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Foundations III: Languages, Tools and Services

Deborah McGuinness

Semantic eScience Fall 2011

Week 5, Oct. 3, 2011

Review of reading Assignment• Ontology Tool Summary, Pellet, OWL-S,

SAWSDL, Wine Agent

• Assignment 2 clarifications?

• Any comments, questions?

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Contents• Review of reading, comments, questions?

• Languages

• Tools

• Services

• Summary and assignments

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Semantic Web Methodology and Technology Development Process

• Establish and improve a well-defined methodology vision for Semantic Technology based application development

• Leverage controlled vocabularies, et c.

Use Case

Small Team, mixed skills

Analysis

Adopt Technology Approach

Leverage Technology

Infrastructure

Rapid Prototype

Open World: Evolve, Iterate,

Redesign, Redeploy

Use Tools

Science/Expert Review & Iteration

Develop model/

ontology

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Semantic Web Layers

http://www.w3.org/2003/Talks/1023-iswc-tbl/slide26-0.html, http://flickr.com/photos/pshab/291147522/

Languages• RDFS – Resource Description Framework

Schema

• OWL – Web Ontology Language OWL

• SKOS – Simple Knowledge Organization System

• RIF – Rule Interchange Framework

• SPARQL- SPARQL Protocol and RDF Query Language

• OWL-S – OWL for Services 6

RDFS• Note: While XMLS was aimed at schemas, it

has little expressive power if it is to be an ontology language– Changes format of DTDs (document schemas) to be

XML– Adds an extensible type hierarchy

• Integers, Strings, etc.

• Can define sub-types, e.g., positive integers

• RDFS is recognizable as an ontology language– Classes and properties– Sub/super-classes (and properties)– Range and domain (of properties)

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However• RDFS too weak to describe resources in sufficient

detail for many applications– No localized range and domain constraints

• Can’t say that the range of hasChild is person when applied to persons and elephant when applied to elephants

– No existence/cardinality constraints• Can’t say that all instances of person have a mother that is also a

person, or that persons have exactly 2 parents

– No transitive, inverse or symmetrical properties• Can’t say that isPartOf is a transitive property, that hasPart is the

inverse of isPartOf or that touches is symmetrical

– …

• Difficult to provide reasoning support– No “native” reasoners for non-standard semantics

– May be possible to reason via First Order axiomatisation8

OWL requirementsDesirable features identified for Web Ontology

Language:

• Extends existing Web standards – Such as XML, RDF, RDFS

• Easy to understand and use– Should be based on familiar KR idioms

• Formally specified

• Of “adequate” expressive power

• Possible to provide automated reasoning support9

The Original OWL language:• Original three species of OWL

– OWL full is union of OWL syntax and RDF– OWL DL restricted to FOL fragment (¼ DAML+OIL)– OWL Lite is “easier to implement” subset of OWL DL

• OWL DL based on SHIQ Description Logic– In fact it is equivalent to SHOIN(Dn) DL

• OWL DL Benefits from many years of Description Logic research– Well defined semantics– Formal properties well understood (complexity, decidability)– Known reasoning algorithms– Implemented systems (highly optimized)

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OWL Class Constructors

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OWL axioms

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OWL Layering

13See http://www.w3.org/TR/owl-features/ section 2 for features and relation to RDF or OWL species

OWL 2• http://www.w3.org/2007/OWL/wiki/OWL_Working_G

roup• Recommendation as of Oct. 27, 2009

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W3C OWL 2 User Documents• Document Overview - The place to start – light introduction to OWL

2 and its relationship to OWL

http://www.w3.org/TR/owl2-overview/

• New Features and Rationale - More details of the new features in OWL 2 along with their motivations

http://www.w3.org/TR/owl2-new-features/

• Primer - An introduction to OWL using a running example

http://www.w3.org/TR/owl2-primer/

• Quick Reference A brief synopsis of the features of OWL along with links into relevant documents (both to user and specification documents)

http://www.w3.org/TR/owl2-quick-reference/

• Next generation of the OWL 1 Guide - Next generation of a portion of the OWL 1 Overview combined with UMBC’s quick reference card

– Meetings: ISWC, OWLED, ESWC, Web Science, DL, Protégé, …

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Why Some Users May Care about OWL 2

• Datatype support: Many applications need more datatype support including things such as numerical comparisons (e.g., VSTO, SWEET, etc.)

• Selected additional expressive power: Different applications may need or benefit from features such as qualified cardinality.

• More support for annotations (e.g., for more support for knowledge provenance )

• Definition and support for profiles

McGuinness – SemTech June 16, 2009

OWL 2• Extends OWL with a small set of features

– That are motivated from application usage– For which semantics and reasoning techniques are well understood– That tool builders are willing and able to support

• Is fully backwards compatible with OWL: – Every OWL ontology is a valid OWL 2 ontology– Every OWL 2 ontology not using new features is a valid OWL

ontology

– OWL Lite & OWL DL are both sublanguages of OWL 2, along with the new profiles (EL, QL, RL)

• Already supported by popular OWL tools & infrastructure:– Protégé, Pellet, FaCT++, OWL API

New OWL 2 Features : Expressiveness– qualified cardinality restrictions, e.g.:

ObjectMinCardinality(2 friendOf hacker)– property chains, e.g.:

SubObjectPropertyOf(SubObjectPropertyChain(parent brother) uncle)– local reflexivity restrictions, e.g.:

ObjectExistsSelf(likes) [for narcissists]– reflexive, irreflexive, symmetric, and antisymmetric properties,

e.g.:ReflexiveObjectProperty(knows); IrreflexiveObjectProperty(husbandOf)

flowsInto rdf:type owl:IrreflexiveProperty. Nothing can flow into itself.

