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

doi:10.1186/1471-2105-7-21

BMC Bioinformatics

Volume 7

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Durand P
Labarre L
Meil A
Divo1 JL
Vandenbrouck Y
Viari A
Wojcik J

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Labarre L
Meil A
Divo1 JL
Vandenbrouck Y
Viari A
Wojcik J
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GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins

Patrick Durand¹^,5 , Laurent Labarre¹^,2 , Alain Meil¹ , Jean-Louis Divo1¹ , Yves Vandenbrouck³^,6 , Alain Viari⁴ and Jérôme Wojcik¹^,7

¹Hybrigenics SA, 3–5 Impasse Reille, 75014 Paris, France

²AGC, UMR CNRS 8030 – Genoscope, 2 rue Gaston Crémieux, 91000 Evry, France

³Genome Express, 11 Chemin des Prés, 38944 Meylan, France

⁴INRIA Rhône-Alpes, 655 Avenue de l'Europe, 38334 Saint-Ismier Cedex, France

⁵IRISA-INRIA, Campus de Beaulieu, 35402 Rennes Cedex, France

⁶DRDC/BIM, CEA-Grenoble, 17 Avenue des martyrs, 38054 Grenoble Cedex 9, France

⁷Serono Genetics Institute, Route Nationale 7, 91030 Evry Cedex, France

author email corresponding author email

BMC Bioinformatics 2006, 7:21doi:10.1186/1471-2105-7-21


Published:	17 January 2006

Abstract

Background

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.

Results

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.

Conclusion

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 academy@genostar.com. A commercial licence form can be obtained for profit company at info@genostar.com. See also http://www.genostar.org webcite.