Curation, Visualization and Analysis of Biological Pathways

Pathway diagrams are found everywhere: in textbooks, in review articles, on posters and on whiteboards. Their utility to biologists as conceptual models is obvious. They have also become immensely useful for computational analysis and interpretationof large-scale experimental data when properly modeled. We will highlight the latest developments and newest features of WikiPathways (www.wikipathways.org), a community curated pathway database that enables researchers to capture rich, intuitive models of pathways. WikiPathways and the associated tools PathVisio and pathvisio.js are developed as open source projects with a lot of community engagement.

The new interactive JavaScript-based pathway viewer, pathvisio.js (https://github.com/wikipathways/pathvisiojs/), is integrated in the WikiPathways website and enables users to zoom in and click on pathway elements to show linkouts to other databases. In the future pathvisio.js will replace the Java applet editor and introduce a quick and simple way to curate and edit pathways.

The standalone pathway editor and analysis and visualization tool, PathVisio (www.pathvisio.org), was refactored with the goal to achieve a better, modular system that can be easily extended with plugins. Plugins are accessible through the new plugin repository and can be installed through the plugin manager from within the application. This is an important aspect of usability that will allow users to build an application with all the necessary modules relevant for their work. The WikiPathways plugin of PathVisio allows searching and browsing WikiPathways from within PathVisio. Furthermore users can upload new pathways or update existing pathways.