Help:WikiPathways Webservice

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(fixed perl example)
Line 188: Line 188:
# Create service interface with fault handler
# Create service interface with fault handler
my $wp_soap = SOAP::Lite
my $wp_soap = SOAP::Lite
-
        ->proxy('http://www.wikipathways.org/wpi/webservice/webservice.php')
+
->proxy('http://www.wikipathways.org/wpi/webservice/webservice.php')
-
        ->uri('http://www.wikipathways.org/webservice')
+
->uri('http://www.wikipathways.org/webservice')
-
        ->on_fault(sub {
+
->on_fault(sub {
-
                my $soap = shift;
+
my $soap = shift;
-
                my $res = shift;
+
my $res = shift;
-
                # Map faults to exceptions
+
 
-
                if(ref($res) eq '') {
+
# Map faults to exceptions
-
                        die($res);
+
if(ref($res) eq '') {
-
                } else {
+
die($res);
-
                        die($res->faultstring);
+
} else {
-
                }
+
die($res->faultstring);
-
                return new SOAP::SOM;
+
}
-
          } );
+
return new SOAP::SOM;
 +
} );
# listOrganisms (no args; returns array of strings)
# listOrganisms (no args; returns array of strings)
Line 214: Line 215:
print "\ngetPathwayInfo(pwId=WP274):\n";
print "\ngetPathwayInfo(pwId=WP274):\n";
foreach my $key (keys %{$pathwayInfo}) {
foreach my $key (keys %{$pathwayInfo}) {
-
        print "\t$key: $pathwayInfo->{$key}\n";
+
print "\t$key: $pathwayInfo->{$key}\n";
}
}
# findPathwaysByXref (multiple args; returns array of hash references)
# findPathwaysByXref (multiple args; returns array of hash references)
my $argsXrefData = SOAP::Data->name(
my $argsXrefData = SOAP::Data->name(
-
                        id => '201746_at',
+
ids => '201746_at',
-
                        code => 'X',
+
codes => 'X',
-
                        pass => '',
+
);
-
                        revision => ''
+
-
                        );
+
my @foundPathwayRefList = $wp_soap->findPathwaysByXref($argsXrefData)->paramsout;
my @foundPathwayRefList = $wp_soap->findPathwaysByXref($argsXrefData)->paramsout;
unshift(@foundPathwayRefList, $wp_soap->findPathwaysByXref($argsXrefData)->result); #add first result to list
unshift(@foundPathwayRefList, $wp_soap->findPathwaysByXref($argsXrefData)->result); #add first result to list
print "\nfindPathwaysByXref(id=201746_at, code=X):\n";
print "\nfindPathwaysByXref(id=201746_at, code=X):\n";
foreach my $ref (@foundPathwayRefList){
foreach my $ref (@foundPathwayRefList){
-
        foreach my $key (keys %{ $ref}){
+
foreach my $key (keys %{ $ref}){
-
                if ($key =~ /^fields$/){ # Another hash reference to deconstruct
+
if ($key =~ /^fields$/){ # Print all fields
-
                        foreach my $fieldkey (keys %{ $ref->{$key}}){
+
foreach my $f (@{ $ref->{$key} }) {
-
                                print "\t$key.$fieldkey: $ref->{$key}->{$fieldkey}\n";
+
my $name = $f->{'name'};
-
                        }
+
my $value = $f->{'values'};
-
                } else {
+
print "$name: $value";
-
                        print "\t$key: $ref->{$key}\n";
+
}
-
                }
+
} else {
-
        }
+
print "\t$key: $ref->{$key}\n";
 +
}
 +
}
}
}
</pre>
</pre>

Revision as of 07:26, 16 May 2011

Web Services for WikiPathways

WikiPathways can be accessed programmatically through a SOAP web service. Web services provide powerful means to query, access and interact with the pathway content at WikiPathways. Read all about it in this PLoS ONE article.

Contents

Showcase

Search
WikiPathwaysSearch200.png
Use the web service to search for pathways more info
Query interactions
Cytoscape200.png
Load pathways as interaction networks in Cytoscape
Build workflows
Taverna200.png
Use pathway information in your Taverna workflows

Note: The Atlas Mapper showcase has been discontinued, as the ArrayExpress Atlas team took down the SOAP service that this showcase depends on. On this page, you can still find the source code for examples of how to use the WikiPathways web service.

