how do we teach anatomy to the computer? structural informatics group university of washington

How do We Teach Anatomy How do We Teach Anatomy to the Computer?to the Computer?

Structural Informatics GroupStructural Informatics GroupUniversity of WashingtonUniversity of Washington

American Association of Clinical Anatomists American Association of Clinical Anatomists 20012001

Why do we need to teach anatomy to the Why do we need to teach anatomy to the computer?computer?

What to teach to the computer?What to teach to the computer?

How do we do it?How do we do it?

How to Teach Anatomy to the Computer?How to Teach Anatomy to the Computer?

Current status of computer programs in Current status of computer programs in anatomyanatomy

Knowledge representationKnowledge representation

Information accessInformation access

Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?

Current status: Knowledge representationCurrent status: Knowledge representation

Traditional sourcesTraditional sourcesSpatial: cadaver, radiology, Spatial: cadaver, radiology,

atlasesatlasesSymbolic: textbooks, Symbolic: textbooks,

Unique to the computerUnique to the computerSpatial: volumetric data setsSpatial: volumetric data sets

3D graphical models3D graphical models

Symbolic: ???Symbolic: ???


Current status of computer programs in anatomyCurrent status of computer programs in anatomy

Information accessInformation access

CD-ROM, InternetCD-ROM, Internet

One piece of information One piece of information for one mouse clickfor one mouse click



The Semantic Web: The Semantic Web: A new form of Web content that A new form of Web content that is meaningful to computers will is meaningful to computers will unleash a revolution of new unleash a revolution of new possibilities.possibilities.

By: By: Tim Berners-LeeTim Berners-LeeJames HendlerJames HendlerOra LassilaOra Lassila


Need forNeed for Knowledge-based (smart) applicationsKnowledge-based (smart) applications

in: in: educationeducationclinical medicineclinical medicineresearchresearch

Anatomical knowledge in Anatomical knowledge in computer-understandable formcomputer-understandable form

Leading toLeading toQualitative change in role of teacherQualitative change in role of teacher

How Do We Teach Anatomy to the Computer?How Do We Teach Anatomy to the Computer?

The Digital AnatomistThe Digital AnatomistInformation SystemInformation System

James F. Brinkley M.D., Ph.D. James F. Brinkley M.D., Ph.D. Cornelius Rosse M.D., D.Sc.Cornelius Rosse M.D., D.Sc.


Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System

Anatomy Knowledge SourcesAnatomy Knowledge SourcesAnatomy Knowledge SourcesAnatomy Knowledge Sources

Image Repository

Symbolic Knowledge

Source

NetworkNetwork

Authoring Programs

End-UserPrograms

Servers


Symbolic Knowledge

Source

NetworkNetwork

Authoring Programs

End-UserPrograms

Servers

Image RepositoryImage Repository

2-DImages

2-DAnnotations

3-DModel

3-D ImageVolumes


Symbolic Knowledge

Source

NetworkNetwork

End-UserPrograms

Servers

Image RepositoryImage Repository

2-DImages

2-DAnnotations

3-DModel

3-D ImageVolumes

SceneGenerator

SceneGeneratorAnnotatorAnnotatorSkandhaSkandha

Graphical Authoring ProgramsGraphical Authoring Programs


Symbolic Knowledge SourcesSymbolic Knowledge SourcesSymbolic Knowledge SourcesSymbolic Knowledge Sources

Image Repository

NetworkNetwork

End-UserPrograms

Servers

FoundationalModel

FoundationalModel

Meta-knowledge

Meta-knowledge

ClinicalInfo

ClinicalInfo

ProtégéProtégéFoundational

ModelBuilder

FoundationalModelBuilder

Symbolic Authoring ProgramsSymbolic Authoring Programs



Image Repository

Symbolic Knowledge

Source

NetworkNetwork

Authoring Programs

Servers

End User InterfacesEnd User Interfaces

DigitalAnatomist

Atlases

DigitalAnatomist

Atlases

BrainMapper

BrainMapper

RadiationOncology

RadiationOncology



Image Repository

Symbolic Knowledge

Source

NetworkNetwork

KnowledgeServer

KnowledgeServer

ImageServer

ImageServer

DataServer

DataServer

GraphicsServer

GraphicsServer

DigitalAnatomistAtlases

SymbolicSymbolicGraphicalGraphical

Authoring ProgramsAuthoring Programs End-User InterfacesEnd-User Interfaces

Web-based Web-based Digital Anatomist Atlas of Digital Anatomist Atlas of

Thoracic visceraThoracic viscera

Digital Anatomist Information SystemDigital Anatomist Information System



Image Repository

Symbolic Knowledge

Source

NetworkNetwork

Authoring Programs

Servers


DigitalAnatomist

Atlases

DigitalAnatomist

Atlases

BrainMapper

BrainMapper

RadiationOncology

RadiationOncology

SuperimposedFMRI and corticallanguage maps



Image Repository

Symbolic Knowledge

Source

NetworkNetwork

Authoring Programs

Servers


DigitalAnatomist

Atlases

DigitalAnatomist

Atlases

BrainMapper

BrainMapper

RadiationOncology

RadiationOncology

Radiation Treatment Planning Radiation Treatment Planning

PRISM PRISM

Structural Informatics Group

AnatomistsAnatomistsCornelius Rosse, MD, DScCornelius Rosse, MD, DScJose Mejino, MDJose Mejino, MDAugusto Agoncillo, MDAugusto Agoncillo, MDRichard Martin, PhDRichard Martin, PhDKate Mulligan, PhDKate Mulligan, PhDJohn Sundsten, PhDJohn Sundsten, PhDDoug Bowden, MDDoug Bowden, MD

