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Understanding Realworld Ontologies

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Title: Understanding Realworld Ontologies


1
Understanding Real-world Ontologies

2
Outline
  • Analysis of real-world ontologies
  • The (simplified) GALEN ontology.
  • The National Cancer Institute (NCI) Thesaurus.
  • The TAMBIS ontology.
  • Advanced issues and design patterns
  • Qualified versus unqualified number restrictions.
  • Transitive propagation of properties.
  • Nominals and pseudo-nominals.

3
Analysis of Real-world Ontologies
4
GALEN
  • Ontology about medical terms and surgical
    procedures.
  • Constructed in the 90s within the OpenGALEN
    project.
  • Main applications
  • Integration of clinical records, and
  • decision support.
  • GALEN
  • is very large (35.000 concepts),
  • is fairly expressive (SHIF description logic),
  • has not been classified yet by any DL reasoner
  • In this tutorial we use a smaller version, which
  • is still large (3000 concepts),
  • is similarly expressive as full GALEN,
  • was first classified by the FaCT system.

5
GALEN The Ontology at a Glance
  • Size
  • 3000 classes
  • 500 object properties
  • no individuals or datatypes
  • Expressivity
  • 350 General Concept Inclusion Axioms (GCIs).
  • Concept constructors
  • Conjunction (intersectionOf)
  • Existential restrictions (someValuesFrom)
  • 150 functional properties
  • 26 transitive properties

6
GALEN The (Unclassified) Hierarchies
  • The class hierarchy
  • Number of subsumption relations 1978
  • Maximum depth of the tree 13
  • No multiple inheritance
  • Browse through it!
  • The property hierarchy
  • 4 properties with multiple inheritance
  • Browse through it!

7
GALEN Concept definitions and GCIs
  • Concept definition
  • Axiom of the form A C with
  • A a concept name
  • C a (possibly complex) concept
  • A definition assigns a name A to a complex
    concept C
  • Some examples
  • LungPathology Pathology u 9 locativeAttribute.Lu
    ng
  • RenalTransplant Transplanting u 9
    actsOn.Kindney

8
GALEN Concept definitions and GCIs
  • Inclusion axioms
  • Axioms of the form A v C
  • A is a concept name
  • C is a possibly complex concept
  • Represent an incomplete (partial) definition
  • Examples
  • XRayMachine v ImagingDevice
  • Candida v 9 hasFunction.AerobicMetabolicProcess
  • In GALEN, some of these can be very complex
  • check out the definitions of Knee Joint and
    Kidney!

9
GALEN Concept definitions and GCIs
  • General Concept Inclusion Axioms (GCIs)
  • Axioms of the form C D
  • C,D can be complex
  • May describe general (background) knowledge about
    the ontology
  • Examples
  • Secretion u 9 actsSpecificallyOn.Leucocidin v
  • 9 isFunctionOf.StraphilococcusAureus
  • 9 actsOn.Glucose u Transport u 9
    carriesFrom.Blood v
  • 9 carriesTo.Cell

10
Classifying GALEN
  • Ontology statistics (revisited)
  • Number of class subsumption relations 6729
  • 1978 of which are told and the rest inferred
  • Maximum depth of the class tree 15
  • As opposed to 13 in the case of the unclassified
    tree
  • Classes with multiple inheritance 408
  • All multiple inheritance relations have been
    inferred!
  • This was intended in the design of GALEN
  • Maximum depth of the property tree 9
  • No change with respect to the told tree
  • Properties with multiple inheritance 4
  • Again, no change with respect to the told
    tree
  • Reasoning is mostly performed on classes and not
    on properties

11
Modeling Choices
  • The upper part
  • Composed of the domain-independent concepts and
    roles.
  • Examples
  • TopCategory, DomainCategory, GeneralisedStructure
  • Shallowly defined (mostly a taxonomy)
  • The domain specific part
  • Examples
  • Plant, LungPathology,
  • Richly defined
  • Much more than just a taxonomy!

