Biological Pathway Workshop

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Mining biological pathways using the WikiPathways
web service
Web service
Website
Thomas Kelder thomas.kelder_at_bigcat.unimaas.nl
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www.wikipathways.org

• Resource for biological pathways
• Free and open source
• Wiki, editable by users

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Recent contributions
An Lebacq
Shamith Samarajiwa
Andreas Neerincx
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GPML
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Web service
SOAP / WSDL
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Implementation

• SOAP / WSDL
• Platform Language independent
• Widely supported
• Client Java libraries (PathVisio)
• High-level API to web service

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Available services

• Find pathways by keywords or entity id
• Download pathways as XML or image formats
• Access to complete revision history
• Download pathway as identifier list

HMDB HMDB00121 HMDB01846 HMDB01056 HMDB01396 HMDB
00972 HMDB01354 HMDB00696 HMDB00043 HMDB01185 HMDB
00939
Entrez Gene 123263 6948 10588 23382 4143 275 1719
643509 10840
UniProt A4UU12 A4UU13 A9CB79 Q04609 Q04609-2 Q04
609-3 Q2VPJ0 Q541A4 Q7Z5D2
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Who would use the web service?

• Developers
• Connect your tool / website to WikiPathways
• Feed your pathway analysis algorithms
• Create pathway visualizations
• Researchers
• Pathway analysis in your R scripts
• Use pathways in your Taverna workflows

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Search engine
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www.biogps.org
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Visualizing gene expression
Integrates data from ArrayExpress Atlas with
WikiPathways
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Cytoscape plugin
Search and open WikiPathways pathways directly
from Cytoscape.
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Taverna workflows
- Include pathway information in Taverna
workflows. - Get basic workflows you can use as
building blocks at http//www.myexperiment.org/pa
cks/40
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GSEA in R
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Why use the web service?

• Easier programmatic access
• Query pathway information
• Less parsing
• Always up-to-date with latest pathways

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• http//www.wikipathways.org/webservice
• Example applications and source code
• API Documentation
• Links to useful libraries

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Want to write open source code? Want to make
money? Want to do both? Look for mentor
organization GenMAPP