User:Pathwaybot/query examples

< User:Pathwaybot

Welcome to WikiProject Gene Wiki
This page documents the Pathway bot, that it is maintained within the Wikiproject Gene Wiki. It is a WikiProject dedicated to make and maintiain Wikidata as a central hub of linked knowledge on Genes, Proteins, Diseases, Drugs, and related concepts.

On this page query examples on pathway content on Wikidata. Query suggestion or requests are more than welcome. Request and suggestion can be submitted to the Discussion page

Source specific queries

WikiPathways

List all items sourced from WikiPathways

SELECT * WHERE {
   ?item wdt:P2410 ?wpid ;
}

List all items sourced from WikiPathways and the last update in Wikidata

The following query uses these:

Properties: WikiPathways ID (P2410)  
```
SELECT ?item ?itemLabel ?dateModifier WHERE {
   ?item wdt:P2410 ?wpid ;
         schema:dateModified ?dateModifier .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
```

Chromosomal positions of genes in a WikiPathways

For pathway WP534 in this case:

The following query uses these:

Items: genome assembly GRCh38 (Q20966585)

Properties: has part(s) (P527)   , WikiPathways ID (P2410)   , chromosome (P1057)   , short name (P1813)   , HGNC gene symbol (P353)   , genomic start (P644)   , genomic end (P645)   , genomic assembly (P659)  
```
SELECT DISTINCT ?name ?chr ?start ?stop WITH {
  SELECT DISTINCT ?gene ?name ?chr WHERE {
    VALUES ?pathwayID { "WP534" }
    ?pathway wdt:P527 ?gene ;
             wdt:P2410 ?pathwayID .
    ?gene wdt:P1057/wdt:P1813 ?chr ;
          wdt:P353 ?name .
  }
} AS %result
WHERE {
  INCLUDE %result
  ?gene p:P644 [
    pq:P659 wd:Q20966585 ;
    ps:P644 ?start
  ] .
  ?gene p:P645 [
    pq:P659 wd:Q20966585 ;
    ps:P645 ?stop
  ]
}
```

And try this visualisation too.

Reactome

List all items sourced from Reactome

The following query uses these:

Properties: Reactome ID (P3937)  
```
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {
    ?pathway wdt:P3937 ?reactomeID .
            
   SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
```

List all items sourced from Reactome and the last update in Wikidata

The following query uses these:

Properties: Reactome ID (P3937)  
```
SELECT ?item ?itemLabel ?dateModifier WHERE {
   ?item wdt:P3937 ?wpid ;
         schema:dateModified ?dateModifier .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
```

Get all top level entries from Reactome

The following query uses these:

Properties: Reactome ID (P3937)   , has part(s) (P527)  
```
SELECT DISTINCT ?item ?itemLabel WHERE {
   ?item wdt:P3937 ?reactome_id ;
         wdt:P527 ?pwpart .
    FILTER NOT EXISTS {
       ?parent wdt:P527 ?item .
      }       
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
```

Get all child nodes from Reactome

The following query uses these:

Items: biological pathway (Q4915012)   , biological process (Q2996394)

Properties: Reactome ID (P3937)   , has part(s) (P527)   , instance of (P31)  
```
SELECT DISTINCT ?item ?itemLabel  WHERE {
   ?item wdt:P3937 ?reactome_id ;
         wdt:P527 ?pwpart .
    FILTER NOT EXISTS {
       {?pwpart wdt:P31 wd:Q4915012 }
        UNION 
       {?pwpart wdt:P31 wd:Q2996394 }
       ?pwpart wdt:P527 ?child_node .
      }       
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
```

Visualize the hierarchies captured in Reactome

The following query uses these:

Items: Metabolism of steroids (Q34340147)

Properties: Reactome ID (P3937)   , part of (P361)

Features: Graph (Q24515287)  

#defaultView:Graph
SELECT ?item ?itemLabel ?pwpart ?pwpartLabel WHERE {
  #VALUES ?pwpart {wd:Q34340147}
   ?item wdt:P3937 ?reactomeID1 .
   ?item wdt:P361+ ?pwpart .

  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

Chromosomal positions of genes in a Reactome

For pathway R-HSA-532668 in this case:

The following query uses these:

Items: genome assembly GRCh38 (Q20966585)

Properties: has part(s) (P527)   , encoded by (P702)   , Reactome ID (P3937)   , chromosome (P1057)   , short name (P1813)   , HGNC gene symbol (P353)   , genomic start (P644)   , genomic end (P645)   , genomic assembly (P659)  
```
SELECT DISTINCT ?name ?chr ?start ?stop WITH {
  SELECT DISTINCT ?gene ?name ?chr WHERE {
    VALUES ?pathwayID { "R-HSA-532668" }
    ?pathway wdt:P527+/wdt:P702 ?gene ;
             wdt:P3937 ?pathwayID .
    ?gene wdt:P1057/wdt:P1813 ?chr ;
          wdt:P353 ?name .
  }
} AS %result
WHERE {
  INCLUDE %result
  ?gene p:P644 [
    pq:P659 wd:Q20966585 ;
    ps:P644 ?start
  ] .
  ?gene p:P645 [
    pq:P659 wd:Q20966585 ;
    ps:P645 ?stop
  ]
}
```

And try this visualisation too.

