examples021

rq turtle/ttl

List possible interactions of plants that can produce Norhyocyamine (wd:Q27107545), a plant secondary metabolite.

Use at

• https://biosoda.unil.ch/emi/sparql/

PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX emi: <https://purl.org/emi#>
PREFIX sosa: <http://www.w3.org/ns/sosa/>
SELECT DISTINCT ?sourceWD ?sourceName ?intxnName ?intxnId ?targetWD ?targetName WHERE {
	# interaction data
	{
        	?intxn emi:hasSource ?xOrg ; # retrieve interaction-pairs
                	emi:hasTarget ?yOrg ;
                        emi:isClassifiedWith ?intxnId .
                ?intxnId rdfs:label ?intxnName .
                ?xOrg emi:inTaxon ?sourceWD ;
			rdfs:label ?sourceName .
		?yOrg emi:inTaxon ?targetWD ;
			rdfs:label ?targetName .
        }

	# metabolite data
	FILTER (?xWD = ?sourceWD || ?xWD = ?targetWD)	# ensure that xWD can be both source/target from the interaction-pairs retrieved before
        {
		SELECT DISTINCT ?xWD ?wd_chem WHERE {
                	?material sosa:hasSample ?extract ;
                        	sosa:isSampleOf ?organe .
                        ?organe emi:inTaxon ?xWD .
                        ?extract sosa:isFeatureOfInterestOf ?lcms .
                        ?lcms sosa:hasResult ?feature_list .
                        ?feature_list emi:hasLCMSFeature ?feature .
                        ?feature emi:hasAnnotation ?sirius_annotation .
                        ?sirius_annotation a emi:StructuralAnnotation ;
                        	emi:hasChemicalStructure ?ik2d .
                        ?ik2d emi:hasSMILES ?smiles ;
                        	emi:isInChIKey2DOf ?ik .
                        ?ik emi:isInChIKeyOf ?wd_chem .
                        VALUES ?wd_chem { wd:Q27107545 }
                }
	}  UNION # union with data from wikidata (lotus)
	{ 
		SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> {
			?wd_chem wdt:P235 ?ik ;
   				wdt:P703 ?xWD .
			VALUES ?wd_chem { wd:Q27107545 }
		}
	}
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v12("?extract")
  v16("?feature")
  v15("?feature_list")
  v20("?ik")
  v18("?ik2d")
  v4("?intxn")
  v7("?intxnId"):::projected 
  v8("?intxnName"):::projected 
  v14("?lcms")
  v11("?material")
  v13("?organe")
  v17("?sirius_annotation")
  v19("?smiles")
  v9("?sourceName"):::projected 
  v2("?sourceWD"):::projected 
  v10("?targetName"):::projected 
  v3("?targetWD"):::projected 
  v22("?wd_chem")
  v5("?xOrg")
  v1("?xWD")
  v6("?yOrg")
  c13(["emi:StructuralAnnotation"]):::iri 
  f0[["(?xWD = ?sourceWD || ?xWD = ?targetWD)"]]
  f0 --> v1
  f0 --> v2
  f0 --> v3
  v4 --"emi:hasSource"-->  v5
  v4 --"emi:hasTarget"-->  v6
  v4 --"emi:isClassifiedWith"-->  v7
  v7 --"rdfs:label"-->  v8
  v5 --"emi:inTaxon"-->  v2
  v5 --"rdfs:label"-->  v9
  v6 --"emi:inTaxon"-->  v3
  v6 --"rdfs:label"-->  v10
  subgraph union0[" Union "]
  subgraph union0l[" "]
    style union0l fill:#abf,stroke-dasharray: 3 3;
    subgraph s1["https://qlever.cs.uni-freiburg.de/api/wikidata"]
      style s1 stroke-width:4px;
      v22 --"wdt:P235"-->  v20
      v22 --"wdt:P703"-->  v1
      bind1[/VALUES ?wd_chem/]
      bind1-->v22
      bind10(["wd:Q27107545"])
      bind10 --> bind1
    end
  end
  subgraph union0r[" "]
    style union0r fill:#abf,stroke-dasharray: 3 3;
    v11 --"sosa:hasSample"-->  v12
    v11 --"sosa:isSampleOf"-->  v13
    v13 --"emi:inTaxon"-->  v1
    v12 --"sosa:isFeatureOfInterestOf"-->  v14
    v14 --"sosa:hasResult"-->  v15
    v15 --"emi:hasLCMSFeature"-->  v16
    v16 --"emi:hasAnnotation"-->  v17
    v17 --"a"-->  c13
    v17 --"emi:hasChemicalStructure"-->  v18
    v18 --"emi:hasSMILES"-->  v19
    v18 --"emi:isInChIKey2DOf"-->  v20
    v20 --"emi:isInChIKeyOf"-->  v22
    bind2[/VALUES ?wd_chem/]
    bind2-->v22
    bind20(["wd:Q27107545"])
    bind20 --> bind2
  end
  union0r <== or ==> union0l
  end