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

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

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

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

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

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

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

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

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

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

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

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

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

30. Superimposed FMRI and cortical language maps

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

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

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

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

40. 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 Why Teach Anatomy to the Computer?

41. GALEN* AnatomicalConceptStructureBodyStructureBodyPartGeneralizedCavityConventionalCavity [ AbdominalCavity] TrueCavityActualCavity [ AnatomicalSinus Lumen ] PotentialCavity PleuralSpace ] PleuralSpace *Rector et al. MIE 94 Proc. 1994:229 MIE 94 Proc. 1994:229Why Teach Anatomy to the Computer?

42. Pleural Cavity

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

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

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

46. "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 What to teach to the computer?

47. 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. What to teach to the computer?

48. ”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' What to teach to the computer?

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

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

51. What kind of symbols? Thought “Concept” Symbol “Term” Referent Triangle of Meaning

52. “The oesophagus is a muscular tube … connecting the pharynx to the stomach. It begins in the neck, level with the lower border of the cricoid cartilage and the sixth cervical vertebra; descending largely anterior to the vertebral column through the superior and posterior mediastina.” Gray’s Anatomy, 38th edition, p. 1751 What kind of symbols?

53. “The oesophagus is a muscular tube … connecting the pharynx to the stomach. It begins in the neck, level with the lower border of the cricoid cartilage and the sixth cervical vertebra; descending largely anterior to the vertebral column through the superior and posterior mediastina.” Gray’s Anatomy, 38th edition, p. 1751 What kind of symbols?

54. “The oesophagus is a muscular tube … connecting the pharynx to the stomach. It begins in the neck, level with the lower border of the cricoid cartilage and the sixth cervical vertebra; descending largely anterior to the vertebral column through the superior and posterior mediastina.” Gray’s Anatomy, 38th edition, p. 1751 What kind of symbols?

55. Symbolic model = symbols of {anatomical structure} + symbols of {structural relationship} mirrors graphical model scales to non-structural relationships What to teach first to the computer?

56. What is a symbolic model? Symbolic model, a conceptualization of a domain of discourse represented with non-graphical symbols; in computer-processible (“understandable”) form; supports inference (reasoning).

57. What is the Foundational Model of Anatomy (FM)? Foundational Model of Anatomy is a symbolic model of the physical organization of the human body; declares the principles for including concepts and relationships that are implicitly assumed when knowledge of anatomy is applied in different contexts; explicitly defines concepts and relationships necessary and sufficient for consistently modeling the structure of the human body.

58. where: Ao= Anatomy ontology ASA= Anatomical Structural Abstraction ATA= Anatomical Transformation Abstraction Mk= Metaknowledge (principles, rules, axioms) where: Ao= Anatomy ontology ASA= Anatomical Structural Abstraction ATA= Anatomical Transformation Abstraction Mk= Metaknowledge (principles, rules, axioms) Foundational Model of Anatomy Fm = (Ao, ASA, ATA, Mk)

59. ASA = (Do, Bn, Pn, SAn) (2) where: Do= Dimensional ontology Bn= Boundary network Pn= Part-of network SAn= Spatial Association network where: Do= Dimensional ontology Bn= Boundary network Pn= Part-of network SAn= Spatial Association network Fm = (Ao, ASA, ATA, Mk) (1) Anatomical Structural Abstraction Foundational Model of Anatomy

60. ASA = (Do, Bn, Pn, SAn) (2) where: Ln = Location On = Orientation Cn = Connectivity where: Ln = Location On = Orientation Cn = Connectivity Fm = (Ao, ASA, ATA, Mk) (1) Spatial Association Network SAn = (Ln, On, Cn) (3) Foundational Model of Anatomy

61. Right Ventricle Networks of ASA

62. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a-

63. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a- Polyhedron Volume (3-D) Dimensional Ontology Dimensional Ontology

64. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a- Polyhedron Volume (3-D) Spatial Ontology Sternocostal Surface Sternocostal Surface Diaphragmatic Surface Diaphragmatic Surface bounded by boundary of Anatomical Surface Anatomical Surface Surface (2-D) bounded by Right Coronary Sulcus Right Coronary Sulcus Anterior Interventricular Sulcus Anterior Interventricular Sulcus Line (1-D) bounded by Coronary Sulcus Coronary Sulcus Inferior margin of heart Inferior margin of heart Apex Boundary Network -is a- Posterior IV Sulcus Posterior IV Sulcus Crux of heart Anatomical Landmark Anatomical Landmark Point (1-D) -is a-

65. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a- Polyhedron Volume (3-D) Spatial Ontology Sternocostal Surface Sternocostal Surface Diaphragmatic Surface Diaphragmatic Surface bounded by boundary of Anatomical Surface Anatomical Surface Surface (2-D) bounded by Right Coronary Sulcus Right Coronary Sulcus Anterior Interventricular Sulcus Anterior Interventricular Sulcus Line (1-D) bounded by Coronary Sulcus Coronary Sulcus Inferior margin of heart Inferior margin of heart Apex Boundary Network -is a- Posterior IV Sulcus Posterior IV Sulcus Crux of heart Anatomical Landmark Anatomical Landmark Point (1-D) -is a- Part-of Network Part-of Network HeartHeart super- object super- object Inflow part of RV of RV Inflow part of RV of RV Infundibulum Wall of RV Cavity of RV subobject -is a- has Cavity of infund. infund. Cavity of infund. infund. Cavity of infl.part infl.part

66. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a- Polyhedron Volume (3-D) Spatial Ontology Sternocostal Surface Sternocostal Surface Diaphragmatic Surface Diaphragmatic Surface bounded by boundary of Anatomical Surface Anatomical Surface Surface (2-D) bounded by Right Coronary Sulcus Right Coronary Sulcus Anterior Interventricular Sulcus Anterior Interventricular Sulcus Line (1-D) bounded by Coronary Sulcus Coronary Sulcus Inferior margin of heart Inferior margin of heart Apex Boundary Network -is a- Posterior IV Sulcus Posterior IV Sulcus Crux of heart Anatomical Landmark Anatomical Landmark Point (1-D) -is a- Part-of Network Part-of Network HeartHeart super- object super- object Inflow part of RV of RV Inflow part of RV of RV Infundibulum Wall of RV Cavity of RV subobject -is a- has Cavity of infund. infund. Cavity of infund. infund. Cavity of infl.part infl.part has adjacency adjacency anterioranteriorinferiorinferior to left Left ventricle ventricle Pericardial sac sacPericardial has adjacency adjacency DiaphragmDiaphragm inferiorinferior Spatial Association Network

67. Foundational Model of Anatomy Fm = (Ao, ASA, ATA, Mk) Fm BODY = {Fm ANATOMICAL_ENTITY }

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

69. Foundational Principles Assertions that provide the basis for reasoning and action Constraint principle Definition principle Constitutive principle Organizational unit principle Structural relationship principle Representation principle Constraint principle Definition principle Constitutive principle Organizational unit principle Structural relationship principle Representation principle How to teach the FM to the computer?

70. Explicit Definitions Purpose of FM definitions: Provide the rationale for an inheritance hierarchy in a structural context; Specify the essence of anatomical entities in terms of two sets of structural attributes: those of their genus and differentiae How to teach the FM to the computer?

71. Principled Modeling = Foundational Principles + Explicit Definitions

72. UMLS

73. Leaf terms (concepts)

74. Multiple layers of meaning

76. Principled Modeling Prototype problems: 1.How to reconcile different naming and classification conventions? 2. How to assure inheritance? 3.How to represent different and overlapping part-whole relationships? 4.How to represent different kinds of location attributes?

77. Esophagus Leaf concept

78. Explicit Definitions Purpose of FM definitions: Provide the rationale for an inheritance hierarchy in a structural context; Specify the essence of anatomical entities in terms of two sets of structural attributes: those of their genus differentiae How to reconcile different classifications?

