![Thea model implementationAxioms Extensional Prolog predicates / facts subClassOf(’http://example.org#Human’,’http://example.org#Mammal’).equivalentClasses([forebrain_neuron, intersectionOf([neuron, someValuesFrom(partof,forebrain) ]) ]).Expressions defined as Prolog termsLists for variable number arguments More programmatic convenience predicates (Intentional)axiom(A) :- classAxiom(A).axiom(A) :- propertyAxiom(A).…property(A) :- dataProperty(A).property(A) :- objectProperty(A).property(A) :- annotationProperty(A).ontologyAxiom(Ontology, Axiom) (Extensional)relates Axioms to specific OntologyAnnotations not as axiom arguments but as separate facts: annotation(Axiom, AnnotationProperty, AnnotationValue) (Extensional)10](https://image.slidesharecdn.com/theaslideshare-100329164242-phpapp01/85/Thea-Processing-OWL-Ontologies-An-application-of-logic-programming-10-320.jpg)
![Thea OWL Parser - Serializer12Parse: owl_parse_rdf(+URI,+Opts:list), owl_parse_xml(File,_Opts), owl_parse_manchester_syntax_file(File,_Opts)options for imports, clear rdf graph, clear axioms owl_repository(URI, LocalURI)Implements owl2_io:load_axioms_hook(File,[owl|mansyn|owlx],Opts)Serialise: owl_generate_rdf(+FileName,+RDF_Load_Mode)Save Axioms as Prolog facts Load Axioms from Prolog files (consult).Possible extensions:Save and Load to/from external ‘OWL-aware’ databases: e.g. OWLgress](https://image.slidesharecdn.com/theaslideshare-100329164242-phpapp01/85/Thea-Processing-OWL-Ontologies-An-application-of-logic-programming-12-320.jpg)
![Manipulate OWL ontologies14Programmatic processing or scripting of ontologies for tasks that would be tedious and repetitive to do by hand:Enforce disjointUnion with exceptionssetof(X,(subClassOf(X,Y), \+ annotationAssertion(status,X,unvetted)), Xs),assert_axiom(disjointUnion(Y,Xs))Populate Abox: generate Axioms from external data: read(Stream, PVTerm), PVTerm :=.. [C,I|PVs],assert_axiom(classAssertion(C,I),forall(member(P-V,PVs), assert_axiom(propertyAssertion(P,I,V)),fail.Assumes Stream contains terms of the form: Class(IndividualID, Property1-Value1, …, PropertyN-ValueN).](https://image.slidesharecdn.com/theaslideshare-100329164242-phpapp01/85/Thea-Processing-OWL-Ontologies-An-application-of-logic-programming-14-320.jpg)
![OWL Link support18Client ApplicationOWL ReasonerRequestResponseXML based Interface based on OWL2 / XML* Successor to DIG, Tell* and Ask requests.Results translated to AxiomsExample:% owl_link(+ReasonerURL, +Request:list, -Response:list, +Options:list)… tell('http://owllink.org/examples/KB_1', [subClassOf('B','A'), subClassOf('C','A'), equivalentClasses(['D','E']), classAssertion('A','iA'), subClassOf('C','A') ]),getAllClasses('http://owllink.org/examples/KB_1'),getEquivalentClasses('http://owllink.org/examples/KB_1','D'),setOfClasses([], [owl:Thing, C, B, E, A, D]), setOfClasses([], [E, D]),](https://image.slidesharecdn.com/theaslideshare-100329164242-phpapp01/85/Thea-Processing-OWL-Ontologies-An-application-of-logic-programming-18-320.jpg)
![Thea RL rule reasoning20RL Profile, RL/RDF rules:Scalable reasoning, trade full expressivity of the language for efficiency.Syntactic subset of OWL 2 which is amenable to implementation using rule-based technologies partial axiomatization of the OWL 2 RDF-Based Semantics in the form of first-order implications inspired by Description Logic ProgramsImplementationDeclarative rule definition (entailments): entails(Rule, AntecedentList, ConsequenttList) entails(prp-dom, [propertyDomain(P,C),propertyAssertion(P,X,_)],[classAssertion(C,X)]).entails(prp-rng, [propertyRange(P,C),propertyAssertion(P,_,Y)],[classAssertion(C,Y)]).Forward