– disjoint properties, e.g.:DisjointObjectProperties(childOf spouseOf)

– keys, e.g.:HasKey( US-Citizen () ( a:hasSSN ) )

New OWL2 features: MetaModelling– Restricted form of metamodelling via “punning”, e.g.

subClassOf(SnowLeopard BigCat)

ClassAssertion(SnowLeopard EndangeredSpecies)

http://www.w3.org/TR/owl2-new-features/#F12:_Punning

– Annotations of axioms as well as entities, e.g.:ClassAssertion(Comment(“source: WWF”) SnowLeopard EndangeredSpecies)

– Including annotations of annotations

• Punning allowed in OWL 2 but OWL 2 DL still imposes:– Name cannot be used for both class and datatype– Name can only be used for one type of property

Annotations•Annotation Assertion

– Construct for annotation of ontology entities and anonymous individuals

• Annotation– Construct for annotation of axioms and ontologies(even annotations themselves)

• Annotations about annotation properties– SubAnnotationPropertyOf

• Syntax example: :narrow_synonymrdfs:subPropertyOf:synonym. (UC#5)

– The annotation property :narrow synonym is a subproperty of :synonym. – AnnotationPropertyDomain

• Syntax example: FMA:UWDAIDrdfs:domainFMA:AnatomicalEntity. (UC#2) – Only FMA: AnatomicalEntitycan have an FMA:UWDAID (that is, an FMA ID) – AnnotationPropertyRange

Syntax example: FMA:UWDAIDrdfs:rangexsd:positiveInteger.

New Features: Syntactic Sugar

– Disjoint unions• Shorthand for combination of disjointWith and unionOf

statements• BrainHemisphereowl:disjointUnionOf( :LeftHemisphere:Rig

htHemisphere) . • BrainHemisphereis exclusively either a :LeftHemisphere or

:RightHemisphere and cannot be both of them. • DisjointUnion(Element Earth Wind Fire Water)

– Negative assertions• States that a property does not hold for a particular

individual• NegativeObjectPropertyAssertion(Deborah hasChild Mary)• NegativeDataPropertyAssertion (Peter hasAge 21)

Profiles• OWL defines only one fragment (OWL Lite)• OWL 2 defines three different fragments with useful

computational properties– EL: polynomial time reasoning for schema and data

• Useful for ontologies with large conceptual part

– QL: fast (logspace) query answering using RDBMs via SQL

• Useful for large datasets already stored in RDBs

– RL: fast (polynomial) query answering using rule-extended DBs

• Useful for large datasets stored as RDF triples

EL (Profiles Document Source)• Supported class restrictions

–existential quantification to a class expression (ObjectSomeValuesFrom) or a data range (DataSomeValuesFrom) –existential quantification to an individual (ObjectHasValue) or a literal (DataHasValue) –self-restriction (ObjectHasSelf) –enumerations involving a singleindividual (ObjectOneOf) or a singleliteral (DataOneOf) –intersection of classes (ObjectIntersectionOf) and data ranges (DataIntersectionOf)

• Supported axioms, restricted to class restrictions–class inclusion (SubClassOf) –class equivalence (EquivalentClasses) –class disjointness(DisjointClasses) –object property inclusion (SubObjectPropertyOf) with or without property chains, and data property inclusion (SubDataPropertyOf) –property equivalence (EquivalentObjectPropertiesand EquivalentDataProperties), –transitive object properties (TransitiveObjectProperty) –reflexive object properties (ReflexiveObjectProperty) –domain restrictions (ObjectPropertyDomainand DataPropertyDomain) –range restrictions (ObjectPropertyRangeand DataPropertyRange) –assertions (SameIndividual, DifferentIndividuals, ClassAssertion, ObjectPropertyAssertion, DataPropertyAssertion, NegativeObjectPropertyAssertion, and NegativeDataPropertyAssertion) –functional data properties (FunctionalDataProperty) –keys (HasKey)

EL does NOT support• universal quantification to a class expression (ObjectAllValuesFrom) or a

data range (DataAllValuesFrom) • –cardinality restrictions (ObjectMaxCardinality, ObjectMinCardinality,

ObjectExactCardinality, DataMaxCardinality, DataMinCardinality, and DataExactCardinality)

• –disjunction (ObjectUnionOf, DisjointUnion, and DataUnionOf) • –class negation (ObjectComplementOf) • –enumerations involving more than one individual (ObjectOneOfand

DataOneOf) • –disjoint properties (DisjointObjectPropertiesand DisjointDataProperties) • –irreflexiveobject properties (IrreflexiveObjectProperty) • –inverse object properties (InverseObjectProperties) • –functional and inverse-functional object properties