79. Definition Esophagus is an ‘organ with an organ cavity’, which connects the pharynx to the stomach

80. DefinitionDefinition Organ with organ cavity is a ‘cavitated organ’, the morphological parts of which surround a continuous cavity, which contains one or more body substances.

81. DefinitionDefinition Cavitated organ is an ‘organ’, the morphological parts of which surround one or more cavities, which contain one or more body substances.

82. DefinitionDefinition Organ is an ‘anatomical structure’,which consists of the maximal set of organ parts so connected to one another that together they constitute a self- contained unit of macroscopic anatomy, morphologically distinct from other such units.

83. DefinitionDefinition Anatomical structure is a ‘material physical anatomical entity’ which is an object generated by the coordinated expression of groups of genes; it consists of parts that are themselves anatomical structures.

84. Principled Modeling Prototype problems: 1.How to reconcile different naming and classification conventions? 2. How to assure inheritance? 3.How to represent different and overlapping part-whole relationships? 4.How to represent different kinds of location attributes?

85. Material Physical Anatomical Entity Material Physical Anatomical Entity -is a- Anatomical Structure Anatomical Structure Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity

86. Material Physical Anatomical Entity Material Physical Anatomical Entity -is a- Anatomical Structure Anatomical Structure Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Conceptual Anatomical Entity Conceptual Anatomical Entity

87. Material Physical Anatomical Entity Material Physical Anatomical Entity -is a- Anatomical Structure Anatomical Structure Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Conceptual Anatomical Entity Conceptual Anatomical Entity

88. MateAA Physical Anatomical Entity MateAA Physical Anatomical Entity -is a- Anatomical Structure Anatomical Structure Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Conceptual Anatomical Entity Conceptual Anatomical Entity Organ Part Organ Part

89. Material Physical Anatomical Entity Material Physical Anatomical Entity -is a- Anatomical Structure Anatomical Structure Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Conceptual Anatomical Entity Conceptual Anatomical Entity Organ Part Organ Part Organ Part Organ Part Tissue Organ component Organ subdivision

90. Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Material Physical Anatomical Entity Material Physical Anatomical Entity Organ Cell Organ Part Organ Part -is a- Anatomical Structure Anatomical Structure Body Part Body Part Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Conceptual Anatomical Entity Conceptual Anatomical Entity Human Body Human Body Organ System Organ System Tissue Organ component Organ subdivision

91. Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Material Physical Anatomical Entity Material Physical Anatomical Entity Organ Cell Organ Part Organ Part -is a- Anatomical Structure Anatomical Structure Body Part Body Part Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Body Substance Body Substance Conceptual Anatomical Entity Conceptual Anatomical Entity Human Body Human Body Organ System Organ System Tissue Organ component Organ subdivision

92. OrganOrgan Solid Organ Cavitated Organ Organ with cavitated organ part Organ with cavitated organ part Organ with organ cavity Organ with organ cavity HeartHeartEsophagusEsophagus -is a- Anatomy Ontology

93. Principled Modeling Fm = (Ao, ASA, ATA, Mk) Ao: taxonomic classification based on explicit definition of concepts, inheritance of definitional structural attributes; consistent with foundational principles.

94. Assurance of inheritance

98. Test What is the brain? To which Ao class would you assign the brain?

99. Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Material Physical Anatomical Entity Material Physical Anatomical Entity Organ Cell Organ Part Organ Part -is a- Anatomical Structure Anatomical Structure Body Part Body Part Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Body Substance Body Substance Conceptual Anatomical Entity Conceptual Anatomical Entity Human Body Human Body Organ System Organ System Tissue Organ component Organ subdivision

100. Organ Definition:Organ is an anatomical structure is an anatomical structure consists ofmaximal sets of organ parts consists ofmaximal sets of organ parts connected to one another constitute self-contained unit distinct from other units connected to other organs connected to other organs constitutesorgan system constitutesorgan system body part

