Foundations of the Semantic Web by jianglifang


									Foundations of the Semantic Web:
     Ontology Engineering

              Building Ontologies 2
               Ontology Patterns
               & Top Ontologies
            Alan Rector & colleagues
  Special acknowledgement to Jeremy Rogers & Chris Wroe
Common patterns & top level ontologies

• Patterns –
   – what links with what by what property
• High level ontologies
   – The top level view of the categories that can exist
• One approach to high top level ontologies
   – The constraints for the common patterns are expressed in the top
     level ontology
   – Top Level ontologies are most easily expressed as a series
     dichotomies1 which capture the distinctions needed for critical
       • Therefore work from ‘bottom up’, looking at patterns and deriving top
         the level ontology

 1Dichotomy:   split into two, from “di”: two; “chotomy” cut.
                  Basic Assumptions

• All primitives disjoint
   – With specified exceptions for “ValueTypes” to be explained
• Primitives separated into a
   – “Top Ontology” which are about broad abstractions
       • “Thing”, “Process”, “Substance”, etc.
           – Corresponds to our most abstract schemas and distinctions (dichotomies)
               » Only some of which are relevant to most domain ontologies
   – A “Domain Ontology Skeleton” – the things we really want to talk
       • Modules, Universities, People, Exams, etc
           – Domain primitives form disjoint pure trees
               » Every domain primitive has exactly one domain primitive parent
               » If not, requires “untangling”

                    Top Ontologies

• There are many proposed top ontologies
   – See OntoClean, SUO, SUMO, Cyc, John Sowa, …
• What is presented here is an amalgam
   – Mostly in plainer English, even at the cost of some loss
     of precision
      • Although I will present some of the technical words
   – Motivated by common engineering issues

       Common Patterns Summary (1)
• Independent things can have modifiers
   – The sky is blue
   – The exam is difficult
• Properties may be “reified”
   – “The food is hot”
   – The food has a temperature which is hot but cooling.
      • NB OWL allows descriptions of concepts only, not properties

      Common Patterns Summary (2)

• Things participate in processes / processes act on
   – Alan participates in the process of lecturing
   – Food participates in digestion
   – Student participates in learning
• Agents are responsible for Acts
   – Doctors order tests
   – People buy and sell things
   – Students take exams

       Common Patterns Summary (3)
• Forms & ‘oeuvres’ are manifest in things
   – “Hamlet” is manifest in a performance of “Hamlet” and
     in script for “Hamlet”
   – “The handouts for this course are manifest in both the
     presentation of power point slides and the physical
     paper handouts”
• Things and processes can be Physical or
  NonPhysical/ “Abstract”
   – A ball, the concept of a ball
   – An plan; an physical action motivated by that plan

       Common patterns Summary (4)

• Things are made of stuff/substances
   – Books are made of paper; The desk is made of wood.
   – Bones are made of bone_tissue; …
   – A Lecture is constituted of speaking, gesturing, pacing about,
     writing on the board,
• Things have parts in many different ways –
   – Part-whole relations are distinct from containment, connection,
     adjacency, branching, and other spatial relationships
       • The study of “merology” – the study of parts and wholes
• Part-whole relations are often ‘reciprocal’ as well as
  having inverses
   – We want to say both
       • “All fingers are parts of some hand” and
          “All hands have parts some fingers”                          8
              Common patterns Summary (5)
• There are many different kinds of collections/aggregations
   – Collections of small things become substances to make up big things
       • Molecules make up substances
       • Cells make up tissue
• Many things come in duals
   – Some are clearly distinguished
       • The “Bacteria causing the infection” is different from the “Infection caused by the
       • The “Degree earned by the study” is different from the “Study earning the degree”
   – Some are often identified
       • The “process of erosion” and the outcome of an “area of erosion”
       • The “process of building” and the “building built”

       • Some of this is a matter of language, but we often use the same word differently in
         the same sentence.
           – “The erosion has been going on for decades and covers thousands of square miles”
     Independent Entities can have modifiers