(FunctionalObjectPropertyand InverseFunctionalObjectProperty) • –symmetric object properties (SymmetricObjectProperty) • –asymmetric object properties (AsymmetricObjectProperty)

QL• Supported class restrictions

–Subclass Expressions a classexistential quantification (ObjectSomeValuesFrom) where the class is limited to owl:Thingexistential quantification to a data range (DataSomeValuesFrom)

–SuperclassExpressionsa classintersection (ObjectIntersectionOf)negation (ObjectComplementOf)existential quantification to a class (ObjectSomeValuesFrom)existential quantification to a data range (DataSomeValuesFrom)

• Supported axioms, compliant with class restriction expressions–subclass axioms (SubClassOf) –class expression equivalence (EquivalentClasses) –class expression disjointness(DisjointClasses) –inverse object properties (InverseObjectProperties) –property inclusion (SubObjectPropertyOfnot involving property chains and SubDataPropertyOf) –property equivalence (EquivalentObjectPropertiesand EquivalentDataProperties) –property domain (ObjectPropertyDomainand DataPropertyDomain) –property range (ObjectPropertyRangeand DataPropertyRange) –disjoint properties (DisjointObjectPropertiesand DisjointDataProperties) –symmetric properties (SymmetricObjectProperty) –reflexive properties (ReflexiveObjectProperty) –irreflexiveproperties (IrreflexiveObjectProperty) –asymmetric properties (AsymmetricObjectProperty) –assertions other than individual equality assertions and negative

QL does not support–existential quantification to a class expression or a data range

(ObjectSomeValuesFromand DataSomeValuesFrom) in the subclass position

–self-restriction (ObjectHasSelf) –existential quantification to an individual or a literal (ObjectHasValue,

DataHasValue) –enumeration of individuals and literals (ObjectOneOf, DataOneOf) –universal quantification to a class expression or a data range

(ObjectAllValuesFrom, DataAllValuesFrom) –cardinality restrictions (ObjectMaxCardinality, ObjectMinCardinality,

ObjectExactCardinality, DataMaxCardinality, DataMinCardinality, DataExactCardinality)

–disjunction (ObjectUnionOf, DisjointUnion, and DataUnionOf) –property inclusions (SubObjectPropertyOf) involving property chains –functional and inverse-functional properties (FunctionalObjectProperty,

InverseFunctionalObjectProperty, and FunctionalDataProperty) –transitive properties (TransitiveObjectProperty) –keys (HasKey) –individual equality assertions and negative property assertions

RL–Subclass expressions

•a class other than owl:Thing•an enumeration of individuals (ObjectOneOf)•intersection of class expressions (ObjectIntersectionOf)•union of class expressions (ObjectUnionOf)•existential quantification to a class expression (ObjectSomeValuesFrom)•existential quantification to a data range (DataSomeValuesFrom)•existential quantification to an individual (ObjectHasValue)•existential quantification to a literal (DataHasValue)

–Superclassexpressions•a class other than owl:Thing•intersection of classes (ObjectIntersectionOf)•negation (ObjectComplementOf)•universal quantification to a class expression (ObjectAllValuesFrom)•existential quantification to an individual (ObjectHasValue)•at-most 0/1 cardinality restriction to a class expression (ObjectMaxCardinality0/1)•universal quantification to a data range (DataAllValuesFrom)•existential quantification to a literal (DataHasValue)•at-most 0/1 cardinality restriction to a data range (DataMaxCardinality0/1)

RL does not supportOWL 2 RL supports all axioms of OWL 2 apart

from disjoint unions of classes (DisjointUnion) and reflexive object property axioms (ReflexiveObjectProperty)

OWL 2 Documentation Roadmap

SKOS propertiesSimple Knowledge Organization System - W3C Recommendation Status on

August 18, 2009 http://www.w3.org/2004/02/skos/• skos:note

e.g. ‘Anything goes.’

• skos:definitione.g. ‘A long curved fruit with a yellow skin and soft, sweet white flesh inside.’

• skos:examplee.g. ‘A bunch of bananas.’

• skos:scopeNotee.g. ‘Historically members of a sheriff's retinue armed with pikes who escorted judges at assizes.’

• skos:historyNotee.g. ‘Deleted 1986. See now Detention, Institutionalization (Persons), or

Hospitalization.’

• skos:editorialNotee.g. ‘Confer with Mr. X. re deletion.’

• skos:changeNotee.g. ‘Promoted “love” to preferred label, demoted “affection” to alternative label, Joe

Bloggs, 2005-08-09.’

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SKOS Vocabulary Elements

• skos:mappingRelation

• skos:closeMatch

• skos:exactMatch

• skos:broadMatch

• skos:narrowMatch

• skos:relatedMatch

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SKOS Class and Property relations• S38 skos:mappingRelation, skos:closeMatch, skos:exactMatch,

skos:broadMatch, skos:narrowMatch and skos:relatedMatch are each instances of owl:ObjectProperty.

• S39 skos:mappingRelation is a sub-property of skos:semanticRelation.