CliniciansCliniciansGeorge Ojemann, MDGeorge Ojemann, MDKen Maravilla, MDKen Maravilla, MDDavid Corina, MDDavid Corina, MDKaren Kinbar, PhDKaren Kinbar, PhD

Computer Science/InformaticsComputer Science/InformaticsJames Brinkley, MD, PhDJames Brinkley, MD, PhDLinda Shapiro, PhDLinda Shapiro, PhDIra Kalet, PhDIra Kalet, PhDWilliam Lober, MDWilliam Lober, MDAndrew Poliakov, PhDAndrew Poliakov, PhDRex Jakobovits, PhDRex Jakobovits, PhDKurt Rickard, PhDKurt Rickard, PhDSara Kim, PhDSara Kim, PhDJeff ProtheroJeff ProtheroRavensara Travillian, MARavensara Travillian, MAPeter MorkPeter MorkZhenrong QianZhenrong QianChia-chi TengChia-chi Teng


The Foundational Model of AnatomyThe Foundational Model of Anatomy

Cornelius Rosse M.D., D.Sc.Cornelius Rosse M.D., D.Sc.


3-D Models of Right Lung and Heart3-D Models of Right Lung and Heart

Digital Anatomist Image RepositoryDigital Anatomist Image Repository



Image Repository

NetworkNetwork

End-UserPrograms

Servers

FoundationalModel

FoundationalModel

Meta-knowledge

Meta-knowledge

ClinicalInfo

ClinicalInfo

Authoring Programs


Need forNeed for Knowledge-based (smart) applicationsKnowledge-based (smart) applications

in: in: educationeducationclinical medicineclinical medicineresearchresearch

Anatomical knowledge in Anatomical knowledge in computer-understandable formcomputer-understandable form

Leading toLeading toQualitative change in role of Qualitative change in role of

teacherteacherhealth care providerhealth care provider


Controlled Medical Terminologies (CMT)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

SNOMEDSNOMED

Topography AxisTopography Axis

20000 Respiratory System20000 Respiratory System

28000 Lung28000 Lung

29000 Pleura29000 Pleura

29050 Pleural Cavity29050 Pleural CavityPleural Cavity


READ CODESREAD CODES

Human Body StructureHuman Body Structure

Body System StructureBody System StructureRespiratory StructureRespiratory StructurePleural StructurePleural StructurePleural CavityPleural Cavity

Body Region StructureBody Region StructureTrunk StructureTrunk StructureBody Cavity StructureBody Cavity StructureThoracic Cavity StructureThoracic Cavity StructurePleural StructurePleural StructurePleural CavityPleural CavityPleural Cavity

Pleural Cavity


GALEN*GALEN*AnatomicalConceptAnatomicalConcept

StructureStructureBodyStructureBodyStructure

BodyPartBodyPartGeneralizedCavityGeneralizedCavity

ConventionalCavityConventionalCavity[[AbdominalCavityAbdominalCavity]]

TrueCavityTrueCavityActualCavityActualCavity

[[AnatomicalSinus LumenAnatomicalSinus Lumen]]PotentialCavityPotentialCavity

PleuralSpacePleuralSpace]]PleuralSpace**Rector et al.Rector et al. MIE 94 Proc. 1994:229MIE 94 Proc. 1994:229


Pleural Cavity


ConclusionConclusion

• Inadequacy of Inadequacy of traditional knowledge sourcestraditional knowledge sources

• New need forNew need forcomputer-processable computer-processable anatomical knowledgeanatomical knowledge

"Anatomy""Anatomy" …….. a …….. a homonym homonym forfor

anatomy (structure)anatomy (structure)e.g., anatomy of the frog, hand, braine.g., anatomy of the frog, hand, brain

anatomy (science)anatomy (science)systematized branch of knowledge accumulated systematized branch of knowledge accumulated about anatomy (structure).about anatomy (structure).


"Structure""Structure" ……. a ……. a homonymhomonym for for

something composed of parts;something composed of parts;(e.g., a building, a cell, a plant, brain)(e.g., a building, a cell, a plant, brain)i.e., a material objecti.e., a material object

the arrangement or interrelation of all the parts the arrangement or interrelation of all the parts of a whole.of a whole.

(e.g., of a sentence, a symphony, (e.g., of a sentence, a symphony, or of society, government,or of society, government,or of the atom, the hand)or of the atom, the hand)

i.e., relationshipsi.e., relationships


Structure of a material objectStructure of a material object

Structure of Structure Structure of Structure == Subobjects (parts) + Structural RelationshipsSubobjects (parts) + Structural Relationships

The components of an object The components of an object and their manner of arrangement in constituting a and their manner of arrangement in constituting a whole.whole.


””Anatomical Structure"Anatomical Structure" … a … a homonymhomonym for for

a material object generated by the coordinated a material object generated by the coordinated expression of an organism's expression of an organism's own structural genes;own structural genes;

the arrangement (physical interrelation) of the arrangement (physical interrelation) of all the parts of an anatomical structure all the parts of an anatomical structure in constituting the whole.in constituting the whole.

