BioPAX/OWL and SPARQL

Tutorial Material

 * start a terminal
 * create a directory jena_workspace, move into that directory
 * download jena.jar
 * download biopax data http://www.biopax.org/Junk/Homosapiens.nt or a smaller file http://www.biopax.org/Junk/Escherichia_coli.nt

BioPAX Level 3 Queries
BASE  PREFIX rdf:    PREFIX bp:  

SELECT ?protein ?pname ?component ?rightcomponent ?rdfT ?pathway where { ?protein rdf:type bp:Protein. ?protein bp:entityReference ?protRef. ?protRef bp:xref ?xref. ?xref bp:id ?pname. ?component bp:component ?protein. ?rightcomponent bp:right ?component. ?pathway bp:pathwayComponent ?rightcomponent. ?rightcomponent rdf:type ?rdfT. } order by ?protein

BASE  PREFIX rdf:    PREFIX bp:  

SELECT distinct ?protein ?pname ?component where { ?protein rdf:type bp:Protein. ?protein bp:entityReference ?protRef. ?protRef bp:xref ?xref. ?xref bp:id ?pname. ?component bp:component ?protein. } order by ?protein

BASE  PREFIX rdf:    PREFIX bp:  

SELECT ?pName ?a ?all ?allvalues WHERE { {?pathway bp:pathwayComponent ?comp. ?pathway bp:standardName ?pName. ?comp rdf:type bp:Catalysis. ?comp bp:controlled ?a. ?comp bp:controller ?b. ?a ?all ?allvalues.} }

BASE  PREFIX rdf:    PREFIX bp:  

SELECT * WHERE { {?pathway bp:pathwayComponent ?comp. ?pathway bp:standardName ?pName. ?comp rdf:type bp:BiochemicalReaction .} UNION {?pathway bp:pathwayComponent ?comp. ?pathway bp:standardName ?pName. ?comp rdf:type bp:Catalysis .} }

BASE  PREFIX rdf:    PREFIX bp:  

SELECT ?comp ?x ?pid ?feature ?pidRef ?type ?name WHERE { ?pathway rdf:type bp:Pathway. ?pathway bp:pathwayComponent ?comp. ?comp rdf:type bp:BiochemicalReaction. ?comp ?x ?pid. ?pid rdf:type bp:Protein. ?pid bp:feature ?feature. ?feature rdf:type ?bp. ?feature bp:modificationType ?type. ?pid bp:entityReference ?pidRef. ?pidRef bp:standardName ?name. }

BASE  PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX bp:  <biopax-level3.owl#>

SELECT ?comp ?x ?pid ?feature ?pidRef ?type ?name WHERE { ?pathway rdf:type bp:Pathway. ?pathway bp:pathwayComponent ?comp. ?comp rdf:type bp:BiochemicalReaction. ?comp ?x ?pid. ?pid rdf:type bp:Protein. ?pid bp:feature ?feature. ?feature rdf:type ?bp. ?feature bp:modificationType ?type. ?pid bp:entityReference ?pidRef. ?pidRef bp:standardName ?name. }

BASE <http://www.biopax.org/release/> PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX bp:  <biopax-level3.owl#>

SELECT ?comp ?x ?pid WHERE { ?pathway rdf:type bp:Pathway. ?pathway bp:pathwayComponent ?comp. ?comp rdf:type bp:BiochemicalReaction. ?comp ?x ?pid. ?pid rdf:type bp:Protein. }

BASE <http://www.biopax.org/release/> PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX bp:  <biopax-level3.owl#>

SELECT ?comp ?name WHERE { ?pathway rdf:type bp:Pathway. ?pathway bp:pathwayComponent ?comp. ?comp bp:standardName ?name FILTER (!REGEX(?name, "survival")) }

BASE <http://www.biopax.org/release/> PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX bp:  <biopax-level3.owl#>

SELECT  ?xref  ?id ?protein where { ?protein rdf:type bp:Protein. ?protein bp:entityReference ?protRef. ?protRef bp:xref ?xref. ?xref bp:id ?id. ?component bp:component ?protein. ?rightcomponent bp:right ?component. ?pathway bp:pathwayComponent ?rightcomponent. ?rightcomponent rdf:type ?rdfT. FILTER (REGEX(str(?xref), "P17174", "i")). }