How we assist knowledge collection Serving the monks Chris Evelo Dept of Bioinformatics – BiGCaT...
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How we assist knowledge collection
Serving
the monks
Chris Evelo
Dept of Bioinformatics – BiGCaTMaastricht University
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Paper:WikiPathways: Pathway Editing for the People. Alexander R. Pico, Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Bruce R. Conklin, Chris Evelo. PLoS Biology 2008: 6: 7. e184
Commentaries:Big data: Wikiomics. Mitch Waldrop. Nature 455, 22-25 (2008) We the curators. Allison Doerr. Nature Methods 5, 754 - 755 (2008)
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WikiPathways
• Public resource for biological pathways
• Wiki:– Anyone can contribute and curate
• More up-to-date representation of biological knowledge
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What are biological pathways?
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How are Pathways used?
• Example: RNA interference in C. elegans
The nematode C. elegans
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Connect to Genome Databases
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Data Visualization
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On to the real thing…Fasten seat belts!
Photo by Timo Arnall
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Search: “One carbon”
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Click
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Click
Editing
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Registration by e-mail address
All edits logged
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Click
Click & drag
Draw the proteins and interactions
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Click
Draw the proteins and interactions
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Draw the proteins and interactions
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Double click
Annotate the proteins
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Annotate the proteins
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Click
Add reference to literature
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Download
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“Wiki’s work because it is easier to undo damage than to create it. Imagine what cities would look like if it was easier to clean graffiti than to create it” – Clay Shirkey
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Revision history
Select two versions
Click
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Diff tool
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September 2008
February 2009
April 2009
GrowthMore users, species, pathways, genes
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Contributions – small edits
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Species• We can add
any speciesthat is in ENSEMBL
• Or anything where youcreate an ENSEMBL like DB
• Just ask!
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MetabolomicsVisualization and statistics fully supported
HMDB
Chebi
NuGOwiki
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Automatic content generation
GO: gene ontology visualization
• Automatic pathway (table) generatorfor any GO level
• Ask for tool or pathways
• Go statistics in GenMAPP, Go_Elite,R (through webservice)
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Automatic content generation
KEGG
• Automatic pathway converter
• Ask for tool or pathways
• We need two versions:– Original– Community updated
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Automatic content generation
BioPAX
• Part of BioPAX already implemented
• Full converter in developmentusing Paxtools
• Can also be used for Reactome(round trip)
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Assisted content generation
Suggestions from:
• HMDB
• KEGG
• BIND
• Text mining (Phasar)
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PortalsNeed one?
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Webservice
Web service
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What for?
• Build web applications
• Extend existing applications
• Include in workflows / analysis pipelines
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Available services
• Download– All pathway information in various formats– Pathway metadata– Colored pathway images– Gene lists
• Find– By keyword searches– By gene / protein / small molecule identifier– Interactions by gene / protein
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Available services
• Update– Notify community by curation tags– Update pathway content– Create new pathways
• Write access upon request
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Search engine
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Visualizing gene expression
Integrates data fromArrayExpress Atlaswith WikiPathways pathways
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Cytoscape plugin
Search and open pathways from WikiPathways directly in Cytoscape.
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Taverna workflows
Include pathway information in Taverna workflows.
http://www.myexperiment.org/packs/40
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R- example: GSEA
• Get all human pathways as gene lists
• Download a GEO dataset (on papillary renal cell carcinoma)
• Perform Parametric Gene Set Enrichment
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Credit system
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Department of Bioinformatics (Maastricht)
Thomas KelderMartijn van Iersel
Chris Evelo
www.wikipathways.org
Gladstone Institutes (San Francisco)Alexander Pico
Kristina Hanspers
Bruce Conklin
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Enjoy!