Synonym:Synonym: 'biological structure' 'biological structure'


Question:Question:

What to teach What to teach firstfirst about anatomy to a computer? about anatomy to a computer?

Answer: Answer:

The structure of anatomical structures The structure of anatomical structures that constitute the body.that constitute the body.

StructureStructureBodyBody = ({= ({SubobjectSubobjectBodyBody }}, , {{Structural relationshipStructural relationship})})


Question:Question:

What to enter in the computer What to enter in the computer to explain (model) anatomy?to explain (model) anatomy?

Answer:Answer:

Symbols for anatomical structuresSymbols for anatomical structures

Symbols for structural relationshipsSymbols for structural relationships


What kind of symbols?

Thought“Concept”

Symbol“Term”

ReferentTriangle of Meaning

““The oesophagus is a muscular tube … The oesophagus is a muscular tube … connecting the pharynx to the stomach. It connecting the pharynx to the stomach. It begins in the neck, level with the lower begins in the neck, level with the lower border of the cricoid cartilage and the sixth border of the cricoid cartilage and the sixth cervical vertebra; descending largely cervical vertebra; descending largely anterior to the vertebral column through the anterior to the vertebral column through the superior and posterior mediastina.”superior and posterior mediastina.”

Gray’s Anatomy, 38th edition, p. Gray’s Anatomy, 38th edition, p. 17511751


““The The oesophagusoesophagus is a is a muscular tubemuscular tube … … connecting the connecting the pharynx pharynx to the to the stomachstomach. It . It begins in the begins in the neckneck, level with the , level with the lower lower border of the cricoid cartilageborder of the cricoid cartilage and the and the sixth sixth cervical vertebracervical vertebra; descending largely ; descending largely anterior to the anterior to the vertebral columnvertebral column through the through the superiorsuperior and and posterior mediastinaposterior mediastina.”.”



““The The oesophagusoesophagus is ais a muscular tubemuscular tube … … connecting connecting the the pharynx pharynx to to the the stomachstomach. . ItIt beginsbegins inin the the neckneck, , level withlevel with the the lower lower border of the cricoid cartilageborder of the cricoid cartilage and the and the sixth sixth cervical vertebracervical vertebra; ; descendingdescending largely largely anterioranterior toto the the vertebral columnvertebral column through through the the superiorsuperior and and posterior mediastinaposterior mediastina.”.”



Symbolic model = Symbolic model = symbols of {anatomical structure} +symbols of {anatomical structure} +symbols of {structural relationship}symbols of {structural relationship}

mirrors graphical modelmirrors graphical model

scales to non-structural relationshipsscales to non-structural relationships

What to teach What to teach first first to the computer?to the computer?

What is a symbolic model?

Symbolic model,Symbolic model,

a conceptualization of a domain of discoursea conceptualization of a domain of discourserepresented with non-graphical symbols;represented with non-graphical symbols;

in computer-processible (“understandable”) form;in computer-processible (“understandable”) form;

supports inference (reasoning).supports inference (reasoning).

What is the Foundational Model of Anatomy (FM)?

Foundational Model of AnatomyFoundational Model of Anatomyis a is a symbolic modelsymbolic model of the physical organization of the human body; of the physical organization of the human body;

declares the principlesdeclares the principles for including concepts and relationships for including concepts and relationships that are implicitly assumed that are implicitly assumed when knowledge of anatomywhen knowledge of anatomyis applied in different contexts;is applied in different contexts;

explicitly definesexplicitly definesconcepts and relationships concepts and relationships

necessary and sufficient for consistently necessary and sufficient for consistently modeling the structure of the modeling the structure of the human body.human body.

where:where:AoAo = Anatomy ontology= Anatomy ontologyASAASA = Anatomical Structural Abstraction= Anatomical Structural AbstractionATAATA = Anatomical Transformation Abstraction= Anatomical Transformation AbstractionMkMk = Metaknowledge = Metaknowledge

(principles, rules, axioms)(principles, rules, axioms)



Foundational Model of AnatomyFoundational Model of Anatomy

Fm = (Ao, ASA, ATA, Mk)Fm = (Ao, ASA, ATA, Mk)

ASA = (Do, Bn, Pn, SAn) ASA = (Do, Bn, Pn, SAn) (2)(2)ASA = (Do, Bn, Pn, SAn) ASA = (Do, Bn, Pn, SAn) (2)(2)

where:where:DoDo = Dimensional ontology= Dimensional ontologyBnBn = Boundary network= Boundary networkPnPn = Part-of network= Part-of networkSAnSAn = Spatial Association network= Spatial Association network


Fm = (Ao, ASA, ATA, Mk) (1)Fm = (Ao, ASA, ATA, Mk) (1)

Anatomical Structural AbstractionAnatomical Structural AbstractionAnatomical Structural AbstractionAnatomical Structural Abstraction


ASA = (Do, Bn, Pn, SAn) (2)ASA = (Do, Bn, Pn, SAn) (2)

where:Ln = LocationOn = OrientationCn = Connectivity



Spatial Association NetworkSpatial Association Network

SAn = (Ln, On, Cn) (3)SAn = (Ln, On, Cn) (3)


RightVentricle

Networks of ASANetworks of ASA

RightVentricle

CardiacChamber CardiacChamber

Organ Subdivision Organ Subdivision

Organ PartOrgan Part

Anatomical StructureAnatomical StructureAnatomy OntologyAnatomy Ontology

-is a--is a-

RightVentricle





-is a--is a-

PolyhedronPolyhedron

Volume (3-D)Volume (3-D)

