WikiPathways: An Experiment in the Communitybased Curation of Biology

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WikiPathways An Experiment in the
Community-based Curation of Biology
Alex Pico The Gladstone Institutes, UCSF June
26th 2008
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Pathway Analysis Tools

• GenMAPP
• Cytoscape
• WikiPathways

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Pathways as Communication Medium

• Intuitive
• Visualization
• Integration
• Analysis

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Pathway Analysis Tools

• GenMAPP
• Cytoscape
• WikiPathways

wiki pathway drawing tool a pathway database
that anyone can edit
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Wikis in Science
RefSeq has collected over 50 million
sequences from 5168 species (May 2008)
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A Wiki for Pathways

• Public resource for biological pathways
• Wiki anyone can contribute and curate
• First biological pathway wiki

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Demo
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Under the Hood
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Under the Hood
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Under the Hood
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Beta Usagesince January 08

• 11 new human pathways
• 10 new mouse pathways
• 6 new zebrafish pathways
• 3 new rat pathways
• A portal for the micro-nutrients community
• Over 230 registered users (10 contributing)

• Dozens of E.coli and plant pathways
• 3 new community portals
• July issue of PLoS Biology

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Future Development

• Automated scripts bots
• Curator tools
• BioPAX import/export
• Web API
• Contribution scores and awards

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When Would I Use WikiPathways?

• As a Reference
• To learn or update your knowledge
• As a Repository
• When studying a new field
• When writing a review article
• Updating your field of interest
• As a Resource
• For pathway analysis

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WikiPathways
Pathway Editing for the People
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WikiPathways
Pathway Editing for the People
Public Community
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Pathway Analysis Tools

• GenMAPP
• Cytoscape
• WikiPathways

Open source software projects

• Licensed for common use
• Sustainable life cycle
• Collaborative development

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Collaborative Development

• Google Summer of Code
• - 1125 student and 175 organizations
• - 90 countries represented
• - 9 students and 14 mentors working on GenMAPP,
  Cytoscape and WikiPathways
• Cytoscape Consortium
• - 15 core developers
• - 7 institutes in 4 countries

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Acknowledgements
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Why Pathway Analysis?

• Intuitive to Biologists
• Provide a biological context for results
• More efficient than searching databases
  gene-by-gene
• Intuitive data display for sharing data
• Computation on Pathway Content
• Analyze over-representation of changed genes on
  pathways
• Compare pathway signatures between conditions