• S40 skos:closeMatch, skos:broadMatch, skos:narrowMatch and skos:relatedMatch are each sub-properties of skos:mappingRelation.

• S41 skos:broadMatch is a sub-property of skos:broader, skos:narrowMatch is a sub-property of skos:narrower, and skos:relatedMatch is a sub-property of skos:related.

• S42 skos:exactMatch is a sub-property of skos:closeMatch.• S43 skos:narrowMatch is owl:inverseOf the property

skos:broadMatch.• S44 skos:relatedMatch, skos:closeMatch and skos:exactMatch are

each instances of owl:SymmetricProperty.• S45 skos:exactMatch is an instance of owl:TransitiveProperty.• http://www.w3.org/2006/07/SWD/SKOS/reference/20081001/skos.txt

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Integrity constraints

• skos:exactMatch is disjoint with each of the properties skos:broadMatch and skos:relatedMatch.

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SKOS example• <?xml version="1.0" encoding="UTF-8"?>

• <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/"

• xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"

• xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"

• xmlns:skos="http://www.w3.org/2004/02/skos/core#">

• <rdf:Description rdf:about="http://zepheira.com/examples/soa-skos#">

• <rdf:type rdf:resource="http://www.w3.org/2004/02/skos/core#ConceptScheme"/>

• <dc:title>SKOS-based service taxonomy for DevX Article</dc:title>

• <skos:hasTopConcept rdf:resource="http://zepheira.com/examples/soa-skos#Service"/>

• </rdf:Description>

• <rdf:Description rdf:about="http://zepheira.com/examples/soa-skos#Service">

• <rdf:type rdf:resource="http://www.w3.org/2000/01/rdf-schema#Class"/>

• <rdfs:comment>An rdfs:Class of services.</rdfs:comment>

• </rdf:Description>

• <rdf:Description rdf:about="http://zepheira.com/examples/soa-skos#PrintingService">

• <rdf:type rdf:resource="http://zepheira.com/examples/soa-skos#Service"/>

• <skos:narrower rdf:resource="http://zepheira.com/examples/soa-skos#LaserPrintingService"/>

• <skos:narrower rdf:resource="http://zepheira.com/examples/soa-skos#PlotterPrintingService"/>

• <skos:prefLabel>Printing Service</skos:prefLabel>

• </rdf:Description>34

SKOS example• <rdf:Description rdf:about="http://zepheira.com/examples/soa-skos#LaserPrintingService">

• <rdf:type rdf:resource="http://zepheira.com/examples/soa-skos#Service"/>

• <skos:narrower rdf:resource="http://zepheira.com/examples/soa-skos#ColorLaserPrintingService"/>

• <skos:narrower rdf:resource="http://zepheira.com/examples/soa-skos#BWLaserPrintingService"/>

• <skos:prefLabel>Laser Printing Service</skos:prefLabel>

• </rdf:Description>

• <rdf:Description rdf:about="http://zepheira.com/examples/soa-skos#PlotterPrintingService">

• <rdf:type rdf:resource="http://zepheira.com/examples/soa-skos#Service"/>

• <skos:prefLabel>Plotter Printing Service</skos:prefLabel>

• </rdf:Description>

• <rdf:Description rdf:about="http://zepheira.com/examples/soa-skos#ColorLaserPrintingService">

• <rdf:type rdf:resource="http://zepheira.com/examples/soa-skos#Service"/>

• <skos:prefLabel>Color Laser Printing Service</skos:prefLabel>

• </rdf:Description>

• <rdf:Description rdf:about="http://zepheira.com/examples/soa-skos#BWLaserPrintingService">

• <rdf:type rdf:resource="http://zepheira.com/examples/soa-skos#Service"/>

• <skos:prefLabel>Black and White Laser Printing Service</skos:prefLabel>

• </rdf:Description>

• </rdf:RDF> 35

SKOS core and RDFS/OWL• Disjoint?

– Should skos:Concept be disjoint with …• rdf:Property ?• rdfs:Class ?• owl:Class ?

• http://www.w3.org/TR/2009/REC-skos-reference-20090818/#L1045

• http://skosapi.sourceforge.net/

• Editors– ThManager http://thmanager.sourceforge.net/– SKOS API and Editor

http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-401/iswc2008pd_submission_88.pdf

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Editors• Protégé (http://protege.stanford.edu)• SWOOP (http://mindswap.org/2004/SWOOP; see

also http://www.mindswap.org/downloads/)

• Altova SemanticWorks (http://www.altova.com/download/semanticworks/semantic_web_rdf_owl_editor.html)

• SWeDE (http://owl-eclipse.projects.semwebcentral.org/InstallSwede.html), goes with Eclipse

• NeON toolkit http://neon-toolkit.org/• ThManager http://thmanager.sourceforge.net/• TopBraid Composer and other commercial tools

CMAP• CMAP Ontology Editor (COE)

– http://cmap.ihmc.us/

Protégé

•http://protege.stanford.edu/•http://protegewiki.stanford.edu/index.php/Protege-OWL•Please check version compatibility when choosing.

•Do you have plugins you like?