Test Drive

Take the WikiPathways web service for a full-featured test drive:

  1. Install the free testing tool, SoapUI (web start version is also available).
  2. Load our WSDL file.

How to cite

Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. (2009) Mining Biological Pathways Using WikiPathways Web Services. PLoS ONE 4(7): doi:10.1371/journal.pone.0006447

API Reference

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

Java libraries

You can get a high-level API to the WikiPathways web service here: source compiled binaries (choose the most recent wikipathways_client_bin-*).

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 our Java libraries.

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.

Example Code

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.bridgedb.Xref;
import org.bridgedb.bio.BioDataSource;
import org.pathvisio.model.ObjectType;
import org.pathvisio.model.Pathway;
import org.pathvisio.model.PathwayElement;
import org.pathvisio.wikipathways.WikiPathwaysClient;
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", BioDataSource.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();
		}
	}
}

Once you downloaded the libraries and compiled the Example class, you can run it with 

java -classpath wikipathways-client.jar:. org.pathvisio.wikipathways.Example

Perl

This is a short example of a few ways to interact with the WikiPathways web service in Perl. 

#!perl -w
use strict;

# Load module
use SOAP::Lite;

# Debugging (optional)
#SOAP::Lite->import(+trace => qw(debug));

# Create service interface with fault handler
my $wp_soap = SOAP::Lite
	->proxy('http://www.wikipathways.org/wpi/webservice/webservice.php')
	->uri('http://www.wikipathways.org/webservice')
	->on_fault(sub {
		my $soap = shift;
		my $res = shift;

		# Map faults to exceptions
		if(ref($res) eq '') {
			die($res);
		} else {
			die($res->faultstring);
		}
		return new SOAP::SOM;
} );

# listOrganisms (no args; returns array of strings)
my @orgList = $wp_soap->listOrganisms()->paramsout;
unshift(@orgList, $wp_soap->listOrganisms()->result); #add first result to list
$" = ", ";  # change list separator
print "listOrganisms: @orgList\n";

# getPathwayInfo (one arg; returns hash reference)
my $pwId = SOAP::Data->name(pwId => "WP274");
my $pathwayInfo =  $wp_soap->getPathwayInfo($pwId)->result;
# Access data via hash reference
print "\ngetPathwayInfo(pwId=WP274):\n";
foreach my $key (keys %{$pathwayInfo}) {
	print "\t$key: $pathwayInfo->{$key}\n";
}

# findPathwaysByXref (multiple args; returns array of hash references)
my $argsXrefData = SOAP::Data->name(
	ids => '201746_at',
	codes => 'X',
);
my @foundPathwayRefList = $wp_soap->findPathwaysByXref($argsXrefData)->paramsout;
unshift(@foundPathwayRefList, $wp_soap->findPathwaysByXref($argsXrefData)->result); #add first result to list
print "\nfindPathwaysByXref(id=201746_at, code=X):\n";
foreach my $ref (@foundPathwayRefList){
	foreach my $key (keys %{ $ref}){
		if ($key =~ /^fields$/){ # Print all fields
			foreach my $f (@{ $ref->{$key} }) {
				my $name = $f->{'name'};
				my $value = $f->{'values'};
				print "$name: $value";
			}
		} else {
			print "\t$key: $ref->{$key}\n";
		}
	}
}


Here's another example that call getColoredPathway() to color an element on the pathway blue: 

use strict;

# Load module
use SOAP::Lite;
use MIME::Base64;

# Debugging (optional)
#SOAP::Lite->import(+trace => qw(debug));

# Create service interface with fault handler
my $wp_soap = SOAP::Lite
       ->proxy('http://www.wikipathways.org/wpi/webservice/webservice.php')
       ->uri('http://www.wikipathways.org/webservice')
       ->on_fault(sub {
               my $soap = shift;
               my $res = shift;
               # Map faults to exceptions
               if(ref($res) eq '') {
                       die($res);
               } else {
                       die($res->faultstring);
               }
               return new SOAP::SOM;
          } );

