sparql-examples

A set of SPARQL examples that are used in different SIB resources

View the Project on GitHub sib-swiss/sparql-examples

001

rq turtle/ttl

Among the SIRIUS structural annotations from Tabernaemontana coffeoides (Apocynaceae) seeds extract, which ones are reported in the Tabernaemontana genus?

Use at

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

SELECT DISTINCT ?ik2d ?genus
WHERE
    {
    ?material sosa:hasSample ?extract ;
        sosa:isSampleOf ?organe .
    ?organe emi:inTaxon ?wd_sp .
    ?wd_sp rdfs:label "tabernaemontana coffeoides" .
    ?extract sosa:isFeatureOfInterestOf ?lcms .
    ?lcms sosa:hasResult ?feature_list .
    ?feature_list emi:hasLCMSFeature ?feature .
    ?feature emi:hasAnnotation ?sirius_annotation .
    ?sirius_annotation a emi:StructuralAnnotation ;
        prov:wasGeneratedBy ?activity ;
        emi:hasChemicalStructure ?ik2d .
    ?activity prov:wasAssociatedWith <https://bio.informatik.uni-jena.de/software/sirius> .
    ?ik2d emi:hasSMILES ?smiles ;
        emi:isInChIKey2DOf ?ik .
    ?ik emi:isInChIKeyOf ?wd_id .
	{
        SELECT DISTINCT ?wd_id ?genus WHERE {
            ?material sosa:hasSample ?extract ;
                sosa:isSampleOf ?organe .
            ?organe emi:inTaxon ?wd_sp .
            ?wd_sp rdfs:label "tabernaemontana coffeoides" .
           # OPTIONAL {
                SERVICE <https://query.wikidata.org/sparql> {
                    ?wd_sp wdt:P225 ?species_name .
                    ?genus wdt:P31 wd:Q16521 ;
                        wdt:P105 wd:Q34740 ;
                        ^wdt:P171* ?wd_sp .
                    ?childtaxa wdt:P171* ?genus .
                    ?wd_id wdt:P703 ?childtaxa
                }
           # }
        } LIMIT 100
    }
}
https://query.wikidata.org/sparql
sosa:hasSample
sosa:isSampleOf
emi:inTaxon
rdfs:label
sosa:isFeatureOfInterestOf
sosa:hasResult
emi:hasLCMSFeature
emi:hasAnnotation
a
prov:wasGeneratedBy
emi:hasChemicalStructure
prov:wasAssociatedWith
emi:hasSMILES
emi:isInChIKey2DOf
emi:isInChIKeyOf
sosa:hasSample
sosa:isSampleOf
emi:inTaxon
rdfs:label
wdt:P225
wdt:P31
wdt:P105
wdt:P171
wdt:P171
wdt:P703
?species_name
?wd_sp
wd:Q16521
?genus
wd:Q34740
?childtaxa
?wd_id
?activity
?extract
?feature
?feature_list
?ik
?ik2d
?lcms
?material
?organe
?sirius_annotation
?smiles
emi:StructuralAnnotation
tabernaemontana coffeoides
https://bio.informatik.uni-jena.de/software/sirius