Ontologie e applicazioniOntologie e applicazioniOntologie e applicazioniOntologie e applicazioni

Marco Brandizi<marco.brandizi@unimib.it>

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Dec 6, 2005

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Dottorato in InformaticaXIX Ciclo

OutlineWhat an ontology is

Informal idea

Applications

Formal definition

Working with ontologies: Description Logics

Ontologies and Semantic Web

The idea of Semantic Web

OWL

An application to microarray data management

Conclusions and future work

Ontologies

OntologiesIssues (relevant in Computer Science, from [Wikipedia])

What is existence?

What physical objects?

What are essential attributes of objects?

Being an apple and being red

What constitutes the identity of an object?

Categories:

Mind: a real entity or a set of states?

Physical objects and substances

Relationships, type of relations

“finger part-of body”? “embryo part-of child-development”?

Ontologies and Computer Science

From [Mc Guinness]

Ontologies and Computer ScienceFrom [Mc Guinnes], required properties:

Finite controlled (extensible) vocabulary

Unambiguous interpretation of classes and term relationships

Strict hierarchical subclass relationships between classes

Typical, although not required

Property specification on a per-class basis

Individual inclusion in the ontology

Value restriction specification on a per-class basis

Desirable:

Specification of disjoint classes

Specification of arbitrary logical relationships between terms

Distinguished relationships such as inverse and part-whole

Toy ontology example

Example of queries

“nails is-part-of elephant”? yes, because:

“has-legs” and “has-nails” are particular “has-parts”

transitive relation

“is-part-of” is the inverse

of “has-parts”

Example of queries

“giraffe is-eaten-by lion”? yes, because:

giraffe is-a herbivore => is-a animal

lion is-a carnivore => lion eats animal => lion eats giraffe“is-eaten” is the inverse of “eats”

Uses (of ontologies and “ontologies”)Reasoning (as in query examples)

Consistency checking

DUMBO is-a Kenian-Elephant AND DUMBO is-a Lion is wrong

Interoperability

Two applications may talk together

Browsing

Searching

Sense disambiguation, synonyms, subsumption

Completion and interaction

Patient is a man => is a male and pregnant is not a cause of its

symptoms

Natural Language Processing

Defining ontologies

[Gruber 93]: “An ontology is an explicit specification

of a conceptualization”

(Variant: it is a shared explicit spec. ...)

Problems [Guarino, 98]:

The specification depends by the language which is

used for the specification

A conceptualization is a more abstract entity, w.r.t. a

formal specification which is expressed with a given

language

What is a conceptualizationConceptualization: the formal structure of reality as perceived and organized by an agent, independently of:

the vocabulary used (i.e., the language used)

the actual occurence of a specific situation

Different situations involving the same objects, described by different vocabularies, may share the same conceptualization.

apple

mela

same conceptualization

LI

LE

From [Guarino Tut1]

Conceptualizations and ontologies

on(x,y) expresses the general idea of on, it has subsets in possible worldsit has restrictions that excludes “impossible” cases for all worlds

W1: on_1(a,d) is admitted W2: on_2(a,d) is not admittedhere

Conceptualizations and ontologies

a

a

a

b

a

Excluded from conceptualization => Impossible in all worlds

c

From [Guarino Tut1]

From [Guarino Tut1]

From [Guarino Tut1]

Formal definition of the ontologiesAn ontology O for a language L (a set of axioms added to

L)approximates a conceptualization C:

If there exist a onto. commitment K such that:

the intended models of L according to K are included in the

models of O

An Ontology O commits to C if:

has been designed with the purpose of characterizing C

Approximates C

A language L commits to an ontology O if it commits to some

conceptualization C such that O agrees on C

Formal definition of the ontologies

From [Guarino Tut2]

Applying ontologies

From [Guarino 98]

Designing ontologiesFormalized in [Guarino, 94]

Apple(A): Apple is a substantial sortal unary predicate

Defines A in such a way that a is no longer a apple if ~Apple(A)

Red(A): Red is not a sortal, is a characterizing property, if ~Red(A) A is

still an Apple

Formalized in [Gangemi et al. 2001]:

Take account of general, upper level, ontological relations

P1)Part(x,x) P2) Part(x,y) and Part(y,x)->x=y

P3)Part(x,y) and Part(y,z) -> Part(x,z)

Similar work in [ISMB 04]

Considers the basic relations and properties that occurs in Biological

ontologies

Designing ontologiesSimilar work in [ISMB 04], the OBO relational ontology

Considers the basic relations and properties that occurs in

Biological ontologies

Continuants: entities which endure or continue to exist,

changing over time.

fetus and embryo are continuants, related one each

another by transformation relation

Both participate to the Process named

human_being_development

OutlineWhat an ontology is

Informal idea

Applications

Formal definition

Working with ontologies: Description Logics

Ontologies and Semantic Web

The idea of Semantic Web

OWL

An application to microarray data management

Conclusions and future work

Formalizing Ontologies: Logics

From [Franconi Tut]

From [Franconi Tut]

From [Franconi Tut]

From [Franconi Tut]

