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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
affiliationaffiliation
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