Jump to content

Clinical Interpretations of Variants in Cancer (E70)

From Wikidata
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	
			]
Retrieved from "https://www.wikidata.org/w/index.php?title=EntitySchema:E70&oldid=1163717254"