how do we teach anatomy to the computer? structural informatics group university of washington...
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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
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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?
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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?
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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: ???
Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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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
Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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
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Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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
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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.
Structural Informatics GroupStructural Informatics GroupUniversity of WashingtonUniversity of Washington
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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
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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
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Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
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
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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
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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
Servers
End User InterfacesEnd User Interfaces
DigitalAnatomist
Atlases
DigitalAnatomist
Atlases
BrainMapper
BrainMapper
RadiationOncology
RadiationOncology
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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
KnowledgeServer
KnowledgeServer
ImageServer
ImageServer
DataServer
DataServer
GraphicsServer
GraphicsServer
DigitalAnatomistAtlases
SymbolicSymbolicGraphicalGraphical
Authoring ProgramsAuthoring Programs End-User InterfacesEnd-User Interfaces
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Web-based Web-based Digital Anatomist Atlas of Digital Anatomist Atlas of
Thoracic visceraThoracic viscera
Digital Anatomist Information SystemDigital Anatomist Information System
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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
Servers
End User InterfacesEnd User Interfaces
DigitalAnatomist
Atlases
DigitalAnatomist
Atlases
BrainMapper
BrainMapper
RadiationOncology
RadiationOncology
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SuperimposedFMRI and corticallanguage maps
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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
Servers
End User InterfacesEnd User Interfaces
DigitalAnatomist
Atlases
DigitalAnatomist
Atlases
BrainMapper
BrainMapper
RadiationOncology
RadiationOncology
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Radiation Treatment Planning Radiation Treatment Planning
PRISM PRISM
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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
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How Do We Teach Anatomy to the Computer?How Do We Teach Anatomy to the Computer?
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
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3-D Models of Right Lung and Heart3-D Models of Right Lung and Heart
Digital Anatomist Image RepositoryDigital Anatomist Image Repository
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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
Authoring Programs
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Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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
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Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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
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SNOMEDSNOMED
Topography AxisTopography Axis
20000 Respiratory System20000 Respiratory System
28000 Lung28000 Lung
29000 Pleura29000 Pleura
29050 Pleural Cavity29050 Pleural CavityPleural Cavity
Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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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
Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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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
Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
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Pleural Cavity
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Why Why Teach Anatomy to the Computer?Teach Anatomy to the Computer?
ConclusionConclusion
• Inadequacy of Inadequacy of traditional knowledge sourcestraditional knowledge sources
• New need forNew need forcomputer-processable computer-processable anatomical knowledgeanatomical knowledge
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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?
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"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).
What to teach to the computer?What to teach to the computer?
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"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
What to teach to the computer?What to teach to the computer?
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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.
What to teach to the computer?What to teach to the computer?
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””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'
What to teach to the computer?What to teach to the computer?
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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})})
What to teach to the computer?What to teach to the computer?
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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 to teach to the computer?What to teach to the computer?
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What kind of symbols?
Thought“Concept”
Symbol“Term”
ReferentTriangle of Meaning
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““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 symbols?
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““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 symbols?
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““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 symbols?
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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?
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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).
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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.
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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)
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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
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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
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RightVentricle
Networks of ASANetworks of ASA
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RightVentricle
CardiacChamber CardiacChamber
Organ Subdivision Organ Subdivision
Organ PartOrgan Part
Anatomical StructureAnatomical StructureAnatomy OntologyAnatomy Ontology
-is a--is a-
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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
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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-
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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
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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
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Foundational Model of AnatomyFoundational Model of Anatomy
Fm = (Ao, ASA, ATA, Mk)Fm = (Ao, ASA, ATA, Mk)
FmFmBODYBODY = { = {FmFmANATOMICAL_ENTITYANATOMICAL_ENTITY}}
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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?Teach the FM to the computer.Teach the FM to the computer.
How to Teach Anatomy to the Computer?How to Teach Anatomy to the Computer?
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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?
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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
How to teach the FM to the computer?How to teach the FM to the computer?
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How to teach the FM to the computer?How to teach the FM to the computer?
