GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins

Patrick Durand (1, 2) , Laurent Labarre (1, 3) , Alain Meil (1) , Jean-Louis Divo1 (1) , Yves Vandenbrouck (4, 5) , Alain Viari (6) , Jérôme Wojcik (1, 7)

1 Hybrigenics [Paris]
2 SYMBIOSE - Biological systems and models, bioinformatics and sequences
3 UMR 8030 - Génomique métabolique
4 GENOME Express - GENOME Express
5 DRDC/BIM [Grenoble]
6 HELIX - Computer science and genomics
7 Serono Genetics Institute S.A.[Evry]

A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs. GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces. GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at [e-mail]. A commercial licence form can be obtained for profit company at [e-mail]. See also http://www.genostar.org.

Domaines: Génomique, Transcriptomique et Protéomique [q-bio.GN]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Bio-informatique [q-bio.QM]

Patrick Durand, Laurent Labarre, Alain Meil, Jean-Louis Divo1, Yves Vandenbrouck, et al.. GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. BMC Bioinformatics, 2006, 7 (1), pp.21. ⟨10.1186/1471-2105-7-21⟩. ⟨hal-00784481⟩