American Association of Clinical Anatomists
2001
How do We Teach Anatomy
to the Computer?
Structural Informatics Group
University of Washington
How to Teach Anatomy to the Computer?
Why do we need to teach anatomy to the
computer?
What to teach to the computer?
How do we do it?
Why
Teach Anatomy to the Computer?
Current status of computer programs in
anatomy
Knowledge representation
Information access
Why
Teach Anatomy to the Computer?
Current status: Knowledge representation
Traditional sources
Spatial: cadaver, radiology, atlases
Symbolic: textbooks,
Unique to the computer
Spatial: volumetric data sets
3D graphical models
Symbolic: ???
Why
Teach Anatomy to the Computer?
Current status of computer programs in anatomy
Information access
CD-ROM, Internet
One piece of information
for one mouse click
Why
Teach Anatomy to the Computer?
The Semantic Web:
A new form of Web content that
is meaningful to computers will
unleash a revolution of new
possibilities.
By:
Tim Berners-Lee
James Hendler
Ora Lassila
Why
Teach Anatomy to the Computer?
Need for
Knowledge-based (smart) applications
in: education
clinical medicine
research
Anatomical knowledge in
computer-understandable form
Leading to
Qualitative change in role of teacher
How Do We Teach Anatomy to the Computer?
The Digital Anatomist
Information System
James F. Brinkley M.D., Ph.D.
Cornelius Rosse M.D., D.Sc.
Structural Informatics Group
University of Washington
Digital Anatomist Information System
End-User
Programs
Authoring
Programs
Network
Servers
Image
Repository
Symbolic
Knowledge
Source
Anatomy Knowledge Sources
Digital Anatomist Information System
Authoring
Programs
End-User
Programs
Network
Servers
2-D
Images
2-D
Annotations
3-D
Model
Image Repository
3-D Image
Volumes
Symbolic
Knowledge
Source
Digital Anatomist Information System
Graphical Authoring Programs
Skandha
Annotator
End-User
Programs
Scene
Generator
Network
Servers
2-D
Images
2-D
Annotations
3-D
Model
Image Repository
3-D Image
Volumes
Symbolic
Knowledge
Source
Digital Anatomist Information System
Symbolic Authoring Programs
Foundational
Model
Builder
End-User
Programs
Protégé
Network
Servers
Image
Repository
Foundational
Model
Metaknowledge
Clinical
Info
Symbolic Knowledge Sources
Digital Anatomist Information System
End User Interfaces
Authoring
Programs
Digital
Anatomist
Atlases
Brain
Mapper
Network
Servers
Image
Repository
Symbolic
Knowledge
Source
Anatomy Knowledge Sources
Radiation
Oncology
Digital Anatomist Information System
Authoring Programs
Graphical
End-User Interfaces
Digital
Anatomist
Atlases
Symbolic
Network
Graphics
Server
Image
Repository
Image
Server
Data
Server
Knowledge
Server
Symbolic
Knowledge
Source
Anatomy Knowledge Sources
Digital Anatomist Information System
Web-based
Digital Anatomist Atlas of
Thoracic viscera
Digital Anatomist Information System
End User Interfaces
Authoring
Programs
Digital
Anatomist
Atlases
Brain
Mapper
Network
Servers
Image
Repository
Symbolic
Knowledge
Source
Anatomy Knowledge Sources
Radiation
Oncology
Superimposed
FMRI and cortical
language maps
Digital Anatomist Information System
End User Interfaces
Authoring
Programs
Digital
Anatomist
Atlases
Brain
Mapper
Network
Servers
Image
Repository
Symbolic
Knowledge
Source
Anatomy Knowledge Sources
Radiation
Oncology
Radiation Treatment Planning
PRISM
Structural Informatics Group
Anatomists
Computer Science/Informatics
Cornelius Rosse, MD, DSc
Jose Mejino, MD
Augusto Agoncillo, MD
Richard Martin, PhD
Kate Mulligan, PhD
John Sundsten, PhD
Doug Bowden, MD
James Brinkley, MD, PhD
Linda Shapiro, PhD
Ira Kalet, PhD
William Lober, MD
Andrew Poliakov, PhD
Rex Jakobovits, PhD
Kurt Rickard, PhD
Sara Kim, PhD
Jeff Prothero
Ravensara Travillian, MA
Peter Mork
Zhenrong Qian
Chia-chi Teng
Clinicians
George Ojemann, MD
Ken Maravilla, MD
David Corina, MD
Karen Kinbar, PhD
How Do We Teach Anatomy to the Computer?
The Foundational Model of Anatomy
Cornelius Rosse M.D., D.Sc.