Principled Modeling = Principled Modeling = Foundational Principles + Explicit DefinitionsFoundational Principles + Explicit Definitions
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UMLS
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Leaf terms(concepts)
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Multiple layersof meaning
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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?
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Esophagus
Leaf conceptLeaf concept
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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?
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DefinitionDefinition
Esophagus is an ‘organ with an organ cavity’, which connects the pharynx to the stomach
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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.
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DefinitionDefinitionDefinitionDefinition
Cavitated organ is an ‘organ’, the morphological parts of which surround one or more cavities, which contain one or more body substances.
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DefinitionDefinitionDefinitionDefinition
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.
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DefinitionDefinitionDefinitionDefinition
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.
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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?
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Material Physical Anatomical Entity
Material Physical Anatomical Entity -is a--is a-
AnatomicalStructure
AnatomicalStructure
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
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Material Physical Anatomical Entity
Material Physical Anatomical Entity -is a--is a-
AnatomicalStructure
AnatomicalStructure
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
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Material Physical Anatomical Entity
Material Physical Anatomical Entity -is a--is a-
AnatomicalStructure
AnatomicalStructure
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
Anatomical EntityAnatomical Entity
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Mate ꈤ A ꈤ A Physical Anatomical Entity
Mate ꈤ A ꈤ A Physical Anatomical Entity -is a--is a-
AnatomicalStructure
AnatomicalStructure
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
Anatomical EntityAnatomical Entity
OrganOrgan OrganPart
OrganPart
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Material Physical Anatomical Entity
Material Physical Anatomical Entity -is a--is a-
AnatomicalStructure
AnatomicalStructure
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
Anatomical EntityAnatomical Entity
OrganOrgan OrganPart
OrganPartOrganPart
OrganPart
TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision
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Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
OrganOrganCellCell OrganPart
OrganPart
-is a--is a-
AnatomicalStructure
AnatomicalStructure
BodyPart
BodyPart
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
HumanBody
HumanBody
OrganSystem
OrganSystem
TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision
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Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
OrganOrganCellCell OrganPart
OrganPart
-is a--is a-
AnatomicalStructure
AnatomicalStructure
BodyPart
BodyPart
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
BodySubstance
BodySubstance
ConceptualAnatomical Entity
ConceptualAnatomical Entity
HumanBody
HumanBody
OrganSystem
OrganSystem
TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision
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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
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Principled ModelingPrincipled Modeling
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.
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Assurance of inheritanceAssurance of inheritance
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Assurance of inheritanceAssurance of inheritance
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Assurance of inheritanceAssurance of inheritance
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Assurance of inheritanceAssurance of inheritance
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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?
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Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
OrganOrganCellCell OrganPart
OrganPart
-is a--is a-
AnatomicalStructure
AnatomicalStructure
BodyPart
BodyPart
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
BodySubstance
BodySubstance
ConceptualAnatomical Entity
ConceptualAnatomical Entity
HumanBody
HumanBody
OrganSystem
OrganSystem
TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision
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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
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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
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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:
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What is the brain?What is the brain?
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What is the brain?What is the brain?
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What is the brain?What is the brain?
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What is the brain?What is the brain?
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Summary: Principled ModelingSummary: Principled 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?
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Revisit: Principled ModelingRevisit: Principled 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?
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How Do We Teach Anatomy to the Computer?How Do We Teach Anatomy to the Computer?
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.