•(Prompt not compatible with version 4.0)

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Query• Querying knowledge representations in OWL and/or RDF

• OWL-QL (for OWL) http://projects.semwebcentral.org/projects/owl-ql/

• SPARQL for RDF http://www.sparql.org/ and http://www.w3.org/TR/rdf-sparql-query/ – W3C Recommendation as of January 15, 2008

• XQUERY (for XML)• SeRQL (for SeSAME)• RDFQuery (RDF)• Few as yet for natural language representations

(ROO – Dolbear, et al., …)

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What is Query?• http://esw.w3.org/SPARQL

• Languages– SPARQL for RDF (http://www.sparql.org/ and

http://www.w3.org/TR/rdf-sparql-query/ )– RDFQuery for RDF– SeRQL for RDF (SeSAME)– OWL-QL for OWL (

http://projects.semwebcentral.org/projects/owl-ql/ )– XQUERY for XML

• Few as yet for natural language representations (ROO – Dolbear, et al., …)

SPARQL• W3 Recommendation, Jan 2008

• SPARQL has 4 result forms:– SELECT – Return a table of results.– CONSTRUCT – Return an RDF graph, based on

a template in the query.– DESCRIBE – Return an RDF graph, based on

what the query processor is configured to return.– ASK – Ask a Boolean query.

• The SELECT form directly returns a table

• DESCRIBE and CONSTRUCT use the outcome of matching to build RDF graphs.

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SPARQL Solution Modifiers• Pattern matching produces a set of solutions.

This set can be modified in various ways:– Projection - keep only selected variables– OFFSET/LIMIT - chop the number solutions (best

used with ORDER BY)– ORDER BY - sorted results– DISTINCT - yield only one row for one

combination of variables and values.

• The solution modifiers OFFSET/LIMIT and ORDER BY always apply to all result forms.

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Query examples

PREFIX foaf: <http://xmlns.com/foaf/spec/>

SELECT ?url

FROM <bloggers.rdf>

WHERE {

?contributor foaf:name "Jon Foobar" .

?contributor foaf:weblog ?url .

}

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Returns a table in ‘url’ (can use $)

namespace

Triple patterns usingTurtle syntax

What happens• These triples together comprise a graph pattern.• The query attempts to match the triples of the graph pattern to

the model. • Each matching binding of the graph pattern's variables to the

model's nodes becomes a query solution, and the values of the variables named in the SELECT clause become part of the query results.

• In this example, the first triple in the WHERE clause's graph pattern matches a node with a foaf:name property of "Jon Foobar," and binds it to the variable named contributor.

• In the bloggers.rdf model, contributor will match the foaf:Agent blank-node at the top of the figure.

• The graph pattern's second triple matches the object of the contributor's foaf:weblog property.

• This is bound to the url variable, forming a query solution.45

Using SPARQL with Jena• Jena calls RDF graphs "models" and triples

"statements" because that is what they were called at the time the Jena API was first designed

• ARQ's query engine can also parse queries expressed in RDQL or its own internal query language. ARQ is under active development, and is not yet part of the standard Jena distribution.

• http://jena.sourceforge.net/ARQ/Tutorial/data.html• Can also use SPARQL from the command line

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com.hp.hpl.jena.query package// Open the bloggers RDF graph from the filesystem

InputStream in = new FileInputStream(new File("bloggers.rdf"));

// Create an empty in-memory model and populate it from the graph

Model model = ModelFactory.createMemModelMaker().createModel();

model.read(in,null); // null base URI, since model URIs are absolute

in.close();

// Create a new query

String queryString =

"PREFIX foaf: <http://xmlns.com/foaf/0.1/> " +

"SELECT ?url " +

"WHERE {" +

" ?contributor foaf:name \"Jon Foobar\" . " +

" ?contributor foaf:weblog ?url . " +

" }”;

Query query = QueryFactory.create(queryString);

// Execute the query and obtain results

QueryExecution qe = QueryExecutionFactory.create(query, model);

ResultSet results = qe.execSelect();

// Output query results

ResultSetFormatter.out(System.out, results, query);

// Important - free up resources used running the query

qe.close();

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More complex queries@prefix foaf: <http://xmlns.com/foaf/spec/> .

_:a foaf:name "Jon Foobar" ;

foaf:mbox <mailto:jon@foobar.xx> ;

foaf:depiction <http://foobar.xx/2005/04/jon.jpg> .

_:b foaf:name "A. N. O'Ther" ;

foaf:mbox <mailto:a.n.other@example.net> ;

foaf:depiction <http://example.net/photos/an-2005.jpg> .

_:c foaf:name "Liz Somebody" ;

foaf:mbox_sha1sum "3f01fa9929df769aff173f57dec2fe0c2290aeea"

_:d foaf:name "M Benn" ;

foaf:depiction <http://mbe.nn/pics/me.jpeg> . 48

Querying FOAF data with an optional block

PREFIX foaf: <http://xmlns.com/foaf/spec>

SELECT ?name ?depiction

WHERE {

?person foaf:name ?name .

OPTIONAL {

?person foaf:depiction ?depiction .

} .