1) The entitites which have the Role R with range R being in C2) The entities that have some y linked to them, as target of role R

1)

2)

From [Franconi Tut]

DL and computability

From [Franconi Tut]

DL and computability

From [Franconi Tut]

OutlineWhat an ontology is

Informal idea

Applications

Formal definition

Working with ontologies: Description Logics

Ontologies and Semantic Web

The idea of Semantic Web

OWL

An application to microarray data management

Conclusions and future work

Applications: Semantic WebWeb was designed for humans

Knowledge on the web is unstructured and meaning is not explicitly

represented. It is not machine-readable

We would need:

Metadata

Languages for Data Exchange (XML)

Linking Web resources and representing the links meaning (RDF)

More advanced representation of Semantics (OWL)

Retrieving metadata (SPARQL, SWIRL)

Reasoning/Inferencing with metadata (OWL + Rules + Logics)

Applications: Semantic Web“The Semantic Web is an extension of the current web in whichinformation is given well-defined meaning, better enabling computersand people to work in cooperation.”

Tim Berners-Lee, James Hendler, Ora Lassila, The Semantic Web, Scientific American, May 2001

(http://owl.mindswap.org)

RDF

Statements is basic simple structure (Like in Sem Networks)

May be represented in XML (as well as in N3)

Subject/Property(or verb)/Object may reference public resources,

identified by URIs (like Web pages)

A given resource may flexibly be annotated by many statements

Meaning of statements may be defined by other statements and

higher level languages (which still are RDF representable)

May be queried with simple query languages (SPARQL, RQL)

RDF example

From [RDF Nature 05]

RDF Example

From [RDF Nature 05]

RDF Schema (RDF-S)Allow to define simple “ontologies” by means of triples

Pro

Easy to use

Efficiently computable

Cons

Not enough expressive in several cases:

rdfs:range doesn't allow scope management

No disjointness of classes

No boolean combinations of classes

Cannot define a property as transitive/unique/inverse

OWL

SHIQ Description Logics plus other tools (ex.:

imports)

Several versions of DL

Lite – Fastest, least expressive

DL – Computable and expressive, slower

Full – Undecidable, most expressiveness

XML format

Built on top of RDF

OWL

<rdf:RDF xml:base="http://www.co-ode.org/ontologies/pizza/..."> <owl:Ontology rdf:about=""> <owl:imports rdf:resource="http://.."/> <owl:versionInfo rdf:datatype="..."> version 1.2 </owl:versionInfo>- <rdfs:comment xml:lang="en"> A "final stage" that contains all constructs required </rdfs:comment> <protege:defaultLanguage rdf:datatype="..."> en </protege:defaultLanguage></owl:Ontology>

OWL<owl:Class rdf:about="#DeepPanBase"> <rdfs:subClassOf rdf:resource="#PizzaBase"/>

<owl:disjointWith rdf:resource="#ThinAndCrispyBase"/> <rdfs:label xml:lang="pt">BaseEspessa</rdfs:label></owl:Class>

<owl:Class rdf:about="#DeepPanBase"> <rdfs:subClassOf rdf:resource="#PizzaBase"/>

<owl:disjointWith rdf:resource="#ThinAndCrispyBase"/> <rdfs:label xml:lang="pt">BaseEspessa</rdfs:label></owl:Class>

<owl:ObjectProperty rdf:ID="isIngredientOf"> <rdfs:comment xml:lang="en"> The inverse property tree to hasIngredient ... </rdfs:comment>- <owl:inverseOf> <owl:ObjectProperty rdf:ID="hasIngredient"/> </owl:inverseOf> <rdf:type rdf:resource="http://www.w3.org/..."/></owl:ObjectProperty>

OutlineWhat an ontology is

Informal idea

Applications

Formal definition

Working with ontologies: Description Logics

Ontologies and Semantic Web

The idea of Semantic Web

OWL

An application to microarray data management

Conclusions and future work

DNA

gene

mRNA

protein

Genes Machine

Cell/Life

Microarray Data

MIAME Experiment Modelling

From [RDF Nature 05]

The mA Experiments Cycle

“Closing the loop”

What we need to model

What we need to model

What we need to model

Microarrays Annotation Ontology

Microarray entities

Annotation entities

Microarrays Annotation OntologyAnnotation (source, target, child, parent, rank)

Microarrays Annotation Ontology

Microarrays Annotation Ontology

OutlineWhat an ontology is

Informal idea

Applications

Formal definition

Working with ontologies: Description Logics

Ontologies and Semantic Web

The idea of Semantic Web

OWL

An application to microarray data management

Conclusions and future work

mA-Anno Ontology: How could it evolve?

MGED-2/FuGE

Development of some simple tool

Methodologies and ontological distinctions

Annotation could be an independent ontology

Theory of annotations?

Named Graphs [NG, NG1]

C-OWL [Bouquet et. al.]

Context and situations [Gangemi et. al. 2004]

mA-Anno Ontology: How could it evolve?

From [NG1]

b0skill(Peter, Programming

R. Stallmann

FSF

e-macs getxtext

assertedBy

authority

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