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.

API Reference

See the API reference 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.

• Java:
• Perl:
• Php:
• Python:
• R

Groovy

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

Shell script

Andra Waagmeester contributed several linux shell scripts to call the web service: download the scripts here. The xmlstarlet tool makes it easy to parse the results. Below is an example on how to parse the results.

./listPathways.sh |\
sed "s/<[A-Za-z0-9]*:/</g"|\ # remove the namespaces
sed "s/<\/[A-Za-z0-9]*:/<\//g"|\ # remove the closing namespaces

xml sel -t -m //pathways -v "concat(id,',',name,',',species,',',revision,',',url)" -n

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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