

🚀 Exploring the BioPax-Based Ontology with SPARQL Queries 🎶

Overview

This repository contains a Jupyter Notebook for exploring a BioPax-based ontology using SPARQL queries. Whether you're interested in finding interactions between SL_GENE and TSG_GENE, discovering cross-references to external databases, or just diving into some fun ontology querying, this is a good starting point.

What's Inside:

  • A Jupyter Notebook with pre-defined SPARQL queries
  • Examples based on BioPax ontology for exploring gene interactions, evidence, biological processes, and more
  • Guidance on how to run these queries interactively and customize them for your own exploration

🔥 Getting Started

Requirements:

To run this notebook, you'll need:

  • Python 3.11: some of the Python libraries I've started to use have convinced me I need to embrace 3.11. One of the more interesting libraries is trafilatura, which works well with parsing foreign language content from html.

  • The following libraries:

    pip install -r requirements.txt

Loading the Ontology

The ontology is hosted on GitHub. You can load the .ttl (Turtle) file directly into the notebook or use a local copy.

How to Use This Repository:

  1. Clone the repository:

    git clone https://github.com/donbr/gene-interactions-ontology.git
cd gene-interactions-ontology

  2. Open the Jupyter Notebook...

  3. Run the SPARQL queries from the notebook to start exploring the ontology!