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Biomolecule and bioentity interaction databases in systems biology: a comprehensive review
Baltoumas, F.A.; Zafeiropoulou, S.; Karatzas, E.; Koutrouli, M.; Thanati, F.; Voutsadaki, K.; Gkonta, M.; Hotova, J.; Kasionis, I.; Hatzis, P.; Pavlopoulos, G.A. (2021). Biomolecule and bioentity interaction databases in systems biology: a comprehensive review. Biomolecules 11(8): 1245. https://dx.doi.org/10.3390/biom11081245
In: Biomolecules. MDPI AG: Basel. ISSN 2218-273X, more
Peer reviewed article  

Available in  Authors 

Author keywords
    biomedical networks; associations; biological interactions; network biology; databases; data integration

Authors  Top 
  • Baltoumas, F.A.
  • Zafeiropoulou, S.
  • Karatzas, E.
  • Koutrouli, M.
  • Thanati, F.
  • Voutsadaki, K.
  • Gkonta, M.
  • Hotova, J.
  • Kasionis, I.
  • Hatzis, P.
  • Pavlopoulos, G.A.

Abstract
    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.

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