Introduction to Ontologies

1. Introduction to Ontologies

2. Reusable Specifications as Ontologies An ontology is a partial specification of a conceptual vocabulary to be used for formulating knowledge-level theories about a domain of discourse. The fundamental role of an ontology is to support knowledge sharing and reuse. Example: Ontology Simple-TimeDefines classes, relations and axioms to support the modelling of time-dependent activities

3. Classes Day-Name Day-Number Duration Hour-Number Minute-Number Month-Name Month-Number Second-Number Time-Point Calendar-Date Calendar-Year Universal-Time-Spec Time-Range Year-Number Relations < > After After= Before Before= Disjoint-Time-Ranges During During= Equals Finishes Finishes= Meets Overlaps Overlaps= Start= Starts Classes and Relations in Simple Time

4. Definition of Time Point (def-class TIME-POINT (time-position) "A point in time" ((second-of :type second-in-time :max-cardinality 1 ) (minute-of :type minute-in-time :max-cardinality 1 ) (hour-of :type hour-in-time :max-cardinality 1 ) (day-of :type day-in-time :max-cardinality 1) (month-of :type month-in-time :max-cardinality 1) (year-of :type year-in-time :max-cardinality 1 )) :constraint (and (not (and (month-of ?x 2) (> (the ?day (day-of ?x ?day)) 29))) (not (and (member-of ?x (4 6 9 11)) (> (the ?day (day-of ?x ?day)) 30)))))

5. Ontology for medical guidelines • What is a medical guideline? • A specification (often partial) of a protocol of care • Aims to define “best practice” • Examples • Protocols for treating AIDS patients • Protocols for the prevention of bed sores • The Ontology • Defines classes, relations and axioms to support the specification of medical guidelines • Builds on a generic medical ontology • Supports both guideline design and execution.

6. Advantages of Ontologies (1): Reuse base-ontology simple-time common-concepts generic-events bibliographic-data generic-technologies organization-ontology medical-ontology medical-guidelines

7. Class Hierarchy for Medical Guidelines Simple-time Ontology Temporal-thing Common Concepts Ontology Plan Medical-Guidelines Ontology Medical-Guideline Preventive-Guideline Therapeutic-Guideline Diagnostic-Guideline

8. Advantages of Ontologies (2) • Formal Community View • Make it possible to formalise a shared viewpoint over a certain universe of discourse • E.g., agreement on how to model time • Interoperability • Can support communication and cooperation between systems developed at different sites • The ontological commitments made by a system are made explicit • E.g., diagnostic and therapy-control medical systems may share the same underlying generic medical ontology • e.,g., notion of pathological state, therapeutic procedure

9. Advantages of Ontologies (3) • Model-based knowledge acquisition • E.g., use the medical guideline ontology to acquire knowledge about particular medical guidelines in a structured way • Knowledge-level validation and verification • E.g., use the medical guideline ontology to check guideline documents

11. Criteria for Ontology Design (Gruber, 1995) • Clarity • User-centred definitions • Documentation • Alternative choices • Coherence • Logical consistency • Coherent Style (e.g., naming conventions) • Minimal ontological commitments • Do not impede extensibility by making unnecessary knowledge-level commitments • Minimal encoding bias • Do not pre-judge reuse by making symbol-level commitments

12. Example of not-so-good definition Physical Quantity = <Unit, Magnitude> Example: <second, 5> (defrelation PHYSICAL-QUANTITY (<=> (PHYSICAL-QUANTITY ?q) (and (defined (quantity.magnitude ?q)) (double-float (quantity.magnitude ?q)) (defined (quantity.unit ?q)) (member (quantity.unit ?q) (setof meter second kilogram ampere kelvin mole candela)))

13. Example of not-so-good definition Physical Quantity = <Unit, Magnitude> Example: <second, 5> (defrelation PHYSICAL-QUANTITY (<=> (PHYSICAL-QUANTITY ?q) (and (defined (quantity.magnitude ?q)) (double-float (quantity.magnitude ?q)) (defined (quantity.unit ?q)) (member (quantity.unit ?q) (setof meter second kilogram ampere kelvin mole candela))) Encoding Bias Unnecessary Ontological Commitment

14. AKT Reference Ontology • Task: Develop a common ontology to describe academic resources • Rationale: • Ontology to provide a common semantic basis to support variety of AKT services • Gather data about collaborative development • Test tools • Take Integration and Collaboration seriously AKT is a 6-year UK €11M focusing on knowledge technologies, involving 5 universities

15. Organization of AKT Reference Ontology • 100% self-contained • Two-subontologies • AKT-Support • Frames, Sets, Numbers, Lists, Relations, Time, Micro Top Level • AKTive-Portal • Technologies, Events, People & Organizations, Documents, Research Areas and Projects

16. Publishing through D3E

17. Setup for collaborative ontology design Screen 1OntologyBrowsers Screen 2Discussion/RationaleCapture in Compendium

18. Capturing ontology design, discussions, and rationale

19. Publishing through D3E

21. Typology of Comments

22. AKT-2 Architecture Southampton RDF OKBC Triple Store RDF Edinburgh. RDF AKT Reference Ontology Aberdeen. RDF RDF Sheffield. E-print server Amilcare RDF OU News server Wilbur AKT Portal Client Freaky OCML OCML AKT Portal KB AKT Reference Ontology Aktive Portal Server

23. Exercise: Analysis of AKT Reference Ontology

25. Class Medical-Guideline (def-class medical-guideline (plan) "Each guideline is associated with a medical condition. It also targets a particular population" ((outcome-measure :type string) (target-population :type population-specification) (full-name :type string) (associated-medical-condition :type medical-condition) (temporal-constraints :type string) (location-constraints :type guideline-application-location) (associated-documents :type document-reference) (has-guideline-user-type :type guideline-user-type)))