Help:WikiPathways Webservice

From WikiPathways

(Difference between revisions)
Jump to: navigation, search
(→Available functions)
Current revision (19:15, 30 August 2021) (view source)
m (Protected "Help:WikiPathways Webservice" [edit=sysop:move=sysop])
 
(108 intermediate revisions not shown.)
Line 1: Line 1:
-
'''<span style="color:#FF0000"><BIG>This page is under construction</BIG></span>'''
+
__NOEDITSECTION__
 +
= Web Services for WikiPathways =
 +
{|
 +
|
 +
WikiPathways can be accessed programmatically through a REST web service. These services provide powerful means to query, access and interact with the pathway content at WikiPathways.
 +
|rowspan="2" valign="top"|__TOC__
 +
|-
 +
|
-
WikiPathways can be accessed through a SOAP webservice. This page contains documentation for the webservice API.
+
== API Reference ==
 +
See the [https://webservice.wikipathways.org Swagger] page for a list of available web service functions and data structures.
-
== WSDL ==
+
=== Java libraries ===
-
The WSDL file for the WikiPathways webservice can be downloaded from:
+
-
[http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl]
+
-
== Available functions ==
+
You can get a high-level API to the WikiPathways web service here: [http://developers.pathvisio.org/browser/trunk/modules/org.wikipathways.client source] [http://developers.pathvisio.org/data/releases compiled binaries] (choose the most recent wikipathways_client_bin-*).
-
=== listOrganisms ===
+
 
-
Get a list of all available organisms.
+
=== Working with GPML ===
-
{|class=wikitable
+
The pathways on WikiPathways are stored in the GPML format. This is an XML format and can be processed in any programming language. See [http://developers.pathvisio.org/wiki/EverythingGpml here] for the GPML specification. If you are developing in Java, we recommend using our [[#Java libraries|Java libraries]].
-
|colspan=3 | '''returns'''
+
 
-
|-
+
=== Libraries ===
-
|array of string
+
Below is a short list of libraries for popular programming languages that might help you work with the WikiPathways web service.
-
|The names of the supported organisms
+
 
-
|}
+
* R: The rWikiPathways package with vignettes at [https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html bioconductor].
-
=== listPathways ===
+
* Java: Java API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-java github].
-
Get a list of all available pathways.
+
* Perl: Perl API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-perl github].
-
{|class=wikitable
+
* Php: Example scripts at [https://github.com/wikipathways/scripts/ github].
-
|colspan=3 | '''returns'''
+
* Python: Python API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-py github].
-
|-
+
 
-
|array of object WSPathwayInfo
+
== Other Examples ==
-
|The available pathways.
+
 
-
|}
+
=== Groovy ===
-
=== getPathway ===
+
 
-
=== getRecentChanges ===
+
[http://www.helixsoft.nl/blog/?p=153 This blog post] contains an example of how to use the WikiPathways webservice in Groovy.
-
=== login ===
+
 
-
=== getPathwayAs ===
+
== How to cite ==
-
=== updatePathway ===
+
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): [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006447 doi:10.1371/journal.pone.0006447]
-
=== findPathwaysByText ===
+
-
=== findPathwaysByXref ===
+
-
== Examples ==
+
-----
-
=== Java ===
+
<p>[[:Help:Contents|Return to Help Contents]]</p>
-
Check out [http://svn.bigcat.unimaas.nl/pathvisio/trunk/tools/soap-axis2/ the subversion repository] for example code on how to call the webservice from Java with [http://ws.apache.org/axis2/ Apache Axis 2].
+
-
=== Taverna ===
+
-
You can use the WikiPathways webservice to integrate WikiPathways functions in your Taverna workflows. See [http://www.myexperiment.org/packs/30 myexperiment.org] for a set of example workflows that show how to call WikiPathways from Taverna.
+

Current revision

Web Services for WikiPathways

WikiPathways can be accessed programmatically through a REST web service. These services provide powerful means to query, access and interact with the pathway content at WikiPathways.

Contents

API Reference

See the Swagger 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.

Libraries

Below is a short list of libraries for popular programming languages that might help you work with the WikiPathways web service.

  • R: The rWikiPathways package with vignettes at bioconductor.
  • Java: Java API client with code examples at github.
  • Perl: Perl API client with code examples at github.
  • Php: Example scripts at github.
  • Python: Python API client with code examples at github.

Other Examples

Groovy

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

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

Return to Help Contents
Retrieved from "https://classic.wikipathways.org/index.php/Help:WikiPathways_Webservice"
Personal tools