cse-291: ontologies in data integration department of computer science & engineering university...
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CSE-291: Ontologies in Data Integration
Department of Computer Science & Engineering Department of Computer Science & Engineering University of California, San DiegoUniversity of California, San Diego
CSE-291: Ontologies in Data IntegrationCSE-291: Ontologies in Data IntegrationSpring 2003Spring 2003
Bertram LudBertram Ludää[email protected]@SDSC.EDU
CSE-291: Ontologies in Data Integration
OutlineOutline
• Wrapping up last weekWrapping up last week• What is a representation?What is a representation?• [Thesauri, Topic Maps][Thesauri, Topic Maps]• Predicate Logic PrimerPredicate Logic Primer• Description logicsDescription logics• [RDF & RDF Schema][RDF & RDF Schema]• [F-logic][F-logic]• Topic SelectionTopic SelectionSpecial thanksSpecial thanks: : • Alexander Maedche, Steffen Staab:Alexander Maedche, Steffen Staab:
– ECAI’2002 Tutorial on Ontologies
CSE-291: Ontologies in Data Integration
Ontologies … For What?Ontologies … For What?
• Lack of a Lack of a shared understandingshared understanding leads to poor leads to poor communicationcommunication
=> People, organizations and software systems
must communicate between and amongthemselves
• Disparate modeling paradigms, languages and software Disparate modeling paradigms, languages and software tools limittools limit
=> Interoperability
=> Knowledge => Knowledge sharingsharing & & reusereuse [Uschold, Gruninger, 96]
CSE-291: Ontologies in Data Integration
Origin and History (I)Origin and History (I)
• Ontology ....Ontology .... a philosophical discipline, branch of philosophy that deals with the nature and the organisation of reality
• Science of Being (Aristotle, Metaphysics, IV, 1)Science of Being (Aristotle, Metaphysics, IV, 1)
• Tries to answer the questions:Tries to answer the questions:
What is being?
What are the features common to all beings?
CSE-291: Ontologies in Data Integration
Origin and History (II)Origin and History (II)
• Humans require words (or at least symbols) to communicate efficiently. The mapping of words to things is only indirect possible. We do it by creating concepts that refer to things.
• The relation between symbols and things has been described in the form of the meaning triangle:
“Jaguar“
Concept
[Ogden, Richards, 1923]
CSE-291: Ontologies in Data Integration
Origin and History (III)Origin and History (III)
• In recent years ontologies have become a hot topic of interest.
• Here, an ontology refers to an engineering artifact: • It is constituted by a specific vocabulary used to describe a
certain reality, plus • a set of explicit assumptions regarding the intended meaning
of the vocabulary.
• Thus, ontologies describe a formal partial specification of a specific domain:• Shared understanding of a domain of interest• Formal and machine executeable model of a domain of interest
CSE-291: Ontologies in Data Integration
Human and machine communication (I)Human and machine communication (I)
• ... MachineAgent 1
Things
HumanAgent 2
Ontology Description
MachineAgent 2
exchange symbol,e.g. via nat. language
‘‘JAGUAR“
Internalmodels
Concept
Formalmodels
exchange symbol,e.g. via protocols
MA1HA1 HA2
MA2
Symbol
commit commit
a specific domain, e.g.animals
commitcommitOntology
Formal Semantics
HumanAgent 1
MeaningTriangle
[Maedche et al., 2002]
CSE-291: Ontologies in Data Integration
Ontology & Natural LanguageOntology & Natural Language
• It is important to emphasize that there is a m:n relationship It is important to emphasize that there is a m:n relationship between words and conceptsbetween words and concepts
• This means practically:This means practically:
– different words may refer to the same concept
– a word may refer to several concepts
• Ontologies languages should provide means for making this Ontologies languages should provide means for making this difference explicit. difference explicit.
CSE-291: Ontologies in Data Integration
ExampleExample
Ontology: C = {c1,c2, c3}, R = {r1}, HC(c2,c1), r1(c2,c3),
c3
c1
...
c2
..
