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- Title
BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways.
- Authors
Agapito, Giuseppe; Pastrello, Chiara; Guzzi, Pietro Hiram; Jurisica, Igor; Cannataro, Mario
- 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.
- Subjects
WEB-based user interfaces; INTERNET servers; SOFTWARE development tools; NONPROFIT organizations; DISEASE progression; PEAS
- Publication
Bioinformatics, 2020, Vol 36, Issue 15, p4377
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btaa529