Help:WikiPathways RDF

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Two subsets of pathways from WikiPathways are now available in the RDF format: There is a subset for the WP vocabulary and a subset for the GPML vocabulary. The WP vocabulary is for the semantic information about the pathway, datanodes, and interactions and the GPML vocabulary is for the graphical information about how the pathway diagram is laid out and represented.

 Contained in the RDF collection for both the WP and the GPML vocabulary sets, is the Curated and the Reactome collections.

Information for the collection about the interactions is also available included in the RDF.

Updates are currently not immediate. Meaning that if you add a new pathway or edit an existing one these updates will not be available in the RDF immediately. We do test builds of the RDF daily though. If you need an RDF update please contact us (on the mailing is best) and we can see what can be done.

The RDF was created using these vocabularies and database identifiers are given as URIs.


Download RDF

You can download the WikiPathways RDF from here.

SPARQL Endpoint

We provide an (experimental) SPARQL endpoint where data queries can be done.

WikiPathways Example SPARQL Queries

We have a large collection of example queries.


The Open PHACTS projects provides an alternative to work with the WikiPathways RDF, as it is loaded in the data cache of Open PHACTS. The Open PHACTS API provides various queries, like "give me all targets in a pathway". It requires a (free) account to use this system.

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