Project Summary

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.

Principal Investigators

• Alexander Pico
• Chris Evelo

Institute

• Gladstone Institutes, San Francisco, CA, USA
• Maastricht University, The Netherlands

Funding

• The WikiPathways project is funded by the National Institute for General Medical Sciences (R01-GM100039)
• The BioRange program of the Netherlands Bioinformatics Centre (NBIC)
• Broad Research Strategy Program Part 2 (BOS2)
• Transnational University Limburg (tUL)

Publications

• Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo C, Pico AR. (2011) WikiPathways: building research communities on biological pathways. NAR doi: 10.1093/nar/gkr1074
• 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
• 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
• Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, jaiswal P. (2013) WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. Rice 2013, 6:14 doi:10.1186/1939-8433-6-14.

Data

WikiPathways supplies pathway data in the form of GPML, a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio. 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. The pathway content at WikiPathways is freely available for download in a variety of data and image formats, including GPML.
Pathway collections download

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Wikipathways Plants Portal: Accecss here