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

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.

Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY

“…The ApiNATOMY method seeks to progress on the representation of biological pathways which, in the field of systems biology has been primarily focused on databases depicting pathways of biochemical transformation from one molecular species to another (e.g., Orchard et al, 2014 ; de Bono et al, 2016b ; Baltoumas et al, 2021 ; Kanehisa et al, 2021 ). Specifically, ApiNATOMY manages knowledge about anatomical pathways that are represented in the form of conduits for multiscale transport (i.e., pathways of linked conduit compartments in which, for instance, molecular species reside).…”

A roadmap for the functional annotation of protein families: a community perspective

“…expression data in model microbes or proteomics data, or ChIP-Seq data), such as the FitnessBrowser developed to analyze Tn-Seq data ( 120 ), would allow for the capture of all HTP data available for a given protein family. User-friendly tools for analyzing and comparing co-expression data from different organisms exist [see Table 1 of ( 121 )] but vary greatly in the number of organisms covered and the usefulness of their respective outputs. Established databases like UniProt are always interested in ways to incorporate HTP data, but the lack of metadata and standards makes this objective difficult.…”

PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

“…The time is ripe for tools that integrate all this knowledge and henceforth assist researchers to tackle major challenges like climate change [36], sustainability [37], and synthetic ecology [38]. Many resources have emerged in this realm [39], each one serving a specific purpose, such as BacDive [40]. BacDive is a large-scale curated database with prokaryotic information about phenotypic, morphological, and metabolic information.…”