Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

Area of Science:

• Network Biology
• Bioinformatics
• Computational Biology

Background:

• High-throughput techniques generate vast biological datasets on biomolecular interactions.
• Computational tools and databases aid in managing this data deluge, addressing integration, visualization, and complexity.
• Increasing numbers of repositories make it difficult for users to discern their scope, focus, and information redundancy.

Purpose of the Study:

• To provide a comprehensive categorization, comparison, and evaluation of biomolecular interaction repositories.
• To assist users in understanding the scope, content, and interconnectivity of various biological databases.
• To serve as a reference for researchers in the field of Network Biology.

Main Methods:

• Review and categorization of publicly available biomolecular interaction repositories.
• Analysis of repositories based on content, data sources, and representation methods.
• Evaluation of repositories considering user-friendliness, scope, and interconnectivity.

Main Results:

• Identification of diverse repositories with general or specialized scopes (e.g., specific organisms).
• Assessment of strengths and weaknesses of various databases, highlighting issues with self-contained or poorly maintained resources.
• Discussion of data integration, visualization, exploration, organization, scalability, and complexity challenges.

Conclusions:

• A clear categorization and evaluation of biomolecular interaction repositories are needed.
• This review offers a framework for understanding and utilizing these resources effectively.
• The article aims to benefit a broad audience, from beginners to experts in biomedical research and Network Biology.