Help:WikiPathways Webservice
From WikiPathways
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. |
| ||||||||||||
Showcase
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 DriveTake the WikiPathways web service for a full-featured test drive:
How to citeKelder 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 ReferenceSee the API reference page for a list of available web service functions and data structures. Java librariesYou can get a high-level API to the WikiPathways web service here: source compiled binaries (choose the most recent wikipathways_client_bin-*). Working with GPMLThe 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 librariesFor 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 CodeBelow you find some small example scripts in various languages that may help to get you started. JavaUse 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 PerlThis 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";
}
}
}
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);
PythonThis 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': ('ids', 'codes') }
# findPathwaysByXref (multiple args; returns list of dictionary references)
sc = 'X'; gi = '201746_at'
probeset_containing = server.findPathwaysByXref(codes=sc, ids=gi )
print '\nPathways containing the gene ID "%s" for system code "%s"' % (gi,sc)
printOutput(probeset_containing)
RUsing 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')));
?>
GroovyThis blog post contains an example of how to use the WikiPathways webservice in Groovy. Shell scriptAndra 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 |
|||||||||||||