101. Organ system Definition: Organ system anatomical structure is an anatomical structure members of predominantly one organ subclass; consists ofmembers of predominantly one organ subclass; interconnected by zones of continuity; interconnected by zones of continuity; connected to other organ systems constitutesthe human body

102. Definition of neuraxis Neuraxis is... NeuroNames central nervous system NeuroNames "the axial, unpaired part of the central nervous system....in contrast to the paired cerebral hemispheres” Stedman’s Stedman’s an axon; central nervous system. Dorland’s:

103. What is the brain?

107. Summary: Principled Modeling Prototype problems: 1.How to reconcile different naming and classification conventions? 2. How to assure inheritance? 3.How to represent different and overlapping part-whole relationships? 4.How to represent different kinds of location attributes?

108. Revisit: Principled Modeling Prototype problems: 1.How to reconcile different naming and classification conventions? 2. How to assure inheritance? 3.How to represent different and overlapping part-whole relationships? 4.How to represent different kinds of location attributes?

109. How Do We Teach Anatomy to the Computer? Correlation of the Foundational Model with Traditional Sources of Anatomical Knowledge Augusto Agoncillo M.D., José L.V. Mejino Jr., M.D., Cornelius Rosse M.D., D.Sc. Structural Informatics Group University of Washington

110. Problem Semantic expressivity Semantic specificity Conflicts between Traditional Sources and Foundational Model: Conflicts between Traditional Sources and Foundational Model: homonyms ambiguous use of synonyms homonyms ambiguous use of synonyms

111. Semantic Specificity and Expressivity Thought “Concept” Symbol “Term” Referent Triangle of Meaning

112. Authoring program: Protégé Semantic Specificity: synonyms

116. Semantic Specificity: Homonyms Homonym: ‘Base of heart’ Anteriorview Posteriorview

121. Foundational Model Builder

122. Foundational Model Builder

123. Preferred term: Base of heart (anatomical)

124. Foundational Model Builder

125. Preferred term: Base of heart (clinical)

126. Semantic Specificity: Ambiguous use of synonyms Transferred meaning: ‘Left border of heart’ Left border of heart Left surface of heart

127. Semantic Specificity one preferred name for each anatomical entity associate synonyms with each preferred name disallow homonyms; use extensions disallow transferred meanings one preferred name for each anatomical entity associate synonyms with each preferred name disallow homonyms; use extensions disallow transferred meanings Assured in FM by:

128. Foundational Model Builder

129. Foundational Model Builder

130. Problem Semantic expressivity Semantic specificity Conflicts between Traditional Sources and Foundational Model: Conflicts between Traditional Sources and Foundational Model: classification of anatomical entities relationships between anatomical entities classification of anatomical entities relationships between anatomical entities

131. Semantic Expressivity: Classification Alimentary System Mouth Tongue Pharynx Esophagus Stomach Small intestine Large intestine CaecumAppendix Colon Rectum Liver Gall Bladder Alimentary System Mouth Tongue Pharynx Esophagus Stomach Small intestine Large intestine CaecumAppendix Colon Rectum Liver Gall Bladder Lymphoid System Primary Lymphoid Bone Marrow Thymus Secondary Lymphoid Spleen Pharyngeal lymphoid ring Lymph node Lymphoid System Primary Lymphoid Bone Marrow Thymus Secondary Lymphoid Spleen Pharyngeal lymphoid ring Lymph node Terminologia Anatomica

132. Semantic Expressivity: Classification Alimentary System Mouth Tongue Pharynx Esophagus Stomach Small intestine Large intestine CaecumAppendix Colon Rectum Liver Gall Bladder Alimentary System Mouth Tongue Pharynx Esophagus Stomach Small intestine Large intestine CaecumAppendix Colon Rectum Liver Gall Bladder Lymphoid System Primary Lymphoid Bone Marrow Thymus Secondary Lymphoid Spleen Pharyngeal lymphoid ring Lymph node Lymphoid System Primary Lymphoid Bone Marrow Thymus Secondary Lymphoid Spleen Pharyngeal lymphoid ring Lymph node Terminologia Anatomica