Structural Informatics GroupStructural Informatics GroupUniversity of WashingtonUniversity of Washington
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Problem
• Semantic expressivity• Semantic expressivity
• Semantic specificity• Semantic specificity
Conflicts between Traditional Sources and Foundational Model:
Conflicts between Traditional Sources and Foundational Model:
• homonyms• ambiguous use of synonyms
• homonyms• ambiguous use of synonyms
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Semantic Specificity and ExpressivitySemantic Specificity and Expressivity
Thought“Concept”
Symbol“Term”
ReferentTriangle of Meaning
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Authoring program: Protégé Authoring program: Protégé
Semantic Specificity: synonymsSemantic Specificity: synonyms
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Semantic Specificity: synonymsSemantic Specificity: synonyms
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Semantic Specificity: synonymsSemantic Specificity: synonyms
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Semantic Specificity: synonymsSemantic Specificity: synonyms
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SemanticSemantic Specificity: Homonyms Specificity: Homonyms
Homonym: ‘Base of heart’Homonym: ‘Base of heart’
Anterior Anterior viewview
Posterior Posterior viewview
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Foundational ModelBuilder
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Foundational ModelBuilder
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Preferred term: Base of heart (anatomical)
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Foundational ModelBuilder
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Preferred term: Base of heart (clinical)
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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
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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:
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Foundational ModelBuilder
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Foundational ModelBuilder
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Problem
• Semantic expressivity• Semantic expressivity
• Semantic specificity• Semantic specificity
Conflicts between Traditional Sources and Foundational Model:
Conflicts between Traditional Sources and Foundational Model:
classification of anatomical entitiesrelationships between anatomical entitiesclassification of anatomical entitiesrelationships between anatomical entities
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Semantic Expressivity: Classification Semantic Expressivity: Classification Semantic Expressivity: Classification Semantic Expressivity: Classification
Alimentary SystemMouthTonguePharynxEsophagusStomachSmall intestineLarge intestine
Caecum
AppendixAppendix
ColonRectum
LiverGall Bladder
Alimentary SystemMouthTonguePharynxEsophagusStomachSmall intestineLarge intestine
Caecum
AppendixAppendix
ColonRectum
LiverGall Bladder
Lymphoid SystemPrimary Lymphoid
Bone MarrowThymus
Secondary Lymphoid
SpleenPharyngeal lymphoid ringLymph node
Lymphoid SystemPrimary Lymphoid
Bone MarrowThymus
Secondary Lymphoid
SpleenPharyngeal lymphoid ringLymph node
Terminologia AnatomicaTerminologia Anatomica
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Semantic Expressivity: ClassificationSemantic Expressivity: ClassificationSemantic Expressivity: ClassificationSemantic Expressivity: Classification
Alimentary SystemMouthTonguePharynxEsophagusStomachSmall intestineLarge intestine
Caecum
AppendixAppendixColonRectum
LiverGall Bladder
Alimentary SystemMouthTonguePharynxEsophagusStomachSmall intestineLarge intestine
Caecum
AppendixAppendixColonRectum
LiverGall Bladder
Lymphoid SystemPrimary Lymphoid
Bone MarrowThymus
Secondary Lymphoid
SpleenPharyngeal lymphoid ringLymph node
Lymphoid SystemPrimary Lymphoid
Bone MarrowThymus
Secondary Lymphoid
SpleenPharyngeal lymphoid ringLymph node
Terminologia AnatomicaTerminologia Anatomica
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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:
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Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
CellCell
-is a--is a-Conceptual
Anatomical Entity
ConceptualAnatomical Entity
Semantic ExpressivitySemantic Expressivity
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
AnatomicalSpace
AnatomicalSpace
AnatomicalSurface
AnatomicalSurface
AnatomicalLine
AnatomicalLine
AnatomicalStructure
AnatomicalStructure
BodySubstance
BodySubstance
OrganOrgan OrganPart
OrganPart
OrganSystem
OrganSystem
BodyPart
BodyPart
HumanBody
HumanBody
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Semantic ExpressivitySemantic Expressivity
Ambiguous part-whole relationships
InfundibulumInfundibulum
Right ventricleRight ventricle
Inflow partInflow part
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Ambiguous part-whole relationships
Right ventricleRight ventricle
Inflow partInflow part
Outflow partOutflow part
Semantic ExpressivitySemantic Expressivity
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Foundational ModelBuilder
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Foundational ModelBuilder
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Preferred Term: Inflow part of right ventricle
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Preferred Term: Outflow part of right ventricle
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Ambiguous part-whole relationships
Right ventricleRight ventricle
Inflow partInflow part
Outflow partOutflow part
Semantic ExpressivitySemantic Expressivity
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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
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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:
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Continued: Principled ModelingContinued: Principled 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?
