the foundational model of anatomy cornelius rosse, m.d., d.sc. structural informatics group

The Foundational Model of AnatomyThe Foundational Model of Anatomy

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

Structural Informatics GroupStructural Informatics GroupUniversity of WashingtonUniversity of Washington

Digital HumanDigital Human

Open Source Software Framework forOpen Source Software Framework forOrgan Modeling and SimulationOrgan Modeling and Simulation

Organ Modeling and SimulationOrgan Modeling and Simulation

ChallengesChallenges

• Interoperability of softwareInteroperability of software

• Representation of biomedical knowledge Representation of biomedical knowledge in machine-processible formin machine-processible form

• Integration and correlation of Integration and correlation of biomedical informationbiomedical information

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

Digital Anatomist Information ProjectDigital Anatomist Information ProjectDigital Anatomist Information ProjectDigital Anatomist Information Project

MotivationMotivation

• Manifestations of health and disease are Manifestations of health and disease are attributes of anatomical attributes of anatomical

structures.structures.• Logical and comprehensive representation of Logical and comprehensive representation of

anatomical knowledge can serve as a anatomical knowledge can serve as a foundation for other types of foundation for other types of

biomedical information.biomedical information.

Digital Anatomist ProjectUniversity of Washington

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 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

What is an Organ?What is an Organ?Organ [L. organum; Gr. organon]Organ [L. organum; Gr. organon]

a somewhat independent part of the body a somewhat independent part of the body that that performs a special function or performs a special function or functions.functions.

Dorland's Medical Dorland's Medical DictionaryDictionary

E.g., liver, heart, lung, kidneyE.g., liver, heart, lung, kidney hand, erythrocytehand, erythrocyte

OrganOrganin animals and plants, a part composed of in animals and plants, a part composed of

several several tissues and adopted to perform a tissues and adopted to perform a specific function or specific function or functions.functions.

Webster’s DictionaryWebster’s DictionaryE.g., liver, heart, lung, kidneyE.g., liver, heart, lung, kidney hand, head of femur, right ventriclehand, head of femur, right ventricle

Organ Modeling and SimulationOrgan Modeling and Simulation

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

Challenges of Anatomical Knowledge RepresentationChallenges of Anatomical Knowledge Representation

ConclusionConclusion

• Inadequacy of Inadequacy of traditional knowledge sourcestraditional knowledge sources

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


Question:Question:

What information should be entered in the What information should be entered in the Foundational Model of AnatomyFoundational Model of Anatomy??

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})})


““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

What kind of information?

““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,

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)

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

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-

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

hashasadjacencyadjacency hashasadjacencyadjacency

anterioranterioranterioranterior inferiorinferiorinferiorinferiorto leftto leftto leftto left

LeftLeftventricleventricle LeftLeftventricleventriclePericardialPericardial

sacsacPericardialPericardial sacsac

hashasadjacencyadjacency hashasadjacencyadjacency

DiaphragmDiaphragmDiaphragmDiaphragm

inferiorinferiorinferiorinferior

Spatial Association NetworkSpatial Association NetworkSpatial Association NetworkSpatial Association Network

Anatomical EntityAnatomical Entity


Physical Anatomical Entity


-is a--is a-Conceptual

Anatomical Entity

ConceptualAnatomical Entity




-is a--is a-Conceptual

Anatomical Entity


Material Physical Anatomical Entity


Non-material Physical Anatomical Entity







-is a--is a-





Anatomical Point

Anatomical Point

Anatomical Line

Anatomical Line

Anatomical Surface

Anatomical Surface

Anatomical Space

Anatomical Space






-is a--is a-





AnatomicalStructure

AnatomicalStructure

BodySubstance

BodySubstance

BodyPart

BodyPart

HumanBody

HumanBody

OrganSystem

OrganSystemOrganOrganCellCell Organ

Part

OrganPart

TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision

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






-is a--is a-





AnatomicalStructure

AnatomicalStructure

BodySubstance

BodySubstance

BodyPart

BodyPart

HumanBody

HumanBody

OrganSystem

OrganSystemOrganOrganCellCell Organ

Part

OrganPart

TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision

Protégé 2000Protégé 2000

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 Structural AbstractionAnatomical Structural AbstractionAnatomical Structural AbstractionAnatomical Structural Abstraction


Protégé 2000Protégé 2000

ASA: Part of NetworkASA: Part of Network


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

FmFmBODYBODY = { = {FmFmANATOMICAL_ENTITYANATOMICAL_ENTITY}}

Conclusions

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.

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.

ConclusionsConclusions

the foundational model of anatomy cornelius rosse, m.d., d.sc. structural informatics group

Documents

kind of information

lower border

muscular tube

grays anatomy

dorlands medical dictionarye

simulationorgan modeling

new form of web content

kidney hand