examples015

rq turtle/ttl

List of possible natural locations of organisms, which produce Bahamaolide A, (wd:Q75068439) which is an antifungal (https://doi.org/10.1021/np3001915).

Use at

• https://purl.org/emi

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/>
PREFIX wgs: <http://www.w3.org/2003/01/geo/wgs84_pos#>
PREFIX prov: <http://www.w3.org/ns/prov#>
SELECT DISTINCT ?organismName ?organismWD ?loc ?lats ?longs WHERE {
	# metabolite data
	{
		SELECT DISTINCT ?organismWD ?organismName WHERE {				
			?material sosa:hasSample ?extract ;
		        	sosa:isSampleOf ?organe .
			?organe emi:inTaxon ?organismWD ; # filter metabolite data which is found in wikidata-ids wdx	
				rdfs:label ?organismName .
			?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 .	# retrieve wikidata-ids for metabolites
			VALUES ?wd_chem { wd:Q75068439 } # filter wikidata_id of metabolites matches wd:Q75068439
		}
	} UNION	#union with data from lotus (integrated in wikidata)
	{ 
		SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> {
			?wd_chem wdt:P235 ?ik ;
	    			wdt:P703 ?organismWD .
			 VALUES ?wd_chem { wd:Q75068439 }
			 FILTER(?organismWD = ?source_wdx || ?organismWD = ?target_wdx)	# ensure that organism-wd is either from source or target
			 OPTIONAL { ?organismWD wdt:P225 ?organismName . }
		}
	}
	# interaction data		
	?intxn emi:hasSource ?source ; #retrieve interaction-pairs
		emi:hasTarget ?target .
	?source emi:inTaxon ?source_wdx . # retrieve wikidata-id of source
	?target emi:inTaxon ?target_wdx . # retrieve wikidata-id of target
	?intxn prov:atLocation ?loc ; # retrieve the location of the interaction, and the latitude/longitude
		wgs:lat ?lats ;					
		wgs:long ?longs .
}