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How Do We Teach Anatomy to the Computer?How Do We Teach Anatomy to the Computer?
Anatomical RelationshipsAnatomical Relationshipsin the in the
Foundational Model of AnatomyFoundational Model of Anatomy
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.
Structural Informatics GroupStructural Informatics GroupUniversity of WashingtonUniversity of Washington
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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)
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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
Anatomical RelationshipsAnatomical Relationships
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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
ASA = ( ASA = ( DoDo, , PnPn, Bn, SAn ), Bn, SAn )ASA = ( ASA = ( DoDo, , PnPn, Bn, SAn ), Bn, SAn )
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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
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-
ASA = ( ASA = ( DoDo, , BnBn, , PnPn, , SAnSAn ) )ASA = ( ASA = ( DoDo, , BnBn, , PnPn, , SAnSAn ) )
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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
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
ASA = ( ASA = ( DoDo, , BnBn, , PnPn, , SAnSAn ) )ASA = ( ASA = ( DoDo, , BnBn, , PnPn, , SAnSAn ) )
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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
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
ASA = ( Do, Bn, Pn, SAnSAn ))
ASA = ( Do, Bn, Pn, SAnSAn ))
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Anatomical RelationshipsAnatomical Relationships
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Anatomical RelationshipsAnatomical Relationships
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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?
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Part_of relationshipsPart_of relationships
Right ventricleRight ventricle
InfundibulumInfundibulum
Outflow partOutflow part
Right ventricleRight ventricle
Inflow partInflow part
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Attributed Part: Shared partsAttributed Part: Shared parts
Tracheobronchial treeTracheobronchial tree
LungsLungs
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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)
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Attributed Part: Shared partsAttributed Part: Shared partsAttributed Part: Shared partsAttributed Part: Shared parts
(Cranial Nerves: Wilson-Pauwels et al.)(Cranial Nerves: Wilson-Pauwels et al.)
Oculomotor NerveOculomotor Nerve
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Attributed Part: Shared partsAttributed Part: Shared partsAttributed Part: Shared partsAttributed Part: Shared parts
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Attributed Part: Anatomical/ArbitraryAttributed Part: Anatomical/Arbitrary
Anterior view Posterior view
Esophagus
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Attributed Part: Anatomical/ArbitraryAttributed Part: Anatomical/ArbitraryAttributed Part: Anatomical/ArbitraryAttributed Part: Anatomical/Arbitrary
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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Granularity of partsGranularity of partsGranularity of partsGranularity of parts
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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
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ASA = (Do, Bn, ASA = (Do, Bn, PnPn, SAn) , SAn) (2)(2)ASA = (Do, Bn, ASA = (Do, Bn, PnPn, SAn) , 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
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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?
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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)
HowHowto represent different location relationships?to represent different location relationships?
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HowHowto represent different location relationships?to represent different location relationships?
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HowHowto represent different location relationships?to represent different location relationships?
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HowHowto represent different location relationships?to represent different location relationships?
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HowHowto represent different location relationships? to represent different location relationships? AdjacencyAdjacency
Anterior view Posterior view
Esophagus
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Esophagus
T2-3
T8
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AnteriorAnterior
PosteriorPosterior
HowHowto represent different location relationships? to represent different location relationships? CoordinatesCoordinates
HowHowto represent different location relationships? to represent different location relationships? CoordinatesCoordinates
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HowHowto represent different location relationships? to represent different location relationships? CoordinatesCoordinates
HowHowto represent different location relationships? to represent different location relationships? CoordinatesCoordinates
AnteriorAnterior
PosteriorPosterior
RightlateralRightlateral
LeftlateralLeft
lateral
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HowHowto represent different location relationships? to represent different location relationships? AdjacencyAdjacency
HowHowto represent different location relationships? to represent different location relationships? AdjacencyAdjacency
Pericardialsac
Pericardialsac
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AnteriorAnterior
PosteriorPosterior
HowHowto represent different location relationships? to represent different location relationships? CoordinatesCoordinates
HowHowto represent different location relationships? to represent different location relationships? CoordinatesCoordinates
RightlateralRightlateral
LeftlateralLeft
lateral
Right AnteriorLeft Anterior
Right PosteriorLeft Posterior
Right Antero-lateral
Right Postero-lateral
Left Postero-lateral
Left Antero-lateral
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T2-3
T8
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HowHowto represent different location relationships? to represent different location relationships? AdjacencyAdjacency
HowHowto represent different location relationships? to represent different location relationships? AdjacencyAdjacency
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ASA = (Do, Bn, ASA = (Do, Bn, Pn, SAnPn, SAn)) (2)(2)ASA = (Do, Bn, ASA = (Do, Bn, Pn, SAnPn, SAn)) (2)(2)
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)
HowHowto represent part_of and location relationships?to represent part_of and location relationships?