12
Inferred Knowledge
  • A trivial subsumption
  • Why is PathologicalCondition a subclass of
    DomainCategory?
  • Simply look at the definition of Pathological
    Condition!
  • Another example
  • Why is PathologicalBehavior a subclass of
    PathologicalCondition?
  • Look at the definition of both classes
  • Notice that Behavior is a subclass of
    DomainCategory
  • A non-trivial subsumption
  • Why are Achalasia Processes Pathological Body
    Processes?
  • Try!
  • If you dont succeed use the pinpointing
    explanation service

13
Classifying GALEN
  • Simple and multiple inheritance
  • Focus, for example, on PathologicalBodyProcess
  • Navigate to its super-classes
  • Fly the mother ship and see what is going on!

14
The NCI Ontology
  • Huge bio-medical ontology describing the Cancer
    domain
  • Maintained by a dozen of domain experts
  • Contains information about
  • genes,
  • diseases,
  • drugs,
  • research institutions,
  • All with a cancer-centric focus
  • Download it!
  • http//www.mindswap.org/2003/CancerOntology

15
NCI The Ontology at a Glance
  • Size
  • 30.000 classes
  • 70 object properties
  • no individuals or datatypes
  • Expressivity
  • Concept constructors
  • Conjunction (intersectionOf)
  • Existential restrictions (someValuesFrom)
  • Axioms
  • Definitions (no GCIs)
  • Domain and range of properties

16
NCI The (Unclassified) Hierarchies
  • The class hierarchy
  • Number of subsumption relations 103.232
  • Maximum depth of the tree 19
  • Classes with multiple inheritance 4636
  • Browse through it!
  • The property hierarchy
  • No properties with multiple inheritance
  • Browse through it!

17
Axioms in NCI
  • Examples
  • Cancer_Gene v Gene u 9 hasFunction.Tumoregenesis
  • Alzheimer_Disease v Dementia
  • Domain(anatomic_Structure_has_Location)
    Anatomy_Kind
  • Range(technique_hasPurpose) Clinical_Or_Research
    _Activity_Kind

18
The NCI Kinds
  • Upper concepts representing the sub-domains of
    NCI
  • Examples
  • Anatomy.
  • Biological processes.
  • Chemicals and drugs.
  • Organisms
  • Properties relating the Kinds

19
NCI
  • Partitioning and crop-circles view of the
    partitioning
  • Here, we give an intuition about the different
    sub-domains in NCI, which ones are central and
    which ones are side domains

20
NCI and GALEN
  • The domains of NCI and GALEN overlap. Both
    ontologies define concepts such as
  • Anatomical parts bone, tissue, etc.
  • Diseases
  • Organisms,
  • Example
  • Check out how Femur is defined in NCI and GALEN
  • Discuss the different modeling decisions and
    focus of interest

21
Tambis
  • TAMBIS is a medical ontology constructed during
    the early days of the Web.
  • The intended application was the integrated
    access to information in a set of databases.
  • The OWL version was generated from the old format
    using a script.

22
Tambis The Ontology at a Glance
  • Size
  • 400 classes
  • 100 object properties
  • no individuals or datatypes
  • Expressivity
  • No General Concept Inclusion Axioms.
  • Concept constructors
  • Conjunction (intersectionOf)
  • Disjunction (unionOf)
  • Existential restrictions (someValuesFrom)
  • Universal restriction (allValuesFrom)
  • Cardinality restrictions
  • Axioms
  • Definitions (complete and partial)
  • Transitive, functional, symmetric and inverse
    properties

23
Tambis the (unclassified) hierarchies
  • Subclass relationships 226
  • No multiple inheritance
  • Maximum depth of class tree 6
  • Maximum depth of property tree 2

24
Tambis Example Axioms
  • Tambis uses cardinality restrictions profusely
  • See definition of anion
  • Use of disjunction
  • See definition of atom
  • Use of universal restrictions
  • See definition of book-title
  • Use of complex nested restrictions
  • See definition of complement-dna
  • See definition of gene
  • Disjointness axioms
  • See definitions of metal, non-metal and metalloid

25
Tambis Classification
  • Subclass relationships 600
  • compared to 226
  • Classes with multiple inheritance 19
  • compared to none
  • Maximum deph of class tree 7
  • compared to 6
  • Maximum depth of property tree 2
  • 144 unsatisfiable concepts!

