WikiPathways:About
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What is WikiPathways
WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.
Why Pathways
Strictly speaking, one could argue that pathways don't exist... there are only networks. Nonetheless, pathways are useful. 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.
How Does it Work
Each pathway at WikiPathways has a dedicated wiki page, displaying the current diagram, description, references, download options, version history, and component gene and protein lists. Any pathway can be edited from within its wiki page by activating an embedded pathway editor. After editing, an updated pathway image is displayed on the wiki page along with the version history and list of component genes and proteins. Users can easily monitor and undo changes, compare differences and search for overlapping pathways. Using the search feature, one can locate particular pathways by name, by the genes and proteins they contain, or by the text displayed in their descriptions and comments. One can also browse the collection of pathways with combinations of species names and ontology-based categories. The pathway content at WikiPathways is freely available for download in a variety of data and image formats, including GPML, which is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio.
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 post a message to the discussion mailinglist:
wikipathways-discuss@googlegroups.com
Or contact:
- Thomas Kelder: Thomas.Kelder[AT]BIGCAT.unimaas.nl
- Alex Pico: apico[AT]gladstone.ucsf.edu
Note that though WikiPathways is inspired by the open philosophy of Wikipedia and other wiki's, it is an independent project and not directly related to Wikipedia or other projects of the Wikimedia foundation
How to cite WikiPathways
When referring to the website or content, please cite:
Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biol 6(7): doi:10.1371/journal.pbio.0060184
When referring to the web services, please cite:
Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. (2009) Mining Biological Pathways Using WikiPathways Web Services. PLoS ONE 4(7): doi:10.1371/journal.pone.0006447
Open Access and Open Source
We are committed to open access and open source. All content is available under our license terms. All source code for WikiPathways and the PathVisio applet is available under the Apache License, Version 2.0.
- http://svn.bigcat.unimaas.nl/wikipathways/trunk/
- http://svn.bigcat.unimaas.nl/pathvisio/branches/wpapplet_rc_1.1/
Funding and Support
- The BioRange program of the Netherlands Bioinformatics Centre (NBIC).
- GenMAPP.org is funded by the National Institute for General Medical Sciences (R01-GM080223), as well as the Gladstone Institutes
- Google Summer of Code 2007 supported 2 students working on WikiPathways under the mentorship of GenMAPP.org
- University Maastricht: Broad Research Strategy Program Part 2 (BOS2)
- Transnational University Limburg (tUL)
