From WikiPathways

Contents 1 The WikiPathways web service 1.1 Getting Started 1.1.1 Java libraries for WikiPathways 1.1.2 Working with GPML 1.1.3 SOAP libraries 1.2 Examples 1.2.1 Scripts 1.2.2 Web applications 1.2.3 Workflows 1.2.4 Extending existing software 1.2.5 Bots 1.3 API Reference

The WikiPathways web service

WikiPathways can be accessed through a SOAP webservice. This page contains documentation for the webservice API.

Getting Started

The web service is described in a WSDL file that can be downloaded from:

http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl

Java libraries for WikiPathways

Coming soon

• PathVisio libraries
• wikipathways-client

Working with GPML

The pathways on WikiPathways are stored in the GPML format. This is an XML format and can be processed in any programming language. See here for the GPML specification.

SOAP libraries

For most programming languages, libraries exist to make working with SOAP web service easier. Below is a short list of SOAP libraries for popular programming languages that might help you work with the WikiPathways web service.

• Java:
  • Apache Axis
  • See the Java section for information on writing Java tools for the web service
• Perl:
  • SOAP::Lite
• Php:
  • SOAP (official php soap library)
  • PHP-SOAP
• Python:
  • SOAPpy
  • soaplib
• R
  • SSOAP

Examples

Scripts

Coming soon: small example scripts in various languages.

Web applications

• Searching WikiPathways
• Visualize gene expression information

Workflows

You can use the WikiPathways webservice to integrate WikiPathways functions in your Taverna workflows. See myexperiment.org for a set of example workflows that show how to call WikiPathways from Taverna.

Extending existing software

See the Cytoscape plugin for an example on how to use the web service to extend the functionality of existing software. You can install the plugin in your local Cytoscape installation from the plug-in manager.

Bots

API Reference

See the API reference page for a list of available web service functions and data structures.

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