Demo queries
From bio2rdf
- You must submit those queries in Bio2RDF's Sparql point http://bio2rdf.org/sparql
- For a complete description of SPARQL query language syntax refer to W3C reference document http://www.w3.org/TR/rdf-sparql-query/
What is hexokinase ?
select ?t1 ?p2 count(*)
where {
?s1 ?p1 ?o1 .
?o1 bif:contains "hexokinase" .
?s1 a ?t1 .
?s1 ?p2 ?o2 .
}
ORDER BY ?t1 ?p2
Litterature queries in PubMed
Who is Jean Morissette ?
Foaf<-() Try it out!
SELECT ?label1, count(*)
WHERE {
?s1 ?p1 ?o1 .
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?o1 bif:contains "morissette" .
}
ORDER BY DESC (count(*))
What subject has Jean Morissette been working on ?
Foaf<-PubMed<-(OMIM, GeneID, GenBank, HGNC) Try it out!
SELECT ?label3, count(*)
WHERE {
?s1 ?p1 ?o1 .
?o1 bif:contains "morissette and (J or Jean)" .
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?s2 ?p2 ?s1 .
?s2 <http://www.w3.org/2000/01/rdf-schema#label> ?label2 .
?s3 ?p3 ?s2 .
?s3 <http://www.w3.org/2000/01/rdf-schema#label> ?label3 .
}
ORDER BY DESC(count(*))
Who are Dr Labrie collaborators ?
Foaf<-PubMed->Foaf Try it out!
SELECT distinct ?s1, ?s3, count (*)
WHERE {
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?label1 bif:contains "Labrie and (F or Fernand)" .
?s2 ?p2 ?s1 .
?s2 <http://purl.org/dc/elements/1.1/creator> ?s3 .
}
ORDER BY DESC (count(*))
Which are Dr Labrie most referenced paper in annotations ?
Foaf<-Pubmed<-(UniProt, GeneID, GenBank, OMIM, HGNC, Reactome) Try it out!
SELECT ?label2, count(*)
WHERE {
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?label1 bif:contains "Labrie and (F or Fernand)" .
?s2 ?p2 ?s1 .
?s2 <http://www.w3.org/2000/01/rdf-schema#label> ?label2 .
?s3 ?p3 ?s2 .
}
ORDER BY DESC(count(*))
Which MeSH terms are associated to Dr Labrie papers ?
Foaf<-PubMed->MeSH->MeSH Try it out!
SELECT ?label3, ?comment3, ?comment4, count(*)
WHERE {
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?label1 bif:contains "Labrie and (F or Fernand)" .
?s2 ?p2 ?s1 .
?s2 <http://bio2rdf.org/bio2rdf#xMeSH> ?mesh2 .
?mesh2 <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?seeAlso3 .
?seeAlso3 <http://www.w3.org/2000/01/rdf-schema#label> ?label3 .
?seeAlso3 <http://www.w3.org/2000/01/rdf-schema#comment> ?comment3 .
?seeAlso3 <http://bio2rdf.org/bio2rdf#isA> ?isA3 .
?isA3 <http://www.w3.org/2000/01/rdf-schema#comment> ?comment4 .
}
ORDER BY DESC(count(*))
What is Hexokinase ?
What is known about Hexokinase gene, HK1, according to the Atlas ?
literal<-rdf:type Try it out!
SELECT ?type1, ?label1, count(*)
WHERE {
?s1 ?p1 ?o1 .
?o1 bif:contains "HK1" .
?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type1 .
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
}
ORDER BY DESC (count(*))
Look for Hexokinase in GO or MeSH controlled vocabulary ?
literal<-(GO, MeSH) Try it out!
SELECT distinct ?label2, ?comment2, ?label1, ?comment1
WHERE {
?s1 ?p1 ?o1 .
?o1 bif:contains "hexokinase" .
?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type1 .
?s1 <http://www.w3.org/2000/01/rdf-schema#comment> ?comment1 .
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?s1 <http://bio2rdf.org/bio2rdf#isA> ?s2 .
?s2 <http://www.w3.org/2000/01/rdf-schema#comment> ?comment2 .
?s2 <http://www.w3.org/2000/01/rdf-schema#label> ?label2 .
}
What is pathway network of mouse metabolism ?
path:mmu->rn->cpd Try it out!
SELECT distinct ?label1, ?label2
WHERE {
?Pathway1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?label1 bif:contains "'mmu*'" .
?Pathway1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/kegg#Pathway> .
?Pathway1 <http://bio2rdf.org/kegg#xreaction> ?xreaction2 .
?xreaction2 <http://bio2rdf.org/kegg#xProduct> ?xProduct2 .
?xProduct2 <http://www.w3.org/2000/01/rdf-schema#label> ?label2 .
}
path:mmu->rn<-cpd Try it out!
SELECT distinct ?label1, ?label2
WHERE {
?Pathway1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?label1 bif:contains "'mmu*'" .
