Help:WikiPathways Webservice

From WikiPathways

Revision as of 12:14, 16 September 2008 by Thomas (Talk | contribs)
Jump to: navigation, search

Contents

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.
Personal tools