Semantic query, rules, tools Inference, triple stores, etc

1
Semantic query, rules, tools (Inference, triple
stores, etc)

• Peter Fox (RPI)
• ESIP Winter Meeting
• Washington D.C., 2009, Jan 6, 4-530pm

2
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.

Adopt Technology Approach
Leverage Technology Infrastructure
Science/Expert Review Iteration
Rapid Prototype
Open World Evolve, Iterate, Redesign, Redeploy
Use Tools
Analysis
Use Case
Develop model/ ontology
Small Team, mixed skills
2
3
Semantic Web Layers
http//www.w3.org/2003/Talks/1023-iswc-tbl/slide26
-0.html, http//flickr.com/photos/pshab/291147522/
4
Terminology

• Ontology (n.d.). The Free On-line Dictionary of
  Computing. http//dictionary.reference.com/browse/
  ontology
• An explicit formal specification of how to
  represent the objects, concepts and other
  entities that are assumed to exist in some area
  of interest and the relationships that hold among
  them.
• Semantic Web
• An extension of the current web in which
  information is given well-defined meaning, better
  enabling computers and people to work in
  cooperation, www.semanticweb.org
• Primer http//www.ics.forth.gr/isl/swprimer/

5
Ontology Spectrum
Thesauri narrower term relation
Selected Logical Constraints (disjointness,
inverse, )
Frames (properties)
Formal is-a
Catalog/ ID
Informal is-a
Formal instance
General Logical constraints
Terms/ glossary
Value Restrs.
Originally from AAAI 1999- Ontologies Panel by
Gruninger, Lehmann, McGuinness, Uschold, Welty
updated by McGuinness. Description in
www.ksl.stanford.edu/people/dlm/papers/ontologies-
come-of-age-abstract.html
6
Ontology - declarative knowledge

• The triple subject-object-predicate
• interferometer is-a optical instrument
• Fabry-Perot is-a interferometer
• Optical instrument has focal length
• Optical instrument is-a instrument
• Instrument has instrument operating mode
• Data archive has measured parameter
• SO2 concentration is-a concentration
• Concentration is-a parameter
• A query select all optical instruments which
  have operating mode vertical
• An inference infer operating modes for a
  Fabry-Perot Interferometer which measures neutral
  temperature

7
What is Query?

• http//esw.w3.org/topic/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., )

8
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.

9
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.

10
Query examples

• PREFIX foaf lthttp//xmlns.com/foaf/0.1/gt
• SELECT ?url
• FROM ltbloggers.rdfgt
• WHERE
• ?contributor foafname "Jon Foobar" .
• ?contributor foafweblog ?url .

11
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
  foafname property of "Jon Foobar," and binds it
  to the variable named contributor.
• In the bloggers.rdf model, contributor will match
  the foafAgent blank-node at the top of the
  figure.
• The graph pattern's second triple matches the
  object of the contributor's foafweblog property.
  
• This is bound to the url variable, forming a
  query solution.

12
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

13
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().c
  reateModel()
• model.read(in,null) // null base URI, since
  model URIs are absolute
• in.close()
• // Create a new query
• String queryString
• "PREFIX foaf lthttp//xmlns.com/foaf/0.1/gt "
• "SELECT ?url "
• "WHERE "
• " ?contributor foafname \"Jon Foobar\" . "
  
• " ?contributor foafweblog ?url . "
• "
• Query query QueryFactory.create(queryString)
• // Execute the query and obtain results
• QueryExecution qe QueryExecutionFactory.create(q
  uery, model)
• ResultSet results qe.execSelect()
• // Output query results

14
More complex queries

• _at_prefix foaf lthttp//xmlns.com/foaf/0.1/gt .
• _a foafname "Jon Foobar"
• foafmbox ltmailtojon_at_foobar.xxgt
• foafdepiction lthttp//foobar.xx/2005/04/jo
  n.jpggt .
• _b foafname "A. N. O'Ther"
• foafmbox ltmailtoa.n.other_at_example.ne
  tgt
• foafdepiction lthttp//example.net/photos/a
  n-2005.jpggt .
• _c foafname "Liz Somebody"
• foafmbox_sha1sum "3f01fa9929df769aff173f57dec
  2fe0c2290aeea"
• _d foafname "M Benn"
• foafdepiction lthttp//mbe.nn/pics/me.jpeggt
  .

