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Related Experiment Video

Updated: Nov 3, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Biomedical Entity Explorer: A Web Server for Biomedical Entity Exploration.

Jinuk Jung1,2, Hyunwhan Joe1, Kyungsik Ha3

  • 1Biomedical Knowledge Engineering Laboratory, Seoul National University School of Dentistry, Seoul, Korea.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|June 3, 2021
PubMed
Summary

Biomedical Entity Explorer (BEE) is a web server for searching biomedical entities like genes and diseases. It integrates data from 16 databases, allowing complex relationship exploration using set operations.

Keywords:
biomedical entity searchdatabase integrationweb server

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accessing and integrating diverse biomedical data is crucial for research.
  • Existing tools may lack comprehensive entity coverage or advanced search functionalities.
  • Biologists and general users need efficient ways to explore relationships between biomedical entities.

Purpose of the Study:

  • To develop a web server, Biomedical Entity Explorer (BEE), for searching and exploring biomedical entities.
  • To integrate data from multiple databases for a comprehensive resource.
  • To enable complex queries using set operations for relationship discovery.

Main Methods:

  • Integrated biomedical entities (gene, miRNA, drug, disease, SNP, pathway) from 16 diverse databases.
  • Built a searchable database containing synonyms, descriptions, and links for each entity.
  • Implemented search functionalities using intersections, unions, and negations for result exploration.

Main Results:

  • Successfully created BEE, a web server with a unified database of biomedical entities and their gene associations.
  • The platform supports searching for six types of biomedical entities.
  • Users can effectively navigate complex relationships using set operations (union, negation, intersection).

Conclusions:

  • BEE provides a valuable resource for biologists seeking complex biomedical entity associations.
  • The tool serves as an accessible starting point for general users interested in biomedical data.
  • BEE enhances biomedical data exploration through integrated databases and advanced search capabilities.