007

Show chemical structures in Melochia umbellata extracts with structural annotations where the cosmic score is greater than 0.5 and the zodiac score is less than 0.8. For ISDB annotations, consider taxon scores less than 6

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 DISTINCT ?ik ?wd_id ?taxon ?taxon_name
WHERE {
    SERVICE <https://query.wikidata.org/sparql> {
        ?wd_id wdt:P31 wd:Q113145171 ;
            wdt:P703 ?taxon .
        ?taxon wdt:P225 ?taxon_name .
    }
    {
        SELECT DISTINCT ?ik ?chemblid ?name ?type ?value ?wd_id
        WHERE {
            ?sample a emi:ExtractSample ;
                sosa:isSampleOf* ?organe ;
                sosa:isFeatureOfInterestOf ?lcms .
            ?organe emi:inTaxon ?taxon .
            ?taxon rdfs:label "melochia umbellata" .
            ?lcms a emi:LCMSAnalysisPos ;
                sosa:hasResult ?feature_list .
            ?feature_list emi:hasLCMSFeature ?feature .
            {
                ?feature emi:hasAnnotation ?annotation .
                ?annotation a emi:StructuralAnnotation ;
                    prov:wasGeneratedBy ?activity .
                ?activity prov:wasAssociatedWith <https://bio.informatik.uni-jena.de/software/sirius> .
                ?annotation emi:hasCosmicScore ?cosmic ;
                    emi:hasZodiacScore ?zodiac .
                FILTER((?cosmic > 0.5) && (?zodiac > 0.8))
            } UNION {
                ?feature emi:hasAnnotation ?annotation .
                ?annotation emi:hasTaxoScore ?taxo .
                FILTER(?taxo >= 6)
            }
            ?annotation emi:hasChemicalStructure ?ik2d .
            ?ik2d emi:hasSMILES ?smiles ;
                emi:isInChIKey2DOf ?ik .
            ?ik emi:isInChIKeyOf ?wd_id .
        }
    }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v12("?activity")
  v11("?annotation")
  v9("?cosmic")
  v8("?feature")
  v7("?feature_list")
  v16("?ik"):::projected 
  v14("?ik2d")
  v6("?lcms")
  v5("?organe")
  v4("?sample")
  v15("?smiles")
  v13("?taxo")
  v2("?taxon"):::projected 
  v3("?taxon_name"):::projected 
  v1("?wd_id"):::projected 
  v10("?zodiac")
  c12(["melochia umbellata"]):::literal 
  c19(["emi:StructuralAnnotation"]):::iri 
  c13(["emi:LCMSAnalysisPos"]):::iri 
  c3(["wd:Q113145171"]):::iri 
  c22([https://bio.informatik.uni-jena.de/software/sirius]):::iri 
  c7(["emi:ExtractSample"]):::iri 
  subgraph s1["https://query.wikidata.org/sparql"]
    style s1 stroke-width:4px;
    v1 --"wdt:P31"-->  c3
    v1 --"wdt:P703"-->  v2
    v2 --"wdt:P225"-->  v3
  end
  v4 --"a"-->  c7
  v4 --"sosa:isSampleOf"-->  v5
  v4 --"sosa:isFeatureOfInterestOf"-->  v6
  v5 --"emi:inTaxon"-->  v2
  v2 --"rdfs:label"-->  c12
  v6 --"a"-->  c13
  v6 --"sosa:hasResult"-->  v7
  v7 --"emi:hasLCMSFeature"-->  v8
  subgraph union0[" Union "]
  subgraph union0l[" "]
    style union0l fill:#abf,stroke-dasharray: 3 3;
    f0[["?taxo >= '6^^xsd:integer'"]]
    f0 --> v13
    v8 --"emi:hasAnnotation"-->  v11
    v11 --"emi:hasTaxoScore"-->  v13
  end
  subgraph union0r[" "]
    style union0r fill:#abf,stroke-dasharray: 3 3;
    f1[["?cosmic > '0.5^^xsd:decimal'?zodiac > '0.8^^xsd:decimal'"]]
    f1 --> v9
    f1 --> v10
    v8 --"emi:hasAnnotation"-->  v11
    v11 --"a"-->  c19
    v11 --http://www.w3.org/ns/prov#wasGeneratedBy-->  v12
    v12 --http://www.w3.org/ns/prov#wasAssociatedWith-->  c22
    v11 --"emi:hasCosmicScore"-->  v9
    v11 --"emi:hasZodiacScore"-->  v10
  end
  union0r <== or ==> union0l
  end
  v11 --"emi:hasChemicalStructure"-->  v14
  v14 --"emi:hasSMILES"-->  v15
  v14 --"emi:isInChIKey2DOf"-->  v16
  v16 --"emi:isInChIKeyOf"-->  v1