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What is WikiPathways

In the “tradition” of Wikipedia and other wiki platforms, WikiPathways is intended to be an open, public space for content editing dedicated to biological pathways to facilitate pathway contributions and maintenance from the scientific community. Each WikiPathways page is focused on a single pathway, displaying the current version and references. A pathway can be edited by activating a webstart version of the pathway editing tool, PathVisio. PathVisio provides a basic palette of objects and annotation needed to represent biological processes, including gene objects which are directly mapped to biological annotations from any source through an extensible identifier synonym database. PathVisio is actively being developed by members of Chris Evelo’s group (BiGCaT, University of Maastricht, The Netherlands) in collaboration with GenMAPP (Gladstone Institutes, UCSF). After editing is complete, the new version of the pathway is displayed on the wiki page along with an updated version of the underlying biological information in various pathway file formats. Pathway information downloaded in these formats can be used in applications such as GenMAPP, to analyze for example gene expression data. While in beta, we are supporting the GenMAPP Pathway Markup Language (GPML) file format native to PathVisio. GPML is an XML file format that is being developed to bridge the annotation-rich, curated style of GenMAPP pathways and the more structured, robust BioPAX format which is emerging as the community standard.

Why Pathways

Biological pathways provide intuitive views of the myriad of interactions underlying biological processes. A typical signaling pathway, for example, can represent receptor-binding events, protein complexes, phosphorylation reactions, translocations and transcriptional regulation, with only a minimal set of symbols, lines and arrows. These powerful representations are essential tools, common among the textbooks and review articles that document any given field of biology. Making these tools available for computational methods of analysis will allow researchers to connect pathways to databases of biological annotations and experimental data, creating effective products of systems biology. Collecting and maintaining pathway information in a robust database, however, is an ongoing challenge.

What's Next

As WikiPathways evolves, we plan to produce an embedded version of PathVisio directly into the wiki pages, eliminating the need for a webstart application altogether. Analogous to Wikipedia, modifications to pathways will be recorded, thereby creating a revision history for each pathway and allowing visual comparison between different versions of a pathway. We will also support additional pathway file formats to encourage exchange across current applications and research preferences. We also recognize that the success of WikiPathways will depend heavily on clear and fair standards with regards to handling competing opinions and controversial findings. During beta, we will be gaining critical experience on managing style guides, versions and disputes. We are confident that WikiPathways will be a useful resource to the research community and provide a much needed forum for pathway curation.

Who is Involved

WikiPathways is maintained by BiGCaT Bioinformatics (University of Maastricht) and the Conklin Lab at the Gladstone Institutes (University of California, San Francisco). The current WikiPathways team includes Thomas A.J. Kelder, Alexander R. Pico, Martijn van Iersel, Kristina Hanspers, Bruce R. Conklin and Chris T.A. Evelo.

For questions, comments or suggestions, please contact:

  • Thomas Kelder: Thomas.Kelder[AT]
  • Alex Pico: apico[AT]

Funding and Support

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