From WikiPathways

Contents 1 Web Services for WikiPathways 1.1 Showcase 1.2 Test Drive 1.3 API Reference 1.3.1 Java libraries for WikiPathways 1.3.2 Working with GPML 1.3.3 SOAP libraries 1.4 Examples 1.4.1 Java 1.4.2 R

Web Services for WikiPathways

WikiPathways can be accessed programmatically through a SOAP web service. This page provides documentation and examples of what you can do with the web service.

Showcase

Search Use the web service to search for pathways	View data View gene expression data on pathways
Query interactions Load pathways as interaction networks in Cytoscape	Build workflows Use pathway information in your Taverna workflows

Test Drive

Take the WikiPathways Web Service for a test drive: 1. Install the free testing tool, SoapUI. 1. Load our WSDL file.

API Reference

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

Java libraries for WikiPathways

• wikipathways-client: A high-level API to the WikiPathways web service.
• PathVisio libraries: Libraries to process GPML and use the synonym databases.

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. If you are developing in Java, we recommend using the PathVisio library.

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

Below you find some small example scripts in various languages that may help to get you started.

Java

Use the wikipathways-client and PathVisio libraries to access the WikiPathways web service from Java. Below is a short example program in Java.

package org.pathvisio.wikipathways;

import java.io.File;
import java.net.URL;

import org.pathvisio.model.DataSource;
import org.pathvisio.model.ObjectType;
import org.pathvisio.model.Pathway;
import org.pathvisio.model.PathwayElement;
import org.pathvisio.model.Xref;
import org.pathvisio.wikipathways.webservice.WSPathway;
import org.pathvisio.wikipathways.webservice.WSPathwayInfo;
import org.pathvisio.wikipathways.webservice.WSSearchResult;

public class Example {
	public static void main(String[] args) {
		try {
			//Create a client to the WikiPathways web service
			WikiPathwaysClient client = new WikiPathwaysClient(
					new URL("http://www.wikipathways.org/wpi/webservice/webservice.php")	
			);
			
			//Find a pathway by affymetrix probeset
			Xref affy = new Xref("201746_at", DataSource.AFFY);
			System.out.println("Searching for pathways with Affymetrix probeset " + affy);

			WSSearchResult[] result = client.findPathwaysByXref(affy);
			for(WSSearchResult r : result) {
				System.out.println("Found pathway: " + r.getName() + " (" + r.getSpecies() + ")");
			}
			
			//Download a pathway from WikiPathways
			WSPathway wsPathway = client.getPathway("WP274");
			System.out.println("Downloaded pathway " + wsPathway.getName() + 
					", revision " + wsPathway.getRevision());
			//Create a pathway object
			Pathway pathway = WikiPathwaysClient.toPathway(wsPathway);
			
			//Get all genes, proteins and metabolites for a pathway
			for(PathwayElement pwElm : pathway.getDataObjects()) {
				//Only take elements with type DATANODE (genes, proteins, metabolites)
				if(pwElm.getObjectType() == ObjectType.DATANODE) {
					//Print information to the screen
					System.out.println(pwElm.getTextLabel());
					System.out.println("\t" + pwElm.getXref());
					System.out.println("\t" + pwElm.getDataNodeType());
				}
			}
			
			//Save the pathway locally
			pathway.writeToXml(new File(wsPathway.getName() + ".gpml"), true);
			
			//Print info for all WikiPathways pathways
			WSPathwayInfo[] pathwayList = client.listPathways();
			
			for(WSPathwayInfo pathwayInfo : pathwayList) {
				System.out.println("Pathway:");
				System.out.println("\tIdentifier:\t" + pathwayInfo.getId());
				System.out.println("\tName:\t" + pathwayInfo.getName());
				System.out.println("\tOrganism:\t" + pathwayInfo.getSpecies());
			}
		} catch(Exception e) {
			e.printStackTrace();
		}
	}
}

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=""))
}

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