....r1(c2,c3),
HC(c2,c1)person
employee
organisation
works at
Lexicon: LC = {person, employee, organisation}, LR = {works at}
F(person) = c1, F(employee) = c2, F(organisation) = c3,
G(works at) = r1
CSE-291: Ontologies in Data Integration
Ontology vs. Knowledge BasesOntology vs. Knowledge Bases• There is no clear separation between ontology and knowledge There is no clear separation between ontology and knowledge
basebase
• Example:Example:
• Often it remains a modeling decision if something is modeled Often it remains a modeling decision if something is modeled as concept or as instance. In many applications meta-modeling as concept or as instance. In many applications meta-modeling means are required.means are required.
person
Ann
medication Aspirin
Aspirin pill-1 pill-2
cured-with
taken-aspirins
taken-aspirins
CSE-291: Ontologies in Data Integration
Types of Ontologies (I)Types of Ontologies (I) [Guarino, 98]
describe very general concepts like space, time, event, which are independent of a particular problem or domain. It seems reasonable to have unified top-level ontologies for large
communities of users.
describe the vocabulary related
to a generic domain by specializing the
concepts introduced in the top-level
ontology.
describe the vocabulary related to a generic task
or activity by specializing the
top-level ontologies.
These are the most specific ontologies. Concepts in application ontologies often correspond to roles played by domain entities while performing a certain activity.
CSE-291: Ontologies in Data Integration
Ontologies and their Relatives (I)Ontologies and their Relatives (I)
• There are many relatives around:There are many relatives around:
– Controlled vocabularies, thesauri and classification systems available in the WWW, see http://www.lub.lu.se/metadata/subject-help.html
• Classification Systems (e.g. UNSPSC, Library Science, etc.)• Thesauri (e.g. Art & Architecture, Agrovoc, etc.)
– Lexical Semantic Nets • WordNet, see http://www.cogsci.princeton.edu/~wn/• EuroWordNet, see http://www.hum.uva.nl/~ewn/
– Topic Maps, http://www.topicmaps.org (e.g. used within knowledge management applications)
• In general it is difficult to find the border line! In general it is difficult to find the border line!
CSE-291: Ontologies in Data Integration
Ontologies and their Relatives (II)Ontologies and their Relatives (II)
Catalog / ID
Terms/Glossary
Thesauri
InformalIs-a
FormalIs-a
FormalInstance
Frames
ValueRestric-tions
Generallogical
constraints
AxiomsDisjointInverse Relations,...
CSE-291: Ontologies in Data Integration
Some Ontologies (and Friends) in Some Ontologies (and Friends) in ActionAction
(coming soon to a project near you)(coming soon to a project near you)
CSE-291: Ontologies in Data Integration
GEON ArchitectureGEON Architecture
Rocky Mountains
Midatlantic Region
CSE-291: Ontologies in Data Integration
SMART (Meta)data I: Logical Data ViewsSMART (Meta)data I: Logical Data Views
Source: NADAM Team(Boyan Brodaric et al.)
Adoption of a standard (meta)data model => wrap data sets into unified virtual views
CSE-291: Ontologies in Data Integration
SMART Metadata II: Multihierarchical Rock Classification for “Thematic SMART Metadata II: Multihierarchical Rock Classification for “Thematic Queries” (GSC) –– or: Queries” (GSC) –– or: Taxonomies are not only for biologists ...Taxonomies are not only for biologists ...
Composition
Genesis
Fabric
Texture
“smart discovery & querying” via multiple, independent concept hierarchies (controlled vocabularies)• data at different description levels can be found and processed
CSE-291: Ontologies in Data Integration
Biomedical InformaticsResearch Networkhttp://nbirn.net
Biomedical InformaticsResearch Networkhttp://nbirn.net
SMART Metadata III:SMART Metadata III: Source Source Contextualization & Ontology RefinementContextualization & Ontology Refinement
Focused GEON ontology working meeting last week ... (GEON, SCEC/KR, GSC, ESRI)
CSE-291: Ontologies in Data Integration
EcoCycEcoCyc
CSE-291: Ontologies in Data Integration
Gene Ontology Gene Ontology http://www.geneontology.orghttp://www.geneontology.org
“a dynamic controlled vocabulary that can be applied to all eukaryotes”
Built by the community for the community.
