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Ontologies and OWLwith some notes on
XML Schema, E-R Diagrams and UML
in 15 minutes
Dave ThauUniversity of Kansas
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XML Schema Fiesta!
• Darwin Core
• ABCD
• SDD
• TCS
• Linnean Core
• And more to come
< > < > < > < >
Yippee!
Yahoo!
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XML Schema Is Good For
• Describing the format of documents– How elements nest– Which elements are necessary – The order in which they may appear– What attributes an element can have
• Describing the element types
• Ensuring valid syntax
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XML Schema Not Made For
• Semantics– When are two things the same?– How do two concepts relate?– How do I know what kind of thing this is?
• These matter in:– SDD terminologies– Schema mapping
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Erect hairs on mesosoma
Erect hairs on trunk
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Same Idea, Different Names
Taxonomic Concept Schema v0.80
SDD v0.91b11
Publication SourcePublication
DatePublished PublicationDate
Rank RankLevel
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Ontologies
• An ontology defines a common vocabulary for researchers who need to share information in a domain
• It includes machine-interpretable definitions of basic concepts in the domain and relations among them.
• Ontologies enable reuse of domain knowledge
• They assist mediation between heterogeneous data sources – XML documents among them.
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Example Ontology
Ontologies have:
ConceptsPropertiesInstances
hasColor
BodyPart
Color
Mesosoma Pronotum
brown
hasPartPronotum
Of Ant #100
MesosomaOf
Ant #100
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OWL
• W3C Standard Web Ontology Language
• OWL builds on RDF and RDFS which can be represented using XML
• Vocabulary designed to describe concepts and relationships between them
• Based on Description Logics, varieties of predicate logic, so supports reasoning
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Some Handy OWL Terms• Relationships between classes
– equivalentClass– subClassOf– Intersection, union, complement, disjunction
• Relationships between instances– sameAs, differentFrom
• Properties of properties– Cardinality– Transitive, Symmetric– allValuesFrom, someValuesFrom– Functional, InverseFunctional
• Relationships between properties– subPropertyOf– inverseOf– samePropertyAs
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OWL Example
<owl:Class rdf:ID=”ParasiticHost”><rdfs:subClassOf rdf:resource=” http://ecofax.org/ontologies#Host”/><rdfs:subClassOf>
<owl:Restriction><owl:onProperty>
<owl:ObjectProperty rdf:about=”#hasParasite”/></owl:onProperty><owl:minCardinality rdf:datatype=”&xsd:int”>
1</owl:minCardinality>
</owl:Restriction></rdfs:subClassOf>
</owl:Class>
<owl:ObjectProperty rdf:ID=”hasParasite”><rdfs:domain rdf:resource=”#parasiticHost”/><rdfs:range rdf:resource=“http://ecofax.org/ontologies#Parasite”/>
</owl:ObjectProperty>
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Reconciling Ontologies
hasColor
BodyPart
Color
Pronotum MesosomahasPart Trunkequivalent
ONTOLOGY 1 ONTOLOGY 2
Segment
What trunk colors doI know about?
isColored
Hueequivalent
equivalent
Meso ofAnt #100 Trunk of
Ant #210
BrownRed
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Ontologies and XML Schema
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Mapping Standards
DarwnCoreSchema
DarwnCoreSchema
ABCDSchema
ABCDSchema
LinneanCoreSchema
LinneanCoreSchema
mappings. Not so good! n!(n-2)!
12
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Mapping Standards
DarwnCoreschema
DarwnCoreschema
ABCDschema
ABCDschema
LinneanCoreschema
LinneanCoreschema
mappings. Better! n
Specimenschema
Specimenschema
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Deriving XML Schema From Ontologies
DarwnCoreOntology
DarwnCoreOntology
ABCDOntology
ABCDOntology
LinneanCoreOntology
LinneanCoreOntology
SpecimenOntology
SpecimenOntology
DarwnCoreSchema
DarwnCoreSchema
ABCDSchema
ABCDSchema
LinneanCoreSchema
LinneanCoreSchema
Mapping Using OWL
Mapping Using XLink?Maybe extendingXML type Elements?
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Ontology Analogy
From “The Relations Between Ontologies and XML SchemaKlein, Fensel, van Harmelen and Horricks, 2001http://www.cs.man.ac.uk/~horrocks/Publications/download/2001/etai01.pdf
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Why bother?
• Ontologies can add semantics to XML schema elements and attributes
• Semantics are necessary for interoperability between different schemata
• Nailing down your data model before implementation is a good idea– Don’t build a building w/o blueprints– Make sure you know what you need– Make sure you know how things relate
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UML
• UML is an graphical notation for software development
• Good for describing object-oriented design• UML can sort-of be used to model OWL• However:
– Properties in OWL are first class citizens – not true of associations in UML
– OWL has built-in descriptions like subProperty, sameAs, transitive
• UML may be MMTT in this case
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Conclusion• XML Schema is great for
describing document structure• Not great for interoperability
between systems using different schemata
• If we can’t live in perfect harmony, need to reconcile schemata
• That’s what ontologies are for• Schemata can be derived from
ontologies• We can have both!
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Ontology Tools I Know and Love
●Specification -- http://www.w3.org/TR/owl-features/ ●Protege -- http://protege.standford.edu/
● The XML Spy of ontology editors● Nice viewer for OWL
● Pellet -- http://www.mindswap.org● My current favorite Description Logic reasoner
for OWL ● Jena2 -- http://jena.sourceforge.net
● Java based OWL reasoner and parser●SWI-Prolog -- http://www.swi-prolog.org/
● Has modules for semantic web support (rdf, rdfs, owl)