}

| name | depiction |

| "A. N. O'Ther" | <http://example.net/photos/an-2005.jpg> |

| "Jon Foobar" | <http://foobar.xx/2005/04/jon.jpg> |

| "Liz Somebody" | |

| "M Benn" | <http://mbe.nn/pics/me.jpeg>

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Query with alternative matches, and its results

PREFIX foaf: <http://xmlns.com/foaf/spec/>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT ?name ?mbox

WHERE {

?person foaf:name ?name .

{

{ ?person foaf:mbox ?mbox } UNION { ?person foaf:mbox_sha1sum ?mbox }

}

}

| name | mbox |

| "Jon Foobar" | <mailto:jon@foobar.xx> |

| "A. N. O'Ther" | <mailto:a.n.other@example.net> |

| "Liz Somebody" | "3f01fa9929df769aff173f57dec2fe0c2290aeea" |50

Filter to retrieve RSS feed items published in April 2005

PREFIX rss: <http://purl.org/rss/1.0/>

PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

PREFIX dc: <http://purl.org/dc/elements/1.1/>

SELECT ?item_title ?pub_date

WHERE {

?item rss:title ?item_title .

?item dc:date ?pub_date .

FILTER xsd:dateTime(?pub_date) >= "2005-04-01T00:00:00Z"^^xsd:dateTime &&

xsd:dateTime(?pub_date) < "2005-05-01T00:00:00Z"^^xsd:dateTime

} 51

Find people described in two named FOAF graphs

PREFIX foaf: <http://xmlns.com/foaf/spec/>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT ?name

FROM NAMED <jon-foaf.rdf>

FROM NAMED <liz-foaf.rdf>

WHERE {

GRAPH <jon-foaf.rdf> {

?x rdf:type foaf:Person .

?x foaf:name ?name .

} .

GRAPH <liz-foaf.rdf> {

?y rdf:type foaf:Person .

?y foaf:name ?name .

} .

} 52

Which graph describes different people

PREFIX foaf: <http://xmlns.com/foaf/spec/>

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT ?name ?graph_uri

FROM NAMED <jon-foaf.rdf>

FROM NAMED <liz-foaf.rdf>

WHERE {

GRAPH ?graph_uri {

?x rdf:type foaf:Person .

?x foaf:name ?name .

}

}

| name | graph_uri |

| "Liz Somebody" | <file://.../jon-foaf.rdf> |

| "A. N. O'Ther" | <file://.../jon-foaf.rdf> |

| "Jon Foobar" | <file://.../liz-foaf.rdf> |

| "A. N. O'Ther" | <file://.../liz-foaf.rdf> | 53

Personalized feed by query filterPREFIX foaf: <http://xmlns.com/foaf/spec/>

PREFIX rss: <http://purl.org/rss/1.0/>

PREFIX dc: <http://purl.org/dc/elements/1.1/>

SELECT ?title ?known_name ?link

FROM <http://planetrdf.com/index.rdf>

FROM NAMED <phil-foaf.rdf>

WHERE {

GRAPH <phil-foaf.rdf> {

?me foaf:name "Phil McCarthy" .

?me foaf:knows ?known_person .

?known_person foaf:name ?known_name .

} .

?item dc:creator ?known_name .

?item rss:title ?title .

?item rss:link ?link .

?item dc:date ?date.

}

ORDER BY DESC[?date] LIMIT 10

54

Returning as XML• SPARQL allows query results to be returned as

XML, in a simple format known as the SPARQL Variable Binding Results XML Format.

• This schema-defined format acts as a bridge between RDF queries and XML tools and libraries.

• There are a number of potential uses for this capability. You could transform the results of a SPARQL query into a Web page or RSS feed via XSLT, access the results via XPath, or return the result document to a SOAP or AJAX client.

• To output query results as XML, use the ResultSetFormatter.outputAsXML() method, or specify --results rs/xml on the command line.

55

Final examplePREFIX dc: <http://purl.org/dc/elements/1.1/>

PREFIX rss: <http://purl.org/rss/1.0/>

SELECT ?link ?title

FROM <http://rss.slashdot.org/Slashdot/slashdotScience>

FROM <http://www.nature.com/nprot/current_issue/rss/index.html>

WHERE {

?i rss:link?link .

?i dc:date?date . FILTER (?date > "2008-08-31")

?i rss:description?desc. FILTER regex(?desc,"biolog|mathematic","i")

?i rss:title?title

} 56

SPARQL 2-page reference guide

• http://www.dajobe.org/2005/04-sparql/SPARQLreference-1.8-us.pdf

57

58

Using Protégé• SPARQL plug-in to run queries on your

ontology

59

Semantic Web with Rules• Metalog• RuleML• SWRL• WRL• Cwm• N3 - http://hydrogen.informatik.tu-cottbus.de/wiki/index.php/N3_Notation

• Jess• Jena• RIF

60

Rules - expressing logic• Notation - e.g. Horn rules

– (P1 ∧ P2 ∧ ...) → C– parent(?x,?y) ∧ brother(?y,?z) ⇒ uncle(?x,?z)

– for any X, Y and Z: if Y is a parent of X, and Z is a brother of Y then Z is the uncle of X

61

Examples from http://www.w3.org/Submission/SWRL/

• A simple use of these rules would be to assert that the combination of the hasParent and hasBrother properties implies the hasUncle property. Informally, this rule could be written as:– hasParent(?x1,?x2) ∧ hasBrother(?x2,?x3) ⇒ hasUncle(?x1,?x3)

• In the abstract syntax the rule would be written like:– Implies(Antecedent(hasParent(I-variable(x1) I-variable(x2)) hasBrother(I-variable(x2) I-variable(x3)))Consequent(hasUncle(I-variable(x1) I-variable(x3))))

• From this rule, if John has Mary as a parent and Mary has Bill as a brother then John has Bill as an uncle.

