Presenting and exploring biological pathways with PathVisio

By M. V. Iersel, Thomas Kelder, Alexander R. Pico, Kristina Hanspers, S. Coort, Bruce R. Conklin, Chris T. A. Evelo. BMC Bioinformatics, 2008

371 citations recorded by the source corpus.

BackgroundBiological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help biological research. PathVisio is a new visualization tool for biological pathways that mimics the popular GenMAPP tool with a completely new Java implementation that allows better integration with other open source projects. The GenMAPP MAPP file format is replaced by GPML, a new XML file format that provides seamless exchange of graphical pathway information among multiple programs.ResultsPathVisio can be combined with other bioinformatics tools to open up three possible uses: visual compilation of biological knowledge, interpretation of high-throughput expression datasets, and computational augmentation of pathways with interaction information. PathVisio is open source software and available at http://www.pathvisio.org.ConclusionPathVisio is a graphical editor for biological pathways, with flexibility and ease of use as primary goals.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1028c33ca9c0d222dea200fc4c163a029b3e902e

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In Molecular Biology

Citations in the corpus

PathVisio 3: An Extendable Pathway Analysis Toolbox (2015, methodology): “In 2008, we presented the first version of our pathway visualization and analysis tool PathVisio [1].”
WikiPathways: building research communities on biological pathways (2011, methodology): “We provide pathways in an open, XML standard format, called GPML, which is explicitly compatible with a handful of analysis tools, such as GenMAPP (11), PathVisio (12), Cytoscape (13) and GO-Elite (14).”
Into the Eye of the Cytokine Storm (2012, methodology): “PathVisio was used for data visualization (143) of the acute-phase response signaling pathway from IPA (Ingenuity Systems).”
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology (2010, methodology): “Development, visualization and web publishing of organism-specific DBs Metabolic pathway information Other software systems for managing metabolic pathway information are KEGG [89, 90], PUMA2 [91] (inactive), Amaze [92] (inactive), GenMAPP [93, 94], PathCase [95, 96], VisANT [97], and Reactome [98–1”