User:Pathwaybot/query examples
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[edit]
WikiPathways[edit]
List all items sourced from WikiPathways[edit]
SELECT * WHERE {
?item wdt:P2410 ?wpid ;
}
List all items sourced from WikiPathways and the last update in Wikidata[edit]
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[edit]
For pathway WP534 in this case:
The following query uses these:
- 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[edit]
List all items sourced from Reactome[edit]
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[edit]
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[edit]
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[edit]
The following query uses these:
- 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[edit]
The following query uses these:
- 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[edit]
For pathway R-HSA-532668 in this case:
The following query uses these:
- 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[edit]
WikiPathways and Reactome[edit]
[edit]
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[edit]
Biological pathways with protein structures in the PDB database[edit]
The following query uses these:
- 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[edit]
All compounds which are potentially targeting Parkinsons Disease Pathway (Q29883419) (Wikipathways)[edit]
The following query uses these:
- 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)[edit]
The following query uses these:
- 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[edit]
Get known variants reported in CIViC database (Q27612411) for genes reported in a WikiPathways pathway : Bladder cancer (Q30230812)[edit]
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[edit]
Wikidata and the SPARQL endpoint of WikiPathways[edit]
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[edit]
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[edit]
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.[edit]
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[edit]
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[edit]
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[edit]
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". } }