Help:WikiPathways Webservice

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'''<span style="color:#FF0000"><BIG>This page is under construction</BIG></span>'''
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__NOEDITSECTION__
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= Web Services for WikiPathways =
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{|
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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.
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|rowspan="2" valign="top"|__TOC__
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WikiPathways can be accessed through a SOAP webservice. This page contains documentation for the webservice API.
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== API Reference ==
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See the [https://webservice.wikipathways.org Swagger] page for a list of available web service functions and data structures.
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== WSDL ==
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=== Java libraries ===
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The WSDL file for the WikiPathways webservice can be downloaded from:
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[http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl]
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== Examples ==
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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-*).
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=== Java ===
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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].
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=== Taverna ===
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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.
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== API Reference ==
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=== Working with GPML ===
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=== Objects ===
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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]].
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This section explains the different object classes defined in the WSDL.
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==== WSPathwayInfo ====
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Container for pathway metadata, such as name, organism and url.
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{|class=wikitable
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|colspan=3 | '''fields'''
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|-
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|name
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|string
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|The name of the pathway
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|species
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|string
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|The species (organism) of the pathway
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|url
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|string
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|The url to the pathway
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|revision
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|string
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|The revision number of the pathway ('0' can be used for the most recent revision)
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|}
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==== WSPathway ====
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=== Libraries ===
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'''Extends WSPathwayInfo'''.
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Below is a short list of libraries for popular programming languages that might help you work with the WikiPathways web service.
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Container for pathway metadata and content. This object inherits all fields from WSPathwayInfo and
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* R: The rWikiPathways package with vignettes at [https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html bioconductor].
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has one additional field:
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* Java: Java API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-java github].
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{|class=wikitable
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* Perl: Perl API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-perl github].
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|colspan=3 | '''fields'''
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* Php: Example scripts at [https://github.com/wikipathways/scripts/ github].
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|-
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* Python: Python API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-py github].
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|gpml
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|string
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|The content of the pathway (as [http://www.pathvisio.org/EverythingGPML GPML]).
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|}
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==== WSAuth ====
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== Other Examples ==
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Container for authentication data for a logged in WikiPathways session.
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{|class=wikitable
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|colspan=3 | '''fields'''
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|-
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|user
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|string
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|The username of a WikiPathways account
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|key
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|string
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|The authentication key of the session (can be obtained by calling the login function).
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|}
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==== WSSearchResult ====
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=== Groovy ===
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Container for a single search result.
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{|class=wikitable
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|colspan=3 | '''fields'''
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|score
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|double
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|The score of the search result
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|-
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|fields
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|array of object WSIndexField
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|An array of index fields that were returned with the search. The included fields may vary among different search functions.
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|}
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==== WSIndexField ====
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[http://www.helixsoft.nl/blog/?p=153 This blog post] contains an example of how to use the WikiPathways webservice in Groovy.
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Container for a single index field.
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{|class=wikitable
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|colspan=3 | '''fields'''
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|-
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|name
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|string
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|The name of the index field.
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|-
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|fields
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|array of string
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|An array with the value(s) of the field.
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|}
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=== Functions ===
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== How to cite ==
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==== listOrganisms ====
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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]
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Get a list of all available organisms.
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{|class=wikitable
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|colspan=3 | '''returns'''
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|array of string
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|The names of the supported organisms
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|}
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==== listPathways ====
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Get a list of all available pathways.
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{|class=wikitable
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|colspan=3 | '''returns'''
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|array of object [[Help:WikiPathways_Webservice#WSPathwayInfo|WSPathwayInfo]]
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|The available pathways.
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|}
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==== getPathway ====
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Download the pathway from WikiPathways.
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{|class=wikitable
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|colspan=3 | ''Arguments''
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|-
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|'''Type'''
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|'''Name'''
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|'''Description'''
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|-
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|string
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|pwName
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|The pathway name
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|-
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|string
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|pwSpecies
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|The pathway species
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|-
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|integer
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|revision
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|The revision number of the pathway (use '0' for most recent version)
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|-
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|colspan=3 | ''Returns''
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|-
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|colspan=2 | array of object [[Help:WikiPathways_Webservice#WSPathwayInfo|WSPathwayInfo]]
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|| The available pathways.
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|}
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==== getRecentChanges ====
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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.
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{|class=wikitable
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|colspan=3 | ''Arguments''
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|-
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|'''Type'''
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|'''Name'''
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|'''Description'''
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|-
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|string
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|timestamp
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|Only get changes from after this time. Timestamp format: yyyymmddMMHHSS.
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|-
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|colspan=3 | ''Returns''
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|-
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|colspan=2 | array of object [[Help:WikiPathways_Webservice#WSPathwayInfo|WSPathwayInfo]]
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|| The changed pathways.
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|}
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==== login ====
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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).
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{|class=wikitable
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|colspan=3 | ''Arguments''
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|-
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|'''Type'''
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|'''Name'''
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|'''Description'''
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|-
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|string
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|name
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|The username of the WikiPathways account
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|string
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|pass
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|The password of the WikiPathways account
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|-
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|colspan=3 | ''Returns''
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|-
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|colspan=2 | string
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| The authentication code for this session
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|}
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=== getPathwayAs ====
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-----
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==== updatePathway ====
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<p>[[:Help:Contents|Return to Help Contents]]</p>
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==== findPathwaysByText ====
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==== findPathwaysByXref ====
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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"
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