Help:WikiPathways Webservice

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WikiPathways can be accessed programmatically through a [http://wikipedia.org/wiki/Representational_state_transfer REST web service]. These services provide powerful means to query, access and interact with the pathway content at WikiPathways.  
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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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== API Reference ==
== API Reference ==
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See the [[{{FULLPAGENAME}}/API|API reference]] page for a list of available web service functions and data structures.
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See the [https://webservice.wikipathways.org Swagger] page for a list of available web service functions and data structures.
=== Java libraries ===
=== Java libraries ===
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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.
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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* R: The rWikiPathways package with vignettes at [https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html bioconductor].
* Java: Java API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-java github].
* Java: Java API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-java github].
* Perl: Perl API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-perl github].
* Perl: Perl API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-perl github].
* Php: Example scripts at [https://github.com/wikipathways/scripts/ github].
* Php: Example scripts at [https://github.com/wikipathways/scripts/ github].
* Python: Python API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-py github].
* Python: Python API client with code examples at [https://github.com/wikipathways/wikipathways-api-client-py github].
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* R: Example scripts at [https://github.com/wikipathways/scripts/ github].
 
== Other Examples ==
== Other Examples ==
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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.
[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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=== Shell script ===
 
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Andra Waagmeester contributed several linux shell scripts to call the web service: [http://www.bigcat.unimaas.nl/~andra/WP_bashscripts/ download the scripts here].
 
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The [http://xmlstar.sourceforge.net xmlstarlet] tool makes it easy to parse the results. Below is an example on how to parse the results.
 
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<pre><nowiki>
 
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./listPathways.sh |\
 
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sed "s/<[A-Za-z0-9]*:/</g"|\ # remove the namespaces
 
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sed "s/<\/[A-Za-z0-9]*:/<\//g"|\ # remove the closing namespaces
 
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xml sel -t -m //pathways -v "concat(id,',',name,',',species,',',revision,',',url)" -n
 
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</nowiki></pre>
 
== How to cite ==
== How to cite ==

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

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