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

features

Programming/building request with immutables objects
Querying several RDF content (SPARQL Endpoint, RDF File, RDF content)
Federated Query
Handling lazy page results
Subscribe to SPARQL query status events
Stringify request and configuration to ease transport
Decorating the building nodes with additional information

Dependencies - RDF Software libraries

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

Documentation

further information and documentation, visit https://p2m2.github.io/discovery/

Html/Js example

Html import

<script type="text/javascript" src="https://cdn.jsdelivr.net/gh/p2m2/discovery@develop/dist/discovery-web.min.js"> </script> 
<script>
      var config = SWDiscoveryConfiguration
                    .init()
                    .sparqlEndpoint("https://metabolights.semantic-metabolomics.fr/sparql");

      SWDiscovery(config)
          .prefix("obo","http://purl.obolibrary.org/obo/")
          .prefix("metabolights","https://www.ebi.ac.uk/metabolights/property#")
          .prefix("rdfs","http://www.w3.org/2000/01/rdf-schema#")
          .something()
            .set(URI("obo:CHEBI_4167"))
              .isObjectOf(URI("metabolights:Xref"),"study")
                .datatype(URI("rdfs: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

Install

sbt

libraryDependencies += "com.github.p2m2" %% "discovery" % "0.4.0"

scalajs

libraryDependencies += "com.github.p2m2" %%% "discovery" % "0.4.0"

npm

npm i @p2m2/discovery

Running docker proxy image

docker command

docker run -d --network host -t inraep2m2/service-discovery-proxy:latest

docker-compose file

version: '3.9'
services:
  service-discovery-proxy:
    image: inraep2m2/service-discovery-proxy:latest
    command: ./mill -w app.runBackground --port 8085 --verbose
    network_mode: "host"
    restart: on-failure

p2m2 / discovery 0.4.3