Combinatorial queries

WikiPathways and Reactome

WikiPathways and Reactome entries that share the same citation

The following query uses these:

Properties: WikiPathways ID (P2410)   , cites work (P2860)   , Reactome ID (P3937)  
```
SELECT ?wp_pathway ?wp_pathwayLabel ?cites ?citesLabel ?reactome_pathway ?reactome_pathwayLabel WHERE {
  ?wp_pathway wdt:P2410 ?wpid ;
              wdt:P2860 ?cites .
  ?reactome_pathway wdt:P3937 ?reactomeid ;
                    wdt:P2860 ?cites .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
```

Pathways and PDB

Biological pathways with protein structures in the PDB database

The following query uses these:

Items: biological pathway (Q4915012)   , biological process (Q2996394)

Properties: instance of (P31)   , has part(s) (P527)   , encodes (P688)   , PDB structure ID (P638)   , WikiPathways ID (P2410)   , Reactome ID (P3937)  
```
SELECT ?pathway ?pathwayLabel ?WikiPathways ?Reactome (COUNT(DISTINCT ?protein) as ?count) WHERE {
  VALUES ?pathwayType { wd:Q4915012 wd:Q2996394 }
  ?pathway wdt:P31 ?pathwayType .
  { ?pathway wdt:P527/wdt:P688 ?protein . } UNION { ?pathway wdt:P527 ?protein . }
  ?protein wdt:P638 ?PDBID .
  OPTIONAL { ?pathway wdt:P2410 ?WikiPathways }
  OPTIONAL { ?pathway wdt:P3937 ?Reactome }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
} GROUP BY ?pathway ?pathwayLabel ?WikiPathways ?Reactome
  ORDER BY DESC(?count)
```

Compounds and Pathways

All compounds which are potentially targeting Parkinsons Disease Pathway (Q29883419) (Wikipathways)

The following query uses these:

Items: Parkinsons Disease Pathway (Q29883419)

Properties: WikiPathways ID (P2410)   , has part(s) (P527)   , encodes (P688)   , physically interacts with (P129)  
```
SELECT ?wpid ?gene ?geneLabel ?protein ?proteinLabel ?compound ?compoundLabel WHERE {
  wd:Q29883419 wdt:P2410 ?wpid;
    wdt:P527 ?gene.
  ?gene wdt:P688 ?protein.
  
  ?protein wdt:P129 ?compound .
   SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
```

All compounds which are potentially targeting Signaling by NOTCH1 in Cancer (Q37753018) (Reactome)

The following query uses these:

Items: Signaling by NOTCH1 in Cancer (Q37753018)

Properties: part of (P361)   , has part(s) (P527)   , UniProt protein ID (P352)   , encodes (P688)   , physically interacts with (P129)  
```
SELECT DISTINCT  ?gene ?geneLabel ?protein ?proteinLabel ?compound ?compoundLabel WHERE {
  VALUES ?item {wd:Q37753018} 
  ?pwpart wdt:P361* ?item ;
          wdt:P527 ?protein .
  ?protein wdt:P352 ?uniprot .
  ?gene wdt:P688 ?protein .
  ?protein wdt:P129 ?compound .
   SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
```

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". }
}
```

Federated queries

Wikidata and the SPARQL endpoint of WikiPathways

The endpoint has a UI at https://sparql.wikipathways.org and the SPARQL endpoint lives at https://sparql.wikipathways.org/sparql

Known interaction types in WikiPathways for a pathway with Identifier WP716

PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
SELECT DISTINCT ?interaction_type WHERE {
  VALUES ?wpid {"WP716"}
  ?item wdt:P2410 ?wpid ;
        wdt:P2888 ?source_pathway .
 
  SERVICE <http://sparql.wikipathways.org/sparql> {
     ?wp_pathway dc:identifier ?source_pathway .
     ?s dcterms:isPartOf ?wp_pathway, ?interaction .
     ?interaction rdf:type wp:Interaction .
     ?interaction rdf:type ?interaction_type .
     ?interaction wp:participants ?participants .
  }
}

Local annotations from WikiPathways using Federated query on a Pathway with identifier WP716

The following query uses these:

Properties: WikiPathways ID (P2410)   , exact match (P2888)  
```
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
SELECT DISTINCT ?item ?pw_annotation  WHERE {
  VALUES ?wpid {"WP716"}
  ?item wdt:P2410 ?wpid ;
        wdt:P2888 ?source_pathway .
 
