Skip to Main content Skip to Navigation
Journal articles

Pathway Preserving Representation of Metabolic Networks

Antoine Lambert 1, 2 Jonathan Dubois 2, 1 Romain Bourqui 2, 1
1 GRAVITE - Graph Visualization and Interactive Exploration
CNRS - Centre National de la Recherche Scientifique : UMR, École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Inria Bordeaux - Sud-Ouest, Université Sciences et Technologies - Bordeaux 1
Abstract : Improvements in biological data acquisition and genomes sequencing now allow to reconstruct entire metabolic networks of many living organisms. The size and complexity of these networks prohibit manual drawing and thereby urge the need of dedicated visualization techniques. An efficient representation of such a network should preserve the topological information of metabolic pathways while respecting biological drawing conventions. These constraints complicate the automatic generation of such visualization as it raises graph drawing issues. In this paper we propose a method to lay out the entire metabolic network while preserving the pathway informa- tion as much as possible. That method is flexible as it enables the user to define whether or not node duplication should be performed, to preserve or not the network topology. Our technique combines partitioning, node place- ment and edge bundling to provide a pseudo-orthogonal visualization of the metabolic network. To ease pathway information retrieval, we also provide complementary interaction tools that emphasize relevant pathways in the entire metabolic context.
Document type :
Journal articles
Complete list of metadata

Cited literature [31 references]  Display  Hide  Download

https://hal.inria.fr/inria-00579267
Contributor : Antoine Lambert Connect in order to contact the contributor
Submitted on : Tuesday, February 28, 2012 - 6:09:16 PM
Last modification on : Saturday, December 4, 2021 - 3:05:54 AM
Long-term archiving on: : Friday, November 23, 2012 - 3:11:02 PM

File

PathwayPreservingRepresentatio...
Publisher files allowed on an open archive

Identifiers

  • HAL Id : inria-00579267, version 1

Citation

Antoine Lambert, Jonathan Dubois, Romain Bourqui. Pathway Preserving Representation of Metabolic Networks. Computer Graphics Forum, Wiley, 2011, Special Issue Bergen, Norway 1 - 3 June 2011, 30 (3), pp.1021 - 1030. ⟨inria-00579267⟩

Share

Metrics

Record views

524

Files downloads

796