Clinical Interpretations of Variants in Cancer (E70)

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language codelabeldescriptionaliasesedit
enClinical Interpretations of Variants in Cancerbasic schema for items sourced from clinical interpretations in variants in cancerCIViC schemaedit
ja癌のバリアントに対する臨床上の解釈CIViCのから取得したデータ項目に対する基本的なスキーマCIViCスキーマedit
check entities against this Schemaedit
# Data: SELECT * WHERE {?reactome wdt:P3329 ?civicId } LIMIT 10

PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX schema: <http://schema.org/>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX pr: <http://www.wikidata.org/prop/reference/>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>

start = @<#wikidata-civic-variant-record>

<#wikidata-civic-variant-record> EXTRA p:P3354 EXTRA p:P3355 p:P3356 p:P3357 p:P3358  {
 	p:P31 @<#P31_instance_of> ;
 	p:P279 @<#P279_subclass_of>* ;
	p:P3433 @<#P3433-biological-variant-of>;
	
	# The properties genomic start and genomic end are both optional, but if one exist the others needs to exist as well
	# P644 = genomic start
	# P645 = genomic end
	(
		p:P644 @<#genomic-location-provenance>+;	
		p:P645 @<#genomic-location-provenance>+;
	)* ;

 	p:P1057 @<#P1057-chromosome>* ;	 
 	p:P3354 @<#P3354-positive-therapeutic-predictor>* ; # P3354 = positive therapeutic predictor			
 	p:P3355 @<#P3355-negative-therapeutic-predictor>* ; # P3355 = negative therapeutic predictor
 	p:P3356 @<#P3356-positive-diagnostic-predictor>* ; # P3356 = positive diagnostic predictor	
 	p:P3357 @<#P3357-negative-diagnostic-predictor>* ; # P3357 = negative diagnostic predictor
 	p:P3358 @<#P3358-positive-prognostic-predictor>* ; # P3358 = positive prognostic predictor
 	p:P3359 @<#P3359-negative-prognostic-predictor>* ; # P3359 = negative prognostic predictor

## IDENTIFIERS	
 	p:P3329 @<#P3329-civicid> ; # P3329 = CIViCid
} 

<#P31_instance_of> { 
            ps:P31	@<#variant_types> ;
	        prov:wasDerivedFrom @<#civic-variant-reference>;
		  } 

<#variant_types> {
	wdt:P3986 .
}

<#P279_subclass_of> { 
	        ps:P279	@<#variant_type> ;
	        prov:wasDerivedFrom @<#civic-variant-reference>;
		  } 

<#P3433-biological-variant-of> { 
	        ps:P3433	@<#human_gene> ;
	        prov:wasDerivedFrom @<#civic-variant-reference>;
		    } 

<#P1057-chromosome> {
 	   ps:P1057 @<#human-chromosomes> ;
 	   pq:P659  @<#genomic-assembly>+ ;  
 	   prov:wasDerivedFrom @<#civic-variant-reference>+ ;   
 	} 

<#P3354-positive-therapeutic-predictor> { 
	          ps:P3354 @<#pharmaceutical_drug> ;
	          # P2175 = medical condition treated 
	          pq:P2175  @<#wikidata-disease> ;
 	          prov:wasDerivedFrom @<#wikicite>+ ;
			} 

<#P3355-negative-therapeutic-predictor> { 
	          ps:P3355 @<#pharmaceutical_drug> ;
	          # P2175 = medical condition treated 
	 		  pq:P2175 @<#wikidata-disease> ;
 	          prov:wasDerivedFrom @<#wikicite>+ ;
			} 
<#P3356-positive-diagnostic-predictor> { 
	          ps:P3356	@<#wikidata-disease> ;
 	          prov:wasDerivedFrom @<#wikicite>+;
			}

<#P3357-negative-diagnostic-predictor> { 
	          ps:P3356	@<#wikidata-disease> ;
 	          prov:wasDerivedFrom @<#wikicite>+;
			}
<#P3358-positive-prognostic-predictor> { 
	          ps:P3358	@<#wikidata-disease> ;
 	          prov:wasDerivedFrom @<#wikicite>+;
			}
<#P3359-negative-prognostic-predictor> {
			  ps:P3359  @<#wikidata-disease> ;
			  prov:wasDerivedFrom @<#wikicite>+ ;
}

