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Example queries

WikiPathways and CIViC

Get known variants reported in CIViC database (Q27612411) for genes reported in a WikiPathways pathway : Bladder cancer (Q30230812)

The following query uses these:

• Items: bladder cancer (Q504775)   

• Properties: WikiPathways ID (P2410)   , has part(s) (P527)   , subclass of (P279)   , CIViC variant ID (P3329)   , biological variant of (P3433)   , positive therapeutic predictor for (P3354)   , negative therapeutic predictor for (P3355)   , positive diagnostic predictor for (P3356)   , negative diagnostic predictor for (P3357)   , positive prognostic predictor for (P3358)   , negative prognostic predictor for (P3359)   , medical condition treated (P2175)   

  SELECT DISTINCT ?pathway ?pathwayLabel ?pwpart ?pwpartLabel ?variant ?variantLabel ?disease?diseaseLabel WHERE {
  
     VALUES ?predictor {p:P3354 p:P3355 p:P3356 p:P3357 p:P3358 p:P3359}
     VALUES ?predictorQualifier {pq:P2175}
     VALUES ?wpID {"WP2828"}
    
     ?pathway wdt:P2410 ?wpID ; # Pathways has a WikiPathways identifier
            wdt:P527 ?pwpart . # which contains pathways parts
    
     ?disease wdt:P279+ wd:Q504775 .  # The disease is a subclass of urinary bladder cancer 
                                      # based on annotations in the Disease ontology
     ?variant wdt:P3329 ?civicID ; # a variant known in CIViC 
               ?predictor ?node ; # has a predicting relation with diseases
                                     # labeled as being a subclass of urinary bladder cancer
               wdt:P3433 ?pwpart .  # variant is biological variant of
     
     {?node ?predictorStatement ?drug_label ;
                ?predictorQualifier ?disease .}
     UNION 
     {
        ?node ?predictorStatement ?disease  .
     }
     SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
  }
  

Try it!