15
Querying FOAF data with an optional block

• PREFIX foaf lthttp//xmlns.com/foaf/0.1/gt
• SELECT ?name ?depiction
• WHERE
• ?person foafname ?name .
• OPTIONAL
• ?person foafdepiction ?depiction .
• .
• name depiction
  
• "A. N. O'Ther" lthttp//example.net/photos/an-2
  005.jpggt
• "Jon Foobar" lthttp//foobar.xx/2005/04/jon.j
  pggt
• "Liz Somebody"
  
• "M Benn" lthttp//mbe.nn/pics/me.jpeggt

16
Query with alternative matches, and its results

• PREFIX foaf lthttp//xmlns.com/foaf/0.1/gt
• PREFIX rdf lthttp//www.w3.org/1999/02/22-rdf-synt
  ax-nsgt
• SELECT ?name ?mbox
• WHERE
• ?person foafname ?name .
• ?person foafmbox ?mbox UNION ?person
  foafmbox_sha1sum ?mbox
• name mbox
  
• "Jon Foobar" ltmailtojon_at_foobar.xxgt
  
• "A. N. O'Ther" ltmailtoa.n.other_at_example
  .netgt
• "Liz Somebody" "3f01fa9929df769aff173f57dec
  2fe0c2290aeea"

17
Filter to retrieve RSS feed items published in
April 2005

• PREFIX rss lthttp//purl.org/rss/1.0/gt
• PREFIX xsd lthttp//www.w3.org/2001/XMLSchemagt
• PREFIX dc lthttp//purl.org/dc/elements/1.1/gt
• SELECT ?item_title ?pub_date
• WHERE
• ?item rsstitle ?item_title .
• ?item dcdate ?pub_date .
• FILTER xsddateTime(?pub_date) gt
  "2005-04-01T000000Z"xsddateTime
• xsddateTime(?pub_date) lt
  "2005-05-01T000000Z"xsddateTime

18
Find people described in two named FOAF graphs

• PREFIX foaf lthttp//xmlns.com/foaf/0.1/gt
• PREFIX rdf lthttp//www.w3.org/1999/02/22-rdf-synt
  ax-nsgt
• SELECT ?name
• FROM NAMED ltjon-foaf.rdfgt
• FROM NAMED ltliz-foaf.rdfgt
• WHERE
• GRAPH ltjon-foaf.rdfgt
• ?x rdftype foafPerson .
• ?x foafname ?name .
• .
• GRAPH ltliz-foaf.rdfgt
• ?y rdftype foafPerson .
• ?y foafname ?name .
• .

19
Which graph describes different people

• PREFIX foaf lthttp//xmlns.com/foaf/0.1/gt
• PREFIX rdf lthttp//www.w3.org/1999/02/22-rdf-synt
  ax-nsgt
• SELECT ?name ?graph_uri
• FROM NAMED ltjon-foaf.rdfgt
• FROM NAMED ltliz-foaf.rdfgt
• WHERE
• GRAPH ?graph_uri
• ?x rdftype foafPerson .
• ?x foafname ?name .
• name graph_uri
  
• "Liz Somebody" ltfile//.../jon-foaf.rdfgt
  
• "A. N. O'Ther" ltfile//.../jon-foaf.rdfgt
  
• "Jon Foobar" ltfile//.../liz-foaf.rdfgt
  
• "A. N. O'Ther" ltfile//.../liz-foaf.rdfgt
  

20
Personalized feed by query filter

• PREFIX foaf lthttp//xmlns.com/foaf/0.1/gt
• PREFIX rss lthttp//purl.org/rss/1.0/gt
• PREFIX dc lthttp//purl.org/dc/elements/1.1/gt
• SELECT ?title ?known_name ?link
• FROM lthttp//planetrdf.com/index.rdfgt
• FROM NAMED ltphil-foaf.rdfgt
• WHERE
• GRAPH ltphil-foaf.rdfgt
• ?me foafname "Phil McCarthy" .
• ?me foafknows ?known_person .
• ?known_person foafname ?known_name .
• .
• ?item dccreator ?known_name .
• ?item rsstitle ?title .
• ?item rsslink ?link .
• ?item dcdate ?date.
• ORDER BY DESC?date LIMIT 10

21
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.

22
Final example

• PREFIX dc lthttp//purl.org/dc/elements/1.1/gt
• PREFIX rss lthttp//purl.org/rss/1.0/gt
• SELECT ?link ?title
• FROM lthttp//rss.slashdot.org/Slashdot/slashdotSci
  encegt
• FROM lthttp//www.nature.com/nprot/current_issue/rs
  s/index.htmlgt
• WHERE
• ?i rsslink?link .
• ?i dcdate?date . FILTER (?date gt "2008-08-31")
• ?i rssdescription?desc. FILTER
  regex(?desc,"biolog mathematic","i")
• ?i rsstitle?title

23
2-page reference guide

• http//www.dajobe.org/2005/04-sparql/SPARQLreferen
  ce-1.8-us.pdf

24
Using Protégé

• SPARQL plug-in to run queries on your ontology

25
Semantic Web with Rules

• Metalog
• RuleML
• SWRL
• WRL
• Cwm
• N3 - http//hydrogen.informatik.tu-cottbus.de/wiki
  /index.php/N3_Notation
• Jess
• Jena
• RIF

26
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

27
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.