Dimensional OntologyDimensional Ontology

RightVentricle





-is a--is a-



Spatial OntologySpatial Ontology

Sternocostal SurfaceSternocostal Surface

Diaphragmatic SurfaceDiaphragmatic Surface

bounded bybounded by

boundary ofboundary of

Anatomical SurfaceAnatomical Surface

Surface (2-D)Surface (2-D)

bounded bybounded by RightCoronary Sulcus

RightCoronary Sulcus

AnteriorInterventricular Sulcus


Line (1-D)Line (1-D)


Coronary SulcusCoronary Sulcus

Inferior margin of heartInferior margin of heart

ApexApex

Boundary NetworkBoundary NetworkBoundary NetworkBoundary Network

-is a--is a-

Posterior IV SulcusPosterior IV Sulcus

Crux of heartCrux of heart

Anatomical LandmarkAnatomical Landmark

Point (1-D)Point (1-D)

-is a--is a-

RightVentricle





-is a--is a-


















ApexApex


-is a--is a-





-is a--is a-

Part-ofNetworkPart-of

Network

HeartHeartHeartHeart

super-objectsuper-object

Inflow partInflow part of RVof RVInflow partInflow part of RVof RV

InfundibulumInfundibulum

Wall of RVWall of RVWall of RVWall of RVCavity of RVCavity of RVCavity of RVCavity of RV

subobject subobject

-is a--is a-

hashas

hashas

Cavity ofCavity of infund.infund.Cavity ofCavity of infund.infund.

Cavity ofCavity ofinfl.partinfl.partCavity ofCavity ofinfl.partinfl.part

RightVentricle





-is a--is a-


















ApexApex


-is a--is a-





-is a--is a-


Network






subobject subobject

-is a--is a-

hashas

hashas



hashasadjacencyadjacency hashasadjacencyadjacency

anterioranterioranterioranterior inferiorinferiorinferiorinferiorto leftto leftto leftto left

LeftLeftventricleventricle LeftLeftventricleventriclePericardialPericardial

sacsacPericardialPericardial sacsac


DiaphragmDiaphragmDiaphragmDiaphragm

inferiorinferiorinferiorinferior

Spatial Association NetworkSpatial Association NetworkSpatial Association NetworkSpatial Association Network



FmFmBODYBODY = { = {FmFmANATOMICAL_ENTITYANATOMICAL_ENTITY}}



How do we do it?How do we do it?Teach the FM to the computer.Teach the FM to the computer.


Foundational PrinciplesFoundational PrinciplesFoundational PrinciplesFoundational Principles

Assertions that provide the basis for reasoning and actionAssertions that provide the basis for reasoning and actionAssertions that provide the basis for reasoning and actionAssertions 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?How to teach the FM to the computer?

Explicit DefinitionsExplicit Definitions

Purpose of FM definitions:Purpose of FM definitions:

Provide the rationale for an Provide the rationale for an inheritance hierarchyinheritance hierarchyin a structural context;in a structural context;

Specify the Specify the essenceessence of anatomical entities of anatomical entitiesin terms of two sets of structural attributes:in terms of two sets of structural attributes:

those of their those of their genusgenus

and and differentiaedifferentiae



Principled Modeling = Principled Modeling = Foundational Principles + Explicit DefinitionsFoundational Principles + Explicit Definitions

Leaf terms(concepts)

Multiple layersof meaning

Principled ModelingPrincipled Modeling

Prototype problems:Prototype problems:

1.1. How to reconcile different How to reconcile different naming and classification naming and classification

conventions?conventions?

2. 2. How to assure inheritance?How to assure inheritance?

3.3. How to represent different and How to represent different and overlappingoverlapping

part-whole relationships?part-whole relationships?

4.4. How to represent different kinds How to represent different kinds of of

location attributes?location attributes?

Esophagus

Leaf conceptLeaf concept

Explicit DefinitionsExplicit Definitions

Purpose of FM definitions:Purpose of FM definitions:

Provide the rationale for an Provide the rationale for an inheritance hierarchyinheritance hierarchyin a structural context;in a structural context;

Specify the Specify the essenceessence of anatomical entities of anatomical entitiesin terms of two sets of structural attributes:in terms of two sets of structural attributes:

those of their those of their genusgenus

differentiaedifferentiae

How to reconcile different classifications?How to reconcile different classifications?

DefinitionDefinition

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

DefinitionDefinitionDefinitionDefinition

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


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


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.


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--is a-

AnatomicalStructure

AnatomicalStructure

Non-material Physical Anatomical Entity




AnatomicalStructure

AnatomicalStructure



Physical Anatomical Entity


ConceptualAnatomical Entity




AnatomicalStructure

AnatomicalStructure







Anatomical EntityAnatomical Entity

Mate ꈤ A ꈤ A Physical Anatomical Entity

Mate ꈤ A ꈤ A Physical Anatomical Entity -is a--is a-

AnatomicalStructure

AnatomicalStructure








OrganOrgan OrganPart

OrganPart



AnatomicalStructure

AnatomicalStructure









OrganPartOrganPart

OrganPart

TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision






OrganOrganCellCell OrganPart

OrganPart

-is a--is a-

AnatomicalStructure

AnatomicalStructure

BodyPart

BodyPart





HumanBody

HumanBody

OrganSystem

OrganSystem








OrganPart

-is a--is a-

AnatomicalStructure

AnatomicalStructure

BodyPart

BodyPart



BodySubstance

BodySubstance



HumanBody

HumanBody

OrganSystem

OrganSystem


OrganOrganOrganOrgan

Solid OrganSolid Organ Cavitated OrganCavitated Organ

Organ with cavitatedorgan part

Organ with cavitatedorgan part

Organ with organ cavity

Organ with organ cavity

HeartHeartHeartHeart EsophagusEsophagusEsophagusEsophagus--is ais a----is ais a--

