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The Foundational Model of Anatomy Cornelius Rosse, M.D., D.Sc. Structural Informatics Group

Digital Human Open Source Software Framework for Organ Modeling and Simulation. The Foundational Model of Anatomy Cornelius Rosse, M.D., D.Sc. Structural Informatics Group University of Washington. Organ Modeling and Simulation. Challenges Interoperability of software

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The Foundational Model of Anatomy Cornelius Rosse, M.D., D.Sc. Structural Informatics Group

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  1. Digital Human Open Source Software Framework for Organ Modeling and Simulation The Foundational Model of Anatomy Cornelius Rosse, M.D., D.Sc. Structural Informatics Group University of Washington

  2. Organ Modeling and Simulation • Challenges • Interoperability of software • Representation of biomedical knowledge in machine-processible form • Integration and correlation of • biomedical information

  3. 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

  4. Digital Anatomist Information Project • Motivation • Manifestations of health and disease are attributes of anatomical structures. • Logical and comprehensive representation of anatomical knowledge can serve as a foundation for other types of biomedical information.

  5. Digital Anatomist Project University of Washington

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

  7. 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

  8. 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

  9. Organ Modeling and Simulation • What is an Organ? • Organ [L. organum; Gr. organon] • a somewhat independent part of the body that performs a special function or functions. • Dorland's Medical Dictionary • E.g., liver, heart, lung, kidney • hand, erythrocyte • Organ • in animals and plants, a part composed of several tissues and adopted to perform a specific function or functions. • Webster’s Dictionary • E.g., liver, heart, lung, kidney • hand, head of femur, right ventricle

  10. Challenges of Anatomical Knowledge Representation 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

  11. Challenges of Anatomical Knowledge Representation • Conclusion • Inadequacy of • traditional knowledge sources • New need for • computer-processable • anatomical knowledge

  12. Challenges of Anatomical Knowledge Representation • Question: • What information should be entered in the • Foundational Model of Anatomy? • Answer: • The structure of anatomical structures • that constitute the body. • StructureBody= ({SubobjectBody}, {Structural relationship})

  13. What kind of information? • “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

  14. What kind of information? • “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

  15. What kind of information? • “The oesophagusis amuscular tube … connecting the pharynx to the stomach. Itbeginsin the neck, level with the lower border of the cricoid cartilage and the sixth cervical vertebra; descending largely anteriorto the vertebral columnthrough the superior and posterior mediastina.” • Gray’s Anatomy, 38th edition, p. 1751

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

  17. 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.

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

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

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

  21. Networks of ASA Right Ventricle

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

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

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

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

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

  27. Anatomical Entity

  28. -is a- Physical Anatomical Entity Conceptual Anatomical Entity Anatomical Entity

  29. Material Physical Anatomical Entity Non-material Physical Anatomical Entity Anatomical Entity -is a- Physical Anatomical Entity Conceptual Anatomical Entity

  30. Anatomical Entity -is a- Physical Anatomical Entity Conceptual Anatomical Entity Material Physical Anatomical Entity Non-material Physical Anatomical Entity Anatomical Space Anatomical Surface Anatomical Line Anatomical Point

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

  32. Organ • Definition: • Organ • is ananatomical structure • consists of maximal sets of organ parts • connected to one another • constitute self-contained unit • distinct from other units • connected to other organs • constitutes organ system • body part

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

  34. Protégé 2000

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

  36. Protégé 2000

  37. ASA: Part of Network

  38. ASA: Part of Network

  39. ASA: Part of Network

  40. ASA: Part of Network

  41. ASA: Part of Network

  42. ASA: Part of Network

  43. Foundational Model of Anatomy Fm = (Ao, ASA, ATA, Mk) FmBODY = {FmANATOMICAL_ENTITY}

  44. Conclusions • 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.

  45. Conclusions • 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.

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