009

Which samples have features annotated as Aspidosperma_type alkaloids by CANOPUS with a probability score above 0.5, ordered by the decreasing count of features?

Use at

• https://biosoda.unil.ch/graphdb/repositories/emi-dbgi

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX emi: <https://purl.org/emi#>
PREFIX sosa: <http://www.w3.org/ns/sosa/>

SELECT ?extract ?organe ?species_name ?genus_name ?family_name ?count_of_selected_class
WHERE {
    ?material sosa:hasSample ?extract ;
        sosa:isSampleOf ?organe .
    ?organe emi:inTaxon ?wd_sp .
    OPTIONAL {
        SERVICE <https://query.wikidata.org/sparql> {
            ?wd_sp wdt:P225 ?species_name .
            ?family wdt:P31 wd:Q16521 ;
                wdt:P105 wd:Q35409 ;
                wdt:P225 ?family_name ;
                ^wdt:P171* ?wd_sp .
            ?genus wdt:P31 wd:Q16521 ;
                wdt:P105 wd:Q34740 ;
                wdt:P225 ?genus_name ;
                ^wdt:P171* ?wd_sp .
        }
    }
    {
        SELECT ?extract (COUNT(DISTINCT ?feature) AS ?count_of_selected_class)
        WHERE {
            ?extract a emi:ExtractSample ;
                sosa:isFeatureOfInterestOf ?lcms .
            ?lcms a emi:LCMSAnalysis ;
                emi:hasLCMSFeatureSet ?feature_list .
            ?feature_list emi:hasLCMSFeature ?feature .
            ?feature emi:hasAnnotation ?canopus .
            ?canopus a emi:ChemicalTaxonAnnotation ;
                emi:hasClass ?np_class ;
                emi:hasClassProbability ?class_prob .
            ?np_class rdfs:label "Aspidosperma type" .
            FILTER((?class_prob > 0.5)) .
        } GROUP BY ?extract ORDER BY DESC(?count_of_selected_class)
    }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v15("?canopus")
  v11("?class_prob")
  v17("?count_of_selected_class"):::projected 
  v2("?extract"):::projected 
  v6("?family")
  v7("?family_name"):::projected 
  v14("?feature")
  v13("?feature_list")
  v8("?genus")
  v9("?genus_name"):::projected 
  v12("?lcms")
  v1("?material")
  v16("?np_class")
  v3("?organe"):::projected 
  v5("?species_name"):::projected 
  v4("?wd_sp")
  c20(["emi:ChemicalTaxonAnnotation"]):::iri 
  c9(["wd:Q35409"]):::iri 
  c14(["emi:ExtractSample"]):::iri 
  c16(["emi:LCMSAnalysis"]):::iri 
  c11(["wd:Q34740"]):::iri 
  c24(["Aspidosperma type"]):::literal 
  c7(["wd:Q16521"]):::iri 
  v1 --"sosa:hasSample"-->  v2
  v1 --"sosa:isSampleOf"-->  v3
  v3 --"emi:inTaxon"-->  v4
  subgraph optional0["(optional)"]
  style optional0 fill:#bbf,stroke-dasharray: 5 5;
    subgraph s1["https://query.wikidata.org/sparql"]
      style s1 stroke-width:4px;
      v4 -."wdt:P225".->  v5
      v6 --"wdt:P31"-->  c7
      v6 --"wdt:P105"-->  c9
      v6 --"wdt:P225"-->  v7
      v4 --"wdt:P171"-->  v6
      v8 --"wdt:P31"-->  c7
      v8 --"wdt:P105"-->  c11
      v8 --"wdt:P225"-->  v9
      v4 --"wdt:P171"-->  v8
    end
  end
  f0[["?class_prob > '0.5^^xsd:decimal'"]]
  f0 --> v11
  v2 --"a"-->  c14
  v2 --"sosa:isFeatureOfInterestOf"-->  v12
  v12 --"a"-->  c16
  v12 --"emi:hasLCMSFeatureSet"-->  v13
  v13 --"emi:hasLCMSFeature"-->  v14
  v14 --"emi:hasAnnotation"-->  v15
  v15 --"a"-->  c20
  v15 --"emi:hasClass"-->  v16
  v15 --"emi:hasClassProbability"-->  v11
  v16 --"rdfs:label"-->  c24
  bind2[/"count(?feature)"/]
  v14 --o bind2
  bind2 --as--o v17