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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?
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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)
ConclusionsConclusions
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““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.”.”
Gray’s Anatomy, 38th edition, p. Gray’s Anatomy, 38th edition, p. 17511751
Conclusions
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Conclusions
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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
ConclusionsConclusions
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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
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Evolving knowledge-based application for Evolving knowledge-based application for Anatomy education:Anatomy education:
““Intelligent” Digital AnatomistIntelligent” Digital Anatomist
ConclusionsConclusions
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Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
Image Repository
NetworkNetwork
End-UserPrograms
Servers
Symbolic Knowledge SourcesSymbolic Knowledge SourcesSymbolic Knowledge SourcesSymbolic Knowledge Sources
FoundationalModel
FoundationalModel
Meta-knowledge
Meta-knowledge
ClinicalInfo
ClinicalInfo
Authoring Programs
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Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
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
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Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
NetworkNetwork
Authoring Programs
““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
KnowledgeServer
KnowledgeServer
ImageServer
ImageServer
DataServer
DataServer
GraphicsServer
GraphicsServer
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Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
NetworkNetwork
Authoring Programs
““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
KnowledgeServer
KnowledgeServer
ImageServer
ImageServer
DataServer
DataServer
GraphicsServer
GraphicsServer
DIGITAL ANATOMISTMetaknowledgeMetaknowledge
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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)
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Evaluation of FM byEvaluation of FM by
AnatomistsAnatomistsCliniciansCliniciansResearchersResearchers
ConclusionsConclusions
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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)
Fm = (Ao, ASA, ATA, Mk)Fm = (Ao, ASA, ATA, Mk)
ConclusionsConclusions
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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
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Spare slides
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Portal Venous Tree
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Vena Caval Tree
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Systemic Arterial Tree
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Pericardial Effusion
Interactive Radiology ExercisesInteractive Radiology Exercises
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•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
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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
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Authoring program: Protégé Authoring program: Protégé
Semantic Specificity: synonymsSemantic Specificity: synonyms
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Semantic Specificity: synonymsSemantic Specificity: synonyms
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Semantic Specificity: synonymsSemantic Specificity: synonyms
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Semantic Specificity: synonymsSemantic Specificity: synonyms
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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.
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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.
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Dynamic 3-D Scene Generator
Evolving knowledge-based applicationEvolving knowledge-based application
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Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
NetworkNetwork
Authoring Programs
““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
KnowledgeServer
KnowledgeServer
ImageServer
ImageServer
DataServer
DataServer
GraphicsServer
GraphicsServer
DIGITAL ANATOMISTMetaknowledgeMetaknowledge
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FM ServerFM Server “Data Server”“Data Server”
FMFM 3-D Primitives
3-D Primitives CorrespondencesCorrespondences
Graphics ServerGraphics Server
Web BrowserWeb Browser
CGI ScriptCGI Script
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Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
NetworkNetwork
Authoring Programs
““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
KnowledgeServer
KnowledgeServer
ImageServer
ImageServer
DataServer
DataServer
GraphicsServer
GraphicsServer
DIGITAL ANATOMISTMetaknowledgeMetaknowledge
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Pleural Cavity