133. Semantic Expressivity state defining attributes of anatomical entities in terms of constituent parts entities they constitute state defining attributes of anatomical entities in terms of constituent parts entities they constitute Definition principle:

134. Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Material Physical Anatomical Entity Material Physical Anatomical Entity Cell -is a- Conceptual Anatomical Entity Conceptual Anatomical Entity Semantic Expressivity Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Anatomical Space Anatomical Space Anatomical Surface Anatomical Surface Anatomical Line Anatomical Line Anatomical Structure Anatomical Structure Body Substance Body Substance Organ Part Organ Part Organ System Organ System Body Part Body Part Human Body Human Body

135. Semantic Expressivity Ambiguous part-whole relationships Infundibulum Right ventricle Inflow part

136. Ambiguous part-whole relationships Right ventricle Inflow part Outflow part Semantic Expressivity

137. Foundational Model Builder

138. Foundational Model Builder

139. Preferred Term: Inflow part of right ventricle

140. Preferred Term: Outflow part of right ventricle

141. Ambiguous part-whole relationships Right ventricle Inflow part Outflow part Semantic Expressivity

142. Summary Principled representation of Foundational Model calls for: greater specificity and expressivity than traditional sources definition of new classes of anatomical entities definition of new classes of anatomical entities introduction of new descriptive terms introduction of new descriptive terms modification of existing terms modification of existing terms Principled representation of Foundational Model calls for: greater specificity and expressivity than traditional sources definition of new classes of anatomical entities definition of new classes of anatomical entities introduction of new descriptive terms introduction of new descriptive terms modification of existing terms modification of existing terms

143. Conclusions Establishes an inheritance hierarchy (Ao) based on inherent structural properties Establishes an inheritance hierarchy (Ao) based on inherent structural properties Specifies structural relationships between anatomical entities Specifies structural relationships between anatomical entities Explicitly represents classes and relationships implied in traditional sources Explicitly represents classes and relationships implied in traditional sources Conflicts can be solved:

144. Continued: Principled Modeling Prototype problems: 1.How to reconcile different naming and classification conventions? 2. How to assure inheritance? 3.How to represent different and overlapping part-whole relationships? 4.How to represent different kinds of location attributes?

145. How Do We Teach Anatomy to the Computer? Anatomical Relationships in the Foundational Model of Anatomy José L.V. Mejino Jr., M.D., Cornelius Rosse M.D., D.Sc. Structural Informatics Group University of Washington

146. where: Ao= Anatomy ontology ASA= Anatomical Structural Abstraction ATA= Anatomical Transformation Abstraction Mk= Metaknowledge (principles, rules, axioms) where: Ao= Anatomy ontology ASA= Anatomical Structural Abstraction ATA= Anatomical Transformation Abstraction Mk= Metaknowledge (principles, rules, axioms) Foundational Model of Anatomy Fm = (Ao, ASA, ATA, Mk)

147. ASA = (Do, Bn, Pn, SAn) (2) where: Do= Dimensional ontology Bn= Boundary network Pn= Part-of network SAn= Spatial Association network where: Do= Dimensional ontology Bn= Boundary network Pn= Part-of network SAn= Spatial Association network Fm = (Ao, ASA, ATA, Mk) (1) Anatomical Structural Abstraction Anatomical Relationships

148. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a- Polyhedron Volume (3-D) Dimensional Ontology Dimensional Ontology ASA = ( Do, Pn, Bn, SAn )

149. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a- Polyhedron Volume (3-D) Dimensional Ontology Dimensional Ontology Sternocostal Surface Sternocostal Surface Diaphragmatic Surface Diaphragmatic Surface bounded by boundary of Anatomical Surface Anatomical Surface Surface (2-D) bounded by Right Coronary Sulcus Right Coronary Sulcus Anterior Interventricular Sulcus Anterior Interventricular Sulcus Line (1-D) bounded by Coronary Sulcus Coronary Sulcus Inferior margin of heart Inferior margin of heart Apex Boundary Network -is a- Posterior IV Sulcus Posterior IV Sulcus Crux of heart Anatomical Landmark Anatomical Landmark Point (1-D) -is a- ASA = ( Do, Bn, Pn, SAn )

150. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a- Polyhedron Volume (3-D) Dimensional Ontology Dimensional Ontology Sternocostal Surface Sternocostal Surface Diaphragmatic Surface Diaphragmatic Surface bounded by boundary of Anatomical Surface Anatomical Surface Surface (2-D) bounded by Right Coronary Sulcus Right Coronary Sulcus Anterior Interventricular Sulcus Anterior Interventricular Sulcus Line (1-D) bounded by Coronary Sulcus Coronary Sulcus Inferior margin of heart Inferior margin of heart Apex Boundary Network -is a- Posterior IV Sulcus Posterior IV Sulcus Crux of heart Anatomical Landmark Anatomical Landmark Point (1-D) -is a- Part-of Network Part-of Network HeartHeart super- object super- object Inflow part of RV of RV Inflow part of RV of RV Infundibulum Wall of RV Cavity of RV subobject -is a- has Cavity of infund. infund. Cavity of infund. infund. Cavity of infl.part infl.part ASA = ( Do, Bn, Pn, SAn )

151. Right Ventricle Cardiac Chamber Cardiac Chamber Organ Subdivision Organ Subdivision Organ Part Anatomical Structure Anatomy Ontology -is a- Polyhedron Volume (3-D) Dimensional Ontology Dimensional Ontology Sternocostal Surface Sternocostal Surface Diaphragmatic Surface Diaphragmatic Surface bounded by boundary of Anatomical Surface Anatomical Surface Surface (2-D) bounded by Right Coronary Sulcus Right Coronary Sulcus Anterior Interventricular Sulcus Anterior Interventricular Sulcus Line (1-D) bounded by Coronary Sulcus Coronary Sulcus Inferior margin of heart Inferior margin of heart Apex Boundary Network -is a- Posterior IV Sulcus Posterior IV Sulcus Crux of heart Anatomical Landmark Anatomical Landmark Point (1-D) -is a- Part-of Network Part-of Network HeartHeart super- object super- object Inflow part of RV of RV Inflow part of RV of RV Infundibulum Wall of RV Cavity of RV subobject -is a- has Cavity of infund. infund. Cavity of infund. infund. Cavity of infl.part infl.part has adjacency adjacency anterioranteriorinferiorinferior to left Left ventricle ventricle Pericardial sac sacPericardial has adjacency adjacency DiaphragmDiaphragm inferiorinferior Spatial Association Network SAn ) ASA = ( Do, Bn, Pn, SAn )

152. Anatomical Relationships

154. Principled Modeling Prototype problems: 1.How to reconcile different naming and classification conventions? 2. How to assure inheritance? 3.How to represent different and overlapping part-whole relationships? 4.How to represent different kinds of location attributes?

155. Part_of relationships Right ventricle Infundibulum Outflow part Right ventricle Inflow part

156. Attributed Part: Shared parts Tracheobronchial tree Lungs

157. Attributed Part: Shared parts (Netter’s Atlas of Human Anatomy)

158. Attributed Part: Shared parts (Cranial Nerves: Wilson-Pauwels et al.) Oculomotor Nerve

159. Attributed Part: Shared parts

160. Attributed Part: Anatomical/Arbitrary Anterior viewPosterior view Esophagus

161. Attributed Part: Anatomical/Arbitrary

162. Granularity of parts

175. (Alberts et al.: Molecular Biology of the Cell) Nuclear pore complex

176. ASA = (Do, Bn, Pn, SAn) (2) where: Do= Dimensional ontology Bn= Boundary network Pn= Part-of network SAn= Spatial Association network where: Do= Dimensional ontology Bn= Boundary network Pn= Part-of network SAn= Spatial Association network Fm = (Ao, ASA, ATA, Mk) (1) Anatomical Structural Abstraction Foundational Model of Anatomy

177. Principled Modeling Prototype problems: 1.How to reconcile different naming and classification conventions? 2. How to assure inheritance? 3.How to represent different and overlapping part-whole relationships? 4.How to represent different kinds of location attributes?

