Why LexGrid?

2. Why LexGrid? Existing medical records • Various forms of coding and classification in use since the early 1500’s • ‘Modern’ records from the 1960’s to present include various forms of codes • Medical records are still on a “per-institution basis”

3. Why LexGrid? Emerging medical records Multiple factors forcing new levels of interoperability • Economic • Regulatory • Technical

4. Why LexGrid? Bioinformatics • Large volumes of information • Large cross sections • Detailed – what is important may not (and cannot) be anticipated • Interoperability of • Medical (Phenomics) • Genomics • Environmental • GeoSpatial

5. The GAP (In Western Medicine) “Terminologies” Coding and Classification ICD-10-PCS ICD-9-CM MGED SNOMED-III CPT-4 SNOMED CT ChEBI MESH SNOP ... GO FMA Countries Languages Many, many more to come GMOD Mime Types “Ontologies” Computable DL Frameworks

6. LexGridThe purpose behind LexGrid Communication

7. Language and the Communication Process • Language - a “specification” that enables communication • Semantics - the association between signs or symbols and their intended “meaning” • Syntax - the rules for ordering and structuring the signs into phrases and sentences • Pragmatics - the relationship between signs and symbols and the recipient. Broadly, the shared context.

8. Ogden’s Semiotic Triangle Thought or Reference Refers to Symbolises Symbol Referent Stands for C.K Ogden and I. A. Richards. The Meaning of Meaning.

9. Ogden’s Semiotic Triangle Thought or Reference Refers to Symbolises Symbol Referent Stands for “Rose”, “ClipArt” C.K Ogden and I. A. Richards. The Meaning of Meaning.

10. The Communication Process CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “I see a ClipArt image of a rose” “Rose”, “ClipArt” “Rose”, “ClipArt” Stands For Stands For Referent Symbol Symbol

11. The Communication Process Semantics CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “I see a ClipArt image of a rose” “Rose”, “ClipArt” “Rose”, “ClipArt” Stands For Stands For Referent Symbol Symbol

12. The Communication Process Semantics CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “I see a ClipArt image of a rose” “Rose”, “ClipArt” “Rose”, “ClipArt” Stands For Stands For Referent Symbol Symbol Syntax

13. Context The Communication Process Semantics CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “I see a ClipArt image of a rose” “Rose”, “ClipArt” “Rose”, “ClipArt” Stands For Stands For Referent Symbol Symbol Context Syntax Shared Context

14. Shared Context Impacts how much information can be contained in a symbol. Information / Symbol No Shared Context Shared Sun Shared Species Common Culture Common Profession Shared Universe Shared Planet Common Language Similar Education Common Specialty

15. Minimum Shared Context

16. The impact of context on communication Shared context: • Allows information to be communicated in larger, more succinct “chunks”. • Drug, analgesic and NSAID are all “chunks”, yet differ markedly in conceptual complexity. • Enables specialized symbol sets: • Contrast the amount of information contained in the formula E=MC2 versus that contained in this presentation...

17. Contextual Formalism The degree of formality in a shared context can vary across a wide spectrum: • Tacit context which is simply presumed • Contextual negotiation proceeding the actual message • Rigorous and formal rules and documents describing the form and possible meanings behind every message and phrase.

18. Factors Effecting the Degree Contextual Formalism • Number of participating parties • Formalism needs to increase as number of participants increase • Geographic, cultural and temporal proximity of communicators • The further apart communicators are, the less they can assume • Amount of shared context • The more you have, the more important it becomes to be organized

19. Factors Effecting the Degree Contextual Formalism • The cost of imprecise communication • Poetry and literature - low cost (some may argue actual gain) • Technical and professional - high to very high cost • What is the cost of assuming the units of a thrust specification? • What is the cost of assuming the dose of a prescription? • What is the cost of assuming the century in which the communication originated?

20. Common Forms of Contextual Formalism • Dictionaries • Thesauri • Textbooks, college courses, etc. • Operations manuals • Data dictionaries • Terminologies

21. Context The Communication Process Semantics CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “I see a ClipArt image of a rose” “Rose”, “ClipArt” “Rose”, “ClipArt” Stands For Stands For Referent Symbol Symbol Context Syntax Shared Context

22. Context Context Making Shared Context Explicit CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “I see a ClipArt image of a rose” “Rose”, “ClipArt” “Rose”, “ClipArt” Stands For Stands For Referent Symbol Symbol Formal Shared Context Terminologies Terminologies

23. Context Context Context Terminologies Terminologies Terminologies Shared Context Least Common Denominator CONCEPT CONCEPT “I see a ClipArt image of a red flower with ...” Symbolises Refers To Refers To Symbolises “I see a ClipArt image of a rose” “Rose”, “ClipArt” “Rose”, “ClipArt” Stands For Stands For Referent Symbol Symbol ... increase the symbol complexity Reduce the Shared Context...

