From WikiPathways

Contents 1 Webservice documentation 1.1 WSDL 1.2 Examples 1.2.1 Java 1.2.2 Taverna 1.3 API Reference 1.3.1 Functions 1.3.1.1 listOrganisms 1.3.1.2 listPathways 1.3.1.3 getPathway 1.3.1.4 getRecentChanges 1.3.1.5 login 1.3.1.6 getPathwayAs 1.3.1.7 updatePathway 1.3.1.8 findPathwaysByText 1.3.1.9 findPathwaysByXref 1.3.2 Objects 1.3.2.1 WSPathwayInfo 1.3.2.2 WSPathway 1.3.2.3 WSAuth 1.3.2.4 WSSearchResult 1.3.2.5 WSIndexField

Webservice documentation

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

WSDL

The WSDL file for the WikiPathways webservice can be downloaded from: http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl

Examples

Java

Check out the subversion repository for example code on how to call the webservice from Java with Apache Axis 2.

Taverna

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.

API Reference

Functions

listOrganisms

Get a list of all available organisms.

returns
array of string	The names of the supported organisms

listPathways

Get a list of all available pathways.

returns
array of object WSPathwayInfo	The available pathways.

getPathway

Download the pathway from WikiPathways.

Arguments
Type	Name	Description
string	pwName	The pathway name
string	pwSpecies	The pathway species
integer	revision	The revision number of the pathway (use '0' for most recent version)
Returns
array of object WSPathwayInfo		The available pathways.

getRecentChanges

Get the recently changed pathways.

Note: the recent changes table only retains items for a limited time (2 months), so there is no guarantee that you will get all changes when the timestamp points to a date that is more than 2 months in the past.

Arguments
Type	Name	Description
string	timestamp	Only get changes from after this time. Timestamp format: yyyymmddMMHHSS.
Returns
array of object WSPathwayInfo		The changed pathways.

login

Start a logged in session, using an existing WikiPathways account. This function will return an authentication code that can be used to excecute methods that need authentication (e.g. updatePathway).

Arguments
Type	Name	Description
string	name	The username of the WikiPathways account
string	pass	The password of the WikiPathways account
Returns
string		The authentication code for this session

getPathwayAs

Download a pathway in the specified file format.

Arguments
Type	Name	Description
string	fileType	The file format. This can be one of: gpml png svg pdf txt pwf See the download page for an explanation of these file formats.
string	pwName	The pathway name
string	pwSpecies	The pathway species
integer	revision	The revision number of the pathway (use '0' for most recent version)
Returns
base64Binary		The file contents (base64 encoded)

updatePathway

Update a pathway on the wiki with the given GPML code.

Arguments
Type	Name	Description
string	pwName	The pathway name
string	pwSpecies	The pathway species
string	description	A description of the modifications
string	gpml	The updated GPML code
integer	revision	The revision number of the version this GPML code was based on. This is used to prevent edit conflicts in case another client edited the pathway after this client downloaded it.
object WSAuth	auth	The authentication info.	Returns
boolean		True if the pathway was updated sucessfully.

findPathwaysByText

Find pathways using a textual search on the description and text labels of the pathway objects.

Arguments
Type	Name	Description
string	query	The search query (e.g. 'apoptosis' or 'p53').
string	species	The species to limit the search to (leave blank to search on all species).
Returns
array of object WSSearchResult		An array of search results.

findPathwaysByXref

Find pathways by searching on the external references of DataNodes (gene/protein/metabolite identifiers).

Arguments
Type	Name	Description
string	id	The DataNode identifier (e.g. 'P45985').
string	code	The code of the database system to limit the search to. Leave blank to search on all database systems. See this page for an overview of available system codes.
Returns
array of object WSSearchResult		An array of search results.

Objects

This section explains the different object classes defined in the WSDL.

WSPathwayInfo

Container for pathway metadata, such as name, organism and url.

fields
name	string	The name of the pathway
species	string	The species (organism) of the pathway
url	string	The url to the pathway
revision	string	The revision number of the pathway ('0' can be used for the most recent revision)

WSPathway

Extends WSPathwayInfo.

Container for pathway metadata and content. This object inherits all fields from WSPathwayInfo and has one additional field:

fields
gpml	string	The content of the pathway (as GPML).

WSAuth

Container for authentication data for a logged in WikiPathways session.

fields
user	string	The username of a WikiPathways account
key	string	The authentication key of the session (can be obtained by calling the login function).

WSSearchResult

Container for a single search result.

fields
score	double	The score of the search result
fields	array of object WSIndexField	An array of index fields that were returned with the search. The included fields may vary among different search functions.

WSIndexField

Container for a single index field.

fields
name	string	The name of the index field.
fields	array of string	An array with the value(s) of the field.