-is a--is a--is a--is a-

Anatomy OntologyAnatomy OntologyAnatomy OntologyAnatomy Ontology


Fm = (Fm = (AoAo, ASA, ATA, Mk), ASA, ATA, Mk)

AoAo: : taxonomic classification based ontaxonomic classification based onexplicit definition of concepts,explicit definition of concepts,inheritance of definitional inheritance of definitional

structural attributes;structural attributes;consistent with foundational principles.consistent with foundational principles.

Assurance of inheritanceAssurance of inheritance

TestTest

What is the brain?What is the brain?

To which Ao class would you assign the brain?To which Ao class would you assign the brain?







OrganPart

-is a--is a-

AnatomicalStructure

AnatomicalStructure

BodyPart

BodyPart



BodySubstance

BodySubstance



HumanBody

HumanBody

OrganSystem

OrganSystem


OrganOrganDefinition:Definition:

OrganOrgan

is anis an anatomical structureanatomical structure

• consists ofconsists of maximal sets of organ partsmaximal sets of organ partsconnected toconnected to one another one anotherconstituteconstitute self-contained unit self-contained unitdistinct fromdistinct from other units other units

• connected toconnected to other organsother organs• constitutesconstitutes organ systemorgan system

body partbody part

Organ systemOrgan systemDefinition:

OrganOrgan system system

is an anatomical structureanatomical structure

• consists of members of predominantly one members of predominantly one organ subclass; organ subclass;

interconnected by zones interconnected by zones of of continuity;continuity; • connected to other organ systems• constitutes the human body

Definition of neuraxisDefinition of neuraxis

Neuraxis Neuraxis is ...is ...

central nervous system NeuroNamesNeuroNames

"the axial, unpaired part of the central nervous "the axial, unpaired part of the central nervous system....in contrast to the paired cerebral hemispheres”system....in contrast to the paired cerebral hemispheres”

Stedman’sStedman’s

an axon; an axon; central nervous system.central nervous system.

Dorland’s:Dorland’s:

What is the brain?What is the brain?

Summary: Principled ModelingSummary: Principled Modeling









Revisit: Principled ModelingRevisit: Principled Modeling










Correlation of Correlation of the Foundational Model with the Foundational Model with

Traditional Sources of Anatomical KnowledgeTraditional Sources of Anatomical Knowledge

Augusto Agoncillo M.D., Augusto Agoncillo M.D., José L.V. Mejino Jr., M.D.,José L.V. Mejino Jr., M.D.,

Cornelius Rosse M.D., D.Sc.Cornelius Rosse M.D., D.Sc.


Problem

• Semantic expressivity• Semantic expressivity

• Semantic specificity• Semantic specificity

Conflicts between Traditional Sources and Foundational Model:


• homonyms• ambiguous use of synonyms

• homonyms• ambiguous use of synonyms

Semantic Specificity and ExpressivitySemantic Specificity and Expressivity

Thought“Concept”

Symbol“Term”

ReferentTriangle of Meaning

Authoring program: Protégé Authoring program: Protégé

Semantic Specificity: synonymsSemantic Specificity: synonyms

SemanticSemantic Specificity: Homonyms Specificity: Homonyms

Homonym: ‘Base of heart’Homonym: ‘Base of heart’

Anterior Anterior viewview

Posterior Posterior viewview

Foundational ModelBuilder

Preferred term: Base of heart (anatomical)

Preferred term: Base of heart (clinical)

Semantic Specificity: Ambiguous use of synonymsSemantic Specificity: Ambiguous use of synonyms

Transferred meaning: ‘Left border of heart’Transferred meaning: ‘Left border of heart’

Left borderLeft borderof heartof heart

Left surfaceLeft surfaceof heartof heart

Semantic SpecificitySemantic Specificity

• one preferred name for each anatomical entity

• associate synonyms witheach preferred name

• disallow homonyms;use extensions

• disallow transferred meanings

• one preferred name for each anatomical entity

• associate synonyms witheach preferred name

• disallow homonyms;use extensions

• disallow transferred meanings

Assured in FM by:

Problem

• Semantic expressivity• Semantic expressivity

• Semantic specificity• Semantic specificity



classification of anatomical entitiesrelationships between anatomical entitiesclassification of anatomical entitiesrelationships between anatomical entities

Semantic Expressivity: Classification Semantic Expressivity: Classification Semantic Expressivity: Classification Semantic Expressivity: Classification

Alimentary SystemMouthTonguePharynxEsophagusStomachSmall intestineLarge intestine

Caecum

AppendixAppendix

ColonRectum

LiverGall Bladder


Caecum

AppendixAppendix

ColonRectum

LiverGall Bladder

Lymphoid SystemPrimary Lymphoid

Bone MarrowThymus

Secondary Lymphoid

SpleenPharyngeal lymphoid ringLymph node


Bone MarrowThymus

Secondary Lymphoid


Terminologia AnatomicaTerminologia Anatomica

Semantic Expressivity: ClassificationSemantic Expressivity: ClassificationSemantic Expressivity: ClassificationSemantic Expressivity: Classification