Indepenent                  Refining
  Entity                     Entity



         Ontology Patterns 1
Independent entities can haves modifiers
• Examples
   –    “Tom is tall”
   –   “CS646 exams are easy”
   –   “Dolphin’s swimming is fast”
   –   “Night is dark”
   –   “This is my left hand”
   –   “My left hand is resting on the right side of the desk”
        • (We’ll work on this one properly later)
   – The flow in the river is fast
• Modifiers/refiners
   – Usually expressed by adjectives or adverbs in English
        • Can be turned into nouns but this often makes odd reading, e.g.
             – “The tallness of john”

                Common dichotomy 1:
              Independent vs Dependent
               SelfStanding vs Refining
• Some things are “self-standing”
    – We can talk about them on their own
    – We cannot give an exhaustive list of their kinds
         • People, books, modules, buildings, ideas, …
• Some things are “refining”
    – They only make sense when applied to something else
    – Their kinds are arbitrary or measured
         • height – short, medium, tall – or 6ft
         • quality – good, indifferent, bad
         • laterality – left right
• “Self-standing” vs “Independent”
    – Engineering justification vs philosophical justification
         • treat as synonyms for now
              – Explain more in advanced course

 Refining concepts include “ValueTypes” & are
  linked to self-standing concepts by properties
• SizeValueType
• Department hasSize someValuesFrom SizeValueType
• Values normally are
    – disjoint
    – Cover value type
        • SizeValueType = small or medium_sized or small
• Refining properties are normally functional
  (aka “single valued”, “unique”)
    – It does not make sense to have two sizes

                         Example 2

• LateralityValueType = Left or Right
• Example
  – Hand hasLaterality someValuesFrom LateralityValueType
  – Screw hasThreatHandedness someValuesFrom LateralityValueType

  – Hmm… perhaps we have a poor name for LateralityValueType
     • “LeftOrRightValueType”?

                     Technical Pattern 1:
                   Reification1 of Properties
• We can re-express
          Department has_size someValuesFrom Large
          Department hasFeature someValuesFrom
                     (Size hasStateValue someValuesFrom Large).
• Any expression of the form

          Object property someValuesFrom value|

     can be re-expressed as

           Object hasFeature someValuesFrom
              (ReifiedProperty hasStateValue someValuesFrom state)
1 Reification– The process of making real. In knowledge representation, making
 something a object which can have properties in is own right and be a value.
 Closely related to the linguistic phenomenon of “nominalisation” – forming a              15
 noun from an adjective, adverb, or verb. (NB There is a second usage to be covered later)
                    Technical Pattern 1 (cont)

• We must be careful of cardinalities, when we re-express
   Department has_size someValuesFrom Large
     Department hasFeature someValuesFrom
                 (Size hasStateValue someValuesFrom Large).
• A Department should only have one Size – but can have many other
   – Solution 1: Qualified Number Restrictions – works in OilEd but not in official
     OWL (yet)
       • restriction Continuant1 hasFeature max-cardinality=1 Size
       • restriction Department hasFeature someValuesFrom
                                      (Size hasStateValue2 someValuesFrom Large)
                1 “Continuant” is a very high level notion in the top ontology which subsumes
                2 “hasStateValue” is functional                                             16
                 Why Reify Properties

• In order to say something about the relationship
   – i.e. in order to restrict the relationship
       • Restrictions only apply to classes, not properties
   – Example
     “Departments that are large by comparison with Computer Science

   – Department and hasFeature SomeValuesFrom (Size and
       (restriction hasValue someValuesFrom Large) and
       (restriction hasTrend someValuesFrom Increasing))

   Value, Trend, Temporal Pattern, Quantity

• Many features have a qualitative value, quantitative value,
  trend, and temporal pattern, e.g.
• “Trains that are delayed, becoming more delayed, whose delay
  is now 60 minutes, and whose delay is recurrent”
   – Train and hasFeature SomeValuesFrom (Timekeeping and
                    hasQualitativeValue someValuesFrom Delayed
                    hasQuantitativeValueInMinutes value 601
                    hasTrend someValuesFrom Increasing
                    hasTemporalPattern someValuesFrom Recurrent)

     1   NB “Concrete domains” – e.g. numbers and literals –
         are in OWL standard but not currently implemented in
         OilEd FaCT or Racer.