Structural Informatics Group
University of Washington
Digital Anatomist Image Repository
3-D Models of Right Lung and Heart
Digital Anatomist Information System
End-User
Programs
Authoring
Programs
Network
Servers
Image
Repository
Foundational
Model
Metaknowledge
Clinical
Info
Symbolic Knowledge Sources
Why
Teach Anatomy to the Computer?
Need for
Knowledge-based (smart) applications
in: education
clinical medicine
research
Anatomical knowledge in
computer-understandable form
Leading to
Qualitative change in role of
teacher
health care provider
Why
Teach Anatomy to the Computer?
Controlled Medical Terminologies (CMT)
• MeSH (Medical Subject Headings)
• SNOMED (Systematized Nomenclature of Medicine)
• The Read Codes
• GALEN (General Architecture for Languages
Encyclopedias and Nomenclatures in Medicine)
• NeuroNames (University of Washington)
• UMLS (Unified Medical Language Systems)
US National Library of Medicine
Why
Teach Anatomy to the Computer?
SNOMED
Topography Axis
20000 Respiratory System
28000 Lung
29000 Pleura
PleuralCavity
Cavity
29050 Pleural
Why
Teach Anatomy to the Computer?
READ CODES
Human Body Structure
Body System Structure
Respiratory Structure
Pleural Structure
Pleural Cavity
Cavity
Pleural
Body Region Structure
Trunk Structure
Body Cavity Structure
Thoracic Cavity Structure
Pleural Structure
Pleural
Pleural Cavity
Cavity
Why
Teach Anatomy to the Computer?
GALEN*
AnatomicalConcept
Structure
BodyStructure
BodyPart
GeneralizedCavity
ConventionalCavity
[AbdominalCavity]
TrueCavity
ActualCavity
[AnatomicalSinus Lumen]
PotentialCavity
PleuralSpace]
PleuralSpace
*Rector et al.
MIE 94 Proc. 1994:229
Pleural Cavity
Why
Teach Anatomy to the Computer?
Conclusion
•
Inadequacy of
traditional knowledge sources
• New need for
computer-processable
anatomical knowledge
How to Teach Anatomy to the Computer?
Why do we need to teach anatomy to the
computer?
What to teach to the computer?
How do we do it?
What to teach to the computer?
"Anatomy" …….. a homonym for
anatomy (structure)
e.g., anatomy of the frog, hand, brain
anatomy (science)
systematized branch of knowledge accumulated
about anatomy (structure).
What to teach to the computer?
"Structure" ……. a homonym for
something composed of parts;
(e.g., a building, a cell, a plant, brain)
i.e., a material object
the arrangement or interrelation of all the parts
of a whole.
(e.g., of a sentence, a symphony,
or of society, government,
or of the atom, the hand)
i.e., relationships
What to teach to the computer?
Structure of a material object
Structure of Structure =
Subobjects (parts) + Structural Relationships
The components of an object
and their manner of arrangement in constituting a
whole.
What to teach to the computer?
”Anatomical Structure" … a homonym for
a material object generated by the coordinated
expression of an organism's
own structural genes;
the arrangement (physical interrelation) of
all the parts of an anatomical structure
in constituting the whole.
Synonym: 'biological structure'
What to teach to the computer?
Question:
What to teach first about anatomy to a computer?
Answer:
The structure of anatomical structures
that constitute the body.
StructureBody = ({SubobjectBody }, {Structural relationship})
What to teach to the computer?
Question:
What to enter in the computer
to explain (model) anatomy?
Answer:
Symbols for anatomical structures
Symbols for structural relationships
What kind of symbols?
Triangle of Meaning
Thought
“Concept”
Referent
Symbol
“Term”
What kind of symbols?
“The oesophagus is a muscular tube …
connecting the pharynx to the stomach. It
begins in the neck, level with the lower
border of the cricoid cartilage and the sixth
cervical vertebra; descending largely
anterior to the vertebral column through the
superior and posterior mediastina.”
Gray’s Anatomy, 38th edition, p. 1751
What kind of symbols?
“The oesophagus is a muscular tube …
connecting the pharynx to the stomach. It
begins in the neck, level with the lower
border of the cricoid cartilage and the sixth
cervical vertebra; descending largely
anterior to the vertebral column through the
superior and posterior mediastina.”
Gray’s Anatomy, 38th edition, p. 1751
What kind of symbols?
“The oesophagus is a muscular tube …
connecting the pharynx to the stomach. It
begins in the neck, level with the lower
border of the cricoid cartilage and the sixth
cervical vertebra; descending largely
anterior to the vertebral column through the
superior and posterior mediastina.”
