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 1.2.1.1 R 1.3 Showcase 1.3.1 Web applications 1.3.2 Workflows 1.3.3 Extending existing software 1.3.4 Bots 1.4 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.

R

Using the SSOAP package in R, you can retrieve pathway information from the WikiPathways web service and use it in your R scripts (e.g. for gene set enrichment or pathway statistics). Below are a few code snippets that show you how to use SSOAP with the WikiPathways web service.

## Install SSOAP from Bioconductor ##
source("http://bioconductor.org/biocLite.R")
biocLite("SSOAP")

## Load the SSOAP library ##
library(SSOAP)

## Create a SOAPServer instance for the web service ##
srv = SOAPServer("http://www.wikipathways.org/wpi/webservice/webservice.php");

## List all organisms on WikiPathways ##
reply = .SOAP(srv, "listOrganisms", action=I("listOrganisms"), handlers=NULL)
doc = xmlParse(reply$content, asText=TRUE)
organismNodes = xmlElementsByTagName(xmlRoot(doc), "organisms", TRUE)

for(node in organismNodes) {
	print(xmlValue(node)) #Print the organism name to the screen
}

## Find all pathways for the 'apoptosis' keyword ##
reply = .SOAP(srv, "findPathwaysByText", query="apoptosis", species="", action=I("findPathwaysByText"), handlers=NULL)
doc = xmlParse(reply$content, asText=TRUE)

# Find the result nodes with an xpath query
resultNodes = getNodeSet(doc, "//*[local-name()='result']")
# Print the pathway name, species and url for each result
for(node in resultNodes) {
	children = xmlChildren(node, addNames= TRUE)
	url = xmlValue(children$url)
	name = xmlValue(children$name);
	species = xmlValue(children$species);
	
	print(paste(name, " (", species, "): ", url, sep=""))
}

Showcase

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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