• Add the difficulty of exams and size to the
  department ontology
   – Allow for an exam’s difficulty to be given a reason, e.g.
     too long, material obscure, questions ambiguous, etc.
• Add size, publication output, and research income
  to the Department
   – Allow for trends

Feature-State pairs vs Intrinsic Properties (“Selectors”)
       • Some modifiers can change -
           – “Being late”, “tall”,” beautiful”, “being to the right of something”
           – Usually thought of as ‘accidental’
           – Often something useful to say about the relationship
             therefore useful to reify
                • Making reification a consistent pattern often helpful – otherwise
                  difficult to remember which are reified.
           – We have called the reifications “Features” 1
                • values are often called ‘states’ because they are true during some time
                     – See temporal discussion later.

   1    Guarino calls them “qualities” and some other authors use “feature” to mean
        other things. However “feature-state pairs” is fairly common usage.            20
                Dichotomy (cont)
    Feature-state pairs vs Intrinsic Properties
• Some modifiers are intrinsic and help identify the object
    – being a right hand, a philips screwdriver, a flatbed truck, the first rib,…
    – Usually thought of as ‘intrinsic’
    – Do not change during the life of the subject
    – Nothing to say about the relationship, therefore
      No value in reification
    – Nomenclature unsettled. Called “selectors” in GALEN
• StateValues can have further modifiers
    – “A very severe cold”
    – “A moderately good wine”
• Intrinsic properties cannot
    – “A very right hand”?
    – “A very third finger”?

          relates_to                                has_part1

         Things             participate_in          Processes
      (Continuants)                                (Occurrents)

                           Agent                      Act
PhysicalSructures           Organisation               Lecture
 Buildings                   University                Exam
                    owns                    isAgentOf
 Computers                   Department                Module
 …                           Research_group            …
                                             1   Should strictly        22
                                                 distinguish “monads”
                     Common Pattern
                  Processes act on things
                     Things “participate in” Processes
                  “Continuants” participate in “Occurrents”
                   “Endurants” participate in “Perdurants”

•   Person participatesIn Journey
•   Student participatesIn Study
•   Water participatesIn Flow
•   Lecturer and student each participatesIn Lecture
•   Ball and Footballer each participatesIn Kick

•   Numerous different kinds of participation
•   Can distinguish discrete and continuous “Occurrents”
     – discrete – Journey, Kick, Lecture
     – continuous – Flow, Study, Speaking, Listening
     But not always easy or useful to do so

                           Lenat termed continuous Occurrents “Activities”   23
                              Basic Dichotomy

• Continuants vs Occurrents
    – Roughly Things vs Processes
         • Processes change the state of things
              – Exact relationship left to philosophers
• “Continuants”  “Endurants”  “Things”
    – Entities which endure in time
    – Their parts likewise endure in time and are separated in spatial dimensions
         • Books, people, ideas, software, buildings, metal, plastic, …
              – May have “versions” and be modified by “feature-state” pairs at different periods
                of time, but have an identity which endures through time
• “Occurrents”  “Perdurants”  “Processes & Events”
    – Occur at or during some point or period of time
    – Their parts are separated in time (as well as space)
         • “Subprocesses”, “subevents”

             Important observation
Not All Ontological Patterns are relevant to all Ontologies
 Not of the Top Ontology are relevant to all applications

• The pizza ontology didn’t have any processes or events
   – The pizza menu is about things not processes
• A model of baking pizzas would need processes
• A model of pizza recipes would need processes
• A model of pizza menus does not need processes