Gray’s Anatomy, 38th edition, p. 1751
What to teach first to the computer?
Symbolic model =
symbols of {anatomical structure} +
symbols of {structural relationship}
mirrors graphical model
scales to non-structural relationships
What is a symbolic model?
Symbolic model,
a conceptualization of a domain of discourse
represented with non-graphical symbols;
in computer-processible (“understandable”) form;
supports inference (reasoning).
What is the Foundational Model of Anatomy (FM)?
Foundational Model of Anatomy
is a symbolic model of the physical organization of the human body;
declares the principles
for including concepts and relationships
that are implicitly assumed
when knowledge of anatomy
is applied in different contexts;
explicitly defines
concepts and relationships
necessary and sufficient for consistently
modeling the structure of the
human body.
Foundational Model of Anatomy
Fm = (Ao, ASA, ATA, Mk)
where:
Ao
ASA
ATA
Mk
= Anatomy ontology
= Anatomical Structural Abstraction
= Anatomical Transformation Abstraction
= Metaknowledge
(principles, rules, axioms)
Foundational Model of Anatomy
Anatomical Structural Abstraction
Fm = (Ao, ASA, ATA, Mk)
ASA = (Do, Bn, Pn, SAn)
where:
Do
Bn
Pn
SAn
(1)
(2)
= Dimensional ontology
= Boundary network
= Part-of network
= Spatial Association network
Foundational Model of Anatomy
Spatial Association Network
Fm = (Ao, ASA, ATA, Mk)
(1)
ASA = (Do, Bn, Pn, SAn)
(2)
SAn = (Ln, On, Cn)
(3)
where:
Ln = Location
On = Orientation
Cn = Connectivity
Networks of ASA
Right
Ventricle
Anatomy Ontology
Anatomical Structure
Organ Part
Organ
Subdivision
Cardiac
Chamber
-is a-
Right
Ventricle
Dimensional
Ontology
Anatomy Ontology
Anatomical Structure
Volume (3-D)
Organ Part
Polyhedron
Organ
Subdivision
Cardiac
Chamber
-is a-
Right
Ventricle
Spatial Ontology
Anatomy Ontology
Boundary Network
Anatomical Structure
Volume (3-D)
Polyhedron
Line (1-D)
Surface (2-D)
Organ Part
Anterior
Interventricular
Sulcus
Anatomical
Surface
Organ
Subdivision
Cardiac
Chamber
-is a-
-is a-
Sternocostal
Surface
bounded by
bounded by
Right
Ventricle
Right
Coronary
Sulcus
Inferior margin
of heart
boundary of
Diaphragmatic
Surface
bounded by
Posterior
IV Sulcus
Anatomical
Landmark
-is aPoint (1-D)
Coronary
Sulcus
Apex
Crux of heart
Spatial Ontology
Anatomy Ontology
Boundary Network
Anatomical Structure
Volume (3-D)
Polyhedron
-is a-
Line (1-D)
Surface (2-D)
Organ Part
Anterior
Interventricular
Sulcus
Anatomical
Surface
Organ
Subdivision
-is a-
Heart
Part-of
Network
has
superobject
Wall of RV
-is a-
Sternocostal
Surface
bounded by
bounded by
Infundibulum
Inflow part
of RV
Cardiac
Chamber
has
subobject
Cavity of RV
Cavity of Cavity of
infund. infl.part
Right
Ventricle
Right
Coronary
Sulcus
Inferior margin
of heart
boundary of
Diaphragmatic
Surface
bounded by
Posterior
IV Sulcus
Anatomical
Landmark
-is aPoint (1-D)
Coronary
Sulcus
Apex
Crux of heart
Spatial Ontology
Anatomy Ontology
Boundary Network
Anatomical Structure
Volume (3-D)
Surface (2-D)
Organ Part
Anterior
Interventricular
Sulcus
Anatomical
Surface
Organ
Subdivision
Polyhedron
-is a-
Line (1-D)
-is a-
Heart
Part-of
Network
Cardiac
Chamber
has
-is a-
superobject
Wall of RV
bounded by
bounded by
Infundibulum
Inflow part
of RV
Sternocostal
Surface
has
subobject
Right
Ventricle
Cavity of RV
Cavity of Cavity of
infund. infl.part
Inferior margin
of heart
boundary of
Diaphragmatic
Surface
bounded by
has
adjacency
has
adjacency
to left
anterior
Pericardial
sac
inferior
Left
ventricle
Right
Coronary
Sulcus
Coronary
Sulcus
Posterior
IV Sulcus
Anatomical
Landmark
inferior
Diaphragm
Spatial Association Network
-is aPoint (1-D)
Apex
Crux of heart
Foundational Model of Anatomy
Fm = (Ao, ASA, ATA, Mk)
FmBODY = {FmANATOMICAL_ENTITY}
How to Teach Anatomy to the Computer?