# Color the pathway element on pathway WP722 identified by GraphID 'c8d79' blue.
my $pwId = SOAP::Data->name(pwId => "WP722");
my $color=SOAP::Data->name(color => "0000FF");
my $graphId=SOAP::Data->name(graphId=>"c8d79");
# Use the latest revision of the pathway.
my $revision=SOAP::Data->name(revision => 0);
# Return image in SVG format.
my $fileType=SOAP::Data->name(fileType => 'svg');

my $graph=$wp_soap->getColoredPathway($pwId,$revision,$graphId,$color,$fileType)->result;
open (FILE, ">test.svg");
binmode(FILE);
my $decoded = decode_base64($graph);
syswrite(FILE, $decoded);
close(FILE);

Python

This is a short example of a few ways to interact with the WikiPathways web service in Python. 

# Print out function for query results (see code below function first)
def printOutput(ws_output):
    #Loops through a list of dictionary items
    index=1
    for object in ws_output:
        #calls select dictionary keys to print out values
        print_output = '   '+str(index)+')'+'species:'+object['species']+'\t '
        print_output+= 'id:'+object['id']+'\t '+'name:'+object['name']
        print print_output
        index+=1

# Load SOAPpy and dependent modules (fpconst) and access the remote
# SOAP server through a proxy class, SOAPProxy - see:
# (http://diveintopython.org/soap_web_services/first_steps.html)
from SOAPpy import SOAPProxy      
url = 'http://www.wikipathways.org/wpi/webservice/webservice.php'
namespace = 'http://www.wikipathways.org/webservice'
server = SOAPProxy(url, namespace)

# listOrganisms (no args; returns list of strings)
wp_organisms = server.listOrganisms()
print '\nSupported organisms at WikiPathways'
index=1
for organism in wp_organisms:
    print '   '+str(index)+')',organism; index+=1

# getPathwayInfo (one arg; returns dictionary reference)
pathway = 'WP274'
pathway_info = server.getPathwayInfo(pwId = pathway)
print '\nPathway information for %s' % pathway
# Access data via dictionary reference
printOutput([pathway_info])

# findPathwaysByText (multiple args; returns list of dictionary references)
pathway = 'apoptosis'    
apoptosis_containing = server.findPathwaysByText(query= pathway, species = "")
print '\nPathways containing the term %s' % pathway 
printOutput(apoptosis_containing)

# Define the order of args: needed for this service
server.config.argsOrdering = {'findPathwaysByXref': ('id', 'code') }

# findPathwaysByXref (multiple args; returns list of dictionary references)
sc = 'X'; gi = '201746_at'
probeset_containing = server.findPathwaysByXref(code=sc, id=gi )
print '\nPathways containing the gene ID "%s" for system code "%s"' % (gi,sc) 
printOutput(probeset_containing)

R

Using the SSOAP package in R, you can retrieve pathway information from the WikiPathways web service and use it in your R scripts. Below are a few code snippets that show you how to use SSOAP with the WikiPathways web service. See this page for a more extensive example, where we perform gene set enrichment on WikiPathways pathways using the PGSEA library. 

## 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=""))
}

PHP 

<?php

$client = new
SoapClient('http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl');
//Show all functions in the WikiPathways webservice 
var_dump($client->__getFunctions());

// Show all pathways in an object
var_dump($client->listPathways());

//List all pathway names
$pathways = $client->listPathways();
foreach ($pathways->pathways as $pathway){
    print $pathway->name."\n";
}

//Get pathway Info of Pathway with pwId WP274
var_dump($client->getPathwayInfo(array('pwId'=>'WP274')));

//Get pathway history
var_dump($client->getPathwayHistory(array('pwId'=>'WP716', 'timestamp' 
=> '0')));

?>

Groovy

This blog post contains an example of how to use the WikiPathways webservice in Groovy.

Shell script

Andra Waagmeester contributed several linux shell scripts to call the web service: download the scripts here. The xmlstarlet tool makes it easy to parse the results. Below is an example on how to parse the results. 

./listPathways.sh |\
sed "s/<[A-Za-z0-9]*:/</g"|\ # remove the namespaces
sed "s/<\/[A-Za-z0-9]*:/<\//g"|\ # remove the closing namespaces

xml sel -t -m //pathways -v "concat(id,',',name,',',species,',',revision,',',url)" -n

Return to Help Contents

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