MIE 2006 Tutorial Standards and Ontology Part 3: SNOMED - CT Sunday August 27th, 2006

1. MIE 2006 TutorialStandards and OntologyPart 3: SNOMED - CTSunday August 27th, 2006 Werner Ceusters, MD Ontology Research Group Center of Excellence in Bioinformatics & Life Sciences SUNY at Buffalo, NY

2. Objectives • Use the history of the development of SNOMED-CT to show the differences between a terminological and an ontological approach; • Look at some problematic features of concept-based thinking and how they are addressed in SNOMED-CT; • Make you think “ontologically”  ?

3. The “real” MIE2006 SNOMED-CT Tutorial • logical definitions; • integrated broad content; • table structures; • interaction between the relational model (three core tables) and the concept model used to represent medical content (hierarchies and relationship types linking the hierarchies); • related mappings; • support for data recording, retrieval and analysis; • quality assurance processes; • highlights of the SNOMED CT January 2006 release. Kent A Spackman Sunday, 27 August 2006; 09.30 – 12.30 http://www.mie2006.org/documents/ TutorialSpackman.pdf

4. Presentation outline • Ontology versus Terminology • Terminological thinking in SNOMED: • From SNOP to SNOMED-CT • Mistakes in SNOMED-CT due to terminological thinking • How to make SNOMED-CT better using real ontology

5. Terminology

6. ‘Terminology’ hastwo meanings • The discipline of terminology management • synonymous with terminology work (used in ISO 704) • The set of designations used in the special language of a subject field, such as the terminology of medicine • Used in in both the singular and plural • Used with an article in the singular: a terminology

7. Terminology is VERY standardised • ISO 704:2000Terminology work – Principles and methods • ISO 860:1996Terminology work – Harmonization of concepts and terms • ISO 1087-1:2000Terminology work – Vocabulary – Part 1: Theory and application • ISO 15188:2001Project management guidelines for terminology standardization • ISO 1087-2:2000Terminology work – Vocabulary – Part 2: Computer applications • ISO 12620:1999Computer applications in terminology – Data categories • ISO 16642:2003Computer applications in terminology – Terminological markup framework • ISO 2788:1986Documentation – Guidelines for the establishment and development of monolingual thesauri ?

8. ISO Standards in Terminology: building blocks • Objects • perceived or conceived, concrete or abstract • abstracted or conceptualized into concepts • Concepts • depict or correspond to a set of objects based on a defined set of characteristics • represented or expressed in language by designations or by definitions • organized into concept systems • Designations • represented as terms, names (appellations) or symbols • designate or represent a concept • attributed to a concept by consensus within a special language community ?

9. Fundamental Activities of Terminology Work • Identifying ‘concepts’ and ‘concept relations’; • Analyzing and modeling concept systems on the basis of identified concepts and concept relations; • Establishing representations of concept systems through concept diagrams; • Crafting concept-oriented definitions; • Attributing designations (predominantly terms) to each concept in one or more languages; and, • Recording and presenting terminological data, principally in terminological entries stored in print and electronic media (terminography).

10. Origin: Peirce, Ogden & Richards, Wüster Unit of Thinking (Concept) (Unit of Thought, Unit of Knowledge) Referent (Concrete Object, Real Thing, Conceived Object) Designation (Symbol, Sign, Term, Formula etc.)

11. ‘cancer’ in SNOMED-CT

12. ‘Cancer’ as disease versus morphology

13. Why terminologies ? • As such ? • Fixing/stabilizing the language within a domain and a linguistic community; • Unambiguous communication. • In Healthcare Information Technology ? • Semantic Indexing; • Information exchange and linking between heterogeneous systems; • Terminologies as basis for documentation through coding and classification

14. Coding versus classification • Coding: • Annotate terms in the EHR with codes from a coding system •  synonyms, translations, hierarchies • Classification: • Assign patients exhibiting certain features to a predefined class •  purpose oriented, culture dependent • Frequently mixed up !

15. Fracturednose= Fractureofnose ?

16. Coding / classification confusion • “patient with fractured nose” = “patient with fracture of nose” • But therefor not “fractured nose” = “fracture of nose” !

17. Ontology

18. Ontology • Ontology: the science of what things exist and how they relate to each other • An ontology is a representation of some pre-existing domain of realitywhich • (1) reflects the properties of the objects within its domain in such a waythat there obtains a systematic correlation between realityand the representation itself, • (2) is intelligible to a domain expert • (3) is formalized in a way that allows it to support automatic information processing OWL (DLs) does only this bit !

19. A division of labour • Terminology: • Communication amongst humans • Communication between human and machine • Ontology: • Representation of “reality” inside a machine • Communication amongst machines • Interpretation by machines

20. SNOMED-CT

21. SNOMED-CT SNOMED CT is a comprehensive and precise clinicalreference terminology that makes healthcare informationaccessible and useable, whenever and wherever it isneeded. Global in scope, yet adaptable for nationalpurposes,SNOMED CT provides a “common language” ofunsurpassed depth that enables a consistent way ofcapturing, sharing and aggregating health dataacrossclinical specialties and sites of care. http://www.snomed.org/news/pdfs/CTbrochure0902.pdf

22. SNOMED International www.snomed.org

23. Milestones in the development of SNOMED • SNOP – 1965 • SNOMED – 1974 • SNOMED II – 1979 • SNOMED Version 3.0 – 1993 • LOINC codes integrated into SNOMED – 1997 • SNOMED Version 3.5 – 1998 • SNOMED RT – 2000 • SNOMED CT (SNOMED RT + CTV3) – First release January 2002 • SNOMED CT Spanish Edition – April 2002 • SNOMED CT German Edition - April 2003 • Last version: SNOMED-CT English – July 2006

24. Systematized Nomenclature of Pathology (1965) • Author: • CAP Committee on Nomenclature and Classification of Disease • 4 coding axes: • Topography(physical/natural features), • Morphology(structure/form), • Etiology(causes), and • Function

25. 4 Hierarchies of SNOP • Topography T-terms • names of body sites • MorphologyM-terms • names of structural changes that occur in tissues as a result of disease • EtiologyE-terms • causative agents of disease (chemicals, bacteria, viruses) • FunctionF-terms • names of the physiological manifestations associated with disease (also symptoms and some viral diseases) ?