<#P3329-civicid> { 
	ps:P3329	xsd:string ;
	prov:wasDerivedFrom @<#civic-variant-reference>; 
}

<#civic-variant-reference> {
      pr:P248	[wd:Q27612411] ;
	  # P854 = reference URL
	  pr:P854	IRI ;
	  # P813 = retrieved
	  pr:P813	xsd:dateTime ;
} 

<#civic-evidence-reference> {
      # P248 = Stated in
      pr:P248	[wd:Q27612411] ;
	  # P854 = reference URL
	  pr:P854	IRI ;
	  # P813 = retrieved
	  pr:P813	xsd:dateTime ;
} 

<#genomic-location-provenance> {
	pq:P659	@<#genomic-assembly>+ ;
	prov:wasDerivedFrom @<#civic-variant-reference>+ ;  
} 

<#ensembl-gene-reference> {
      pr:P248	[wd:Q27975061
	                 wd:Q30227110
                         wd:Q27975061 ] ;
	  pr:P594	LITERAL ;
}

<#wikicite> {
       pr:P1640 [wd:Q27612411] ; # CIViC database
       pr:P813 xsd:dateTime ;
       pr:P854 . ;
       pr:P248 { wdt:P31 [wd:Q13442814]} ;
} 

<#pharmaceutical_drug> EXTRA p:P31 {
    # P31 = instance of & wd:Q12140 = Pharmaceutical drug
 	p:P31 { ps:P31	[
                                          wd:Q12140 # Pharmaceutical drug
                                          wd:Q11173 # chemical compound
                                          wd:Q35456 # essential medicine 
                                        ] ;
 	           prov:wasDerivedFrom @<#civic-evidence-reference>+ ;
			}* ;
			
    # P274 = chemical formula
 	p:P274 { ps:P274	LITERAL ;
 	          prov:wasDerivedFrom @<#pubchem-compound-reference>+ ;
			}* ;
} 

<#pubchem-compound-reference> {
	pr:P248 [wd:Q278487] ;
	pr:P662	LITERAL ;
	pr:P1476	LITERAL ;
	pr:P813	xsd:dateTime ;
} 

<#variant_type> {
   p:P3986 {
      ps:P3986	LITERAL ;
	  ps:P2888	IRI ;
   } ;
} 

<#human_gene> {
   p:P31 { 
    ps:P31 [wd:Q7187] ;
   } ;
   p:P703 {	
        ps:P703 [wd:Q15978631] ;
   }  ;
   p:P351 {
	ps:P351 LITERAL ;
   } ;
}

<#wikidata-disease> {
   p:P699 {
     ps:P699	xsd:string+;  
   } ;
}

## LISTS
<#human-chromosomes> [
				wd:Q430258  # human chromosome 1
				wd:Q638893  # human chromosome 2
				wd:Q668633  # human chromosome 3
				wd:Q836605  # human chromosome 4
				wd:Q840741  # human chromosome 5
				wd:Q540857  # human chromosome 6
				wd:Q657319  # human chromosome 7
				wd:Q572848  # human chromosome 8
				wd:Q840604  # human chromosome 9
				wd:Q840737  # human chromosome 10
				wd:Q847096  # human chromosome 11
				wd:Q847102  # human chromosome 12
				wd:Q840734  # human chromosome 13
				wd:Q138955  # human chromosome 14
				wd:Q765245  # human chromosome 15
				wd:Q742870  # human chromosome 16
				wd:Q220677  # human chromosome 17
				wd:Q780468  # human chromosome 18
				wd:Q510786  # human chromosome 19
				wd:Q666752  # human chromosome 20
				wd:Q753218  # human chromosome 21
				wd:Q753805  # human chromosome 22
				wd:Q61333  # human chromosome X
				wd:Q202771  # human chromosome Y
				wd:Q27075  # human chromosome MT
			] 
			
<#genomic-assembly> [
   				wd:Q20966585 # Genome assembly GRCh38
				wd:Q21067546 # Genome assembly GRCh37	
			]
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