178. ASA = (Do, Bn, Pn, SAn) (2) where: Ln = Location On = Orientation Cn = Connectivity where: Ln = Location On = Orientation Cn = Connectivity Fm = (Ao, ASA, ATA, Mk) (1) Spatial Association Network SAn = (Ln, On, Cn) (3) How to represent different location relationships?

179. How

180. How

181. How

182. How to represent different location relationships? Adjacency Anterior viewPosterior view Esophagus

183. T2-3 T8

184. Anterior Posterior How to represent different location relationships? Coordinates How

185. How How Anterior Posterior Right lateral Right lateral Left lateral Left lateral

186. How to represent different location relationships? Adjacency How Pericardial sac Pericardial sac

187. Anterior Posterior How to represent different location relationships? Coordinates How Right lateral Right lateral Left lateral Left lateral Right AnteriorLeft Anterior Right PosteriorLeft Posterior Right Antero- lateral Right Postero- lateral Left Postero- lateral Left Antero- lateral

188. T2-3 T8

189. How to represent different location relationships? Adjacency How

190. ASA = (Do, Bn, Pn, SAn) (2) Fm = (Ao, ASA, ATA, Mk) (1) Spatial Association Network SAn = (Ln, On, Cn) (3) How to represent part_of and location relationships?

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

192. Summary: Foundational Model specifies Anatomy ontology structure-based classification of anatomical entities Structural relationships (ASA) Conclusions

193. “The oesophagus is a muscular tube … connecting the pharynx to the stomach. It begins in the neck, level with the lower border of the cricoid cartilage and the sixth cervical vertebra; descending largely anterior to the vertebral column through the superior and posterior mediastina.” Gray’s Anatomy, 38th edition, p. 1751 Conclusions

195. Summary: Foundational Model specifies Anatomy ontology structure-based classification of anatomical entities Structural relationships (ASA) Foundational Model omits functionpathology clinical cases Conclusions

196. Role of Foundational Model of Anatomy Role of Foundational Model of Anatomy Prototype for symbolic models in other domains e.g., physiology, pathology, cancer therapy Core of biomedical knowledge bases to solve problems in education, research, health care "Foundational" because anatomy is fundamental to all biomedical sciences; anatomical concepts encompassed by FM generalize to all biomedical domains. Conclusions

197. Evolving knowledge-based application for Anatomy education: “Intelligent” Digital Anatomist Conclusions

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

199. Digital Anatomist Information System Network Authoring Programs Servers “Intelligent” applications Anatomy Tutor Anatomy Tutor Anatomy Consultant Anatomy Consultant 2-D Images 2-D Images 2-D Annotations 2-D Annotations 3-D Model 3-D Model 3-D Image Volumes 3-D Image Volumes Clinical data Foundational Model Foundational Model Symbolic Info Image Repository

200. Digital Anatomist Information System Network Authoring Programs “Intelligent” applications Anatomy Tutor Anatomy Tutor Anatomy Consultant Anatomy Consultant 2-D Images 2-D Images 2-D Annotations 2-D Annotations 3-D Model 3-D Model 3-D Image Volumes 3-D Image Volumes Clinical data Foundational Model Foundational Model Symbolic Info Image Repository Knowledge Server Knowledge Server Image Server Image Server Data Server Data Server Graphics Server Graphics Server

201. Digital Anatomist Information System Network Authoring Programs “Intelligent” applications Anatomy Tutor Anatomy Tutor Anatomy Consultant Anatomy Consultant 2-D Images 2-D Images 2-D Annotations 2-D Annotations 3-D Model 3-D Model 3-D Image Volumes 3-D Image Volumes Clinical data Foundational Model Foundational Model Symbolic Info Image Repository Knowledge Server Knowledge Server Image Server Image Server Data Server Data Server Graphics Server Graphics Server DIGITAL ANATOMIST Metaknowledge