24. Information vs. Symbol Information Symbol Symbol CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “I see a ClipArt image of a rose” “Rose”, “ClipArt” “Rose”, “ClipArt” Stands For Stands For Referent Symbol Symbol Information – predicate w/ Range of True/False/.. Symbol - predicate w/ Range of “Concept”

25. Symbol - Definitional Concept -> Symbol Symbol -> Concept Symbol/Symbol translation Symbol validation, organization and mapping Are axioms – not verifiable Information - Propositional Statements True/False/Unknown Convey information Are verifiable Ontologies serve (at least) two roles

26. Symbol A, B C, D R > ? : A C u D 8 R.C 9 R.> Interpretation AI, BI CI, DI RIµI x I I ? In AI CIÅ DI {a 2I | 8 b.(a,b) 2 RI! b 2 CI} {a 2I | 9 b.(a,b) 2 RI} Sample Description Logic

27. Interpretations • An interpretation Isatisfies an inclusion C v D if CIµ DI, and it satisfies an equality C ´ D if CI = DI. • If T is a set of axioms, then I satisfies T iff I satisfies each element of T. • If I satisfies an axiom (resp. a set of axioms) then we say that it is a model of this axiom (resp. set of axioms). • Two axioms or two sets of axioms are equivalent if they have the same models.

28. Symbol A, B C, D R > ? : A C u D 8 R.C 9 R.> Interpretation AI, BI CI, DI RIµI x I I ? In AI CIÅ DI {a 2I | 8 b.(a,b) 2 RI! b 2 CI} {a 2I | 9 b.(a,b) 2 RI} Description Logic Much study (DAML+OIL, OWL, CL, …) But what of this????

29. Interpretation and OWL OWL:AnnotationProperty • … in OWL DL one cannot define subproperties or domain/range constraints for annotation properties • Five annotation properties are predefined by OWL: owl:versionInfo rdfs:label rdfs:comment rdfs:seeAlso rdfs:isDefinedBy

30. A Rose in OWL? <owl:Class rdf:ID=“Rose”> <rdfs:subClassOf rdf:resource=“#FloweringPlant”/> <rdfs:subClassOf> <owl:restriction> <owl:onProperty rdf:resource=“#hasRisk”/> <owl:someValuesFrom rdf:resource=“#Thorn/> </owl:restriction> </rdfs:subClassOf> </owl:Class>

31. A Rose in OWL? <owl:Class rdf:ID=“C”> <rdfs:subClassOf rdf:resource=“#A”/> <rdfs:subClassOf> <owl:restriction> <owl:onProperty rdf:resource=“#R”/> <owl:someValuesFrom rdf:resource=“#D/> </owl:restriction> </rdfs:subClassOf> </owl:Class>

32. Context The Communication Process + CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “rose” “floweringPlant”, “hasRisk” “thorn” Stands For Stands For Referent Symbol Context {x 2I | 9 thorn.(x, thorn) 2 hasRiskIÅ x 2 floweringPlantI }

33. Context The Communication Process A101I = “flower” A102I = “sharp spine” + R1I = “possible misfortune” A101I = “rose” CONCEPT CONCEPT Symbolises Refers To Refers To Symbolises “A101” “A102”, “R1” “A103” Stands For Stands For Referent Symbol Context {x 2I | 9 A102.(x, A102) 2 R1IÅ x 2 A103^\cI}

34. Definitions vs. Propositions • Is this: • The thing that is defined as a procedure that involves an excision of a structure of lobe of lung? (Axiom) 2. A statement saying “All procedures that involve an excision of the structure of lobe of lung are pulmonary lobectomy? (Falsifiable proposition)

35. LexGrid Focus • Definitional Aspects of Ontologies • Making sure that the information (axioms) that are the basis of propositions are accurate, complete and reproducible • Making sure that resulting propositions are verifiable – that the terms that come out match the terms that go in

36. (Reference) Ontologies Reference ontologies are not designed to be nice - they are designed to be big, boring and true. Barry Smith

37. LexGrid Goal 1) Combine: • Lexical Semantics • Names • (Textual) Definitions • Comments • Other non-classification property • Context • Languages and dialects • Communities and specialties • Localizations • Logical Semantics • Roles and Relations

38. LexGrid Goal 2) Use these to integrate, reason about and report: • Existing data & codes • Special contexts • Need formalization • New information • New screens • Metadata

39. The LexGrid Goal Terminology as a commodity resource • Available whenever and wherever it is needed • Online or downloadable • Push or pull update mechanism • Available 24x7 • Revised and updated in “real-time” • Cross-linked and indexed

40. LexGrid Three-Pronged Approach LexGrid Model

41. The Heart of the Lexical Grid The LexGrid Model - a model of terminology that: • Explicitly names and defines the things that the LexGrid tools need to reference explicitly • Represents “non-semantic” entities as name/value pairs

42. Modeling Extremes hyperNormalized hyperSpecified

43. hyperNormalized Model + Incredibly flexible - Doesn’t say a heck of a lot about a given domain. • Specialization is possible • Entity: “Patient” • Attribute: “Name/String” • Relationship: hasName • Many hyperNormalized models already exist ER1 / UML / SQL / … hyperNormalized hyperSpecified

44. hyperSpecified Model

45. hyperSpecified Model + Incredibly precise – you know exactly what you’ve got • Unwieldy and inflexible • Difficult to understand hyperNormalized hyperSpecified

46. Modeling Pragmatics • Make the differences that are important explicit • Use terminology to carry the rest hyperNormalized hyperSpecified

47. The Heart of the Lexical Grid The LexGrid Model - a formal model of terminology that: • Explicitly names and defines the entities and objects used in the LexGrid tooling • Supports as many “non-semantic” entities (from the toolkit perspective) as possible via. Name/value pairs

48. The LexGrid Model Computation Interpretation

49. The LexGrid Model

50. (Short Rave) This is not a model of a concept!!! It is a model of a symbol!!!