Discovery

What is discovery

discovery is a software library which aims to ease the development of decision support tools exploiting omics RDF databases. The library offers a dedicated query language that can be used in several runtime environments (Browser/JS, Node/JS, JVM/Scala).

discovery is developed as part of the work package “Creating FAIR e-resources for knowledge mining” for the national infrastructure for metabolomics and fluxomics - MetaboHUB

Metabolomic example

This example shows how to retrieve “Metabolights Studies” linking to the CHEBI:4167-D-glucopyranose compound. This example uses the following SPARQL endpoint https://metabolights.semantic-metabolomics.fr/sparql

<script 
        type="text/javascript" 
        src="https://cdn.jsdelivr.net/gh/p2m2/discovery@0.2.0/dist/discovery-web.min.js"> 
</script>
<script>
      var config = SWDiscoveryConfiguration.setConfigString(`
          {
          "sources" : [{
          "id"  : "metabolights",
          "url" : "https://metabolights.semantic-metabolomics.fr/sparql"
           }]}
          `);

      SWDiscovery(config)
          .something()
            .set(URI("http://purl.obolibrary.org/obo/CHEBI_4167"))
              .isObjectOf(URI("https://www.ebi.ac.uk/metabolights/property#Xref"),"study")
                .datatype(URI("http://www.w3.org/2000/01/rdf-schema#label"),"label")
          .select("study","label")
             .commit()
             .raw()
             .then((response) => {
                  for (let i=0;i<response.results.bindings.length;i++) {
                    let study=response.results.bindings[i]["study"].value;
                    let label=response.results.datatypes["label"][study][0].value; 
                    console.log(study+"-->"+label);
                  }
            }).catch( (error) => {
              console.error(" -- catch exception --")
              console.error(error)
            } );
</script>

js fiddle example

Documentation

• User documentation

Tutorials / Template

• discovery-tutorial-html-js
• discovery-tutorial-nodejs
• scalajs project template
• scala project template

Metabolomics Applications

• Simple example using an rdf file hosted on github
• Example using the FORUM DiseasesChem endpoint with discovery
• Full example with table view implementation using scalatags
• ChEBI-discovery. ScalaJs implementation of “Improving lipid mapping in Genome Scale Metabolic Networks using ontologies.” [1]. This methodology uses the Chemical Entities of Biological Interest (ChEBI)

Dependencies - RDF Software libraries

this software development is based on RDFJS (RDF JavaScript Libraries) and RDF4J

JavaScript library facades to develop ScalaJS app

• N3.js - source
• data-model-spec - source
• RDF/XML Streaming Parser - source
• Comunica SPARQL RDFJS Init Actor source

Contact/Issues

Add GitHub issue to request bugs, new features or suggest modifications to existing features.

Licence

The software is licensed under MIT and under development.

Authors

• O. Filangi - IGEPP’s Metabolic Profiling and Metabolomic Platform (P2M2, Rennes)
• F. Giacomoni, N. Paulhe - The Platform “Exploration du Métabolisme” (PFEM, Clermont-Ferrand)

References

[1] Poupin, N., Vinson, F., Moreau, A. et al. Improving lipid mapping in Genome Scale Metabolic Networks using ontologies. Metabolomics 16, 44 (2020). https://doi.org/10.1007/s11306-020-01663-5

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