Three organising principles: Molecular function, Biological
process, Cellular component Isa and Part of taxonomy – but
not good! ~10,000 concepts Lightweight ontology, Poor
semantic rigour. Ok when small and used for annotation. Obstacle when large, evolving and used for mining.
CSE-291: Ontologies in Data Integration
Controlled vocabularyControlled vocabulary
• AGROVOC: Agricultural VocabularyAGROVOC: Agricultural Vocabulary
CSE-291: Ontologies in Data Integration
ThesauriThesauri
• AAT: Art & Architecture ThesaurusAAT: Art & Architecture Thesaurus
CSE-291: Ontologies in Data Integration
Ontologies - Some ExamplesOntologies - Some Examples
• General purpose ontologies:General purpose ontologies:– WordNet / EuroWordNet, http://www.cogsci.princeton.edu/~wn– The Upper Cyc Ontology, http://www.cyc.com/cyc-2-1/index.html– IEEE Standard Upper Ontology, http://suo.ieee.org/
• Domain and application-specific ontologies:Domain and application-specific ontologies:– RDF Site Summary RSS, http://groups.yahoo.com/group/rss-dev/files/schema.rdf– UMLS, http://www.nlm.nih.gov/research/umls/– KA2 / Science Ontology, http://ontobroker.semanticweb.org/ontos/ka2.html– RETSINA Calendering Agent, http://ilrt.org/discovery/2001/06/schemas/ical-full/hybrid.rdf– AIFB Web Page Ontology, http://ontobroker.semanticweb.org/ontos/aifb.html– Web-KB Ontology, http://www-2.cs.cmu.edu/afs/cs.cmu.edu/project/theo-11/www/wwkb/– Dublin Core, http://dublincore.org/
• Meta-OntologiesMeta-Ontologies– Semantic Translation, http://www.ecimf.org/contrib/onto/ST/index.html– RDFT, http://www.cs.vu.nl/~borys/RDFT/0.27/RDFT.rdfs– Evolution Ontology, http://kaon.semanticweb.org/examples/Evolution.rdfs
• Ontologies in a wider senseOntologies in a wider sense– Agrovoc, http://www.fao.org/agrovoc/– Art and Architecture, http://www.getty.edu/research/tools/vocabulary/aat/– UNSPSC, http://eccma.org/unspsc/– DTD standardizations, e.g. HR-XML, http://www.hr-xml.org/
CSE-291: Ontologies in Data Integration
Ontology RepresentationOntology Representation
What is a „representation“?What is a „representation“?
“Jaguar“
Concept
CSE-291: Ontologies in Data Integration
Ontology Representation LanguagesOntology Representation Languages
• Machines need communication with formal content to Machines need communication with formal content to restrict meaningrestrict meaning
• What makes a language „formal“?What makes a language „formal“?– model theory (1st order predicate logic)
– proof theory (Gentzen calculus)
But also:
– conventions (e.g. Java)
CSE-291: Ontologies in Data Integration
What makes a language suitable?What makes a language suitable?
For machine communicationFor machine communication
model theory model theory proof theoryproof theory
tracktabilitytracktability
strong conventions of usestrong conventions of use
human readable names human readable names
For human communicationFor human communication
strong conventions of use strong conventions of use human readable names human readable names „ „natural“ primitives natural“ primitives
CSE-291: Ontologies in Data Integration
Representation Paradigms (incomplete)
Ontologies
TopicMaps
extended ER-Modell
Thesauri
Predicate Logics /Description Logics
Semantic Nets
Taxonomies
CSE-291: Ontologies in Data Integration
ThesaurusThesaurus
CSE-291: Ontologies in Data Integration
Thesauri
Example:Fruit
Orange Apfelsine (german)
VegetablesimilarTo
synonymWith
NarrowerTerm
- Well known in library science- cf. terminologies / classifications (Dewey)
- Graph with labels edges (similar, nt, bt, synonym)- Fixed set of edge labels (aka relations)- no instances
CSE-291: Ontologies in Data Integration
CSE-291: Ontologies in Data Integration
Topic Maps are ...Topic Maps are ...