26
Tambis Unsatisfiable concepts
  • Almost half of the concepts in Tambis are
    unsatisfiable
  • The explanations are non-trivial
  • Check out protein-structure and
    macromolecular-part!
  • Distinguishing root and derived unsatisfiable
    classes
  • derived unsatisfiable classes are unsatisfiable
    because they depend on another unsatisfiable
    concept.
  • definition of Enzyme,
  • definition of Binding-site
  • root unsatisfiable classes contain an
    inherent contradiction
  • definition of Metal,
  • definition of Non-metal,
  • definition of Metalloid

27
Tambis Repair
28
Advanced Issues and Design Patterns
29
Qualified Number Restrictions (QCRs)
  • Existential restrictions in OWL DL are qualified
  • Person u 9hasChild.Male
  • Cardinality restrictions can only be qualified
    with gt
  • Person u 9hasChild.Male
  • The lack of QCRs has been identified as a major
    limitation of OWL, especially in biomedical
    applications
  • A quadruped is an animal with exactly four parts
    that are legs
  • A medical oversight committee is a committee
    which consists of at least five members of which
    two are medical doctors, one is a manager and two
    are members of the public.

30
Qualified Cardinality Restrictions
  • Can be approximated using property inclusion
    and property range.
  • Quadruped Animal u ( 4 hasLeg)
  • hasLeg v hasPart
  • Range(hasLeg) Leg

31
Qualified Cardinality Restrictions
  • This approximation is unsound in general
  • MedicalCommittee Committee u (3 hasMember)
    u 1hasMember.MD u 1 hasMember. MD
  • Approximated by
  • MedicalCommittee (3 hasMember) u
    1hasMDMember u
  • 1hasNotMDMember
  • hasMDMember v hasMember
  • hasNotMDMember v hasMember
  • Range(hasMDMember) MD
  • Range(hasNotMDMember) MD

32
Transitive Propagation of Properties
  • In OWL, we can express transitive propagation of
    a property
  • If Paris is located in France and France is
    located in Europe, then France is located in
    Europe.
  • If the hand is a part of the arm and the arm is
    part of the human body, then the hand is a part
    of the human body.
  • In OWL, however, we cannot express transitive
    propagation of a property along a different
    property
  • If an ulcer is located in the gastric mucosa and
    the gastric mucosa is a part of the stomach, then
    the ulcer is located in the stomach
  • If a burn is located in the foot and the foot is
    part of the leg, then the burn is located in the
    leg.

33
Transitive Propagation of Properties
  • Various patterns that approximate transitive
    propagation have been proposed and used in
    ontologies.
  • Use of the property hierarchy and transitivity
  • Part_Of v Located_In
  • Transitive(Part_Of)
  • This pattern may yield to undesired results,
    since part-whole relations may not always imply
    location
  • The orange peal is part of the orange, but is it
    located in the orange?

34
Nominals in OWL-DL
  • Define concepts in terms of individuals.
  • Two constructs in OWL
  • owloneOf, owlhasValue
  • owloneOf - Enumeration of individuals.
  • WineColor ? red, white, rose
  • red, white, rose red t white t rose
  • owlhasValue - Value restrictions.
  • RedWine ? 9hasColor.red
  • RockFan v 9hasIdol.elvis

35
Nominals and Pseudo-nominals
  • Reasoners traditionally do not support nominals
    (only Aboxes)
  • Not enough implementation experience.
  • Believed to be hard.
  • Decision procedure for SHON in 2001!
  • Example Wine ontology
  • Used in OWL guide to demonstrate OWL.
  • Large number of nominals used.
  • No reasoner (even incomplete) could reason with
    it! Only Pellet (very recently)

36
Faking Nominals
  • Pseudonominals Approximation to nominals

SpanishWine Wine u 9producedIn.spain FrenchWi
ne Wine u 9producedIn.france
Unsound!!
SpanishWine Wine u 9producedIn.Spain FrenchWine
Wine u 9producedIn.France France u Spain ?
37
Pseudo-nominals unsoundness
  • Suppose we define the concept of a wine that is
    produced in at least three different countries
  • Wine u 3 producedIn.Country
  • Suppose I have only two countries in my ontology
  • Country Spain,France
  • My concept is then unsatisfiable.
  • Suppose we now use pseudo-nominals and treat
    Spain and France as disjoint atomic concepts.
    Then, our concept is satisfiable.
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