WikiPathways: capturing the full diversity of pathway knowledge.

Martina Kutmon,Anwesha Bohler,Bart Smeets,Jonathan Mélius,Anders Riutta,Chris T Evelo,Elisa Cirillo,Susan L Coort,Andra Waagmeester,Egon L Willighagen,Ryan Miller,Sravanthi R Sinha,Kristina Hanspers,Alexander R Pico,Nuno Nunes

doi:10.1093/nar/gkv1024

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.

Highlights

Launched in 2008 as an experiment to see if crowdsourcing could work for a pathway archive, WikiPathways started out with 500 pathways across six species maintained by four individuals [1]
In terms of coverage of unique human genes, WikiPathways is comparable to KEGG [2] (Figure 1)
With a more centralized curation process, Reactome can benefit from having access to more open, community curation at WikiPathways, in addition to having their content distributed in additional formats, services and analysis tools

Summary

Introduction

Launched in 2008 as an experiment to see if crowdsourcing could work for a pathway archive, WikiPathways started out with 500 pathways across six species maintained by four individuals [1]. We begin with the most recent additions to the breadth and depth of content at WikiPathways, including website and software updates that make this content easy to find and use in data analysis and visualization. With a more centralized curation process, Reactome can benefit from having access to more open, community curation at WikiPathways, in addition to having their content distributed in additional formats, services and analysis tools.

Results

Conclusion