62

Examples• An even simpler rule would be to assert that Students are Persons, as in– Student(?x1) ⇒ Person(?x1).Implies(Antecedent(Student(I-variable(x1)))Consequent(Person(I-variable(x1))))

– However, this kind of use for rules in OWL just duplicates the OWL subclass facility. It is logically equivalent to write instead• Class(Student partial Person) or • SubClassOf(Student Person)

– which would make the information directly available to an OWL reasoner.

63

Rule Interchange Format (RIF)• W3 Recommendation (June 2010)

• Interlingua (similar to KIF)

• http://www.w3.org/2005/rules/wiki/RIF_Working_Group

• Tools starting to emerge

• http://www.w3.org/2005/rules/wiki/RIF_FAQ

• http://www.w3.org/TR/rif-overview/

Test an interchanged RIF rule set• testQuery(Literal) test the literal (= rule head or fact)• testNotQuery(Literal) negatively test the literal with

default negation• testNegQuery(Literal) negatively test the literal with

explicit negation• testNumberOfResults(Literal, Number) test number of results

derived for the literal = stated value• testNumberOfResults(Literal, Var, Number) test number of results for

the variable in the literal• testNumberOfResultsMore(Literal,Number) test number of results for

the literal > given value• testNumberOfResultsLess(Literal,Number) test number of results for

the literal < given value• testNumberOfResultsMore(Literal,Var,Number) test number of results for

the variable in the literal > given value• testNumberOfResultsLess(Literal,Var,Number) test number of results for

the variable in the literal < given value 64

More RIF testing• testResult(QueryLiteral,ResultLiteral) test if the second literal is

an answer of the query literal• testResults(Literal,Var,[<BindingList>]) test if the list of binding

results for the variable in the literal can be derived• testResultsOrder(Literal,Var,[<BindingList>]) test if the list of ordered

binding results for the variable in the literal can be derived• testQueryTime(Literal, MaxTime) test if the literal can be

derived in less than the stated time in milliseconds• testNotQueryTime(Literal, MaxTime) test if the literal can be

derived negatively by default in less than the stated time in milliseconds• testNegQueryTime(Literal, MaxTime) test if the literal can be

derived strongly negative in less than the stated time in milliseconds• getQueryTime(Literal, Time) get the query time for the literal• getNotQueryTime(Literal,Time) get the default negated

query time for the literal• getNegQueryTime(Literal,Time) get the explicitly negated

query time for the literal

65

Testing class membershipDocument(

Prefix(fam http://example.org/family#)

Group (

Forall ?X ?Y (

fam:isFatherOf(?Y ?X) :- And (fam:isSonOf(?X ?Y) fam:isMale(?Y) ?X#fam:Child ?Y#fam:Parent )

)

fam:isSonOf(fam:Adrian fam:Uwe)

fam:isMale(fam:Adrian)

fam:isMale(fam:Uwe)

fam:Adrian#fam:Child

fam:Uwe#fam:Parent

)

)

Conclusion: fam:isFather(fam:Uwe fam:Adrian) 66

XML for conclusion<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Document [

<!ENTITY rif "http://www.w3.org/2007/rif#">

<!ENTITY xs "http://www.w3.org/2001/XMLSchema#">

<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">

]>

<Atom xmlns="&rif;">

<op>

<Const type="&rif;iri">http://example.org/family#isFather</Const>

</op>

<args>

<Const type="&rif;iri">http://example.org/family#Uwe</Const>

<Const type="&rif;iri">http://example.org/family#Adrian</Const>

</args>

</Atom>

<!--XML document generated on Tue Dec 30 12:08:16 EST 2008-->67

Language options that you can implement

• JenaRules is based on RDF(S) and uses the triple representation of RDF descriptions (see also N3 Notation and Turtle Syntax).

68

69

Examples<ex:Driver rdf:about="http://example.com/John">

<ex:state>New York</ex:state>

<ex:hasTrainingCertificate rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</ex:hasTrainingCertificate>

</ex:Driver>

@prefix rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#

@prefix ex: http://example.com/

@prefix xs: http://www.w3.org/2001/XMLSchema#

[eligibleDriver: (?d rdf:type ex:EligibleDriver)

<-

(?d rdf:type ex:Driver)

(?d ex:state "New York")

(?d ex:hasTrainingCertificate "true"^^xs:boolean)]

Any driver living in New York and having training driver certificate is eligible for insurance.

A driver is young if has between 18 and 25 years old.