Why do we need to teach anatomy to the
computer?
What to teach to the computer?
How do we do it?
Teach the FM to the computer.
How to teach the FM to the computer?
Foundational Principles
Assertions that provide the basis for reasoning and action
•
•
•
•
•
•
Constraint principle
Definition principle
Constitutive principle
Organizational unit principle
Structural relationship principle
Representation principle
How to teach the FM to the computer?
Explicit Definitions
Purpose of FM definitions:
Provide the rationale for an inheritance hierarchy
in a structural context;
Specify the essence of anatomical entities
in terms of two sets of structural attributes:
those of their genus
and differentiae
How to teach the FM to the computer?
Principled Modeling =
Foundational Principles + Explicit Definitions
UMLS
Leaf terms
(concepts)
Multiple layers
of meaning
Principled Modeling
Prototype problems:
1.
How to reconcile different
naming and classification conventions?
2.
How to assure inheritance?
3.
How to represent different and overlapping
part-whole relationships?
4.
How to represent different kinds of
location attributes?
Leaf concept
Esophagus
How to reconcile different classifications?
Explicit Definitions
Purpose of FM definitions:
Provide the rationale for an inheritance hierarchy
in a structural context;
Specify the essence of anatomical entities
in terms of two sets of structural attributes:
those of their genus
differentiae
Definition
Esophagus is
an ‘organ with
an organ
cavity’, which
connects the
pharynx to the
stomach
Definition
Organ with organ
cavity is a ‘cavitated
organ’, the
morphological parts
of which surround a
continuous cavity,
which contains one
or more body
substances.
Definition
Cavitated organ
is an ‘organ’, the
morphological
parts of which
surround one or
more cavities,
which contain
one or more
body substances.
Definition
Organ is an ‘anatomical
structure’,which
consists of the maximal
set of organ parts so
connected to one
another that together
they constitute a selfcontained unit of
macroscopic anatomy,
morphologically distinct
from other such units.
Definition
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.
Principled Modeling
Prototype problems:
1.
How to reconcile different
naming and classification conventions?
2.
How to assure inheritance?
3.
How to represent different and overlapping
part-whole relationships?
4.
How to represent different kinds of
location attributes?
Material Physical
Anatomical Entity
-is a-
Non-material Physical
Anatomical Entity
Anatomical
Structure
Physical
Anatomical Entity
Material Physical
Anatomical Entity
Conceptual
Anatomical Entity
-is a-
Non-material Physical
Anatomical Entity
Anatomical
Structure
Anatomical Entity
Physical
Anatomical Entity
Material Physical
Anatomical Entity
Conceptual
Anatomical Entity
-is a-
Non-material Physical
Anatomical Entity
Anatomical
Structure
Anatomical Entity
Physical
Anatomical Entity
MateꈤAꈤA Physical
Anatomical Entity
Conceptual
Anatomical Entity
-is a-
Non-material Physical
Anatomical Entity
Anatomical
Structure
Organ
Organ
Part
Anatomical Entity
Physical
Anatomical Entity
Material Physical
Anatomical Entity
Conceptual
Anatomical Entity
-is a-
Non-material Physical
Anatomical Entity
Anatomical
Structure
Organ
Tissue
Organ
Part
Organ component
Organ subdivision
Anatomical Entity
Physical
Anatomical Entity
-is a-
Material Physical
Anatomical Entity
Conceptual
Anatomical Entity
Non-material Physical
Anatomical Entity
Anatomical
Structure
Cell
Organ
Tissue
Organ
Part
Organ component
Organ
System
Body
Part
Organ subdivision
Human
Body
Anatomical Entity
Physical
Anatomical Entity
-is a-
Material Physical
Anatomical Entity
Non-material Physical
Anatomical Entity
Anatomical
Structure
Body
Substance
Cell
Conceptual
Anatomical Entity
Organ
Tissue
Organ
Part
Organ component
Organ
System
Body
Part
Organ subdivision
Human
Body
Anatomy Ontology
Organ
-is a-
Solid Organ
Cavitated Organ
Organ with cavitated
organ part
Heart
Organ with
organ cavity
-is a-
Esophagus
Principled Modeling
Fm = (Ao, ASA, ATA, Mk)
Ao: taxonomic classification based on
explicit definition of concepts,
inheritance of definitional
structural attributes;
consistent with foundational principles.