• Standardized: ISO/IEC 13250:2000Standardized: ISO/IEC 13250:2000– ISO standard published Jan. 2000
– enabling standard to describe knowledge structures,electronic indices, classification schemes, ...
• Web enabled:Web enabled:– XML Topic Maps (XTM) are ready to use
• Designed to:Designed to:– manage the info glut
– build valuable information networks above any kind of resources / data objects
– enable the structuring of unstructured information
CSE-291: Ontologies in Data Integration
Back-of-the-Book Index “British Virgin Back-of-the-Book Index “British Virgin Islands”Islands”
Gorda Sound see North SoundLittle Dix Bay .................... 89North Sound ....................... 90Road Harbour see also Road Town ... 73Road Town ...................... 69,71Spanish Town ................... 81,82Tortola ........................... 67Virgin Gorda ...................... 77
CSE-291: Ontologies in Data Integration
Back-of-the-Book Index “British Virgin Back-of-the-Book Index “British Virgin Islands”Islands”
Gorda Sound see North SoundLittle Dix Bay .................... 89North Sound ....................... 90Road Harbour see also Road Town ... 73Road Town ...................... 69,71Spanish Town ................... 81,82Tortola ........................... 67Virgin Gorda ...................... 77
Topics
CSE-291: Ontologies in Data Integration
Back-of-the-Book Index “British Virgin Back-of-the-Book Index “British Virgin Islands”Islands”
Gorda Sound see North SoundLittle Dix Bay .................... 89North Sound ....................... 90Road Harbour see also Road Town ... 73Road Town ...................... 69,71Spanish Town ................... 81,82Tortola ........................... 67Virgin Gorda ...................... 77
Occurrences
CSE-291: Ontologies in Data Integration
Back-of-the-Book Index “British Virgin Back-of-the-Book Index “British Virgin Islands”Islands”
Gorda Sound see North SoundLittle Dix Bay .................... 89North Sound ....................... 90Road Harbour see also Road Town ... 73Road Town ...................... 69,71Spanish Town ................... 81,82Tortola ........................... 67Virgin Gorda ...................... 77
Different topic classes
CSE-291: Ontologies in Data Integration
Back-of-the-Book Index “British Virgin Back-of-the-Book Index “British Virgin Islands”Islands”
Gorda Sound see North SoundLittle Dix Bay .................... 89North Sound ....................... 90Road Harbour see also Road Town ... 73Road Town ...................... 69,71Spanish Town ................... 81,82Tortola ........................... 67Virgin Gorda ...................... 77
Different occurrences classes
CSE-291: Ontologies in Data Integration
Back-of-the-Book Index “British Virgin Back-of-the-Book Index “British Virgin Islands”Islands”
Gorda Sound see North SoundLittle Dix Bay .................... 89North Sound ....................... 90Road Harbour see also Road Town ... 73Road Town ...................... 69,71Spanish Town ................... 81,82Tortola ........................... 67Virgin Gorda ...................... 77
Multiple topic names
CSE-291: Ontologies in Data Integration
Back-of-the-Book Index “British Virgin Back-of-the-Book Index “British Virgin Islands”Islands”
Gorda Sound see North SoundLittle Dix Bay .................... 89North Sound ....................... 90Road Harbour see also Road Town ... 73Road Town ...................... 69,71Spanish Town ................... 81,82Tortola ........................... 67Virgin Gorda ...................... 77
Association
CSE-291: Ontologies in Data Integration
Topics – Computerized SubjectsTopics – Computerized Subjects
SurfBVIBVI Welcome CaribNet
Resources
TopicsLittle Dix Bay Tortola
Road TownVirgin GordaSubject
Subject
SubjectSubject
North Sound
