1http://img.cs.man.ac.uk/stevens
Communities building ontologies:
Tensions and Reality
Robert StevensUniversity of Manches...
2http://img.cs.man.ac.uk/stevens
Introduction
• CS & domain experts
• Why do CS people go on about semantics?
• CS version...
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Two Communities
Computer Scientists
Building ontologies
KR
Reasoning
Better Ontologies
Bi...
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So what Counts as an ontology?
[Deborah McGuinness, Stanford]
Catalog/
ID
Thesauri
Terms/...
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Semantics
– An operational semantics for a language is
defined by what a sentence in that...
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Malate Dehydrogenase Activity
• malate dehydrogenase activity
• GO:0016615
• definition: ...
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What are We Saying?
Person
WomanMan
is-ais-a
•Are all instances of Man instances of Perso...
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What are we saying?
• What kinds of class can fill “has chromosome”?
• How many “Y chromo...
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What Does the Computer Know?
#1234
#5678#9101
#1121#1121
•Knows that all instances of #56...
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malate dehydrogenase
class malate dehydrogenase defined
subClassOf enzymatic_function
re...
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Building Ontologies
• No field of Ontological Engineering equivalent to Knowledge or
Sof...
12http://img.cs.man.ac.uk/stevens
The Development Lifecycle
• Two kinds of complementary methodologies emerged:
– Stage-ba...
13http://img.cs.man.ac.uk/stevens
A Provisional Methodology
• A skeletal methodology and life-cycle for building ontologie...
14http://img.cs.man.ac.uk/stevens
Methodology
Conceptualisation
Integrating existing
ontologies
Encoding
Representation
Id...
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An Ontology Building Life-cycle
Identify purpose and scope
Knowledge acquisition
Evaluat...
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Some Reality & Tensions
• Conceptualisation & encoding conflated
• Encoding rarely drive...
17http://img.cs.man.ac.uk/stevens
More Reality & Tensions
• The community must need the ontology
• The community must buil...
18http://img.cs.man.ac.uk/stevens
More Tips from GO
• Policy for updates of concept labels, Ids and definitions
• Separate...
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Some Solutions
• Simple representation often unsustainable
• DL gives better sustainabil...
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Migration path
OWL ontologyDAG like ontology
i. Semantic diff
ii. Delivery in familiar f...
21http://img.cs.man.ac.uk/stevens
Things, Symbols & Concepts
• Humans require words (or at least symbols) to communicate
e...
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Communities building ontologies: Tensions and Reality

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Invited talk at an ontology meeting at harwell 2003

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  • Concept refers to thing
    Symbol stands for Thing
    Symbol evokes concept
    Symbol: “Jaguar”
    Thing: car or beast
  • Communities building ontologies: Tensions and Reality

