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Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases.

John Erol Evangelista1, Andrew D Lutsky1, Anna I Byrd1

  • 1Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York.

Current Protocols
|September 16, 2025
PubMed
Summary
This summary is machine-generated.

We developed an open-source Knowledge Graph User Interface (KG-UI) to create interactive websites from biomedical data. This tool allows researchers to easily query and visualize complex biological networks, enhancing data accessibility and research collaboration.

Keywords:
data harmonizationdata integrationdata visualizationknowledge graphstranscription factors

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Visualization

Background:

  • Knowledge Graphs (KG) organize biomedical data into interconnected networks.
  • Existing KG databases often lack free, customizable web-based user interfaces (UIs).
  • This limitation hinders interactive data exploration and KG utilization.

Purpose of the Study:

  • To develop an open-source, customizable web-based UI for Knowledge Graph databases.
  • To facilitate the creation of interactive websites for querying and visualizing KG data.
  • To demonstrate the KG-UI's application in bioinformatics projects.

Main Methods:

  • Developed an open-source Knowledge Graph User Interface (KG-UI).
  • Applied KG-UI to eight diverse bioinformatics projects.
  • Created a demo KG of principal investigator (PI) networks using PubMed and grant data.
  • Provided a step-by-step user guide for installation and customization.

Main Results:

  • The KG-UI successfully created interactive websites for eight bioinformatics projects.
  • A demo KG showcasing PI network relationships was successfully constructed and is available.
  • Detailed instructions and source code are provided for KG-UI implementation.
  • The KG-UI enables customization for specific research needs.

Conclusions:

  • The open-source KG-UI provides a valuable, accessible tool for researchers.
  • It enhances the usability and interactivity of biomedical Knowledge Graphs.
  • The KG-UI promotes data sharing and collaborative research in bioinformatics.