Subject
Road Harbour
Subject
Spanish Town
Subject
Bay Island Town Topic classes
CSE-291: Ontologies in Data Integration
SurfBVIBVI Welcome CaribNet
OccurrencesOccurrences
Resources
TopicsLittle Dix Bay Tortola
Road TownVirgin Gorda
North Sound
Road Harbour
Spanish Town
Occurrences
OccurrenceclassesImage
Map
Article
MapMap
Map
MapArticle
Article
Article
ArticleArticle
Article
Image Image
Image
Image
CSE-291: Ontologies in Data Integration
OccurrencesOccurrences
Resources
TopicsLittle Dix Bay Tortola
Road TownVirgin Gorda
North Sound
Road Harbour
Spanish Town
Occurrences
SurfBVIBVI Welcome CaribNet
OccurrenceclassesImage
Map
Article
CSE-291: Ontologies in Data Integration
AssociationsAssociations
Topics
Little Dix Bay TortolaRoad Town
Virgin Gorda
North Sound
Road Harbour
Spanish Town
Associations
Association classes
Vicinity
Part-Whole
Part-Whole
Geo Containment
Geo Containment
Geo Containment
Geo ContainmentVicinityPart-Whole
CSE-291: Ontologies in Data Integration
AssociationsAssociations
Topics
Little Dix Bay TortolaRoad Town
Virgin Gorda
North Sound
Road Harbour
Spanish Town
Associations
Association classes
Geo ContainmentVicinityPart-Whole
CSE-291: Ontologies in Data Integration
Class HierarchiesClass Hierarchies
TopicsLittle Dix Bay Tortola
Road TownVirgin Gorda
North Sound
Road Harbour
Spanish Town
Bay Island Town Topic classes
CSE-291: Ontologies in Data Integration
Class HierarchiesClass Hierarchies
TopicsLittle Dix Bay Tortola
Road TownVirgin Gorda
North Sound
Road Harbour
Spanish Town
Bay
Island
Town Super-classes
Bay forswimming
Anchorbay
Land
Capital
Suburb Sub-classes
CSE-291: Ontologies in Data Integration
ScopesScopes
Brit. Virgin IslandsBrit. Jungferninseln
CaribbeanKaribik
Great BritainGroßbritannien
ImageBild
MapKarte
ArticleArtikel
SurfBVIBVI Welcome CaribNet
Geo ContainmentGeo Umschließung
Political DependencyPolitische Abhängigkeit
CSE-291: Ontologies in Data Integration
ScopesScopes
Brit. Virgin IslandsBrit. Jungferninseln
CaribbeanKaribik
Great BritainGroßbritannien
ImageBild
MapKarte
ArticleArtikel
SurfBVIBVI Welcome CaribNet
Geo ContainmentGeo Umschließung
Political DependencyPolitische Abhängigkeit
Scopes
CSE-291: Ontologies in Data Integration
ScopesScopes
Brit. Virgin IslandsBrit. Jungferninseln
CaribbeanKaribik
Geo ContainmentGeo Umschließung
Great BritainGroßbritannien
Political DependencyPolitische Abhängigkeit
ImageBild
MapKarte
ArticleArtikel
SurfBVIBVI Welcome CaribNet
Names:English
Deutsch
Scopes
CSE-291: Ontologies in Data Integration
ScopesScopes
Brit. Virgin IslandsBrit. Jungferninseln
CaribbeanKaribik
Geo ContainmentGeo Umschließung
Great BritainGroßbritannien
Political DependencyPolitische Abhängigkeit
ImageBild
MapKarte
ArticleArtikel
SurfBVIBVI Welcome CaribNet
Names:English
Deutsch
Scopes
Occurrences:Public
Confidential
CSE-291: Ontologies in Data Integration
ScopesScopes
Brit. Virgin IslandsBrit. Jungferninseln
CaribbeanKaribik
Geo ContainmentGeo Umschließung
Great BritainGroßbritannien
Political DependencyPolitische Abhängigkeit
ImageBild
MapKarte
ArticleArtikel
SurfBVIBVI Welcome CaribNet
Names:English
Deutsch
Scopes
Occurrences:Public
Confidential
Associations:Geography
Politics
CSE-291: Ontologies in Data Integration
Scope Examples: Scope Examples: EnglishEnglish, , PublicPublic, Politics, Politics
Brit. Virgin IslandsCaribbean
Geo Containment
Great Britain
Political Dependency
Image
Map
Article
SurfBVIBVI Welcome CaribNet
Names:English
Deutsch
Scopes
Occurrences:Public
Confidential
Associations:Geography
Politics
CSE-291: Ontologies in Data Integration
In-/Semi-formal approaches: In-/Semi-formal approaches: Topic Maps, ThesauriTopic Maps, Thesauri
AdvantagesAdvantages
• Capture a lot of modeling Capture a lot of modeling experiencesexperiences
• IntuitiveIntuitive