• Most practical ontologies need only a bit of the top

                           False Dichotomy
                          Events vs Processes

• “Process” vs “Event” a point of view rather than intrinsic
    – “John ate dinner at 6:00 pm. He went to the movie at 7:30pm. After the
      movie he went home”
    – “During the dinner the telephone rang at 6:15. The movie lasted two
      hours. During the trip home he stopped to buy petrol”
• “Eating dinner”, “Attending the movie”, “The trip home”
    – Each treated sometimes as occurring at a definitive time point– an event
    – Each treated sometimes as occurring over a time interval - a process
        • NB the way in which verb moods mark processes and events varies even in
          Indo-European languages.
        • Best treated as “points of view” rather than properties of the Entity. (See
             – Not all philosophers agree, but we shall treat “event” and “process” as equivalent in
               this course.

         Many procssses have “Actors” (“Movers) and
          “Objects”/”Targets” and other roles (cases)
•   Actors and Objects
     – The River erodes the valley
     – The Person eats the food
     – The stone breaks the window
•   ActorContinuant isActorOf someValuesFor
     (ProcessOccurrent hasTarget someValuesFor ObjectContinuant)

•   We use “hasTarget” or “actsOn” rather than “hasObject” because it avoids
    confusion with linguistic usage
     – Which verbs are transitive and what prepositions/case they require varies from
        language to language and construction to construction within a language;
          •   I am waiting for John
          •   I await John’s arrival
          •   J’attends Jean
          •   I expect John’s arrival
          •   J’attends à l’arrivée de Jean
    Some actors are “responsible initiators”:
            Agents1 vs nonAgents
    • “Agent” – a key notion for most organisational ontologies
        – Entities that can initiative actions and take responsibility for them
             •   People
             •   Governments
             •   Committees
             •   Companies
             •   Animals?
             •   Gods?
                   – Aristotle’s & the Deists’ notion of God was as “First mover”
                   – “Mover” another alternative label for “Actor”

    • Processes which have responsible agents are called “Acts”
1   NB: There is no agreement on the use of the labels “Actor” and “Agent”. In linguistics
    “agentive” is a case roughly corresponding to “Actor” here We make the distinction in
    this way because many top ontologies use “Agent” in the sense of “responsible initiator”.
    However, in other ontologies, I.e. Schank, “Agent” is used as we use “Actor”.             28
       Being an agent may carry legal
• An adult is a legal agent in most situations and has legal
  responsibilities for their acts
• A child is not a legal agent in most situations
• Organisations may or may not be legal agents
• If needed
   – Distinguish between de facto and de jure (legal) agents
       • de jure agents often derive their agency from an authority
            – The University, the Government, the Bar, the General Medical Council,
   – Agency is complicated in many organisational schemes
       • Best ‘reified’ so that it can be described
            – However, in this course we will keep it simple and make it just a simple
              property isAgentOf
       Many processes have a source or a
• Consider
   –   John gave the book to Mary
   –   John received the book from Peter
   –   John received the book from Peter and gave it to Mary
   –   The surgeon transplanted the kidney from John to Mary
• Often does not matter – useful to have abstractions
   – hasSourceOrRecipient

        Many processes have outcomes

• Consider
   –   John wrote the book
   –   The architect created the design for the house
   –   The gene was expressed as a protein
   –   The student wrote the exam paper
   –   The river eroded the canyon
• Outcomes can in general be more general – i.e. states
   – The storm washed away the beach
        • In this course we will stick to simple cases where outcomes are things
             – Let’s us run together several intervening steps

    Role hierarchy for participates so far

 • Property hierarchy provides means of abstraction
 • Relations between occurrents and continuants
hasParticipant               participatesIn
  hasActor                     isActorOf
    hasAgent                       isAgentOf
  actsOn                       isActedOnBy
    hasTarget                     isTargetOf
    hasSourceOrRecipient          isSourceOrRecipientOf
       hasRecipient                  isRecipientOf
       hasSource                     isSourceOf
    hasOutcome                    isOutcomeOf         32
             Common Dichotomy
        Physical vs NonPhysical/Astract
• Physical things are in the physical world
   – Have mass or energy – or both – or be part of the physical
      • We’ll stick to a fairly naïve physics for this. We don’t need quantum
        mechanics to describe the University!
   – NB not necessarily “tangible” (touchable)
      • Energy, signals, magnetic fields, … are not tangible but are certainly
      • Space & Time (although require such special handling that it hardly
      • Includes both “continuants” and “Occurrents” – “Things” and “Processes”