28
Examples

• An even simpler rule would be to assert that
  Students are Persons, as in
• Student(?x1) ? Person(?x1).Implies(Antecedent(Stud
  ent(I-variable(x1)))Consequent(Person(I-variable(x
  1))))
• 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.

29
Rule Interchange Format (RIF)

• Leading candidate for W3 Recommendation
• Interlingua (similar to KIF)
• http//www.w3.org/2005/rules/wiki/RIF_Working_Grou
  p
• Tools starting (just) to emerge

30
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 gt given value
• testNumberOfResultsLess(Literal,Number) test
  number of results for the literal lt given value
• testNumberOfResultsMore(Literal,Var,Number) test
  number of results for the variable in the literal
  gt given value
• testNumberOfResultsLess(Literal,Var,Number) test
  number of results for the variable in the literal
  lt given value

31
More RIF testing

• testResult(QueryLiteral,ResultLiteral)
  test if the second literal is an answer of the
  query literal
• testResults(Literal,Var,ltBindingListgt)
  test if the list of binding results for the
  variable in the literal can be derived
• testResultsOrder(Literal,Var,ltBindingListgt)
  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

32
Testing class membership

• Document(
• Prefix(fam http//example.org/family)
• Group (
• Forall ?X ?Y (
• famisFatherOf(?Y ?X) - And
  (famisSonOf(?X ?Y) famisMale(?Y) ?XfamChild
  ?YfamParent )
• )
• famisSonOf(famAdrian famUwe)
• famisMale(famAdrian)
• famisMale(famUwe)
• famAdrianfamChild
• famUwefamParent
• )
• )
• Conclusion famisFather(famUwe famAdrian)

33
XML for conclusion

• lt?xml version"1.0" encoding"UTF-8"?gt
• lt!DOCTYPE Document
• lt!ENTITY rif "http//www.w3.org/2007/rif"gt
• lt!ENTITY xs "http//www.w3.org/2001/XMLSchema
  "gt
• lt!ENTITY rdf "http//www.w3.org/1999/02/22-rdf-
  syntax-ns"gt
• gt
• ltAtom xmlns"rif"gt
• ltopgt
• ltConst type"rifiri"gthttp//example.org/fa
  milyisFatherlt/Constgt
• lt/opgt
• ltargsgt
• ltConst type"rifiri"gthttp//example.org/fa
  milyUwelt/Constgt
• ltConst type"rifiri"gthttp//example.org/fa
  milyAdrianlt/Constgt
• lt/argsgt
• lt/Atomgt
• lt!--XML document generated on Tue Dec 30 120816
  EST 2008--gt

34
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).

35
Examples

• ltexDriver rdfabout"http//example.com/John"gt
• ltexstategtNew Yorklt/exstategt
• ltexhasTrainingCertificate rdfdatatype"http//
  www.w3.org/2001/XMLSchemaboolean"gttruelt/exhasTra
  iningCertificategt
• lt/exDrivergt
• _at_prefix rdf http//www.w3.org/1999/02/22-rdf-synt
  ax-ns
• _at_prefix ex http//example.com/
• _at_prefix xs http//www.w3.org/2001/XMLSchema
• eligibleDriver (?d rdftype exEligibleDriver)
• lt-
• (?d rdftype exDriver)
• (?d exstate "New York")
• (?d exhasTrainingCertificate
  "true"xsboolean)
• Any driver living in New York and having training
  driver certificate is eligible for insurance.

