How do We Teach Anatomy to the Computer? Structural Informatics Group University of Washington

2. American Association of Clinical Anatomists 2001 How do We Teach Anatomy to the Computer? Structural Informatics Group University of Washington

3. How to Teach Anatomy to the Computer? • Why do we need to teach anatomy to the computer? • What to teach to the computer? • How do we do it?

4. Why Teach Anatomy to the Computer? • Current status of computer programs in anatomy • Knowledge representation • Information access

5. Why Teach Anatomy to the Computer? • Current status: Knowledge representation • Traditional sources • Spatial: cadaver, radiology, atlases • Symbolic: textbooks, • Unique to the computer • Spatial: volumetric data sets • 3D graphical models • Symbolic: ???

6. Why Teach Anatomy to the Computer? • Current status of computer programs in anatomy • Information access • CD-ROM, Internet • One piece of information • for one mouse click

7. Why Teach Anatomy to the Computer? The Semantic Web: A new form of Web content that is meaningful to computers will unleash a revolution of new possibilities. By: Tim Berners-Lee James Hendler Ora Lassila

8. Why Teach Anatomy to the Computer? • Need for • Knowledge-based (smart) applications • in: education • clinical medicine • research • Anatomical knowledge in • computer-understandable form • Leading to • Qualitative change in role of teacher

9. How Do We Teach Anatomy to the Computer? The Digital Anatomist Information System James F. Brinkley M.D., Ph.D. Cornelius Rosse M.D., D.Sc. Structural Informatics Group University of Washington

10. End-User Programs Authoring Programs Network Servers Anatomy Knowledge Sources Digital Anatomist Information System Symbolic Knowledge Source Image Repository

11. End-User Programs Authoring Programs Servers Digital Anatomist Information System Network 2-D Images 2-D Annotations 3-D Model 3-D Image Volumes Symbolic Knowledge Source Image Repository

12. Graphical Authoring Programs End-User Programs Skandha Annotator Scene Generator Servers Digital Anatomist Information System Network 2-D Images 2-D Annotations 3-D Model 3-D Image Volumes Symbolic Knowledge Source Image Repository

13. End-User Programs Servers Digital Anatomist Information System Symbolic Authoring Programs Foundational Model Builder Protégé Network Foundational Model Meta- knowledge Clinical Info Image Repository Symbolic Knowledge Sources

14. Authoring Programs Network Servers Anatomy Knowledge Sources Digital Anatomist Information System End User Interfaces Digital Anatomist Atlases Brain Mapper Radiation Oncology Symbolic Knowledge Source Image Repository

15. Graphical Symbolic Digital Anatomist Atlases Digital Anatomist Information System Authoring Programs End-User Interfaces Network Graphics Server Image Server Data Server Knowledge Server Symbolic Knowledge Source Image Repository Anatomy Knowledge Sources

16. Digital Anatomist Information System Web-based Digital Anatomist Atlas of Thoracic viscera

28. Authoring Programs Network Servers Anatomy Knowledge Sources Digital Anatomist Information System End User Interfaces Digital Anatomist Atlases Brain Mapper Radiation Oncology Symbolic Knowledge Source Image Repository

30. Superimposed FMRI and cortical language maps

31. Authoring Programs Network Servers Anatomy Knowledge Sources Digital Anatomist Information System End User Interfaces Digital Anatomist Atlases Brain Mapper Radiation Oncology Symbolic Knowledge Source Image Repository

32. Radiation Treatment Planning PRISM

33. Structural Informatics Group Anatomists Cornelius Rosse, MD, DSc Jose Mejino, MD Augusto Agoncillo, MD Richard Martin, PhD Kate Mulligan, PhD John Sundsten, PhD Doug Bowden, MD Clinicians George Ojemann, MD Ken Maravilla, MD David Corina, MD Karen Kinbar, PhD Computer Science/Informatics James Brinkley, MD, PhD Linda Shapiro, PhD Ira Kalet, PhD William Lober, MD Andrew Poliakov, PhD Rex Jakobovits, PhD Kurt Rickard, PhD Sara Kim, PhD Jeff Prothero Ravensara Travillian, MA Peter Mork Zhenrong Qian Chia-chi Teng