Chaining, Crude non-optimized, Repeat cycle until nothing has been entailedforall((entails(Rule,Antecedants,Consequents), hold(Antecedants),member(Consequent,Consequents)), assert_u(entailed(Consequent,Rule,Antecedants)).Backward Chaining %% is_entailed(+Axiom,-Explanation) is nondet% Axiom is entailed if either holds or is a consequent in an% entails/3 rule and all the antecedants are entailed.Simulates tabling: If an Axiom has been entailed it is not tried again to revents endless loops for e.g. s :- s, t.](https://image.slidesharecdn.com/theaslideshare-100329164242-phpapp01/85/Thea-Processing-OWL-Ontologies-An-application-of-logic-programming-20-320.jpg)
![SWRL implementation21Semantic Web Rules.To extend the set of OWL axioms to include Horn-like rules. It thus enables Horn-like rules to be combined with an OWL knowledge base. From (SWRL submission spec)Thea implementationImplies/2 fact to hold rules: implies(?Antecedent:list(swrlAtom), ?Consequent:list(swrlAtom))Convert a prolog clause to SWRL ruleConvert an SWRL rule to OWL axioms?- prolog_clause_to_swrl_rule((hasUncle(X1,X3):- hasParent(X1,X2),hasBrother(X2,X3)),SWRL),swrl_to_owl_axioms(SWRL,Axiom).X1 = v(1), X3 = v(2), X2 = v(3),SWRL = implies(['_d:hasParent'(v(1), v(3)), '_d:hasBrother'(v(3), v(2))], '_d:hasUncle'(v(1), v(2))),Axiom = [subPropertyOf(propertyChain(['_d:hasParent', '_d:hasBrother']), '_d:hasUncle')].](https://image.slidesharecdn.com/theaslideshare-100329164242-phpapp01/85/Thea-Processing-OWL-Ontologies-An-application-of-logic-programming-21-320.jpg)
![DCGterm(T) --> qual_expr(T) ; anat_expr(T).qual_expr(Q and qualityOf some A) --> qual(Q),[of],anat_expr(A).anat_expr(P and partOf some W) --> anat(W),anat_expr(P).anat_expr(A) --> anat(A).anat(A) --> {entailed(subClassOf(A,anatomical_entity)), labelAnnotation_value(A,Label)}, [Label].qual(Q) --> {entailed(subClassOf(Q,quality)), labelAnnotation_value(Q,Label)}, [Label].Non-determinisim of prolog to generate multiple values.](https://image.slidesharecdn.com/theaslideshare-100329164242-phpapp01/85/Thea-Processing-OWL-Ontologies-An-application-of-logic-programming-32-320.jpg)
Thea: Processing OWL Ontologies - An application of logic programming
- 1. Processing OWL2 ontologies using Thea: An application of logic programmingMarch 2010Vangelis Vassiliadissemanticweb.gr1
- 2. Contents - OutlineWhy – MotivationContext: Semantic Web Applications ToolsOWL Tool survey – What we do with themModel, I/O (Parser / Serialisation), Query, Manipulate, Reasoning (Inference)What – can we do with TheaUse of Prolog as an application programming language (host language), rather than as an OWL reasoning engineGet OWL ontologies (ABOX + TBOx) in a prolog program.Use them: Query – Reason Script operationsBuild applicationsHow – ImplementationApplication examples - potential2
- 3. Motivation3Original 2000 stack2008 stack
- 4. OWL Tools4
- 6. Why Prolog?Fact database (Store)Thea uses Prolog as a host programming language, not as a reasoning system, butCan also be used as a Rule-based system. (Reason)SLD resolution, backward chaining.Declarative features, pattern matching (Query)Scripting language – (Manipulation)SWI-Prolog implementation, Semweb package, efficient RDF library (Parse – Serialize) (Load, Save)Http servers Own experience6
- 7. Thea projectProlog library, organized in modules.Depends heavily on SWI-prolog libraries RDF/XML parsing, serializations, http-clientDevelopment HistoryStarted 2004Version 0.5.5 (final for OWL1) in 2006 / SourceForgeMajor redesign for OWL2 in 2009 (presented in OWLED 2009) / GithubCirca 2000 downloads.OWL2 axioms as Prolog facts based on the OWL functional syntax.Extensions / libraries to support:java OWL APISWRLtranslation to DLPRL Reasoning (Forward and backward chaining)OWLLink – act as an OWLLink client.Small set of applications / demos Minimum documentation7
