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

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

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

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

SNOMED Topography Axis Respiratory System Lung Pleura Pleural Cavity Pleural CavityWhy 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 Why Teach Anatomy to the Computer?

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?

Pleural Cavity

"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?

"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?

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?

”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?

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?

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?

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

“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 What kind of symbols?

“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 What kind of symbols?

“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 What kind of symbols?

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).

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.

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)

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

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

Right Ventricle Networks of ASA

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

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

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-

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

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

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

Esophagus Leaf concept

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

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.

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

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.

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.

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

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

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

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

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

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

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

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

Assurance of inheritance

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

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

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

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

Foundational Model Builder

Foundational Model Builder

Preferred Term: Inflow part of right ventricle

Preferred Term: Outflow part of right ventricle

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

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 )

Anatomical Relationships

Part_of relationships Right ventricle Infundibulum Outflow part Right ventricle Inflow part

Attributed Part: Shared parts Tracheobronchial tree Lungs

Attributed Part: Shared parts

Attributed Part: Anatomical/Arbitrary Anterior viewPosterior view Esophagus

Attributed Part: Anatomical/Arbitrary

Granularity of parts

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

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?

How

How

How

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

T2-3 T8

Anterior Posterior How to represent different location relationships? Coordinates How

How How Anterior Posterior Right lateral Right lateral Left lateral Left lateral

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

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

T2-3 T8

How to represent different location relationships? Adjacency How

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?

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

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 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

Portal Venous Tree

Vena Caval Tree

Systemic Arterial Tree