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. 2012 Jan;40(Database issue):D1301-7.
doi: 10.1093/nar/gkr1074. Epub 2011 Nov 16.

WikiPathways: building research communities on biological pathways

Thomas Kelder  1 , Martijn P van Iersel, Kristina Hanspers, Martina Kutmon, Bruce R Conklin, Chris T Evelo, Alexander R Pico
Affiliations

WikiPathways: building research communities on biological pathways

Thomas Kelder et al. Nucleic Acids Res. 2012 Jan.

Abstract

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further.

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Figures

Figure 1.
Figure 1.
The new interactive pathway viewer.
Figure 2.
Figure 2.
Size and growth of the human pathway archive before and after launching WikiPathways. The numbers for years 2005–2008 are derived from the size of the GenMAPP archive, which served as the initial seed content for WikiPathways.
Figure 3.
Figure 3.
Relation between views and edits for the pathways at WikiPathways. Each dot in the graph represents a group of pathways that each has been edited by the same number of unique authors (indicated by color). The size of the dot represents the number of pathways in that group. The x-axis represents the number of times the pathway has been viewed (averaged over each group) and the y-axis represents the number of times the pathway has been edited (averaged over each group).
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