202. where: Ao= Anatomy ontology ASA= Anatomical Structural Abstraction ATA= Anatomical Transformation Abstraction Mk= Metaknowledge (principles, rules, axioms) where: Ao= Anatomy ontology ASA= Anatomical Structural Abstraction ATA= Anatomical Transformation Abstraction Mk= Metaknowledge (principles, rules, axioms) Foundational Model of Anatomy Fm = (Ao, ASA, ATA, Mk)

203. Evaluation of FM by AnatomistsCliniciansResearchers Conclusions

204. where: Ao= Anatomy ontology ASA= Anatomical Structural Abstraction ATA= Anatomical Transformation Abstraction Mk= Metaknowledge (principles, rules, axioms) where: Ao= Anatomy ontology ASA= Anatomical Structural Abstraction ATA= Anatomical Transformation Abstraction Mk= Metaknowledge (principles, rules, axioms) Fm = (Ao, ASA, ATA, Mk) Conclusions

205. How do we teach Anatomy to the Computer? "We are made wise not by the recollection on our past, but by the responsibility to our future." George Bernard Shaw

206. Spare slides

207. Portal Venous Tree

208. Vena Caval Tree

209. Systemic Arterial Tree

210. Pericardial Effusion Interactive Radiology Exercises

212. 296 models of thoracic viscera 17 models of coronary arteries 296 models of thoracic viscera 17 models of coronary arteries rcorartconusrcorartconuslcorartatriallcorartatrial 3-D Structure Primitives FM Server FM 3-D Primitives 3-D Primitives

213. Conus branch of right coronary artery-> rcorartconus Atrial branch of circumflex coronary artery->lcorartatrial Conus branch of right coronary artery-> rcorartconus Atrial branch of circumflex coronary artery->lcorartatrial FM Server “Data Server” FM 3-D Primitives 3-D Primitives Correspondences Data Server

214. Authoring program: Protégé Semantic Specificity: synonyms

218. What is the Foundational Model of Anatomy (FM)? A symbolic model of anatomy (science) represents the physical organization (structure) of biological organisms; currently limited to the human body. "Foundational" because anatomy is fundamental to all biomedical sciences; anatomical concepts encompassed by FM generalize to all biomedical domains.

219. What is a foundational model? Foundational Model is a symbolic model; declares the principles for including concepts and relationships that are implicitly assumed when knowledge of the domain is applied in different contexts; explicitly defines concepts and relationships necessary and sufficient for consistently modeling the structure of the coherent knowledge domain.

220. Dynamic 3-D Scene Generator Evolving knowledge-based application

239. Digital Anatomist Information System Network Authoring Programs “Intelligent” applications Anatomy Tutor Anatomy Tutor Anatomy Consultant Anatomy Consultant 2-D Images 2-D Images 2-D Annotations 2-D Annotations 3-D Model 3-D Model 3-D Image Volumes 3-D Image Volumes Clinical data Foundational Model Foundational Model Symbolic Info Image Repository Knowledge Server Knowledge Server Image Server Image Server Data Server Data Server Graphics Server Graphics Server DIGITAL ANATOMIST Metaknowledge

240. FM Server “Data Server” FM 3-D Primitives 3-D Primitives Correspondences Graphics Server Web Browser CGI Script

241. Digital Anatomist Information System Network Authoring Programs “Intelligent” applications Anatomy Tutor Anatomy Tutor Anatomy Consultant Anatomy Consultant 2-D Images 2-D Images 2-D Annotations 2-D Annotations 3-D Model 3-D Model 3-D Image Volumes 3-D Image Volumes Clinical data Foundational Model Foundational Model Symbolic Info Image Repository Knowledge Server Knowledge Server Image Server Image Server Data Server Data Server Graphics Server Graphics Server DIGITAL ANATOMIST Metaknowledge

242. Pleural Cavity