ontologies and owl with some notes on xml schema, e-r diagrams and uml in 15 minutes

Ontologies and OWLwith some notes on

XML Schema, E-R Diagrams and UML

in 15 minutes

Dave ThauUniversity of Kansas

thau@learningsite.com

XML Schema Fiesta!

• Darwin Core

• ABCD

• SDD

• TCS

• Linnean Core

• And more to come

< > < > < > < >

Yippee!

Yahoo!

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

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

Erect hairs on mesosoma

Erect hairs on trunk

Same Idea, Different Names

Taxonomic Concept Schema v0.80

SDD v0.91b11

Publication SourcePublication

DatePublished PublicationDate

Rank RankLevel

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.

Example Ontology

Ontologies have:

ConceptsPropertiesInstances

hasColor

BodyPart

Color

Mesosoma Pronotum

brown

hasPartPronotum

Of Ant #100

MesosomaOf

Ant #100

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

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

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>

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

Ontologies and XML Schema

Mapping Standards

DarwnCoreSchema

DarwnCoreSchema

ABCDSchema

ABCDSchema

LinneanCoreSchema

LinneanCoreSchema

mappings. Not so good! n!(n-2)!

12

Mapping Standards

DarwnCoreschema

DarwnCoreschema

ABCDschema

ABCDschema

LinneanCoreschema

LinneanCoreschema

mappings. Better! n

Specimenschema

Specimenschema

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?

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

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

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

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!

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)