A Graphical Tool for the Exploration and Visual Analysis of Biomolecular Networks

Cheick Tidiane Ba, Elena Casiraghi, Marco Frasca, Jessica Gliozzo, Giuliano Grossi, Marco Mesiti, Marco Notaro, Paolo Perlasca, Alessandro Petrini, Matteo Re, Giorgio Valentini

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Many interactions among bio-molecular entities, e.g. genes, proteins, metabolites, can be easily represented by means of property graphs, i.e. graphs that are annotated both on the vertices (e.g. entity identifier, Gene Ontology or Human Phenotype Ontology terms) and on the edges (the strength of the relationship, the evidence of the source from which the weight has been taken, etc.). These graphs contain a relevant information that can be exploited for conducting different kinds of analysis, such as automatic function prediction, disease gene prioritization, drug repositioning. However, the number and size of the networks are becoming quite large and there is the need of tools that allow the biologists to manage the networks, graphically explore their structures, and organize the visualization and analysis of the graph according to different perspectives. In this paper we introduce the web service that we have developed for the visual analysis of biomolecular networks. Specifically we will show the different functionalities for exploring big networks (that do not fit in the current canvas) starting from a specific vertex, for changing the view perspective of the network, and for navigating the network and thus identifying new relationships. The proposed system extends the functionalities of off-the-shelf graphical visualization tools (e.g. GraphViz and GeneMania) by limiting the production of big cloud of points and allowing further customized visualizations of the network and introducing their vertex-centric exploration.

Original languageEnglish
Title of host publicationComputational Intelligence Methods for Bioinformatics and Biostatistics - 15th International Meeting, CIBB 2018, Revised Selected Papers
EditorsMaria Raposo, Paulo Ribeiro, Susana Sério, Antonino Staiano, Angelo Ciaramella
PublisherSpringer
Pages88-98
Number of pages11
ISBN (Print)9783030345846
DOIs
Publication statusPublished - Jan 1 2020
Event15th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2018 - Caparica, Portugal
Duration: Sep 6 2018Sep 8 2018

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume11925 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference15th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2018
CountryPortugal
CityCaparica
Period9/6/189/8/18

Keywords

  • Biological network
  • Graph visualization
  • Information visualization
  • Protein function prediction

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Ba, C. T., Casiraghi, E., Frasca, M., Gliozzo, J., Grossi, G., Mesiti, M., Notaro, M., Perlasca, P., Petrini, A., Re, M., & Valentini, G. (2020). A Graphical Tool for the Exploration and Visual Analysis of Biomolecular Networks. In M. Raposo, P. Ribeiro, S. Sério, A. Staiano, & A. Ciaramella (Eds.), Computational Intelligence Methods for Bioinformatics and Biostatistics - 15th International Meeting, CIBB 2018, Revised Selected Papers (pp. 88-98). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11925 LNBI). Springer. https://doi.org/10.1007/978-3-030-34585-3_8