Biology has become a data intensive science. Discovery of new biological facts increasingly relies on the ability to find and match appropriate biological data. For instance for functional annotation of genes of interest or for identification of pathways affected by over-expressed genes. Functional and pathway information about genes and proteins is typically distributed over a variety of databases and the literature.

Pathways are a convenient, easy to interpret way to describe known biological interactions. WikiPathways provides community curated pathways. WikiPathways users integrate their knowledge with facts from the literature and biological databases. The curated pathway is then reviewed and possibly corrected or enriched. Different tools (e.g. Pathvisio and Cytoscape) support the integration of WikiPathways-knowledge for additional tasks, such as the integration with personal data sets. 

Data from WikiPathways is increasingly also used for advanced analysis where it is integrated or compared with other data, Currently, integration with data from different biological sources is mostly done manually. This can be a very time consuming task because the curator often first needs to find the available resources, needs to learn about their specific content and qualities and often spends a lot of time to technically combine the two. 

Semantic web and Linked Data technologies eliminate the barriers between database silos by relying on a set of standards and best practices for representing and describing data. The architecture of the semantic web relies on the architecture of the web itself for integrating and mapping universal resource identifiers (URI), coupled with basic inference mechanisms to enable matching concepts and properties across data sources. Semantic Web and Linked Data technologies are increasingly being successfully applied as integration engines for linking biological elements. 

Exposing WikiPathways content as Linked Open Data to the Semantic Web, enables rapid, semi-automated integration with a the growing amount of biological resources available from the linked open data cloud, it also allows really fast queries of WikiPathways itself. 

We have harmonised WikiPathways content according to a selected set of vocabularies (Biopax, CHEMBL, etc), common to resources already available as Linked Open Data. 
WikiPathways content is now available as Linked Open Data for dynamic querying through a SPARQL endpoint: http://semantics.bigcat.unimaas.nl:8000/sparql