  SERVICE <http://sparql.wikipathways.org/sparql> {
     ?wp_pathway dc:identifier ?source_pathway .
     ?wp_pathway wp:ontologyTag ?pw_annotation .
     # ?pw_annotation rdfs:label ?annotation_label .
   }
}
```

Lists SMILES of substrates and products of metabolic conversions.

The following query uses these:

Properties: canonical SMILES (P233)  

, isomeric SMILES (P2017)  

PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?sourceWD ?sourceWDLabel ?sourceSMILES ?targetWD ?targetWDLabel ?targetSMILES WITH {
  SELECT ?sourceWD ?targetWD WHERE {
    SERVICE <http://sparql.wikipathways.org/sparql> {
      ?pathway a wp:Pathway . 
      ?interaction dcterms:isPartOf ?pathway .
      ?interaction a wp:Interaction, wp:Conversion .
      ?interaction wp:source ?source . ?source a wp:Metabolite; wp:bdbWikidata ?sourceWD .
      ?interaction wp:target ?target . ?target a wp:Metabolite; wp:bdbWikidata ?targetWD .
    }
  }
} AS %results WHERE {
  INCLUDE %results
  OPTIONAL { ?sourceWD wdt:P233 ?sourceSMILEScan }
  OPTIONAL { ?sourceWD wdt:P2017 ?sourceSMILESiso }
  BIND (COALESCE(?sourceSMILESiso, ?sourceSMILEScan) AS ?sourceSMILES)
  OPTIONAL { ?targetWD wdt:P233 ?targetSMILEScan }
  OPTIONAL { ?targetWD wdt:P2017 ?targetSMILESiso }
  BIND (COALESCE(?targetSMILESiso, ?targetSMILEScan) AS ?targetSMILES)
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

Lists metabolites in WikiPathways and InChIKeys from Wikidata

The following query uses these:

Properties: InChIKey (P235)  

PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?metabolite ?wikidata ?inchikey WITH {
  SELECT ?metabolite ?wikidata WHERE {
    SERVICE <http://sparql.wikipathways.org/sparql> {
      ?metabolite a wp:Metabolite ;
                  wp:bdbWikidata ?wikidata .
    }
  }
} AS %results WHERE {
  INCLUDE %results
  ?wikidata wdt:P235 ?inchikey .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

Lists metabolites in WikiPathways with InChIKeys and formal charge from Wikidata

The following query uses these:

Properties: InChIKey (P235)  

PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?metabolite ?wikidata ?inchikey ?charge WITH {
  SELECT ?metabolite ?wikidata WHERE {
    SERVICE <http://sparql.wikipathways.org/sparql> {
      ?metabolite a wp:Metabolite ;
                  wp:bdbWikidata ?wikidata .
    }
  }
} AS %results WHERE {
  INCLUDE %results
  ?wikidata wdt:P235 ?inchikey .
  bind(
    if(substr(?inchikey,27) = "N", "0"^^xsd:integer, 
      if(substr(?inchikey,27) = "M", "-1"^^xsd:integer, 
        if(substr(?inchikey,27) = "O", "+1"^^xsd:integer,
          if(substr(?inchikey,27) = "L", "-2"^^xsd:integer,
            if(substr(?inchikey,27) = "P", "+2"^^xsd:integer,
              if(substr(?inchikey,27) = "K", "-3"^^xsd:integer,
                if(substr(?inchikey,27) = "J", "-4"^^xsd:integer,
                  if(substr(?inchikey,27) = "I", "-5"^^xsd:integer,
                    if(substr(?inchikey,27) = "F", "-8"^^xsd:integer,
                      "999"^^xsd:integer # ERROR
                    )
                  )
                )
              )
            )
          )
        )
      )
    )
    as ?charge
  )
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

Lists metabolites in WikiPathways and chemical formulas and names from Wikidata

The following query uses these:

Properties: chemical formula (P274)  

PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?metabolite ?wikidata ?wikidataLabel ?chemFormula WITH {
  SELECT ?metabolite ?wikidata WHERE {
    SERVICE <http://sparql.wikipathways.org/sparql> {
      ?metabolite a wp:Metabolite ;
                  wp:bdbWikidata ?wikidata .
    }
  }
} AS %results WHERE {
  INCLUDE %results
  ?wikidata wdt:P274 ?chemFormula .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}

Retrieved from "https://www.wikidata.org/w/index.php?title=User:Pathwaybot/query_examples&oldid=1583824030"