TY - JOUR

T1 - Biomolecule and Bioentity Interaction Databases in Systems Biology

T2 - A Comprehensive Review

AU - Baltoumas, Fotis A.

AU - Zafeiropoulou, Sofia

AU - Karatzas, Evangelos

AU - Koutrouli, Mikaela

AU - Thanati, Foteini

AU - Voutsadaki, Kleanthi

AU - Gkonta, Maria

AU - Hotova, Joana

AU - Kasionis, Ioannis

AU - Hatzis, Pantelis

AU - Pavlopoulos, Georgios A.

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - biomedical networks

KW - associations

KW - biological interactions

KW - network biology

KW - databases

KW - data integration

KW - MANUALLY CURATED DATABASE

KW - PROTEIN-PROTEIN INTERACTIONS

KW - GENOMICS DATA SETS

KW - ENRICHMENT ANALYSIS

KW - WEB SERVER

KW - NETWORK ANALYSIS

KW - NONCODING RNAS

KW - INTEGRATIVE ANALYSIS

KW - TOPOLOGICAL ANALYSIS

KW - LIGAND INTERACTIONS

U2 - 10.3390/biom11081245

DO - 10.3390/biom11081245

M3 - Review

C2 - 34439912

VL - 11

JO - Biomolecules

JF - Biomolecules

SN - 2218-273X

IS - 8

M1 - 1245

ER -