• Interesting primitives that Interesting primitives that are not available in other are not available in other approaches (TM)approaches (TM)
DisadvantagesDisadvantages
• No characterization No characterization independent from particular independent from particular implementationimplementation
• May be misinterpreted May be misinterpreted (TM) / few primitives (TM) / few primitives (Thesauri)(Thesauri)
CSE-291: Ontologies in Data Integration
Common errors about Common errors about ontology representation languagesontology representation languages
AI people‘s errorsAI people‘s errors
• „„it is good if it is formal“it is good if it is formal“
• „„it is good if someone with a it is good if someone with a logic background may easily logic background may easily use it“use it“
• „„it is good if the language it is good if the language allows everything“allows everything“
Engineer‘s errorsEngineer‘s errors
• „„it works in my application, it works in my application, thus it is good“thus it is good“
• „„who needs formality who needs formality anyway?“anyway?“
• „„it did not work when I it did not work when I looked at it 10 years ago“looked at it 10 years ago“
CSE-291: Ontologies in Data Integration
Review/Introduction:Review/Introduction:(Classical) First-order [Predicate] Logic:(Classical) First-order [Predicate] Logic:
Short: FO or PL1Short: FO or PL1
CSE-291: Ontologies in Data Integration
But first: Propositional Logic: SyntaxBut first: Propositional Logic: Syntax
• propositionspropositions (no internal structure) can be assigned a (no internal structure) can be assigned a truth-valuetruth-value: : – either true or false (classical 2-valued logic: tertium non datur)
• Logical symbols:Logical symbols:– conjunction: , disjunction: , negation: , – implication: , equivalence: , parentheses:
• Non-logical symbols:Non-logical symbols:– propositional variables p, q, r, ... – signature: set of propositional variables = {p, q, r, ...}
• Formation rules for well-formed formulas (wff)Formation rules for well-formed formulas (wff)– an atomic formula (propositional variable) is a formula– if F, G are formulas, so are:
• FG, F G, F, FG , FG, F
propositional logic<logic> (or "propositional calculus") A system of symbolic logic using symbols to stand for whole propositions and logical connectives. Propositional logic only considers whether a proposition is true or false. In contrast to predicate logic, it does not consider the internal structure of propositions. http://wombat.doc.ic.ac.uk/foldoc/foldoc.cgi?propositional+logic
CSE-291: Ontologies in Data Integration
Propositional Logic: SemanticsPropositional Logic: Semantics
• An An interpretation I interpretation I over a signature over a signature is a mapping is a mapping– I: {true, false} , associating a truth value to every
propositional variable
• Truth tablesTruth tables describe how to extend describe how to extend I I from to from to composite formulas (Boolean Algebra):composite formulas (Boolean Algebra):– FG, F G, F, FG , FG
CSE-291: Ontologies in Data Integration
Boolean Algebra, Truth TablesBoolean Algebra, Truth Tables
http://wombat.doc.ic.ac.uk/foldoc/foldoc.cgi?two-valued+logic
CSE-291: Ontologies in Data Integration
Syntax of First-Order Logic (FO)Syntax of First-Order Logic (FO)
• Logical symbols:Logical symbols: , , , , , , (“for all”), (“exists”), ...
• Non-logical symbols: A FO Non-logical symbols: A FO signature signature consists of consists of– constant symbols: a,b,c, ...
– function symbols: f, g, ...
– predicate (relation) symbols: p,q,r, ....
function and predicate symbols have an associated arity;
– we can write, e.g., p/3, f/2 to denote the ternary predicate p and the function f with two arguments
• First-order First-order variablesvariables: x, y, ...: x, y, ...