<ex:age rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">21</ex:age><br>

</ex:Driver>

@prefix rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#

@prefix ex: http://example.com/

@prefix xs: http://www.w3.org/2001/XMLSchema#

[youngDriver: (?d rdf:type ex:YoungDriver)

<-

(?d rdf:type ex:Driver)

(?d ex:age ?a)

greaterThan(?a,18)

lessThan(?a,25)]

70

Negation<ex:Driver rdf:about="http://example.com/John">

<ex:name>Jojn Smith</ex:name>

</ex:Driver>

@prefix rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#

@prefix ex: http://example.com/

[eligibleDriver: (?d rdf:type ex:TypicalDriver)

<-

(?d rdf:type ex:Driver)

noValue(?d rdf:type ex:YoungDriver)

noValue(?d rdf:type ex:SeniorDriver)]

71

Multiple rules, split disjunction<ex:Driver rdf:about="http://example.com/John">

<ex:state>Vancouver</ex:state>

<ex:accidentsNumber rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</ex:accidentsNumber>

</ex:Driver>

@prefix rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#

@prefix ex: http://example.com/

[eligibleDriver_1: (?d rdf:type ex:EligibleDriver)

<-

(?d rdf:type ex:Driver)

(?d ex:state "New York")

(?d ex:accidentsNumber ?an)

lessThan(?an,2)]

[eligibleDriver_2: (?d rdf:type ex:EligibleDriver)

<-

(?d rdf:type ex:Driver)

(?d ex:state "Vancouver")

(?d ex:accidentsNumber ?an)

lessThan(?an,2)]72

73

Using Protégé• SWRL plugin for editing rules

• Jena (instructions for running the rule engine and using inference: http://hydrogen.informatik.tu-cottbus.de/wiki/index.php/JenaRules)

Inference structure

74

Lastly and briefly• Jess rules (LISP-like)

– Jess rules engine - http://herzberg.ca.sandia.gov/jess/

– http://www.jessrules.com/jess/docs/Jess71p2.pdf

75

Summaries

• Michael Denny’s Table: (a bit out of date)

• http://www.xml.com/2004/07/14/examples/Ontology_Editor_Survey_2004_Table_-_Michael_Denny.pdf

• ESW Wiki: ttp://esw.w3.org/SemanticWebTools

77

Triple Stores• W3C’s list – worth looking at the text around

the listing as well

• http://www.w3.org/wiki/LargeTripleStores

• Jena (http://jena.sourceforge.net/)

• SeSAME/SAIL (http://www.openrdf.org/)

• KOWARI (http://www.kowari.org/) ->

• Mulgara (http://www.mulgara.org/)

• Redland (http://librdf.org/index.html)

• Many others (relational, object-relational)

78

Software development tools• Protégé, 3 or 4, w/ plug-ins - some better

than others• SWOOP (OWL analyzer – species validator,

partitioner)• Jena (http://jena.sourceforge.net/)• Eclipse (full integrated development

environment for Java; http://eclipse.org/)• Top Quadrant suite• Sandsoft (Sandpiper Software)• … see Semantic Technologies

79

Reasoners (aka Inference engines)

• Pellet **• Racer (and Racer Pro) **• SHER (IBM)

http://www.alphaworks.ibm.com/tech/sher • Medius KBS• FACT++• fuzzyDL• KAON2• MSPASS• QuOnto• Jess (for Rules)• …

80

Services• Ontologies of services, provides:

– What does the service provide for prospective clients? The answer to this question is given in the "profile," which is used to advertise the service. To capture this perspective, each instance of the class Service presents a ServiceProfile.

– How is it used? The answer to this question is given in the "process model." This perspective is captured by the ServiceModel class. Instances of the class Service use the property describedBy to refer to the service's ServiceModel.

– How does one interact with it? The answer to this question is given in the "grounding." A grounding provides the needed details about transport protocols. Instances of the class Service have a supports property referring to a ServiceGrounding.

81

Services, not standard…• Now 4 submissions to W3C

– OWL-S - http://www.w3.org/Submission/OWL-S (updated journal publication - http://springerlink.com/content/wp8q2133g5725340/ )

– SWSO/F/L - Semantic Web Services Ontology/Framework/Language - http://www.w3.org/Submission/SWSF/

– WSMO/X/L - Web Services Modeling Ontology/Exection/Language - http://www.w3.org/Submission/WSMX/ www.wsmo.org, www.wsmx.org

– SAWSDL - (WSDL-S)

82

Explanation, Proof (path to Trust)

• Proof markup language (PML)– an interlingua representation for justifications of results

produced by Semantic Web services

• Implemented in InferenceWeb (http://inference-web.org)

• CWM and N3 and theorem provers - not yet adapted to OWL-based languages

• Recent incubator group     http://www.w3.org/2005/Incubator/prov/charter

• Current working group: http://www.w3.org/2011/prov/wiki/Main_Page

83

Assignments for Week 5

• Reading:

• Reminder – look for reference list on class page: then look for

• Class 5: Reading Assignment: – Ontology Evolution (3 papers)– OWL-S editor tutorial – Download cmap if you have not already

• Assignment 2 due next Tuesday