?Pathway1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/kegg#Pathway> .
?Pathway1 <http://bio2rdf.org/kegg#xreaction> ?xreaction2 .
?xreaction2 <http://bio2rdf.org/kegg#xSubstrate> ?xSubstrate2 .
?xSubstrate2 <http://www.w3.org/2000/01/rdf-schema#label> ?label2 .
}
In which pathway is Hk1 gene, mouse hexokinase, involved ?
geneid:15275->(GeneID->KEGG->RN, GeneID->UniProt->Reactome)
Try it out!
SELECT distinct ?type1, ?s1
WHERE {
?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type1 .
?s1 ?p1 ?o1 .
?o1 bif:contains "HK1" .
}
SELECT distinct ?s4
WHERE {
?s1 ?p1 <http://bio2rdf.org/geneid:15275> .
?s1 ?p2 ?s2 .
?s2 ?p3 ?s3 .
?s3 ?p4 ?s4 .
}
http://bio2rdf.org/reactome:10602
http://bio2rdf.org/reactome:1423
What are the genes involved in a KEGG pathway ?
path->relation->object->KEGG:gene=GeneID
Try it out!
SELECT distinct ?label1, ?sameAs5, ?xobject4
WHERE {
?Pathway1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?Pathway1 <http://bio2rdf.org/kegg#xrelation> ?xrelation2 .
?xrelation2 <http://bio2rdf.org/kegg#xentry1> ?xentry3 .
?xentry3 <http://bio2rdf.org/kegg#xobject> ?xobject4 .
?xobject4 <http://www.w3.org/2002/07/owl#sameAs> ?sameAs5 .
FILTER (?Pathway1 = <http://bio2rdf.org/path:mmu00010>)
}
What is known about Paget disease ?
SELECT ?s1 ?type, count(*)
WHERE {
?s1 ?p1 ?o1 .
?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type .
?o1 bif:contains "paget" .
}
ORDER BY DESC (count(*))
Analyse Parkinson
Gene GO annotation from pubmed litterature for nor-1, nur77, nurr1 and rxr about cytoplasm and apoptosis.
literal<-Pubmed<-()->GO Try it out!
SELECT ?label3, count(*)
WHERE {
?s1 ?p1 ?o1 .
?o1 bif:contains "rxr" .
?s2 ?o2 ?s1 .
?s2 <http://bio2rdf.org/bio2rdf#xGO> ?s3 .
?s3 <http://www.w3.org/2000/01/rdf-schema#label> ?label3 .
}
ORDER BY DESC(count(*))
Analyze GO term distribution.
SELECT ?label1, ?label2, ?label3
WHERE {
?s1 ?p1 ?o1 .
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
?o1 bif:contains "rxr and (cytoplasm or apoptosis)" .
?s2 ?o2 ?s1 .
?s2 <http://www.w3.org/2000/01/rdf-schema#label> ?label2 .
?s2 <http://bio2rdf.org/bio2rdf#xGO> ?s3 .
?s3 <http://www.w3.org/2000/01/rdf-schema#label> ?label3 .
}
ORDER BY ASC(?label3)
GO term distribution for GeneID gene.
literal<-GeneID->GO Try it out!
SELECT ?label2 count(*)
WHERE {
?s1 ?p1 ?o1 .
?o1 bif:contains "nur77" .
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
FILTER(regex(?s1,"geneid"))
?s1 ?p2 ?s2 .
?s2 <http://www.w3.org/2000/01/rdf-schema#label> ?label2 .
FILTER(regex(?s2,"go"))
}
ORDER BY DESC(count(*))
GO term distribution for UniProt protein.
literal<-GeneID->GO Try it out!
SELECT ?label2 count(*)
WHERE {
?s1 ?p1 ?o1 .
?o1 bif:contains "nur77" .
?s1 <http://www.w3.org/2000/01/rdf-schema#label> ?label1 .
FILTER(regex(?s1,"uniprot"))
?s1 ?p2 ?s2 .
?s2 <http://www.w3.org/2000/01/rdf-schema#label> ?label2 .
FILTER(regex(?s2,"go"))
}
ORDER BY DESC(count(*))
Pathway analysis
Querying Reactome Biopax pathway
SELECT *
WHERE {
<http://bio2rdf.org/reactome:163685-Integration_of_energy_metabolism> <http://bio2rdf.org/biopax#PATHWAY-COMPONENTS> ?s2 .
?s2 <http://bio2rdf.org/biopax#STEP-INTERACTIONS> ?s3 .
?s3 <http://bio2rdf.org/biopax#PATHWAY-COMPONENTS> ?s4 .
?s4 <http://bio2rdf.org/biopax#STEP-INTERACTIONS> ?s5 .
?s5 <http://bio2rdf.org/biopax#CONTROLLER> ?s6 .
?s6 <http://bio2rdf.org/biopax#PHYSICAL-ENTITY> ?s7 .
?s7 ?p ?s8 .
}
