%0 Journal Article
%T GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins
%A Patrick Durand
%A Laurent Labarre
%A Alain Meil
%A Jean-Louis Divo1
%A Yves Vandenbrouck
%A Alain Viari
%A J¨¦r£¿me Wojcik
%J BMC Bioinformatics
%D 2006
%I BioMed Central
%R 10.1186/1471-2105-7-21
%X 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 academy@genostar.com. A commercial licence form can be obtained for profit company at info@genostar.com. See also http://www.genostar.org webcite.The development of genomic and post-genomic technologies is producing a large amount of heterogeneous data for investigating the functions of the genes and their products. Biological data are spreaded across an increasing number of databases that differ widely in terms of quality, consistency, diversity and availability [1]. The biologists are now faced with the problem of analysing this information and turning it into new knowledge. Simple analysis is usually performed directly on a database through a query language (usually SQL for
%U http://www.biomedcentral.com/1471-2105/7/21