Portal:Semantic Web/Intro

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Welcome to the WikiPathways Semantic Web Portal!

This portal describes the Semantic Web features of the WikiPathways databases, such as the Resource Description Framework (RDF) translation, the ontology, and the new nanopublications.

The WikiPathways RDF is provided as part of the monthly releases and contains the Curated and Reactome pathways. The RDF is split in two parts, the GPMLRDF part which contains a direct translation of the content in the GPML files, and a WPRDF part which contains the biology represented in the GPML

The WikiPathways Vocabularies

The WikiPathways vocabularies are for the semantic information about the pathway, data nodes, and interactions and the GPML vocabulary is for the graphical information about how the pathway diagram is laid out and represented.

How to cite

If you use the RDF, vocabularies, or nanopublication, please cite the following paper:

  • Waagmeester, A., Kutmon, M., Riutta, A., Miller, R., Willighagen, E. L., Evelo, C. T., Pico, A. R., Jun. 2016. Using the semantic web for rapid integration of WikiPathways with other biological online data resources. PLoS Comput Biol 12 (6), e1004989+. doi:10.1371/journal.pcbi.1004989

For the pathway content, please follow these How to cite WikiPathways instructions.

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