- 9. OWL Functional-Style Syntax and Structural SpecificationOntology as a set of AxiomsAxiom := Declaration | ClassAxiom | ObjectPropertyAxiom | DataPropertyAxiom | HasKey | Assertion | AnnotationAxiomDeclaration := 'Declaration' '(' axiomAnnotations Entity ')‘Entity := 'Class' '(' Class ')' | 'Datatype' '(' Datatype ')' | 'ObjectProperty' '(' ObjectProperty ')' | 'DataProperty' '(' DataProperty ')' | 'AnnotationProperty' '(' AnnotationProperty ')' | 'NamedIndividual' '(' NamedIndividual ')‘ClassAxiom := SubClassOf | EquivalentClasses | DisjointClasses | DisjointUnionSubClassOf := 'SubClassOf' '(' axiomAnnotationssubClassExpressionsuperClassExpression ')‘ClassExpression := Class | ObjectIntersectionOf …ObjectIntersectionOf := 'IntersectionOf' '(' ClassExpressionClassExpression { ClassExpression } ')'9SubClassOf(’http://example.org#Human’ ’http://example.org#Mammal’).EquivalentClasses(forebrain_neuron IntersectionOf(neuronSomeValuesFrom(partOf forebrain)))
- 10. Thea model implementationAxioms Extensional Prolog predicates / facts subClassOf(’http://example.org#Human’,’http://example.org#Mammal’).equivalentClasses([forebrain_neuron, intersectionOf([neuron, someValuesFrom(partof,forebrain) ]) ]).Expressions defined as Prolog termsLists for variable number arguments More programmatic convenience predicates (Intentional)axiom(A) :- classAxiom(A).axiom(A) :- propertyAxiom(A).…property(A) :- dataProperty(A).property(A) :- objectProperty(A).property(A) :- annotationProperty(A).ontologyAxiom(Ontology, Axiom) (Extensional)relates Axioms to specific OntologyAnnotations not as axiom arguments but as separate facts: annotation(Axiom, AnnotationProperty, AnnotationValue) (Extensional)10
- 11. Thea OWL Parser - Serializer11
- 12. Thea OWL Parser - Serializer12Parse: owl_parse_rdf(+URI,+Opts:list), owl_parse_xml(File,_Opts), owl_parse_manchester_syntax_file(File,_Opts)options for imports, clear rdf graph, clear axioms owl_repository(URI, LocalURI)Implements owl2_io:load_axioms_hook(File,[owl|mansyn|owlx],Opts)Serialise: owl_generate_rdf(+FileName,+RDF_Load_Mode)Save Axioms as Prolog facts Load Axioms from Prolog files (consult).Possible extensions:Save and Load to/from external ‘OWL-aware’ databases: e.g. OWLgress
- 13. Query OWL ontologies13Simply use Prolog’s declarative pattern matching and symbol manipulation:Tbox:- class(X).:- subClassOf(X,Y).:- class(X), equivalentClasses(Set), select(X,Set,Equivalents).:- propertyDomain(Property,Domain).:- findall(X, subClassOf(Y,X),Superclasses).subclass(X,X).subclass(X,Y) :- owl2_model:subClassOf(X,Z),subclass(Y,Z). (!cyclic graphs)Abox:- classAssertion(C,I).:- propertyAssertion(P,I,V).:- findall(I, classAssertion(C,I),Individuals).:- class(C),aggregate(count,I,classAssertion(C,I),Num).…
- 14. Manipulate OWL ontologies14Programmatic processing or scripting of ontologies for tasks that would be tedious and repetitive to do by hand:Enforce disjointUnion with exceptionssetof(X,(subClassOf(X,Y), \+ annotationAssertion(status,X,unvetted)), Xs),assert_axiom(disjointUnion(Y,Xs))Populate Abox: generate Axioms from external data: read(Stream, PVTerm), PVTerm :=.. [C,I|PVs],assert_axiom(classAssertion(C,I),forall(member(P-V,PVs), assert_axiom(propertyAssertion(P,I,V)),fail.Assumes Stream contains terms of the form: Class(IndividualID, Property1-Value1, …, PropertyN-ValueN).