Caecum

AppendixAppendixColonRectum

LiverGall Bladder


Caecum

AppendixAppendixColonRectum

LiverGall Bladder


Bone MarrowThymus

Secondary Lymphoid



Bone MarrowThymus

Secondary Lymphoid


Terminologia AnatomicaTerminologia Anatomica

Semantic ExpressivitySemantic ExpressivitySemantic ExpressivitySemantic Expressivity

state defining attributes of state defining attributes of anatomical entitiesanatomical entities

in terms ofin terms ofconstituent partsconstituent partsentities they entities they

constituteconstitute

state defining attributes of state defining attributes of anatomical entitiesanatomical entities

in terms ofin terms ofconstituent partsconstituent partsentities they entities they

constituteconstitute

Definition principle:Definition principle:






CellCell

-is a--is a-Conceptual

Anatomical Entity


Semantic ExpressivitySemantic Expressivity



AnatomicalSpace

AnatomicalSpace

AnatomicalSurface

AnatomicalSurface

AnatomicalLine

AnatomicalLine

AnatomicalStructure

AnatomicalStructure

BodySubstance

BodySubstance


OrganPart

OrganSystem

OrganSystem

BodyPart

BodyPart

HumanBody

HumanBody


Ambiguous part-whole relationships


Right ventricleRight ventricle

Inflow partInflow part




Outflow partOutflow part


Preferred Term: Inflow part of right ventricle

Preferred Term: Outflow part of right ventricle

SummarySummary

Principled representation of Foundational Model calls for:Principled representation of Foundational Model calls for:

• greater specificity and expressivity greater specificity and expressivity than traditional sourcesthan traditional sources

• definition of new classes of anatomical entitiesdefinition of new classes of anatomical entities

• introduction of new descriptive termsintroduction of new descriptive terms

• modification of existing termsmodification of existing terms

Principled representation of Foundational Model calls for:Principled representation of Foundational Model calls for:

• greater specificity and expressivity greater specificity and expressivity than traditional sourcesthan traditional sources

• definition of new classes of anatomical entitiesdefinition of new classes of anatomical entities

• introduction of new descriptive termsintroduction of new descriptive terms

• modification of existing termsmodification of existing terms

ConclusionsConclusions

• Establishes an inheritance hierarchy (Ao)Establishes an inheritance hierarchy (Ao)based on inherent structural propertiesbased on inherent structural properties

• Establishes an inheritance hierarchy (Ao)Establishes an inheritance hierarchy (Ao)based on inherent structural propertiesbased on inherent structural properties

• Specifies structural relationshipsSpecifies structural relationshipsbetween anatomical entitiesbetween anatomical entities

• Specifies structural relationshipsSpecifies structural relationshipsbetween anatomical entitiesbetween anatomical entities

• Explicitly represents classes and relationshipsExplicitly represents classes and relationshipsimplied in traditional sourcesimplied in traditional sources

• Explicitly represents classes and relationshipsExplicitly represents classes and relationshipsimplied in traditional sourcesimplied in traditional sources

Conflicts can be solved:

Continued: Principled ModelingContinued: Principled Modeling










Anatomical RelationshipsAnatomical Relationshipsin the in the


José L.V. Mejino Jr., M.D.,José L.V. Mejino Jr., M.D.,Cornelius Rosse M.D., D.Sc.Cornelius Rosse M.D., D.Sc.


ASA = (Do, Bn, Pn, SAn) ASA = (Do, Bn, Pn, SAn) (2)(2)ASA = (Do, Bn, Pn, SAn) ASA = (Do, Bn, Pn, SAn) (2)(2)





Anatomical RelationshipsAnatomical Relationships

RightVentricle





-is a--is a-




ASA = ( ASA = ( DoDo, , PnPn, Bn, SAn ), Bn, SAn )ASA = ( ASA = ( DoDo, , PnPn, Bn, SAn ), Bn, SAn )

RightVentricle





-is a--is a-


















ApexApex


-is a--is a-





-is a--is a-

ASA = ( ASA = ( DoDo, , BnBn, , PnPn, , SAnSAn ) )ASA = ( ASA = ( DoDo, , BnBn, , PnPn, , SAnSAn ) )

RightVentricle





-is a--is a-


















ApexApex


-is a--is a-





-is a--is a-


Network






subobject subobject

-is a--is a-

hashas

hashas



ASA = ( ASA = ( DoDo, , BnBn, , PnPn, , SAnSAn ) )ASA = ( ASA = ( DoDo, , BnBn, , PnPn, , SAnSAn ) )

RightVentricle





-is a--is a-


















ApexApex


-is a--is a-





-is a--is a-


Network






subobject subobject

-is a--is a-

hashas

hashas




anterioranterioranterioranterior inferiorinferiorinferiorinferiorto leftto leftto leftto left

LeftLeftventricleventricle LeftLeftventricleventriclePericardialPericardial

sacsacPericardialPericardial sacsac


DiaphragmDiaphragmDiaphragmDiaphragm

inferiorinferiorinferiorinferior

Spatial Association NetworkSpatial Association NetworkSpatial Association NetworkSpatial Association Network

ASA = ( Do, Bn, Pn, SAnSAn ))

ASA = ( Do, Bn, Pn, SAnSAn ))

Anatomical RelationshipsAnatomical Relationships

Part_of relationshipsPart_of relationships






Attributed Part: Shared partsAttributed Part: Shared parts

Tracheobronchial treeTracheobronchial tree

LungsLungs

Attributed Part: Shared partsAttributed Part: Shared partsAttributed Part: Shared partsAttributed Part: Shared parts

(Netter’s Atlas of Human Anatomy)(Netter’s Atlas of Human Anatomy)


(Cranial Nerves: Wilson-Pauwels et al.)(Cranial Nerves: Wilson-Pauwels et al.)

