examples012

List all metabolites produced by species with near threatened (wd:Q719675) IUCN status (wdt:P141) and with values available (or greater than a specific value) for trait 'Seed dry mass'.

Use at

• https://biosoda.unil.ch/emi/sparql/

PREFIX emi: <https://purl.org/emi#>
		PREFIX wd: <http://www.wikidata.org/entity/>
		PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
		PREFIX enpkg: <https://enpkg.commons-lab.org/kg/>
		PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
		PREFIX wdt: <http://www.wikidata.org/prop/direct/>
		PREFIX sosa: <http://www.w3.org/ns/sosa/>
		PREFIX dcterms: <http://purl.org/dc/terms/>
		PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
		
		SELECT DISTINCT ?structure_inchikey ?wd_chem ?source_wdx ?sourceNameURI WHERE {

			?trySpObs sosa:isSampleOf ?trySpName ;					#retrieve trait/non-trait data for trySpName (scientific name of plant species as listed in trydb)
				  sosa:isFeatureOfInterestOf ?tryObId .
			?tryObId sosa:hasResult ?tryData .
			?trySpName emi:inTaxon ?source_wdx .						#retrieve wikidata-ids wdx for trySpName
			?tryData rdfs:label ?tryDataLab ;					
				 rdf:type emi:Trait ;						#retrieve data which is labelled as "Trait"
				 rdf:value ?tryDataVal .					#retrieve values for Trait data
			FILTER (?tryDataLab = "Seed dry mass" )					#filter on data label 'Seed dry mass'
			FILTER (?tryDataVal >= 626)						#filter on data value >= 626
		 	SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> {
                   		?source_wdx wdt:P141 wd:Q719675 .					#filter wikidata-ids for trySpName, which have IUCN status (wdt:P141) as near threatened (wd:Q719675)
                    	}
			BIND(REPLACE(STR(?trySpName), "%20", " ") AS ?sourceNameX)		#remove percent-encoding for scientific names of trySpName
			BIND(IRI(?sourceNameX) AS ?sourceNameURI)
		 
		      { SELECT ?source_wdx ?structure_inchikey ?wd_chem WHERE {			#retrieve metabolite data
				?material sosa:hasSample ?extract ;				
		        		  sosa:isSampleOf ?organe .	
			    	?organe emi:inTaxon ?source_wdx .					#filter metabolite data which is found in wikidata-ids wdx 
			    	?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 ?structure_inchikey .
				?structure_inchikey emi:isInChIKeyOf ?wd_chem .			#retrieve wikidata-ids for metabolites
			}}
			UNION									#union with data from lotus (integrated in wikidata)
			{ SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> {		
			 	?wd_chem wdt:P235 ?structure_inchikey;				
   			 		 wdt:P703 ?source_wdx .	
			}}
  		} LIMIT 1000
		

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v11("?extract")
  v15("?feature")
  v14("?feature_list")
  v17("?ik2d")
  v13("?lcms")
  v10("?material")
  v12("?organe")
  v16("?sirius_annotation")
  v18("?smiles")
  v9("?sourceNameURI"):::projected 
  v8("?sourceNameX")
  v7("?source_wdx"):::projected 
  v19("?structure_inchikey"):::projected 
  v6("?tryData")
  v2("?tryDataLab")
  v1("?tryDataVal")
  v5("?tryObId")
  v4("?trySpName")
  v3("?trySpObs")
  v20("?wd_chem"):::projected 
  c9(["emi:Trait"]):::iri 
  c17(["emi:StructuralAnnotation"]):::iri 
  c13(["wd:Q719675"]):::iri 
  f0[["?tryDataVal >= '626^^xsd:integer'"]]
  f0 --> v1
  f1[["?tryDataLab = 'Seed dry mass'"]]
  f1 --> v2
  v3 --"sosa:isSampleOf"-->  v4
  v3 --"sosa:isFeatureOfInterestOf"-->  v5
  v5 --"sosa:hasResult"-->  v6
  v4 --"emi:inTaxon"-->  v7
  v6 --"rdfs:label"-->  v2
  v6 --"a"-->  c9
  v6 --"rdf:value"-->  v1
  subgraph s1["https://qlever.cs.uni-freiburg.de/api/wikidata"]
    style s1 stroke-width:4px;
    v7 --"wdt:P141"-->  c13
  end
  bind2[/"replace(str(?trySpName),'%20',' ')"/]
  v4 --o bind2
  bind2 --as--o v8
  bind3[/"?sourceNameX"/]
  v8 --o bind3
  bind3 --as--o v9
  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;
      v20 --"wdt:P235"-->  v19
      v20 --"wdt:P703"-->  v7
    end
  end
  subgraph union0r[" "]
    style union0r fill:#abf,stroke-dasharray: 3 3;
    v10 --"sosa:hasSample"-->  v11
    v10 --"sosa:isSampleOf"-->  v12
    v12 --"emi:inTaxon"-->  v7
    v11 --"sosa:isFeatureOfInterestOf"-->  v13
    v13 --"sosa:hasResult"-->  v14
    v14 --"emi:hasLCMSFeature"-->  v15
    v15 --"emi:hasAnnotation"-->  v16
    v16 --"a"-->  c17
    v16 --"emi:hasChemicalStructure"-->  v17
    v17 --"emi:hasSMILES"-->  v18
    v17 --"emi:isInChIKey2DOf"-->  v19
    v19 --"emi:isInChIKeyOf"-->  v20
  end
  union0r <== or ==> union0l
  end