• Formation rules for Formation rules for termsterms::– constants and variables are terms
– if t_1,...t_k are terms and f is a k-ary function symbols then f(t_1,...,t_k) is a term
CSE-291: Ontologies in Data Integration
Syntax of First-Order Logic (FO)Syntax of First-Order Logic (FO)
• Formation rules for Formation rules for formulasformulas::– if t_1,...t_k are terms and p/k is a predicate symbol (of arity k)
then p(t_1,...,p_k) is an atomic formula (short: atom)• all variable occurrences in p(t_1,..., t_k) are free
– if F,G are formulas and x is a variable, then the following are formulas:
– FG, F G, F, FG , FG, F , x: F (“for all x: F(x,...) is true”) x: F (“there exists x such that F(x,...) is true”)
– the occurrences of a variable x within the scope of a quantifier are called bound occurrences.
CSE-291: Ontologies in Data Integration
ExamplesExamples
x malePerson(x) x malePerson(x) person(x). person(x).
malePerson(bill).malePerson(bill).
child(marriage(bill,hillary),chelsea).child(marriage(bill,hillary),chelsea).
Variable: xVariable: x
Constants (0-ary function symbols): bill/0, hillary/0, chelsea/0Constants (0-ary function symbols): bill/0, hillary/0, chelsea/0
Function symbols: marriage/2Function symbols: marriage/2
Predicate symbols: malePerson/1, person/1, child/2Predicate symbols: malePerson/1, person/1, child/2
CSE-291: Ontologies in Data Integration
Semantics of Predicate LogicSemantics of Predicate Logic
• Let D be a non-empty Let D be a non-empty domaindomain (a.k.a. (a.k.a. domain of domain of discoursediscourse, , universeuniverse). A ). A structurestructure is a pair is a pair I I = (D,I), with = (D,I), with an an interpretationinterpretation I that maps ... I that maps ...– each constant c to an element I(c) D– each predicate symbol p/k to a k-ary relation I(p) Dk,– each function symbol f/k to a k-ary function I(f): DkD
• Given a structure Given a structure I, I, and a set of variables X, a and a set of variables X, a valuationvaluation is a mapping val: X is a mapping val: X D, used to evaluate terms and D, used to evaluate terms and formulas over a given FO signature formulas over a given FO signature – with this: term evaluation val(t) yields a domain element, and
formula evaluation val(F) yields a truth value
CSE-291: Ontologies in Data Integration
ExampleExample
Formula F = Formula F = x malePerson(x) x malePerson(x) person(x). person(x).
Domain D = {b, h, c, d, e}Domain D = {b, h, c, d, e}
Let’sLet’s pick an interpretation I: pick an interpretation I: I(bill) = b, I(hillary) = h, I(chelsea) = c
I(person) = {b, h, c}
I(malePerson) = {b}
Under this I, the formula F evaluates to Under this I, the formula F evaluates to truetrue..
• If we choose IIf we choose I’ like I but I’(malePerson) = {b,d}, then F ’ like I but I’(malePerson) = {b,d}, then F evaluates to evaluates to falsefalse
• Thus, I is a Thus, I is a model model of F, while I’ is not:of F, while I’ is not:– I |= F I’ |=/= F
CSE-291: Ontologies in Data Integration
FO Semantics (cont’d)FO Semantics (cont’d)
• F F entailsentails G (G is a G (G is a logical consequencelogical consequence of F) if every model of F) if every model of F is also a model of G: F |= Gof F is also a model of G: F |= G
• F is F is consistent consistent or or satisfiablesatisfiable if it has at least one model if it has at least one model
• F is F is valid valid or a or a tautology tautology if every interpretation of F is a model if every interpretation of F is a model
Proof TheoryProof Theory: :
Let F,G, ... be FO Let F,G, ... be FO sentences sentences (no free variables). (no free variables).