36
A driver is young if has between 18 and 25 years
old.

• ltexage rdfdatatype"http//www.w3.org/2001/XMLS
  chemainteger"gt21lt/exagegtltbrgt
• lt/exDrivergt
• _at_prefix rdf http//www.w3.org/1999/02/22-rdf-synt
  ax-ns
• _at_prefix ex http//example.com/
• _at_prefix xs http//www.w3.org/2001/XMLSchema
• youngDriver (?d rdftype exYoungDriver)
• lt-
• (?d rdftype exDriver)
• (?d exage ?a)
• greaterThan(?a,18)
• lessThan(?a,25)

37
Negation

• ltexDriver rdfabout"http//example.com/John"gt
• ltexnamegtJojn Smithlt/exnamegt
• lt/exDrivergt
• _at_prefix rdf http//www.w3.org/1999/02/22-rdf-synt
  ax-ns
• _at_prefix ex http//example.com/
• eligibleDriver (?d rdftype exTypicalDriver)
• lt-
• (?d rdftype exDriver)
• noValue(?d rdftype
  exYoungDriver)
• noValue(?d rdftype
  exSeniorDriver)

38
Multiple rules, split disjunction

• ltexDriver rdfabout"http//example.com/John"gt
• ltexstategtVancouverlt/exstategt
• ltexaccidentsNumber rdfdatatype"http//www.w3.
  org/2001/XMLSchemainteger"gt1lt/exaccidentsNumbergt
  
• lt/exDrivergt
• _at_prefix rdf http//www.w3.org/1999/02/22-rdf-synt
  ax-ns
• _at_prefix ex http//example.com/
• eligibleDriver_1 (?d rdftype
  exEligibleDriver)
• lt-
• (?d rdftype exDriver)
• (?d exstate "New York")
• (?d exaccidentsNumber ?an)
• lessThan(?an,2)
• eligibleDriver_2 (?d rdftype
  exEligibleDriver)
• lt-
• (?d rdftype exDriver)
• (?d exstate "Vancouver")
• (?d exaccidentsNumber ?an)
• lessThan(?an,2)

39
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)

40
Inference structure
41
Lastly and briefly

• Jess rules (LISP-like)
• Jess rules engine - http//herzberg.ca.sandia.gov/
  jess/
• http//www.jessrules.com/jess/docs/Jess71p2.pdf

42
Implementation

• Cover language representation choices, and
  knowledge engineering
• Pull apart the use case
• Tools and services
• Architecture considerations and design choices

43
Languages

• OWL
• RDFS
• SKOS
• RIF
• SPARQL
• OWL-S

44
RDFS

• Note XMLS not 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 recognisable as an ontology language
• Classes and properties
• Sub/super-classes (and properties)
• Range and domain (of properties)

45
However

• RDFS too weak to describe resources in sufficient
  detail
• No localized range and domain constraints
• Cant say that the range of hasChild is person
  when applied to persons and elephant when applied
  to elephants
• No existence/cardinality constraints
• Cant 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
• Cant 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
  axiomatisation

46
OWL requirements

• Desirable 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 support

47
The OWL language

• Three species of OWL
• OWL full is union of OWL syntax and RDF
• OWL DL restricted to FOL fragment (¼ DAMLOIL)
• OWL Lite is easier to implement subset of OWL
  DL
• Semantic layering
• OWL DL ¼ OWL full within DL fragment
• DL semantics officially definitive
• OWL DL based on SHIQ Description Logic
• In fact it is equivalent to SHOIN(Dn) DL
• OWL DL Benefits from many years of DL research
• Well defined semantics
• Formal properties well understood (complexity,
  decidability)
• Known reasoning algorithms
• Implemented systems (highly optimized)

48
(No Transcript)
49
OWL Class Constructors
50
OWL axioms
51
SKOS properties

• skosnote
• e.g. Anything goes.
• skosdefinition
• e.g. A long curved fruit with a yellow skin and
  soft, sweet white flesh inside.
• skosexample
• e.g. A bunch of bananas.
• skosscopeNote
• e.g. Historically members of a sheriff's retinue
  armed with pikes who escorted judges at assizes.
• skoshistoryNote
• e.g. Deleted 1986. See now Detention,
  Institutionalization (Persons), or
  Hospitalization.
• skoseditorialNote
• e.g. Confer with Mr. X. re deletion.
• skoschangeNote
• e.g. Promoted love to preferred label, demoted
  affection to alternative label, Joe Bloggs,
  2005-08-09.

52
SKOS core and RDFS/OWL

• Disjoint?
• Should skosConcept be disjoint with
• rdfProperty ?
• rdfsClass ?
• owlClass ?
• DL?
• Should SKOS Core be an OWL DL ontology?
• Means not allowing flexibility in range of
  documentation props
• It is now (2008)!

53
OWL 2

• http//www.w3.org/2007/OWL/wiki/OWL_Working_Group
• http//www.w3.org/2007/OWL/wiki/ImageOwl2-refcard
  _2008-09-24.pdf

54
Tutorial Summary

• Many different options for ontology querying -
  none are standard
• RDF query is most advanced
• Inference needs and choice will depend on
  descriptive requirements (e.g. DL, Full, RDF,
  etc.)