CardioKnowledge Nexus (CKN) Schema

CardioKnowledge Nexus (CKN) is a project aimed at constructing a scholarly knowledge graph focused on cardiovascular diseases. This repository is dedicated to designing and studying the schema and model of this knowledge graph.

This repository is associated with a paper submitted to the 10th International Conference on Web Research. The article was published under the title Advancing Cardiovascular Research: A Tailored Knowledge Graph Schema for Scholarly Data.

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Table of contents

• CardioKnowledge Nexus (CKN) Schema
  • Overview
  • Installation & Setup
    • Prerequisites
    • Project Structure
  • Example Graph Structure
  • Future Improvements
  • Citation
  • Contributing
  • License
  • Contact

Overview

The CKN project leverages graph-based knowledge representation to organize and connect information about diseases, their relationships, and other relevant entities. The repository includes:

• Scripts for schema modeling using OWL (Web Ontology Language).
• Tools for interactive visualization of the knowledge graph.
• Configurable components for extending and refining the model.

Installation & Setup

Prerequisites

Ensure you have Python 3.8+ installed, along with the following dependencies:

pip install -r requirements.txt

Project Structure

ckn-schema/
│-- src/
│   ├── configuration.py      # Configuration settings (e.g., file paths)
│   ├── generator.py          # Graph generation logic
│   ├── color_map.py          # Function for read color map
│-- assets/data/
│   ├── Graph.xlsx            # Example input data for ontology creation
│   ├── color_map.json        # Color Map of node type
│-- output/                   # Stores generated OWL files & visualizations
│-- [main.ipynd](/main.ipynb) # main code for visulization graph and convert
│-- README.md                 # Project documentation

Example Graph Structure

A simplified version of the knowledge graph for CKN schema might look like this:

[Disease] --(affects)--> [AnatomicalStructure]
[AnatomicalStructure]  --(partOf)--> [AnatomicalStructure]

A simplified version of the knowledge graph with sample data might look like this:

[Cardiomyopathy] --(affects)--> [Heart]
[Myocardium]  --(partOf)--> [Heart]

With OWL, these relationships can be formally defined and reasoned upon. You can display the converted ckn_schema.owl file using this web site and it will be displayed as follows.

The graph schema is also drawn using networkX, which is displayed as follows:

We developed a preliminary dataset comprising a limited set of concepts related to the disease "Cardiomyopathy" to serve as the basis for evaluating the proposed graph schema with input from multiple experts. The graph representation was visualized as shown below, and an interactive version was generated as an HTML file using the PyVis library.

Future Improvements

• Expand the ontology with more medical concepts and relationships.
• Extract concepts from medical articles in the field of cardiovascular diseases and complete the content of the graph
• Implement SPARQL queries for advanced knowledge retrieval.
• Improve graph layout and user interface.

Citation

If you use this repository in a scientific publication, we would appreciate references to the following paper:

Plain text:

E. Bitaraf, M. Jafarpour, A. Moeini, S. Shool and M. Tara, "Advancing Cardiovascular Research: A Tailored Knowledge Graph Schema for Scholarly Data," 2025 11th International Conference on Web Research (ICWR), Tehran, Iran, Islamic Republic of, 2025, pp. 553-557, doi: 10.1109/ICWR65219.2025.11006231.

Biblatex entry:

@INPROCEEDINGS{11006231,
  author={Bitaraf, Ehsan and Jafarpour, Maryam and Moeini, Ali and Shool, Sina and Tara, Mahmood},
  booktitle={2025 11th International Conference on Web Research (ICWR)}, 
  title={Advancing Cardiovascular Research: A Tailored Knowledge Graph Schema for Scholarly Data}, 
  year={2025},
  volume={},
  number={},
  pages={553-557},
  keywords={Reviews;Precision medicine;Refining;Knowledge graphs;Ontologies;Metadata;Clinical trials;Knowledge discovery;Drug discovery;Optimization;Scholarly Knowledge Graph (SKG);Cardiovascular Research;Biomedical Ontologies;Drug Discovery;Knowledge Discovery;Disease Modeling;Modular Schema Design;Ontology Engineering},
  doi={10.1109/ICWR65219.2025.11006231}}

Contributing

We welcome contributions to improve CKN Schema! If you'd like to contribute:

1. Fork this repository.
2. Create a new branch (git checkout -b feature-branch).
3. Commit changes and push to GitHub.
4. Open a pull request.

see the contributor guide

License

This project is released under the MIT License.

Contact

For questions or collaborations, feel free to reach out via GitHub Issues or linkedin.

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🚀 CardioKnowledge Nexus – Structuring Medical Knowledge for a Smarter Future!