           Common Dichotomy
      Physical vs NonPhysical/Astract
• Nonphysical things are in the psychosocial world
   – We won’t bother too much about how
       • leave that part for the philosophers
   – Some separate the Psychological from the Social World
       • But then a story which is composed in one person’s mind (Psyche)
         must become something different when it is told to and remembered
         by someone else and enters the social realm)
            – Separating Psyche and Social means we must make this decision
                » Do our potential applications require it?
                   If not, best blur it.
                » an example of an “Ontological Commitment”

• NB: The word “Abstract” is badly overloaded
   – Often used in OO programming for classes that are not allowed to
     have direct instances
       • Including many ontology tools
            – So I will just use “NonPhysical”
     Abstract Patterns are manifests in Physical Entities

      Nonphysical/                           Physical/
        Abstract                              Entities

 Natural Patterns
    Shapes etc                         Copies of Books
 Oeuvres                manifests_in   Performances
    Literature                         Paintings
    Music                              Texts
    Art                                Resources on the Web
                           Common Pattern
Abstract Patterns are manifests in Physical Entities
 • Consider
    – “Hamlet” manifests in a performance of “Hamlet”
    – “Hamlet” manifests in the “Script for Hamlet” manifests in “This copy of
      the script for ‘Hamlet’ held in the University library”
    – “Hamlet” was written by “Shakespeare”
    – “Your project” manifests in the paper copy you hand in or the electronic
      copy you email.
 • What is “Hamlet”
    – The abstract “Pattern” or “Form”
        • Exists in psycho-social space somehow
              – Engineers need not care about the details
    – Abstract “Patterns” which are the outcome of “Acts” by “Agents” we call
        • From the French for “works” but less ambiguous in English than “Works”
          which has 17 meanings in my dictionary.

  Patterns, Oeuvres and their Manifestations

• Our biomedical ontologies ignore the distinction most of
  the time
       • Interested either in bodies or pieces of paper / messages in wires

• Librarians must be very careful of these distinctions – and
  their refinements
   – Must distinguish
       • the abstract notion of a novel, play, symphony, poem, etc.
       • their specific editions (versions)
       • the copies on paper, microfiche, digital media held in their stores.
   – Copyright lawyers and IP specialists likewise
       • Important manifestation on the Web:
         “You may link to this but not copy it to your web site”
                         More NonPhysical Things
     • Mental things
            – ideas, feelings, perceptions, …
     • Social things
            – organisations, governments, languages, …
     • Patterns
            – The patterns manifest in physical things
                  • either composed or abstracted from them
                         – For most purposes can keep it simple
            – Roles – social_roles, physiologic_role, functional_role, etc.
     • Collections and aggregations – (see later in presentation)
            – Aggregations, multiples, and collections other than mathematical sets
     • Symbolic things
            – Mathematical and logical objects

1   A significant proportion of philosophy is devoted to the status o of abstract things such as mathematical objects,
    lost works of Aristotle, etc. We shall content ourselves with a five-way split. In practice, this is actually with four,
    since most symbolic things will end up in “concrete data types”. Since OWL explicitly excludes concrete data
    types from from the general classification lattice, their status has no engineering significance

• Is CS646_2003 a process in the physical world or
  an abstract pattern for that process?
   – How would we know? What questions should we ask?
   – We could probably distinguish
      • a specific instance of a “named pattern” – the thing that
        appears in the syllabus – clearly something nonPhysical
      • the actual course itself with its lectures, labs etc – clearly
      • Would it be helpful to do so?
          – Can you think of examples
              » Do they matter for this application?


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