Category Archives: Biology

WikiPathways: Open Biological Pathways Data on the Semantic Web


The above PathwayWidget provides interactive visualizations of pathways pulled from WikiPathways in real-time. Here we see human pathways active in Alzheimer’s Disease. At right are lists of mitochondrial RNA differentially expressed in Alzheimer’s Disease.

Genes, proteins, and small molecules interact in our bodies through biological pathways to carry out the moment-to-moment work that supports life. WikiPathways is an open, collaborative platform for depositing data gathered through research on biological pathways in all lifeforms including humans.

WikiPathways currently contains over 2400 pathways from over 25 different species. Created by research groups that need a platform to support high-throughput data analysis and visualization, WikiPathways provides a treasure trove of linked-data for data scientists and programmers.

A SPARQL query endpoint is available at the WikiPathways site. For example, you may get an alphabetical list of human pathways from the repository by using the following query.

PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
SELECT DISTINCT str(?title) as ?pathway
WHERE {
   ?pw dc:title ?title ;
      wp:organism ?organism ;
      wp:organismName "Homo sapiens"^^xsd:string .
}
ORDER BY ?pathway

WikiPathways is a site that offers many resources including linked-data and Semantic Web tools and has adopted the Creative Commons CC0 waiver. It’s well worth exploring.