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Review

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

1
Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece
2
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
3
Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
*
Authors to whom correspondence should be addressed.
Academic Editors: Francisco Rodrigues Pinto and Javier De Las Rivas
Biomolecules 2021, 11(8), 1245; https://doi.org/10.3390/biom11081245
Received: 28 July 2021 / Revised: 16 August 2021 / Accepted: 18 August 2021 / Published: 20 August 2021
(This article belongs to the Special Issue Computational Approaches for the Study of Biomolecular Networks)
Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology. View Full-Text
Keywords: biomedical networks; associations; biological interactions; network biology; databases; data integration biomedical networks; associations; biological interactions; network biology; databases; data integration
MDPI and ACS Style

Baltoumas, F.A.; Zafeiropoulou, S.; Karatzas, E.; Koutrouli, M.; Thanati, F.; Voutsadaki, K.; Gkonta, M.; Hotova, J.; Kasionis, I.; Hatzis, P.; Pavlopoulos, G.A. Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. Biomolecules 2021, 11, 1245. https://doi.org/10.3390/biom11081245

AMA Style

Baltoumas FA, Zafeiropoulou S, Karatzas E, Koutrouli M, Thanati F, Voutsadaki K, Gkonta M, Hotova J, Kasionis I, Hatzis P, Pavlopoulos GA. Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. Biomolecules. 2021; 11(8):1245. https://doi.org/10.3390/biom11081245

Chicago/Turabian Style

Baltoumas, Fotis A., Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, and Georgios A. Pavlopoulos. 2021. "Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review" Biomolecules 11, no. 8: 1245. https://doi.org/10.3390/biom11081245

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