Oculomotor NerveOculomotor Nerve

Attributed Part: Anatomical/ArbitraryAttributed Part: Anatomical/Arbitrary

Anterior view Posterior view

Esophagus

Attributed Part: Anatomical/ArbitraryAttributed Part: Anatomical/ArbitraryAttributed Part: Anatomical/ArbitraryAttributed Part: Anatomical/Arbitrary

Granularity of partsGranularity of partsGranularity of partsGranularity of parts

Granularity of partsGranularity of partsGranularity of partsGranularity of parts

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

Nuclear pore complexNuclear pore complex

ASA = (Do, Bn, ASA = (Do, Bn, PnPn, SAn) , SAn) (2)(2)ASA = (Do, Bn, ASA = (Do, Bn, PnPn, SAn) , SAn) (2)(2)






ASA = (Do, Bn, Pn, SAn) (2)ASA = (Do, Bn, Pn, SAn) (2)





SAn = (Ln, On, Cn) (3)SAn = (Ln, On, Cn) (3)

HowHowto represent different location relationships?to represent different location relationships?

HowHowto represent different location relationships?to represent different location relationships?

HowHowto represent different location relationships? to represent different location relationships? AdjacencyAdjacency

Anterior view Posterior view

Esophagus

Esophagus

T2-3

T8

AnteriorAnterior

PosteriorPosterior

HowHowto represent different location relationships? to represent different location relationships? CoordinatesCoordinates




AnteriorAnterior

PosteriorPosterior

RightlateralRightlateral

LeftlateralLeft

lateral



Pericardialsac

Pericardialsac

AnteriorAnterior

PosteriorPosterior



RightlateralRightlateral

LeftlateralLeft

lateral

Right AnteriorLeft Anterior

Right PosteriorLeft Posterior

Right Antero-lateral

Right Postero-lateral

Left Postero-lateral

Left Antero-lateral

T2-3

T8

ASA = (Do, Bn, ASA = (Do, Bn, Pn, SAnPn, SAn)) (2)(2)ASA = (Do, Bn, ASA = (Do, Bn, Pn, SAnPn, SAn)) (2)(2)



SAn = (Ln, On, Cn) (3) SAn = (Ln, On, Cn) (3)

HowHowto represent part_of and location relationships?to represent part_of and location relationships?

Summary: Summary: Foundational Model specifies Foundational Model specifies

Anatomy ontologyAnatomy ontologystructure-based classification of structure-based classification of anatomical entitiesanatomical entities

Structural relationships (ASA)Structural relationships (ASA)


““The The oesophagusoesophagus is ais a muscular tubemuscular tube … … connecting connecting the the pharynx pharynx to the to the stomachstomach. . ItIt beginsbegins in the in the neckneck, , level withlevel with the the lower lower border of the cricoid cartilageborder of the cricoid cartilage and the and the sixth sixth cervical vertebracervical vertebra; ; descendingdescending largely largely anterioranterior to the to the vertebral columnvertebral column through through the the superiorsuperior and and posterior mediastinaposterior mediastina.”.”


Conclusions

Conclusions

Summary: Summary: Foundational Model specifies Foundational Model specifies

Anatomy ontologyAnatomy ontologystructure-based classification of structure-based classification of anatomical entitiesanatomical entities

Structural relationships (ASA)Structural relationships (ASA)Foundational Model omitsFoundational Model omits

functionfunctionpathologypathologyclinical casesclinical cases


Role of Foundational Model of AnatomyRole of Foundational Model of Anatomy

Prototype for symbolic models in other domainsPrototype for symbolic models in other domainse.g., physiology, pathology, cancer therapye.g., physiology, pathology, cancer therapy

Core of biomedical knowledge basesCore of biomedical knowledge basesto solve problems in to solve problems in education, research, health careeducation, research, health care

"Foundational" "Foundational" becausebecauseanatomy is fundamental to all anatomy is fundamental to all

biomedical sciences;biomedical sciences;anatomical concepts encompassed by FManatomical concepts encompassed by FM

generalize to all biomedical domains.generalize to all biomedical domains.