    1. 1. 1http://img.cs.man.ac.uk/stevens Communities building ontologies: Tensions and Reality Robert StevensUniversity of Manchester Robert.stevens@cs.man.ac.uk
    2. 2. 2http://img.cs.man.ac.uk/stevens Introduction • CS & domain experts • Why do CS people go on about semantics? • CS version of building ontologies • Some reality • Resolving some tensions
    3. 3. 3http://img.cs.man.ac.uk/stevens Two Communities Computer Scientists Building ontologies KR Reasoning Better Ontologies Biologists Ontology content Domain Knowledge
    4. 4. 4http://img.cs.man.ac.uk/stevens So what Counts as an ontology? [Deborah McGuinness, Stanford] Catalog/ ID Thesauri Terms/ glossary Informal Is-a Formal Is-a Formal instance Frames (properties) General Logical constraints Value restrictions Disjointness, Inverse, partof Gene Ontology Mouse Anatomy EcoCyc PharmGKB TAMBIS Arom
    5. 5. 5http://img.cs.man.ac.uk/stevens Semantics – An operational semantics for a language is defined by what a sentence in that language will do. – Denotational semantics is a precise mathematical definition of the objects and relations of language in which each sentence of the language names, or denotes, a mathematical object, such as a function. – Natural semantics are the loose ordinary language sense, in which the semantics of a statement is its "meaning". – The term logicist semantics refers to formal models that attempt to represent the natural semantics of some external domain.
    6. 6. 6http://img.cs.man.ac.uk/stevens Malate Dehydrogenase Activity • malate dehydrogenase activity • GO:0016615 • definition: Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate using NAD or NADPH.
    7. 7. 7http://img.cs.man.ac.uk/stevens What are We Saying? Person WomanMan is-ais-a •Are all instances of Man instances of Person? •Can an instance of Person be both a Man and an instance of Woman? •Can there be any more kinds of Person?
    8. 8. 8http://img.cs.man.ac.uk/stevens What are we saying? • What kinds of class can fill “has chromosome”? • How many “Y chromosome” are present? • Does their have to be a “Y chromosome”? • What properties are sufficient to be a Man and which are simply necessary? Y chromosomeMan has chromosome Y chromosomeMan has chromosome X chromosome has chromosome autosome has chromosome 1 1 44
    9. 9. 9http://img.cs.man.ac.uk/stevens What Does the Computer Know? #1234 #5678#9101 #1121#1121 •Knows that all instances of #5678 are members of #1234 •Knows that #5678 & #9101 are disjoint •Knows that #5678 & #9101 are the only kinds of #1234
    10. 10. 10http://img.cs.man.ac.uk/stevens malate dehydrogenase class malate dehydrogenase defined subClassOf enzymatic_function restriction onProperty has_reagent_on_side_A has-class malate restriction onProperty has_reagent_on_side_B has-class oxaloacetate restriction onProperty has_reagent_on_side_A has-class NADP anion restriction onProperty has_reagent_on_side_B has-class NADPH restriction onProperty catalyses has-class ((reducing and (restriction onProperty acts_on has-class NADP)) and (oxidising and (restriction onProperty acts_on has-class malate) and (restriction onProperty acts_on_donar_group has-class CH-OH group))) restriction onProperty catalyses has-class ((reducing and (restriction onProperty acts_on has-class oxaloacetate)) and (oxidising and (restriction onProperty acts_on has-class NADPH))) restriction onProperty catalyses to-class (((reducing and (restriction onProperty acts_on has-class NADP) and (oxidising and (restriction onProperty acts_on has-class malate) and (restriction onProperty acts_on_donar_group has-class CH-OH group))) or ((reducing and (restriction onProperty acts_on has-class oxaloacetate)) and (oxidising and (restriction onProperty acts_on has-class NADPH))))
    11. 11. 11http://img.cs.man.ac.uk/stevens Building Ontologies • No field of Ontological Engineering equivalent to Knowledge or Software Engineering; • Developing standard methodologies for building ontologies; • Such a methodology would include: – a set of stages that occur when building ontologies; – guidelines and principles to assist in the different stages; – an ontology life-cycle which indicates the relationships among stages. • Gruber's guidelines for constructing ontologies are well known.
    12. 12. 12http://img.cs.man.ac.uk/stevens The Development Lifecycle • Two kinds of complementary methodologies emerged: – Stage-based, e.g. TOVE [Uschold96] – Iterative evolving prototypes, e.g. MethOntology [Gomez Perez94]. • Most have TWO stages: – Informal stage • ontology is sketched out using either natural language descriptions or some diagram technique – Formal stage • ontology is encoded in a formal knowledge representation language, that is machine computable • An ontology should ideally be communicated to people and unambiguously interpreted by software – the informal representation helps the former – the formal representation helps the latter.
    13. 13. 13http://img.cs.man.ac.uk/stevens A Provisional Methodology • A skeletal methodology and life-cycle for building ontologies; • Inspired by the software engineering V-process model; • The overall process moves through a life-cycle. The left side charts the processes in building an ontology The right side charts the guidelines, principles and evaluation used to ‘quality assure’ the ontology
    14. 14. 14http://img.cs.man.ac.uk/stevens Methodology Conceptualisation Integrating existing ontologies Encoding Representation Identify purpose and scope Knowledge acquisition Evaluation: coverage, verification, granularity Conceptualisation Principles: commitment, conciseness, clarity, extensibility, coherency Encoding/Representation principles: encoding bias, consistency, house styles and standards, reasoning system exploitation Ontology in Use User Model Conceptualisation Model Implementation Model Ontology Learning Maintenance
    15. 15. 15http://img.cs.man.ac.uk/stevens An Ontology Building Life-cycle Identify purpose and scope Knowledge acquisition Evaluation Language and representation Available development tools Conceptualisation Integrating existing ontologiesEncoding Building Ontology Learning Consistency Checking
    16. 16. 16http://img.cs.man.ac.uk/stevens Some Reality & Tensions • Conceptualisation & encoding conflated • Encoding rarely driven by system requirements • Very difficult to re-use other ontologies • Not really sequential stages, but overlapping • Little support for communal development and comment
    17. 17. 17http://img.cs.man.ac.uk/stevens More Reality & Tensions • The community must need the ontology • The community must build the ontology • There is no one true ontology • Don’t wait for completeness • Don’t wait for correctness • Simple representation gives rapid start • DL too difficult to use
    18. 18. 18http://img.cs.man.ac.uk/stevens More Tips from GO • Policy for updates of concept labels, Ids and definitions • Separate concept labels and Ids • Track obselete terms: “replaces” and “replaced by” • Record provenance of term’s origins • Be open
    19. 19. 19http://img.cs.man.ac.uk/stevens Some Solutions • Simple representation often unsustainable • DL gives better sustainability • Need domain experts to build, but ontologist to refine • DL representation bad for users: Need familiar representation • Reconciling simplicity and sustainability • Applying CS knowledge appropriately
    20. 20. 20http://img.cs.man.ac.uk/stevens Migration path OWL ontologyDAG like ontology i. Semantic diff ii. Delivery in familiar format iii. Consistent and taxonomically complete iv. Property based and reasonable i. Communal knowledge acquisition ii. Provenance of acquisition iii. Communal commentary iv. Consensus i. Report changes ii. Semantic diff Communal ontology development
    21. 21. 21http://img.cs.man.ac.uk/stevens Things, Symbols & Concepts • Humans require words (or at least symbols) to communicate efficiently. The mapping of words to things is only indirectly possible. We do it by creating symbols that stand for things. • The relation between symbols and things has been described in the form of the meaning triangle: “Jaguar“ Concept [Ogden, Richards, 1923]

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