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<p>Abstract</p> <p>Background</p> <p>Gene set analysis is moving towards considering pathway topology as a crucial feature. Pathway elements are complex entities such as protein complexes, gene family members and chemical compounds. The conversion of pathway topology to a gene/protein networks (where nodes are a simple element like a gene/protein) is a critical and challenging task that enables topology-based gene set analyses.</p> <p>Unfortunately, currently available R/Bioconductor packages provide pathway networks only from single databases. They do not propagate signals through chemical compounds and do not differentiate between complexes and gene families.</p> <p>Results</p> <p>Here we present <monospace>graphite</monospace>, a Bioconductor package addressing these issues. Pathway information from four different databases is interpreted following specific biologically-driven rules that allow the reconstruction of gene-gene networks taking into account protein complexes, gene families and sensibly removing chemical compounds from the final graphs. The resulting networks represent a uniform resource for pathway analyses. Indeed, graphite provides easy access to three recently proposed topological methods. The <monospace>graphite</monospace> package is available as part of the Bioconductor software suite.</p> <p>Conclusions</p> <p><monospace>graphite</monospace> is an innovative package able to gather and make easily available the contents of the four major pathway databases. In the field of topological analysis <monospace>graphite</monospace> acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements.</p>