Intro to ontologies, OWL, and reasoning

manyfarmswalkingInternet and Web Development

Oct 21, 2013 (3 years and 7 months ago)

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8/22/2012 1
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Intro to ontologies, OWL, and
reasoning
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Recap
RDF (Resource Description Framework) is one of
the three foundational Semantic Web
technologies, together with SPARQL and the
Web Ontology Language (OWL)
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What is OWL?

Web Ontology Language (OWL) is a language
for writing ontologies for the Web
• What is an ontology?
– Is a formal, logical representation of a domain of
interests that represent knowledge about things,
group of things, and relations between things in
that domain
– An ontology of research resources, and ontology
of people expertise, etc.

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OWL
• The things or objects about which knowledge
is represented (e.g. Brian, Carlo, England) are
called individuals (aka instances)
• Group of things (e.g. person, conference) are
called classes
• Relations between things (e.g. siblings) are
called properties
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Individuals
Carlo


Individuals represent objects in the domain in which we
are interested


URPRRI workshop

Florida

Jon

Melissa

VIVO 2012

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Classes and Subclasses
• OWL classes are interpreted as sets that contain individuals
• SubClasses are subsets of Classes

Instructor rdfs:subClassOf foaf:Person
Carlo

URPRRI Workhsop

Workshop
Person
Instructor
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Object Properties
• Object properties link another individual to an individual
• The above representations means that the individual Carlo and
URPRRI Workshop are related through the teaches property
Carlo

URPRRI Workshop

Workshop
Person
Instructor
teaches

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Object Properties
Properties may have a domain and a range specified. For instance,
the property teaches can have domain Person and range Workshop

teaches rdf:type owl:ObjectProperty
teaches rdfs:domain foaf:Person
teaches rdfs:range workshop
Carlo

URPRRI Workshop

Workshop
Person
Instructor
teaches

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What does OWL add to RDF?
• More meaningful semantics
– OWL allows one to specify more about properties
and classes
•"If Melissa isMarriedTo John" then this implies “John
isMarriedTo Melissa” (symmetric property)
• Have complex class definitions using properties

• Enables “reasoning”
– Check the logical correctness of statements
– Add statements that are implied by other statements


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Complex Class definition
(Equivalent Class)
In OWL, we can say that an instructor is equivalent
to a person that teaches some workshop







Person
teaches
some
workshop
instructor

Class: Instructor
EquivalentTo: Person and teaches some workshop




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Reasoning Example
Assuming we have defined the object property
teaches

with domain
foaf:person
and range
workshop
We assert that
Carlo teaches URPRRI_Workshop

 ????


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Reasoning Example
Assuming we have defined the object property
teaches

with domain
foaf:person
and range
workshop
We assert that
Carlo teaches URPRRI_Workshop

 Carlo rdf:type person
 URPRRI_Workshop rdf:type workshop


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Reasoning Example
Assuming we have defined the object property
teaches

with domain
foaf:person
and range
workshop and
we have defined the equivalent class instructor.
We assert that:
Carlo teaches URPRRI_Workshop

And so infer that:
 Carlo rdf:type instructor



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Open World vs. Closed World
Open world assumption: everything we don’t know is
undefined

Closed world assumption: everything we don’t know is false

Example:
Statement: Erich attends OHSU
Query: “Does Brian attend OHSU?”

Closed world response= no
Open world response= unknown
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Reasoning Example
Assuming we have defined the object property
teaches

with domain
foaf:person
and range
workshop
We assert that
mandy teaches protégé_workshop
protégé_workshop rdf:type animal

 ??


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Reasoning Example
Assuming we have defined the object property
teaches

with domain
foaf:person
and range
workshop
We assert that
mandy teaches protégé_workshop
protégé_workshop rdf:type animal

 protégé_workshop rdf:type workshop



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Reasoning Example
Assuming we have defined the object property
teaches

with domain
foaf:person
and range
workshop
We assert that
mandy teaches protégé_workshop
protégé_workshop rdf:type animal
animal owl:disjointWith workshop


??
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Reasoning Example
Assuming we have defined the object property
teaches

with domain
foaf:person
and range
workshop
We assert that
mandy teaches protégé_workshop
protégé_workshop rdf:type animal
animal owl:disjointWith workshop


Error!!
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OWL Syntaxes
• Many flavors
– Functional OWL Syntax
– RDF based Syntaxes
• RDF/XML
• Turtle
• OWL/XML
• Manchester Syntax
Still they all can be represented as a graph or a
set of triples!

8/22/2012 20
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About VIVO, eagle-i and
CTSAConnect ontologies
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What does VIVO model?

• People, but also organizations, grants, programs,
projects, publications, events, facilities, and
research resources

• Relationships among the above
– Meaningful connections among people and activities
– Bidirectional
– Context and navigation from one point of interest to
another

• Links to URIs outside VIVO
– Concepts
– People, places, organizations, events
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VIVO Ontology
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Context nodes (reified relationships)

• Used for most significant relationships so richer
detail can be captured (time bounds, etc)

• Examples:

Position, Role
• time bounds, and other qualifying information
– Authorship
• to represent author order



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235 object properties





198 Datatype properties
248 Classes





34
62
89
40
19
4
Counts
(approximate)
139
83
9
4
Almost all have
an inverse
73
73
45
Mostly named, with
Asserted subclass
hierarchy
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eagle-i ontology
Research Resources
– Biological specimen
– Document , such as Protocols
– Human studies , such as Clinical Trials
– Instruments
– Organisms and Viruses
– Reagent
– Service
– Software
* All of this things are provided by or generated by a
person or an organization
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https://search.eagle-i.net:8443/model/

eagle
-
i

ontology browser

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e
agle
-
i
: modular import strategy

• Leveraging extenral ontologies
Why go to all this trouble?
At the intersection of Vivo and eagle-i
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CTSAconnect project:
the Agents, Resources and Grants ontology
• Aims to consolidate the Vivo and eagle-i
ontologies
• Including a clinical module
• Refactoring the whole ontology suite for
modular use in applications
• When the CTSAconnect project is over, eagle-
i and VIVO will be driven by ARG modules
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What are all these acronyms?
ISF: The integrated Semantic Framework
The name of the collection of ontology modules that
feed the Vivo and eagle-i, and other applications

CTSAconnect: The funded project that is creating the
ISF and ISF-compliant data

ARG: The namespace of classes and properties
specifcially created in the context of the above
ontology work

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Potential modular structure
– Resources.owl (reagents and so on)
– Diseases.owl (used as topics and to describe resources)
– Anatomy.owl (used as topics and to describe resources)
– People.owl
– Organization.owl
– Clinical_module.owl
– Documents (protocols, publications and the like)
Different applications can use the modules they
need
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ARG clinical module
ARG: Agents, Resources, Grants ontology

CM: Clinical module
IAO: Information Artifact Ontology
OBI: Ontology for Biomedical
Investigations
OGMS: Ontology for General Medical
Science
FOAF: Friend of a Friend vocabulary
BFO: Basic Formal Ontology