Biological Pathway Workshop

1
Web service
2
Outline

• Why a web service?
• SOAP / WSDl
• Functionality
• Code examples
• Application examples

3
Why a web service?

• Programmatic access to WikiPathways
• WikiPathways as a data resource for tools
• Integration with other data-sources

4
SOAP

• Simple Object Access Protocol
• XML-based
• Platform independent
• Language independent
• Extensible
• RPC over HTTP

5
WSDL

• Web Services Description Language
• Defines services as collections of network
  endpoints
• Describes
• Method signatures
• Data structures

6
Available services

• Download
• All pathway information in various formats
• Pathway metadata
• Colored pathway images
• Find
• By keyword searches
• By gene / protein / small molecule identifier
• Interactions by gene / protein

7
Available services

• Update
• Notify community by curation tags
• Update pathway content
• Write access upon request

8

• http//www.wikipathways.org/webservice
• List of available functions
• Documentation and examples

9
Java Examples

• PathVisio and WikiPathways java libraries

org.pathvisio.model Pathway A GPML
pathway PathwayElement An element on the
pathway org.pathvisio.wikipathways WikiPathwaysC
lient Client for web service WikiPathwaysCache Ut
ility that manages cached copy of
WikiPathways org.pathvisio.wikipathways.webservic
e WSPathwayInfo Container for pathway
metadata WSPathway Container for
GPML WSSearchResult Container for a search
result
10

• org.pathvisio.wikipathways.WikiPathwaysClient
• No need to deal with SOAP / WSDL
• Built on Apache Axis

11
(No Transcript)
12

• org.pathvisio.model.Pathway
• No need to deal with XML / GPML

13
(No Transcript)
14
R Examples

• SSOAP
• http//www.omegahat.org/SSOAP/

15
(No Transcript)
16
(No Transcript)
17
(No Transcript)
18
(No Transcript)
19
Applications

• Build web applications
• Extend existing applications
• Include in workflows / analysis pipelines

20
Search engine
21
Visualizing gene expression
Integrates data from ArrayExpress Atlas with
WikiPathways pathways
22
Cytoscape plugin
Search and open pathways from WikiPathways
directly in Cytoscape.
23
Taverna workflows
Include pathway information in Taverna
workflows. http//www.myexperiment.org/packs/40
24
Conclusion

• WikiPathways web service
• Programmatic interface to WikiPathways data
• Direct
• Language-independent
• Java libraries to help you build tools using GPML
  pathways
• http//www.wikipathways.org/webservice