PathVisio 3: An Extendable Pathway Analysis Toolbox

By Martina Kutmon, M. V. Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. A. Evelo. PLoS Comput. Biol., 2015

431 citations recorded by the source corpus.

PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways. Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application. PathVisio can be downloaded from http://www.pathvisio.org and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license (http://www.apache.org/licenses/LICENSE-2.0). It is implemented in Java and thus runs on all major operating systems. The code repository is available at http://svn.bigcat.unimaas.nl/pathvisio. The support mailing list for users is available on https://groups.google.com/forum/#!forum/wikipathways-discuss and for developers on https://groups.google.com/forum/#!forum/wikipathways-devel.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/59d2421e06ee05e32910ca5bd540dfacaba485ea

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression (2017, positive): “A global score based ranking was generated taking into consideration the position of each gene in the 3 cell lines and then was mapped onto the interferon pathways using PathVisio (v 3.2.1) (Kutmon et al., 2015).”
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community (2019, neutral): “PathVisio 3 • Transcriptomics • Proteomics • Metabolomics Unspecified - Integration of omics data - Visualize omics data based on common data nodes and interactions in the pathway Open (Apache) [134]”
WikiPathways: connecting communities (2020, methodology): “Furthermore, WikiPathways provides a variety of options to access the data for use, through downloads in various formats for individual pathways or pathway collections, from the pathway editor and analysis software PathVisio (14), through the WikiPathways REST API and rWikiPathways R package, or thr”
WikiPathways: capturing the full diversity of pathway knowledge (2015, methodology): “The ‘Editing Tour’ video includes the latest updates to the WikiPathways plugin for PathVisio and the Quick Edit feature (see Supplemental Data: Editing Tour).”
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research (2017, methodology): “Pathways are encoded in GPML format and created with PathVisio (14).”
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (2015, methodology): “Briefly, these tools include Omix [8], Cytoscape [5], CellDesigner [9], Vanted [10] with the SBGN-ED add-on [11], VisAnt [12] and PathVisio [13].”
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources (2020, background): “PathVisio provides a user-friendly way to draw pathways and to visualize experimental data on these pathways [232].”