Download - 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
Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
Symbolic Knowledge
Source
NetworkNetwork
Authoring Programs
End-UserPrograms
Servers
Image RepositoryImage Repository
2-DImages
2-DAnnotations
3-DModel
3-D ImageVolumes
Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
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
Challenges of Anatomical Knowledge RepresentationChallenges of Anatomical Knowledge Representation
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})})
Challenges of Anatomical Knowledge RepresentationChallenges of Anatomical Knowledge Representation
““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.”.”
Gray’s Anatomy, 38th edition, p. Gray’s Anatomy, 38th edition, p. 17511751
What kind of information?
““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.”.”
Gray’s Anatomy, 38th edition, p. Gray’s Anatomy, 38th edition, p. 17511751
What kind of information?
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 kind of information?
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
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
Foundational Model of AnatomyFoundational Model of Anatomy
ASA = (Do, Bn, Pn, SAn) (2)ASA = (Do, Bn, Pn, SAn) (2)
where:Ln = LocationOn = OrientationCn = Connectivity
where:Ln = LocationOn = OrientationCn = Connectivity
Fm = (Ao, ASA, ATA, Mk) (1)Fm = (Ao, ASA, ATA, Mk) (1)
Spatial Association NetworkSpatial Association Network
SAn = (Ln, On, Cn) (3)SAn = (Ln, On, Cn) (3)
Foundational Model of AnatomyFoundational Model of Anatomy
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
CardiacChamber CardiacChamber
Organ Subdivision Organ Subdivision
Organ PartOrgan Part
Anatomical StructureAnatomical StructureAnatomy OntologyAnatomy Ontology
-is a--is a-
PolyhedronPolyhedron
Volume (3-D)Volume (3-D)
Dimensional OntologyDimensional Ontology
RightVentricle
CardiacChamber CardiacChamber
Organ Subdivision Organ Subdivision
Organ PartOrgan Part
Anatomical StructureAnatomical StructureAnatomy OntologyAnatomy Ontology
-is a--is a-
PolyhedronPolyhedron
Volume (3-D)Volume (3-D)
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
AnteriorInterventricular Sulcus
Line (1-D)Line (1-D)
bounded bybounded by
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
CardiacChamber CardiacChamber
Organ Subdivision Organ Subdivision
Organ PartOrgan Part
Anatomical StructureAnatomical StructureAnatomy OntologyAnatomy Ontology
-is a--is a-
PolyhedronPolyhedron
Volume (3-D)Volume (3-D)
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
AnteriorInterventricular Sulcus
Line (1-D)Line (1-D)
bounded bybounded by
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-
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
CardiacChamber CardiacChamber
Organ Subdivision Organ Subdivision
Organ PartOrgan Part
Anatomical StructureAnatomical StructureAnatomy OntologyAnatomy Ontology
-is a--is a-
PolyhedronPolyhedron
Volume (3-D)Volume (3-D)
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
AnteriorInterventricular Sulcus
Line (1-D)Line (1-D)
bounded bybounded by
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-
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
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
-is a--is a-Conceptual
Anatomical Entity
ConceptualAnatomical Entity
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
-is a--is a-Conceptual
Anatomical Entity
ConceptualAnatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
-is a--is a-
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
Anatomical Point
Anatomical Point
Anatomical Line
Anatomical Line
Anatomical Surface
Anatomical Surface
Anatomical Space
Anatomical Space
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
-is a--is a-
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
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
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
-is a--is a-
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
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)
where:where:DoDo = Dimensional ontology= Dimensional ontologyBnBn = Boundary network= Boundary networkPnPn = Part-of network= Part-of networkSAnSAn = Spatial Association network= Spatial Association network
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
Foundational Model of AnatomyFoundational Model of Anatomy
Protégé 2000Protégé 2000
ASA: Part of NetworkASA: Part of Network
ASA: Part of NetworkASA: Part of Network
ASA: Part of NetworkASA: Part of Network
ASA: Part of NetworkASA: Part of Network
ASA: Part of NetworkASA: Part of Network
ASA: Part of NetworkASA: Part of Network
Foundational Model of AnatomyFoundational Model of Anatomy
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