Evolving knowledge-based application for Evolving knowledge-based application for Anatomy education:Anatomy education:

““Intelligent” Digital AnatomistIntelligent” Digital Anatomist



Image Repository

NetworkNetwork

End-UserPrograms

Servers


FoundationalModel

FoundationalModel

Meta-knowledge

Meta-knowledge

ClinicalInfo

ClinicalInfo

Authoring Programs


NetworkNetwork

Authoring Programs

Servers

““Intelligent” applicationsIntelligent” applications

Anatomy Tutor

Anatomy Tutor

Anatomy Consultant

Anatomy Consultant

2-DImages

2-DImages

2-DAnnotations

2-DAnnotations

3-DModel

3-DModel

3-D ImageVolumes

3-D ImageVolumes Clinical dataClinical dataFoundational

Model

FoundationalModel

Symbolic InfoSymbolic InfoImage RepositoryImage Repository


NetworkNetwork

Authoring Programs


Anatomy Tutor

Anatomy Tutor

Anatomy Consultant

Anatomy Consultant

2-DImages

2-DImages

2-DAnnotations

2-DAnnotations

3-DModel

3-DModel

3-D ImageVolumes


Model

FoundationalModel


KnowledgeServer

KnowledgeServer

ImageServer

ImageServer

DataServer

DataServer

GraphicsServer

GraphicsServer


NetworkNetwork

Authoring Programs


Anatomy Tutor

Anatomy Tutor

Anatomy Consultant

Anatomy Consultant

2-DImages

2-DImages

2-DAnnotations

2-DAnnotations

3-DModel

3-DModel

3-D ImageVolumes


Model

FoundationalModel


KnowledgeServer

KnowledgeServer

ImageServer

ImageServer

DataServer

DataServer

GraphicsServer

GraphicsServer

DIGITAL ANATOMISTMetaknowledgeMetaknowledge

Evaluation of FM byEvaluation of FM by

AnatomistsAnatomistsCliniciansCliniciansResearchersResearchers


How do we teach How do we teach Anatomy to the Computer?Anatomy to the Computer?

"We are made wise not by the recollection on our past,"We are made wise not by the recollection on our past,but by the responsibility to our future."but by the responsibility to our future."

George Bernard George Bernard ShawShaw

Spare slides

Portal Venous Tree

Vena Caval Tree

Systemic Arterial Tree

Pericardial Effusion

Interactive Radiology ExercisesInteractive Radiology Exercises

•296 models of thoracic viscera

•17 models of coronary arteries

•296 models of thoracic viscera

•17 models of coronary arteries

rcorartconusrcorartconusrcorartconusrcorartconus lcorartatriallcorartatriallcorartatriallcorartatrial

3-D Structure Primitives3-D Structure Primitives

FM ServerFM Server

FMFM 3-D Primitives

3-D Primitives

Conus branch of right coronary artery-> rcorartconusConus branch of right coronary artery-> rcorartconus

Atrial branch of circumflex coronary artery->lcorartatrialAtrial branch of circumflex coronary artery->lcorartatrial

Conus branch of right coronary artery-> rcorartconusConus branch of right coronary artery-> rcorartconus

Atrial branch of circumflex coronary artery->lcorartatrialAtrial branch of circumflex coronary artery->lcorartatrial

FM ServerFM Server“Data Server”“Data Server”

FMFM 3-D Primitives

3-D Primitives CorrespondencesCorrespondences

Data ServerData Server

Authoring program: Protégé Authoring program: Protégé


What is the Foundational Model of Anatomy (FM)?

A symbolic model of anatomy (science)A symbolic model of anatomy (science)

represents the physical organization represents the physical organization (structure)(structure)

of biological organisms;of biological organisms;currently limited to the human body.currently limited to the human body.

"Foundational" "Foundational" becausebecause

anatomy is fundamental to all anatomy is fundamental to all biomedical sciences;biomedical sciences;

anatomical concepts encompassed by anatomical concepts encompassed by FMFM

generalize to all biomedical generalize to all biomedical domains.domains.

What is a foundational model?

Foundational ModelFoundational Modelis a is a symbolic modelsymbolic model;;

declares the principlesdeclares the principles for including concepts and relationships for including concepts and relationships that are implicitly assumed that are implicitly assumed when knowledge of the domain when knowledge of the domain is applied in different contexts;is applied in different contexts;

explicitly definesexplicitly definesconcepts and relationships concepts and relationships

necessary and sufficient for consistently necessary and sufficient for consistently modeling the structure of the modeling the structure of the coherent knowledge domain.coherent knowledge domain.

Dynamic 3-D Scene Generator

Evolving knowledge-based applicationEvolving knowledge-based application


NetworkNetwork

Authoring Programs


Anatomy Tutor

Anatomy Tutor

Anatomy Consultant

Anatomy Consultant

2-DImages

2-DImages

2-DAnnotations

2-DAnnotations

3-DModel

3-DModel

3-D ImageVolumes


Model

FoundationalModel


KnowledgeServer

KnowledgeServer

ImageServer

ImageServer

DataServer

DataServer

GraphicsServer

GraphicsServer


FM ServerFM Server “Data Server”“Data Server”

FMFM 3-D Primitives

3-D Primitives CorrespondencesCorrespondences

Graphics ServerGraphics Server

Web BrowserWeb Browser

CGI ScriptCGI Script


NetworkNetwork

Authoring Programs


Anatomy Tutor

Anatomy Tutor

Anatomy Consultant

Anatomy Consultant

2-DImages

2-DImages

2-DAnnotations

2-DAnnotations

3-DModel

3-DModel

3-D ImageVolumes


Model

FoundationalModel


KnowledgeServer

KnowledgeServer

ImageServer

ImageServer

DataServer

DataServer

GraphicsServer

GraphicsServer


Pleural Cavity

how do we teach anatomy to the computer? structural informatics group university of washington

Documents

d graphical modelssymbolic

new form of web content

semantic web

phdsara kim

phdkate mulligan

mdandrew poliakov

phdjohn sundsten

phddoug bowden