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Updated: Mar 31, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
WikiPathways: capturing the full diversity of pathway knowledge
Martina Kutmon1, Anders Riutta2, Nuno Nunes3
1Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands martina.kutmon@maastrichtuniversity.nl.
Abstract:
WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the diversity and depth of the collected pathways are described from the perspective of researchers interested in using pathway information in their studies. We provide updates on extensions and services to support pathway analysis and visualization via popular standalone tools, i.e. PathVisio and Cytoscape, web applications and common programming environments. We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities. In addition to the latest milestones in our pathway collection and curation effort, we also highlight the latest means to access the content as publishable figures, as standard data files, and as linked data, including bulk and programmatic access.
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