34. How Do We Teach Anatomy to the Computer? The Foundational Model of Anatomy Cornelius Rosse M.D., D.Sc. Structural Informatics Group University of Washington

35. Digital Anatomist Image Repository 3-D Models of Right Lung and Heart

36. End-User Programs Authoring Programs Servers Digital Anatomist Information System Network Foundational Model Meta- knowledge Clinical Info Image Repository Symbolic Knowledge Sources

37. Why Teach Anatomy to the Computer? • Need for • Knowledge-based (smart) applications • in: education • clinical medicine • research • Anatomical knowledge in • computer-understandable form • Leading to • Qualitative change in role of • teacher • health care provider

38. Why Teach Anatomy to the Computer? Controlled Medical Terminologies (CMT) • MeSH (Medical Subject Headings) • SNOMED (Systematized Nomenclature of Medicine) • The Read Codes • GALEN (General Architecture for Languages • Encyclopedias and Nomenclatures in Medicine) • NeuroNames (University of Washington) • UMLS (Unified Medical Language Systems) • US National Library of Medicine

39. Why Teach Anatomy to the Computer? SNOMED Topography Axis 20000 Respiratory System 28000 Lung 29000 Pleura 29050 Pleural Cavity Pleural Cavity

40. Why Teach Anatomy to the Computer? READ CODES Human Body Structure Body System Structure Respiratory Structure Pleural Structure Pleural Cavity Body Region Structure Trunk Structure Body Cavity Structure Thoracic Cavity Structure Pleural Structure Pleural Cavity Pleural Cavity Pleural Cavity

41. Why Teach Anatomy to the Computer? GALEN* AnatomicalConcept Structure BodyStructure BodyPart GeneralizedCavity ConventionalCavity [AbdominalCavity] TrueCavity ActualCavity [AnatomicalSinus Lumen] PotentialCavity PleuralSpace] PleuralSpace *Rector et al. MIE 94 Proc. 1994:229

42. Pleural Cavity

43. Why Teach Anatomy to the Computer? • Conclusion • Inadequacy of • traditional knowledge sources • New need for • computer-processable • anatomical knowledge

44. How to Teach Anatomy to the Computer? • Why do we need to teach anatomy to the computer? • What to teach to the computer? • How do we do it?

45. What to teach to the computer? • "Anatomy" …….. a homonym for anatomy (structure) • e.g., anatomy of the frog, hand, brain anatomy (science) • systematized branch of knowledge accumulated about anatomy (structure).

46. What to teach to the computer? • "Structure" ……. a homonym for something composed of parts; • (e.g., a building, a cell, a plant, brain) • i.e., a material object the arrangement or interrelation of all the parts of a whole. • (e.g., of a sentence, a symphony, • or of society, government, • or of the atom, the hand) • i.e., relationships

47. What to teach to the computer? • Structure of a material object • Structure of Structure = • Subobjects (parts) + Structural Relationships • The components of an object • and their manner of arrangement in constituting a whole.

48. What to teach to the computer? • ”Anatomical Structure" … a homonym for • a material object generated by the coordinated expression of an organism's • own structural genes; • the arrangement (physical interrelation) of • all the parts of an anatomical structure • in constituting the whole. • Synonym: 'biological structure'

49. What to teach to the computer? • Question: • What to teach first about anatomy to a computer? • Answer: • The structure of anatomical structures • that constitute the body. • StructureBody= ({SubobjectBody}, {Structural relationship})

50. What to teach to the computer? • Question: • What to enter in the computer • to explain (model) anatomy? • Answer: • Symbols for anatomical structures • Symbols for structural relationships