Ontologie-basierte Qualitätssicherung medizinischer Terminologien

1. Ontologie-basierte Qualitätssicherung medizinischer Terminologien Barry Smith with thanks to Werner Ceusters, Anand Kumar and Cornelius Rosse ifomis.org

2. Problems with UMLS • Each is a ‘fusion’ of several source vocabularies, some of dubious quality • They were fused without an ontological system being established first • They contain circularities, taxonomic gaps, and unnatural ad hoc determinations • They are representations of concepts, not of reality ifomis.org

3. UMLS Metathesaurus traps ifomis.org

4. Problem: Confusion of concepts and entities in reality ifomis.org

5. Blood Pressure Ontology • The hydraulic equation: • BP = CO*PVR • arterial blood pressure (BP) is directly proportional to the product of blood flow (cardiac output, CO) and peripheral vascular resistance (PVR). ifomis.org

6. UMLS-Semantic Types: • blood pressure is an Organism Function, • cardiac output is a Laboratory or Test Result or Diagnostic Procedure ifomis.org

7. UMLS-Semantic Types: • BP = CO*PVR thus asserts that • blood pressure is proportional either to a laboratory or test result or to a diagnostic procedure ifomis.org

8. ifomis.org

9. SNOMED-CT • 900,000 ‘concepts’ • Description Logic infrastructure • NIH + NHS gesegnet • College of American Pathologists • SNODENT ifomis.org

10. Confused treatment of is_a and part_of • beide_Hoden is_a Hoden • beide_ Gebärmuttern is_a Gebärmutter • teilweise_Entfernung_der_Blase • is_a Entfernung_ der_Blase. ifomis.org

11. Confused treatment of is_a and part_of • Halbextraktion_aus_Steißlage is_a Extraktion_aus_Steißlage • Extraktion_aus_Steißlageis_a vollständige_Steißgeburt • ____________________________ • Halbextraktion_aus_Steißlage is_a vollständige_Steißgeburt ifomis.org

12. Confused treatment of objects and processes • diagnostische_endoskopische_Untersuchung_eines_Mediastinums_NOS • is_a Mediastinoskop. ifomis.org

13. Confusion of object with knowledge about object • Kontrazeption is_a funktionaler_Befund ifomis.org

14. Just plain confusion • labial vein is_a vein of head • labial vein is_a vulval vein • Dupuytren-Krankheit,_ • Knoten_ohne_Kontraktur • is_a • Kontraktur_der_Palmarfaszie ifomis.org

15. Problems with logical combination • ‘Veterinary proprietary drug AND/OR biological’ * • Such terms not designate natural kinds. (Which biological classes exist is not a matter of logical combination of terms or concepts) • *has 2532 children in SNOMED-CT ifomis.org

16. Confusion of part_of and overlaps_with • Struktur_des_Nervus_tibialis • is_a • Oberschenkelteil • Struktur_des_Nervus_tibialis • is_a • Unterschenkelstruktur ifomis.org

17. Missed subsumption detection Missing: is_a neoplasm of heart ifomis.org

18. Are these just isolated examples of errors? ifomis.org

19. Why Description Logicsare not enough SNOMED-RT amputation of toe is_a amputation of foot Hahn-Schulz improvements re part-of in SNOMED-CT ifomis.org

20. ifomis.org

21. National Cancer InstitutecaCORECancer Informatics Infrastructure Backbone caBIO Cancer Bioinformatics Infrastructure Objects: Biomedical objects to facilitate the communication and integration of information from the various initiatives supported by the NCICB ifomis.org

22. caBIO architecture Connectivity at programming interface level ifomis.org

23. Instead of building an ontology of cancer • the NCI builds an ontology (or a ‘model’) of the data in the NCI’s own computers ifomis.org

24. NCI Thesaurus • a biomedical thesaurus created specifically to meet the needs of the NCI • semantically modeled cancer-related terminology built usingDescription Logic ifomis.org

