Portal:Semantic Web

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The WikiPathways Semantic Web Portal

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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News

2017-05-04 - This portal was created

2016-06-23 - Andra Waagmeester's Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources paper is published

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Downloads

The Semantic Web WikiPathways comes in two flavors: as RDF (beta) and as nanopublications (very experimental).

The RDF

You can download the WikiPathways RDF from here.

The WikiPathways 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.

This figure from the 2016 paper shows how the WPRDF can be derived from the GPMLRDF:

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SPARQL

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

WikiPathways Example SPARQL Queries

We have a large collection of example queries.

For example, to list all pathways per instance of a particular gene or protein (wp:GeneProduct), you can use the following SPARQL:

PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dcterms: <http://purl.org/dc/terms/>

SELECT DISTINCT ?pathway str(?label) as ?geneProduct
WHERE {
    ?geneProduct a wp:GeneProduct . 
    ?geneProduct rdfs:label ?label .
    ?geneProduct dcterms:isPartOf ?pathway .
    ?pathway a wp:Pathway .
    
    FILTER regex(str(?label), "CYP"). 
}

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Open PHACTS API

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.

For example, to get the pathways in which SLC25A4 is found, you can use curl:

   curl -X GET --header "Accept: application/json" \
     "https://beta.openphacts.org/2.1/pathways/byTarget?uri=http%3A%2F%2Fidentifiers.org%2Fncbigene%2F282478&app_id=91f5d4d0&app_key=1af5086da757e57c553bfa1351708d5f"

API clients

Besides interacting with the API end point directly, as with curl in the above example, there are also dedicated Open PHACTS API clients that you can use:


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Support

The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement no. 115191, resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in-kind contribution.

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