- 15. Reasoning with OWL 15What is Inference?Broadly speaking, inference on the Semantic Web can be characterized by discovering new relationships. On the Semantic Web, data is modeled as a set of (named) relationships between resources. “Inference” means that automatic procedures can generate new relationships based on the data and based on some additional information in the form of a vocabulary, e.g., a set of rules. Whether the new relationships are explicitly added to the set of data, or are returned at query time, is an implementation issue.From (www.w3c.org) SW activityOWL ReasoningConsistency checkingHierarchy classification Individual classificationOWL (DL) vs. Logic Programming theoretical issues Tableaux algorithms (satisfiability checking).Open world vs. Closed world assumptionNegation as Failure and MonotonicityUnique Name Assumption
- 17. OWLAPI via jpl17JPL is a SWI library to use java from within SWI prolog:Jpl_new(+Class, +Args, -Value)Jpl_call(+Class, +Method, +Args, -RetunrValue)Examplesusing OWLAPI to save files owl_parse_rdf('testfiles/Hydrology.owl'), % parse using prolog/theacreate_factory(Man,Fac),build_ontology(Man,Fac,Ont),save_ontology(Man,Ont,'file:///tmp/foo'). % save using owlapiUsing external pellet reasonercreate_reasoner(Man,pellet,Reasoner),create_factory(Man,Fac),build_ontology(Man,Fac,Ont),reasoner_classify(Reasoner,Man,Ont),save_ontology(Man,Ont,'file:///tmp/foo').writeln(classifying), reasoner_classify(Reasoner,Man,Ont), writeln(classified),class(C), writeln(c=C),reasoner_subClassOf(Reasoner,Fac,C,P), writeln(p=P).
- 18. OWL Link support18Client ApplicationOWL ReasonerRequestResponseXML based Interface based on OWL2 / XML* Successor to DIG, Tell* and Ask requests.Results translated to AxiomsExample:% owl_link(+ReasonerURL, +Request:list, -Response:list, +Options:list)… tell('http://owllink.org/examples/KB_1', [subClassOf('B','A'), subClassOf('C','A'), equivalentClasses(['D','E']), classAssertion('A','iA'), subClassOf('C','A') ]),getAllClasses('http://owllink.org/examples/KB_1'),getEquivalentClasses('http://owllink.org/examples/KB_1','D'),setOfClasses([], [owl:Thing, C, B, E, A, D]), setOfClasses([], [E, D]),
- 19. Description Logic Programs19Grossof and Horrocs, define mapping rules between DL and LPExample An ontology which contains the axioms: subClassOf(cat, mammal). classAssertion(cat, mr_whiskers). inverseProperties(likes,liked_by).will be converted to a program such as: mammal(X) :- cat(X). cat(mr_whiskers). likes(X,Y) :- liked_by(Y,X). liked_by(X,Y) :- likes(Y,X).
- 20. Thea RL rule reasoning20RL Profile, RL/RDF rules:Scalable reasoning, trade full expressivity of the language for efficiency.Syntactic subset of OWL 2 which is amenable to implementation using rule-based technologies partial axiomatization of the OWL 2 RDF-Based Semantics in the form of first-order implications inspired by Description Logic ProgramsImplementationDeclarative rule definition (entailments): entails(Rule, AntecedentList, ConsequenttList) entails(prp-dom, [propertyDomain(P,C),propertyAssertion(P,X,_)],[classAssertion(C,X)]).entails(prp-rng, [propertyRange(P,C),propertyAssertion(P,_,Y)],[classAssertion(C,Y)]).Forward Chaining, Crude non-optimized, Repeat cycle until nothing has been entailedforall((entails(Rule,Antecedants,Consequents), hold(Antecedants),member(Consequent,Consequents)), assert_u(entailed(Consequent,Rule,Antecedants)).Backward Chaining %% is_entailed(+Axiom,-Explanation) is nondet% Axiom is entailed if either holds or is a consequent in an% entails/3 rule and all the antecedants are entailed.Simulates tabling: If an Axiom has been entailed it is not tried again to revents endless loops for e.g. s :- s, t.
