Introduction

The wiki describes and documents FuXi's BackwardsChainingStore - an rdflib Store that serves as a query mediation wrapper over an existing RDFLib graph. The main use is to be able to pose queries involving terms from a ruleset and/or ontology such that either of the top-down algorithms (BFP or SLD) are used to answer the queries and dispatching queries at the bottom of the resolution tree involving EDB predicates against the given graph. Query mediation can also be used against a remote SPARQL service using the generic SPARQL store provided by layercake-python.

Details

The store uses the two "sip strategies" and the in-memory, rdflib SPARQL Algebra implementation as a store-agnostic, top-down decision procedure for semanic web SPARQL (OWL2-RL/RIF/N3) entailment regimes. Queries are mediated over the SPARQL protocol using global schemas captured as SW theories which describe and distinguish their predicate symbols

The store is instantiated this way:

            topDownDPreds = defaultDerivedPreds  if options.ddlGraph else None
            topDownStore=TopDownSPARQLEntailingStore(
                            factGraph.store,
                            factGraph,
                            idb=ruleSet,
                            derivedPredicates = derivedPredicatesIDB,
                            nsBindings=...
                            decisionProcedure = TOP_DOWN_METHOD(0) or 1,
                            identifyHybridPredicates = ..True if you want to scan EDB for predicate symbols ... )
            targetGraph = Graph(topDownStore)
#            queryLiteral = EDBQuery([BuildUnitermFromTuple(goal) for goal in goals],targetGraph)
            result = targetGraph.query(..query string..,initNs=,regular arguments to query)

Example: Influenza SPARQL entailment / query answering via OWL 2 RL document

Use

drugbank:interactionForDrug 
  a owl:ObjectProperty;
  owl:inverseOf drugbank:interactionDrug1, drugbank:interactionDrug2 .

drugbank:InfluenzaDrug a owl:Class.

[
   a owl:Restriction;
   owl:onProperty drugbank:affectedOrganism;
   owl:hasValue "Influenza Virus"
] rdfs:subClassOf drugbank:InfluenzaDrug .

drugbank:affectedOrganism a owl:DatatypeProperty

( 
  drugbank:InfluenzaDrug 
) a ddl:DerivedClassList .

( drugbank:interactionForDrug ) a ddl:DerivedPropertyList .

$ FuXi \
--output=rif --safety=loose --strictness=loose \
--ddlGraph=test/drugBankDDL.n3 --method=sld 
--output=n3 \
--why="SELECT ?label { ?drug a drugbank:InfluenzaDrug; rdfs:label ?label }" 
--debug --ontology=test/drugBankOnt.n3 
--ontologyFormat=n3 
--builtinTemplates=http://fuxi.googlecode.com/hg/RuleBuiltinSPARQLTemplates.n3 
--sparqlEndpoint --dlp http://www4.wiwiss.fu-berlin.de/drugbank/sparql

## Full SPARQL Algebra expression ##
BGP((?drug,rdf:type,drugbank:InfluenzaDrug),(?drug,rdfs:label,?label))
###################################
No SIP graph!
Goal/Query:  (?drug, rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.URIRef('http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/InfluenzaDrug'))
	Solving :InfluenzaDrug(?drug) {}
	Processing rule :InfluenzaDrug_f(?X) :- drugbank:affectedOrganism(?X "Influenza Virus")
		Solving :affectedOrganism(?X "Influenza Virus") {}
SELECT ?X { 	?X <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/affectedOrganism> "Influenza Virus" }-> []
FtWarning: Creation of InputSource without a URI
Evaluating TP against EDB:  SELECT ?label { 	<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00198> <http://www.w3.org/2000/01/rdf-schema#label> ?label }
Time to reach answer Oseltamivir via top-down SPARQL sip strategy: 731.135129929 milli seconds

$ FuXi \
  --output=rif \
  --safety=loose \
  --strictness=loose \
  --ddlGraph=test/drugBankDDL.n3 \
  --method=bfp \
  --output=n3 \
  --why="SELECT ?label { ?drug a drugbank:InfluenzaDrug; rdfs:label ?label }" \
  --debug \
  --ontology=test/drugBankOnt.n3 \
  --ontologyFormat=n3 \
  --builtinTemplates=http://fuxi.googlecode.com/hg/RuleBuiltinSPARQLTemplates.n3 \
  --sparqlEndpoint \
  --dlp http://www4.wiwiss.fu-berlin.de/drugbank/sparql

## Full SPARQL Algebra expression ##
BGP((?drug,rdf:type,drugbank:InfluenzaDrug),(?drug,rdfs:label,?label))
###################################
No SIP graph!
Goal/Query:  (?drug, rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.URIRef('http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/InfluenzaDrug'))
Time to build production rule (RDFLib): 0.000101089477539 seconds
	1. Forall ?X ( :InfluenzaDrug_f(?X) :- drugbank:affectedOrganism(?X "Influenza Virus") )

(a, 1)     : Forall ?X ( :InfluenzaDrug_f(?X) :- And( :OpenQuery(:InfluenzaDrug) bfp:evaluate(rule:1 1) ) )
(b, 1)     : Forall  ( bfp:evaluate(rule:1 0) :- :OpenQuery(:InfluenzaDrug) )
(c, 1, 1) : Forall ?X ( bfp:evaluate(rule:1 1) :- And( bfp:evaluate(rule:1 0) drugbank:affectedOrganism(?X "Influenza Virus") ) )
(d, 1, 1) : Forall ?X ( :affectedOrganism_query(?X "Influenza Virus") :- bfp:evaluate(rule:1 0) )

Asserting initial BFP query  :OpenQuery(:InfluenzaDrug)
Query triggered for  :affectedOrganism_query(?X "Influenza Virus") :- bfp:evaluate(rule:1 0)
FtWarning: Creation of InputSource without a URI
SELECT ?X { 	?X <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/affectedOrganism> "Influenza Virus" }-> []
	Answer to BFP triggered query drugbank:affectedOrganism(:DB00198 "Influenza Virus") : {?X: rdflib.URIRef('http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00198')}
Goal/Query:  (?drug, rdflib.URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'), rdflib.URIRef('http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/InfluenzaDrug'))
Query was not ground
Evaluating TP against EDB:  SELECT ?label { 	<http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00198> <http://www.w3.org/2000/01/rdf-schema#label> ?label }
FtWarning: Creation of InputSource without a URI
Time to reach answer Oseltamivir via top-down SPARQL sip strategy: 725.481987 milli seconds