26. ‘Standard’ SNOP statement • In ‘TMEF-form’: ‘The body site T has undergone morphological change M due to the causative agent E resulting in physiological manifestations F’. • Or more accurate: [Morphology] in [Topography] caused by [Etiology] leads to[Function]

27. SNOP example statement [M: inflammation] in [T: lung] caused by [E: Influenza virus] leads to [F: hypoxia] ?

28. SNOMED International (1995, V3.1) • T Topography 12,385 • M Morphology 4,991 • F Function 16,352 • L Living Organisms 24,265 • C Drugs & Biological Products 14,075 • A Physical Agents, Forces and Activities 1,355 • D Disease/ Diagnosis 28,623 • P Procedures 27,033 • S Social Context 433 • J Occupations 1,886 • G General Modifiers 1,176 • TOTAL RECORDS 132,641 ?

29. Merriam-Webster On-Line Dictionary on ‘diagnosis’ • 1a:the art or act of identifying a disease from its signs and symptoms • 1b:the decision reached by diagnosis • 2:a concise technical description of a taxon • 3a:investigation or analysis of the cause or nature of a condition, situation, or problem • 3b:a statement or conclusion from such an analysis.

30. T - 3 5 3 2 2 Hierarchical structure of Snomed International posterior anatomic leaflet mitral cardiac valve cardiovascular ?

31. SNOMED International’s Hierarchical organization: an example • Bone • Long Bone • Periosteum • Shaft Isa Part or adjacency ? Part of ?

32. SNOMED International:Multiple ways for expressing the same entities D5-46210 Acute appendicitis, NOS D5-46100 Appendicitis, NOS G-A231 Acute M-41000 Acute inflammation, NOS G-C006 In T-59200 Appendix, NOS G-A231 Acute M-40000 Inflammation, NOS G-C006 In T-59200 Appendix, NOS

33. SNOMED-RT: first attempt to make relationships explicit

34. D5-30150:‘Postoperative esophagitis’ • In SNOMED III • Parent term in the hierarchy:D5-30100 Esophagitis, NOS • Cross-reference field :(T-56000)(M-40000)(F-06030) • where: T-56000 Esophagus M-40000 Inflammation F-06030 Post-operative state • In SNOMED-RT(in KRSS syntax) • (defconcept D5-30150 • (and D5-30100 • (some assoc-topography T-56000) • (some assoc-morphology M-40000) • (some assoc-etiology F-06030))) ? Spackman KA, Campbell KE, Cote RA.SNOMED RT: a reference terminology for health care.Proc AMIA Annu Fall Symp. 1997;:640-4.

35. KRSS: an old ‘description logics’ • Description logics: • A decidable fragment of FOL • A propositional modal logic • A classes and properties (concepts and roles)oriented KR language • Subsumption and satisfiability (consistency) are thekey inferences • Most DLs are supersets of ALC • Boolean operators on concepts • Existential and Universal quantifiers • OWL-DL is a large superset (SHOIN): • Property hierarchies & Transitive roles (SH) • Inverse (I) • Nominals (O) (hasValue and one of) • Number restrictions (counting quantifiers)

36. 2002: SNOMED-CT • A merger between • SNOMED-RT, and • the England and Wales National Health Service's Clinical Terms (previously known as the Read Codes). • SNOMED CT is considered to be the first international terminology.

37. Body structure Clinical finding Context-dependent category Environments and geographical locations Event Linkage concept Observable entity Organism Pharmaceutical / biologic product Physical force Physical object Procedure Qualifier value Record artifact Social context Special concept Specimen Staging and scales Substance SNOMED-CT hierarchies ?

38. Administrative statuses Adverse incident outcome categories Clinical history and observation findings Clinical stage finding Deformity Disease (disorder) Drug action Edema Effect of exposure to physical force Finding by method Finding by site Finding of grade Finding related to physiologic substance Finding reported by subject or history provider General clinical state finding Neurological finding Prognosis/outlook finding Sequelae of external causes and disorders Wound finding Clinical Finding hierarchy ?

39. SNOMED-CT evolution

40. Description of Algorithms Ceusters W, Smith B, Kumar A, Dhaen C. Mistakes in Medical Ontologies: Where Do They Come From and How Can They Be Detected? in: Pisanelli DM (ed) IOS Press, Studies in Health Technology and Informatics, vol 102, 2004.

41. ExploitingLexical, semantic and conceptual relations urine bladder gallbladder inflammation gall bladder urinary bladder gall biliary cystitis urine inflammation gall cystitis urinary bladder inflammation gallbladder gallbladder inflammation urinary bladder inflammation

42. Find the mistakes

43. Undetected synonymy ?

44. Undetected synonymy ?

45. Inadequate homonymy ?

46. Mistakes dueto inappropriatelexical mapping ?

47. Total / partial inconsistencies ?

48. Wrongmanually created subsumption ?

49. Wrongmanually created subsumption ?

50. SNOMED-CT (2003) Wrong computed subsumption SNOMED-RT (2000) ?