User talk:Pathwaybot/query examples
Request for queries edit
We are constantly looking for possible ways to combine life science data on Wikidata. Please issue any request for a SPARQL query on pathway data here, we will try to generate the relevant SPARQL query for your request(s)
Hello Pathwaybot! Egon:@Egon_Willighagen: and I:@DeSl: created this query:
\#Query to show genes and proteins encoded by genes, which are linked to a disease with OMIM ID.
SELECT DISTINCT ?pw ?pwLabel ?gene ?geneLabel ?omim ?disease ?diseaseLabel WHERE {
?pw wdt:P2410 ?wpid . { ?pw wdt:P527 ?gene . } UNION { ?pw wdt:P527 ?protein . ?gene wdt:P688 ?protein } ?gene wdt:P492 ?omim . ?disease wdt:P492 ?omim ; wdt:P31 wd:Q12136 . SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
} ORDER BY DESC(?pw)
And a new Query from Egon:@Egon_Willighagen: and me:@DeSl:: (btw this query cannot be done for all species, we reached a time out. Perhaps the query should be optimized even more.)
\#Displays proteins with their associated component of the cell in which this protein is present SELECT DISTINCT ?protein ?proteinLabel ?cell ?cellLabel WITH {
SELECT DISTINCT ?protein WHERE { ?protein wdt:P31 wd:Q8054 ; #instance of protein wdt:P703 wd:Q15978631 . #Restricted to species: homo sapiens }
} AS %result WHERE {
INCLUDE %result ?protein wdt:P681 ?cell . SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
} ORDER BY ?protein
And another query (this time I:@DeSl: made it myself :) ). This query lists all genes related to the biological process 'Brain development'.
\#Displays proteins which are associated with Brain development SELECT DISTINCT ?protein ?proteinLabel WHERE {
?protein wdt:P31 wd:Q8054 ;#instance of protein wdt:P703 wd:Q15978631 . #for species: Homo Sapiens ?protein wdt:P682 wd:Q14330969 #Biological process: brain development SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
} ORDER BY ?protein
Another query, describing which amino acids are in Wikidata and in pathways from WPs linked to Wikidata.
\#defaultView:BubbleChart SELECT ?ID ?IDLabel (COUNT(DISTINCT ?PWID) AS ?count) WHERE{
?ID wdt:P279 wd:Q8066 . ?PWID wdt:P31 wd:Q4915012 . ?PWID wdt:P527 ?ID .
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". } } GROUP BY ?ID ?IDLabel