25. Search for “cancer” ifomis.org

26. Missed subsumption detection ifomis.org

27. Recall SNOMED confusion of ‘part’ and ‘structure’ • Struktur_des_Nervus_tibialis • is_a • Oberschenkelteil • Struktur_des_Nervus_tibialis • is_a • Unterschenkelstruktur ifomis.org

28. Confusion of ‘part’ and ‘structure’ and ‘system’ and ‘substance’ ifomis.org

29. Anatomic Structure, Anatomic System, or Anatomic Substance ? Or ? Does the NCI not know to which category Any item classified there belongs ? Anatomic Substance ? If yes, why is gene product not subsumed by it ? If no, why are drugsandchemicals not subsumed by it ? NCI Thesaurus Root concepts ifomis.org

30. Conceptual entity • Definition: none • Semantic type: • Conceptual entity • Classification • Subconcepts: • Action: • definition: action; a thing done • And: • Definition: an article which expresses the relation of connection or addition, used to conjoin a word with a word, ... ifomis.org

31. Conceptual entity • Action is_a Conceptual Entity • And is_a Conceptual Entity • Swimming is healthy and contains 8 letters ifomis.org

32. Definition of “cancer gene” ifomis.org

33. What diseases have a diameter of over 3 cm ? NCI Thesaurus architecture Findings-And- Disorders-Kind Anatomy-Kind Disease “Formal subsumption” or “inheritance” “Associative” relationships providing “differentiae” “Kinds” restrict the domain and range of associative relationships ISA Breast neoplasm Breast Disease-has-associated-anatomy ifomis.org

34. Confusion of objects and the states in which they participate Findings-And- Disorders-Kind Anatomy-Kind Disease ISA Breast neoplasm Breast Disease-has-associated-anatomy ifomis.org

35. Cancer Data Standards Repository (caDSR) • “One of the problems confronting the biomedical data management community is the panoply of ways that similar or identical concepts are described.” • The real problem is thatconcepts are being described.  ifomis.org

36. Problems with the concept orientation • Ad hoc readings of statements of the type C1-relationship-C2 • California is-part-of United States // California isa name • Concepts do not necessarily correspond to anything in reality: sorcerer, unicorn, leprechaun, ... • Language can make strings of words look as if it were terms • Middle lobe of left lung ifomis.org

37. “Ontology” • In information science: • An ontology is a description (like a formal specification of a program) of the concepts and relationships that can exist for an agent or a community of agents. • In philosophy: • Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ifomis.org

38. Why are conceptsnot enough? • only by looking at referents in reality can we work out how the concepts used by different communities relate to each other ifomis.org

39. Ontology as Bridge for Understanding Cancer Information • Diseases • Pathological Processes • Body site for diseases • Diseases by staging • Risk factors SNOMED • Anatomy • Is-a, part-of • Granular relationship FMA • Biological Processes • Ontology • Classification GO • Swiss-Prot proteins • Annotation: function, structure, mutation ifomis.org

40. Levels of granularity inbiomedical ontology Granularity level Continuants Occurrents ifomis.org

41. SWISS-PROT and OMIM databases have little capability to support reasoning which crosses levels of granularity • also, like SNOMED and GO, they offer no facility for reasoning about time and instances ifomis.org

42. TNM Staging Information • T1: The tumor invades the submucosa, the second layer of the large intestine. • T2: The tumor invades the muscularis propria. … ifomis.org

43. We need an ontological framework with the facility to deal with instance-based information drawn from Patient Records TNM Staging Information Risk factors (Age, Family history) Localization of Tumor (Organ affected, Tissues involved) Pathology (Gross and Miscroscopic pathology, Vessels involved, Nerves involved, Cell types, Nuclear characteristics) ifomis.org

44. Basic Formal Ontology glues the whole thing together at different levels of granularity, from molecular to whole organism level at different stages in time ifomis.org