- 21. SWRL implementation21Semantic Web Rules.To extend the set of OWL axioms to include Horn-like rules. It thus enables Horn-like rules to be combined with an OWL knowledge base. From (SWRL submission spec)Thea implementationImplies/2 fact to hold rules: implies(?Antecedent:list(swrlAtom), ?Consequent:list(swrlAtom))Convert a prolog clause to SWRL ruleConvert an SWRL rule to OWL axioms?- prolog_clause_to_swrl_rule((hasUncle(X1,X3):- hasParent(X1,X2),hasBrother(X2,X3)),SWRL),swrl_to_owl_axioms(SWRL,Axiom).X1 = v(1), X3 = v(2), X2 = v(3),SWRL = implies(['_d:hasParent'(v(1), v(3)), '_d:hasBrother'(v(3), v(2))], '_d:hasUncle'(v(1), v(2))),Axiom = [subPropertyOf(propertyChain(['_d:hasParent', '_d:hasBrother']), '_d:hasUncle')].
- 22. Comparison with other systemsSPARQLNo means of updating dataToo RDF-centric for querying complex TboxesLack of ability to name queries (as in relational views)Lack of aggregate queriesLack of programmabilityBut … extensions (SPARQL update)OPPL (DSL):Simple, SQL – likeIn Protégé…Thea offers a complete programming language.22
- 23. Comparison with OWLAPIOWLAPI: Full featured.Mature.Java API (OO language)Thea: declarative.offers bridge via JPL.easy scripting23Memory usageLoad time (secs)
- 24. Applications OBO label generation (Bioinformatics)eLevator (Product configuration)Open Calais (Semantic Web)Linked data (Semantic Web)24
- 25. ConsumersCustomersConfigurationEngine ServiceeLevatorCustomer PortalCustomer eServicesFinancial dataOrder statusOrder e-guideEnterprise SystemPLM, CRM, ERPAccounting…OrderEntryElevator Cabin configuration Modeling and VisualizationEnterpriseInternet25ASP / SaaS
- 28. Bioinformatics label generation28Challenges in OBO: maintaining consistent class labels that conform to community norms.
- 29. OWL + Prolog Definite Clause Grammars (DCGs) to auto-generate labels or suggestions for labels. Example
- 30. OWL Class: length and qualityOf some (axon and partOf some pyramidal_neuron)
- 31. Derive label length of pyramidal neuron axon.
- 32. DCGterm(T) --> qual_expr(T) ; anat_expr(T).qual_expr(Q and qualityOf some A) --> qual(Q),[of],anat_expr(A).anat_expr(P and partOf some W) --> anat(W),anat_expr(P).anat_expr(A) --> anat(A).anat(A) --> {entailed(subClassOf(A,anatomical_entity)), labelAnnotation_value(A,Label)}, [Label].qual(Q) --> {entailed(subClassOf(Q,quality)), labelAnnotation_value(Q,Label)}, [Label].Non-determinisim of prolog to generate multiple values.
- 33. Useful for automatically generating labels to be indexed for text search.
- 34. The same grammars used to parse controlled natural language expressions.Open Calais 29Web Service by Thomson Reuters. Analyses content (from URLs, or POSTed text) using NLP and semantic techniquesREST interface.Prolog Thea wrapperAccess service from within PrologAccess and process Calais ontology (Tbox) and returned entities (Abox) with TheaOpen CalaisServiceThea Open Calais clientLoad and Parse Ontology (OWL file)Post Content (File, text or URL)RDF responseMarkup Elements(Entities, Relationships) and Metadata
- 36. Linked data31
- 37. Linked dataUse URIs as names for things Use HTTP URIs so that people can look up those names. When someone looks up a URI, provide useful information, using the standards (RDF, SPARQL) Include links to other URIs. so that they can discover more things. 32
- 38. Conclusions Status and Next stepsOWL2 support within PrologFull support of OWL2 structural syntaxEasy programmatic access to query and process Ontologies within Prolog.Import and export to different formatsModules for external reasoning supportNext StepsImprovements in efficiencyComplete modules (other I/Os, Reasoners etc)Complete documentationPortability (other Prolog systems)Use and feedback from the community… Applications33