Giuseppe Agapito1,2, Chiara Pastrello3, Pietro Hiram Guzzi2,4, Igor Jurisica3,5,6, Mario Cannataro2,4. 1. Department of Legal, Economic and Social Sciences. 2. Data Analytics Research Center, Magna Graecia University of Catanzaro, Catanzaro, Italy. 3. Krembil Research Institute, University Health Network, Toronto, Ontario, Canada. 4. Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy. 5. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. 6. Department of Computer Science, University of Toronto, Toronto, ON, Canada.
Abstract
SUMMARY: Biological pathways are fundamental for learning about healthy and disease states. Many existing formats support automatic software analysis of biological pathways, e.g. BioPAX (Biological Pathway Exchange). Although some algorithms are available as web application or stand-alone tools, no general graphical application for the parsing of BioPAX pathway data exists. Also, very few tools can perform pathway enrichment analysis (PEA) using pathway encoded in the BioPAX format. To fill this gap, we introduce BiP (BioPAX-Parser), an automatic and graphical software tool aimed at performing the parsing and accessing of BioPAX pathway data, along with PEA by using information coming from pathways encoded in BioPAX. AVAILABILITY AND IMPLEMENTATION: BiP is freely available for academic and non-profit organizations at https://gitlab.com/giuseppeagapito/bip under the LGPL 2.1, the GNU Lesser General Public License. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Biological pathways are fundamental for learning about healthy and disease states. Many existing formats support automatic software analysis of biological pathways, e.g. BioPAX (Biological Pathway Exchange). Although some algorithms are available as web application or stand-alone tools, no general graphical application for the parsing of BioPAX pathway data exists. Also, very few tools can perform pathway enrichment analysis (PEA) using pathway encoded in the BioPAX format. To fill this gap, we introduce BiP (BioPAX-Parser), an automatic and graphical software tool aimed at performing the parsing and accessing of BioPAX pathway data, along with PEA by using information coming from pathways encoded in BioPAX. AVAILABILITY AND IMPLEMENTATION:BiP is freely available for academic and non-profit organizations at https://gitlab.com/giuseppeagapito/bip under the LGPL 2.1, the GNU Lesser General Public License. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.