Then the following are equivalent:Then the following are equivalent:
1.1. F_1, ..., F_k |= GF_1, ..., F_k |= G
2.2. F_1 F_1 ... ... F_k F_k G is valid G is valid
3.3. F_1 F_1 ... ... F_k F_k G is unsatisfiable (inconsistent) G is unsatisfiable (inconsistent)
CSE-291: Ontologies in Data Integration
Proof TheoryProof Theory
• A A calculus calculus is formal proof system to establish is formal proof system to establish – F_1, ..., F_k |= G
• via formal (syntactic) via formal (syntactic) derivationsderivations – F_1, ..., F_k |– ... |– G, where the “|–” denotes allowed proof steps
• Examples: Examples: – Hilbert Calculus, Gentzen Calculus, Tableaux Calculus, Natural
Deduction, Resolution, ...
• First-order logic is “semi-decidable”:First-order logic is “semi-decidable”:– the set of valid sentences is recursively enumerable, but not recursive
(decidable)
• Some inference engines:Some inference engines:– http://www.semanticweb.org/inference.html
CSE-291: Ontologies in Data Integration
Description LogicsDescription LogicsDecidable Fragments of FODecidable Fragments of FO
(aka (aka terminological logicsterminological logics,,member ofmember of concept languages concept languages))
CSE-291: Ontologies in Data Integration
Formalism for Ontologies: Description LogicFormalism for Ontologies: Description Logic
• DL definition of “Happy Father” DL definition of “Happy Father” (Example from Ian Horrocks, U Manchester, UK)(Example from Ian Horrocks, U Manchester, UK)
CSE-291: Ontologies in Data Integration
Description Logic Statements as RulesDescription Logic Statements as Rules
• Another syntax: first-order logic in rule form (implicit quantifiers):Another syntax: first-order logic in rule form (implicit quantifiers):happyFather(X)
man(X), child(X,C1), child(X,C2), blue(C1), green(C2),
not ( child(X,C3), poorunhappyChild(C3) ).
poorunhappyChild(C)
not rich(C), not happy(C).
• Note: Note: – the direction “” is implicit here (*sigh*)
– see, e.g., Clark’s completion in Logic Programming
CSE-291: Ontologies in Data Integration
Description LogicsDescription Logics
• Terminological Knowledge (TBox)Terminological Knowledge (TBox)– Concept Definition (naming of concepts):
– Axiom (constraining of concepts):
=> a mediators “glue knowledge source”
• Assertional Knowledge (ABox)Assertional Knowledge (ABox)– the marked neuron in image 27
=> the concrete instances/individuals of the concepts/classes that your sources export
CSE-291: Ontologies in Data Integration
Querying vs. ReasoningQuerying vs. Reasoning
• Querying: Querying: – given a DB instance I (= logic interpretation), evaluate a query
expression (e.g. SQL, FO formula, Prolog program, ...)– boolean query: check if I |= (i.e., if I is a model of ) – (ternary) query: { (X, Y, Z) | I |= (X,Y,Z) } => check happyFathers in a given database
• Reasoning:Reasoning:– check if I |= implies I |= for all databases I, – i.e., if => – undecidable for FO, F-logic, etc.– Descriptions Logics are decidable fragments concept subsumption, concept hierarchy, classification semantic tableaux, resolution, specialized algorithms
CSE-291: Ontologies in Data Integration
Formalizing Glue Knowledge:Formalizing Glue Knowledge:Domain Map for Domain Map for SYNAPSESYNAPSE and and NCMIRNCMIR
Domain Map = labeled graph with concepts ("classes") and roles ("associations")• additional semantics: expressed as logic rules
Domain Map = labeled graph with concepts ("classes") and roles ("associations")• additional semantics: expressed as logic rules
Domain Map (DM)
Purkinje cells and Pyramidal cells have dendritesthat have higher-order branches that contain spines.Dendritic spines are ion (calcium) regulating components.Spines have ion binding proteins. Neurotransmissioninvolves ionic activity (release). Ion-binding proteinscontrol ion activity (propagation) in a cell. Ion-regulatingcomponents of cells affect ionic activity (release).
Domain Expert Knowledge
DM in Description Logic
CSE-291: Ontologies in Data Integration
Source Contextualization & DM Source Contextualization & DM RefinementRefinement
In addition to registering (“hanging off”) data relative toexisting concepts, a source may also refine the mediator’s domain map...
sources can register new concepts at the mediator ...