pw.endpoint <- "http://rdf.pathwaycommons.org/sparql/"
query.custom <-
'SELECT DISTINCT * WHERE {
%s bp:pathwayComponent ?reaction .
?reaction bp:displayName ?reaction_name .
?reaction bp:comment ?reaction_comment .
?reaction rdf:type ?reaction_type .
VALUES ?reaction_type{ bp:BiochemicalReaction bp:Degradation bp:TemplateReaction }
OPTIONAL {
?reaction bp:conversionDirection ?direction }
} LIMIT 20'
query.controlreactions <-
'select ?nameController ?reference ?nameControlled where {\n
%s bp:pathwayComponent ?ReactionControl.\n
?ReactionControl a bp:Control .\n
?ReactionControl bp:controller ?controller.\n
?ReactionControl bp:controlled ?controlled.\n
?controller bp:standardName ?nameController.\n
?controlled bp:standardName ?nameControlled.\n
?controller bp:entityReference ?reference. \n}'
query.catalysisreactions <-
'select ?nameController ?reference ?nameControlled where {\n
%s bp:pathwayComponent ?Catalysis.\n
?Catalysis a bp:Catalysis .\n
?Catalysis bp:controller ?controller.\n
?Catalysis bp:controlled ?controlled.\n
?controller bp:entityReference ?reference.\n
?controller bp:standardName ?nameController.\n
?controlled bp:standardName ?nameControlled.\n}'
query.biochemicalreactions <-
'select ?nameReaction ?nleft ?nright ?leftReference ?rightReference where {\n
%s bp:pathwayComponent ?s.\n
?s a bp:BiochemicalReaction.\n
?s bp:left ?left.\n
?s bp:right ?right.\n
?s bp:displayName ?nameReaction.\n
?left bp:displayName ?nleft.\n
?right bp:displayName ?nright.\n
?left <http://www.biopax.org/release/biopax-level3.owl#entityReference> ?leftReference.\n
?right <http://www.biopax.org/release/biopax-level3.owl#entityReference> ?rightReference.\n
}'
query.templatereactions <-
'select * where {\n
%s bp:pathwayComponent ?TemplateReaction.\n
?TemplateReaction a bp:TemplateReaction.\n
?TemplateReaction bp:product ?product. \n
?product bp:displayName ?name.\n
?product bp:entityReference ?reference.\n}'
query.templatereactionsregulations <-
'select ?nameController ?reference ?controller where {\n
%s bp:pathwayComponent ?TemplateReactionRegulation.\n
?TemplateReactionRegulation a bp:TemplateReactionRegulation.\n
?TemplateReactionRegulation bp:controlled ?controlled.\n
?TemplateReactionRegulation bp:controller ?controller.\n
?controller bp:displayName ?nameController.\n
?controller bp:entityReference ?reference.\n}'
query.degradationreactions <-
'select * where {\n
%s bp:pathwayComponent ?Degradation.\n
?Degradation a bp:Degradation .\n
?Degradation bp:displayName ?name. \n}'
query.modulationreactions <-
'select ?nameController ?reference ?nameControlled where {\n
%s bp:pathwayComponent ?Modulation.\n
?Modulation a bp:Modulation.\n
?Modulation bp:controller ?controller.\n
?controller bp:displayName ?nameController.\n
?controller bp:entityReference ?reference.\n
?Modulation bp:controlled ?controlled.\n
?controlled bp:displayName ?nameControlled.\n}'
custom1 <-
'SELECT DISTINCT * WHERE
{ %s bp:pathwayComponent ?reaction .
?reaction bp:displayName ?reaction_name ;
rdf:type ?reaction_type VALUES ?reaction_type {bp:BiochemicalReaction bp:Degradation bp:TemplateReaction}
OPTIONAL { ?reaction bp:conversionDirection ?direction }
OPTIONAL { VALUES ?direction{"LEFT_TO_RIGHT"} }}'
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