How to query SpOdgi to get external Ensembl annotations

[JervenBolleman]

First we modify the example from Ensembl.

PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
PREFIX skos:<http://www.w3.org/2004/02/skos/core#> 
PREFIX owl:<http://www.w3.org/2002/07/owl#> 
PREFIX dc:<http://purl.org/dc/terms/> 
PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> 
PREFIX faldo:<http://biohackathon.org/resource/faldo#> 
PREFIX ensembltranscript:<http://rdf.ebi.ac.uk/resource/ensembl.transcript/> 
PREFIX sio:<http://semanticscience.org/resource/> 
PREFIX dcterms:<http://purl.org/dc/terms/>
PREFIX foaf:<http://xmlns.com/foaf/0.1/>
PREFIX obo:<http://purl.obolibrary.org/obo/>
PREFIX vg:<http://biohackathon.org/resource/vg#>

SELECT *

WHERE {
  ?target a vg:Step ;
    vg:node|vg:reverseNode ?node ;
    faldo:location ?stepLinearLocation .
  ?stepLinearLocation faldo:begin ?bp ;
    faldo:end ?ep .
  ?bp faldo:position ?stepBegin .
  ?ep faldo:position ?stepEnd  .
  BIND(<http://rdf.ebi.ac.uk/resource/ensembl/97/saccharomyces_cerevisiae/R64-1-1/VIII> AS ?ref) .
  SERVICE<https://www.ebi.ac.uk/rdf/services/sparql/>{
    SELECT DISTINCT ?transcript ?ref ?begin ?end {
      ?transcript a <http://rdf.ebi.ac.uk/terms/ensembl/protein_coding> .
      ?transcript faldo:location ?location .
      ?location faldo:begin
        [a faldo:ExactPosition ;
        faldo:position ?begin] .
      ?location faldo:end
        [a faldo:ExactPosition ;
        faldo:position ?end] .
        ?location faldo:reference ?ref .
      FILTER(?begin > ?stepBegin && ?end < ?stepEnd)
    } LIMIT 10
  }
}