Assurance of inheritance
Assurance of inheritance
Assurance of inheritance
Assurance of inheritance
Test
What is the brain?
To which Ao class would you assign the brain?
Anatomical Entity
Physical
Anatomical Entity
-is a-
Material Physical
Anatomical Entity
Non-material Physical
Anatomical Entity
Anatomical
Structure
Body
Substance
Cell
Conceptual
Anatomical Entity
Organ
Tissue
Organ
Part
Organ component
Organ
System
Body
Part
Organ subdivision
Human
Body
Organ
Definition:
Organ
is an
anatomical structure
• consists of
maximal sets of organ parts
connected to
one another
constitute
self-contained unit
distinct from
other units
• connected to
• constitutes
other organs
organ system
body part
Organ system
Definition:
Organ system
is an
anatomical structure
• consists of
members of predominantly one
organ subclass;
interconnected by zones of
continuity;
other organ systems
the human body
• connected to
• constitutes
Definition of neuraxis
Neuraxis is ...
central nervous system
NeuroNames
"the axial, unpaired part of the central nervous
system....in contrast to the paired cerebral hemispheres”
Stedman’s
an axon;
central nervous system.
Dorland’s:
What is the brain?
What is the brain?
What is the brain?
What is the brain?
Summary: Principled Modeling
Prototype problems:
1.
How to reconcile different
naming and classification conventions?
2.
How to assure inheritance?
3.
How to represent different and overlapping
part-whole relationships?
4.
How to represent different kinds of
location attributes?
Revisit: Principled Modeling
Prototype problems:
1.
How to reconcile different
naming and classification conventions?
2.
How to assure inheritance?
3.
How to represent different and overlapping
part-whole relationships?
4.
How to represent different kinds of
location attributes?
How Do We Teach Anatomy to the Computer?
Correlation of
the Foundational Model with
Traditional Sources of Anatomical Knowledge
Augusto Agoncillo M.D.,
José L.V. Mejino Jr., M.D.,
Cornelius Rosse M.D., D.Sc.
Structural Informatics Group
University of Washington
Problem
Conflicts between Traditional Sources
and Foundational Model:
• Semantic specificity
• homonyms
• ambiguous use of synonyms
• Semantic expressivity
Semantic Specificity and Expressivity
Triangle of Meaning
Thought
“Concept”
Referent
Symbol
“Term”
Semantic Specificity: synonyms
Authoring program: Protégé
Semantic Specificity: synonyms
Semantic Specificity: synonyms
Semantic Specificity: synonyms
Semantic Specificity: Homonyms
Homonym: ‘Base of heart’
Anterior
view
Posterior
view
Foundational Model
Builder
Foundational Model
Builder
Preferred term: Base of heart (anatomical)
Foundational Model
Builder
Preferred term: Base of heart (clinical)
Semantic Specificity: Ambiguous use of synonyms
Transferred meaning: ‘Left border of heart’
Left border
of heart
Left surface
of heart
Semantic Specificity
Assured in FM by:
• one preferred name for each
anatomical entity
• associate synonyms with
each preferred name
• disallow homonyms;
use extensions
• disallow transferred meanings
Foundational Model
Builder
Foundational Model
Builder
Problem
Conflicts between Traditional Sources
and Foundational Model:
• Semantic specificity
• Semantic expressivity
classification of anatomical entities
relationships between anatomical entities
Semantic Expressivity: Classification
Terminologia Anatomica
Alimentary System
Lymphoid System
Mouth
Tongue
Pharynx
Esophagus
Stomach
Small intestine
Large intestine
Caecum
Primary Lymphoid
Bone Marrow
Thymus
Secondary Lymphoid
Spleen
Pharyngeal lymphoid ring
Lymph node
Appendix
Colon
Rectum
Liver
Gall Bladder
Semantic Expressivity: Classification
Terminologia Anatomica
Alimentary System
Lymphoid System
Mouth
Tongue
Pharynx
Esophagus
Stomach
Small intestine
Large intestine
Caecum
Primary Lymphoid
Bone Marrow
Thymus
Secondary Lymphoid
Spleen
Pharyngeal lymphoid ring
Lymph node
Appendix
Colon
Rectum
Liver
Gall Bladder
Semantic Expressivity
Definition principle:
state defining attributes of
anatomical entities
in terms of
constituent parts
entities they constitute
Semantic Expressivity
Anatomical Entity
-is a-
Physical
Anatomical Entity
Conceptual
Anatomical Entity
Material Physical
Anatomical Entity
Body
Substance
Cell
Organ
Non-material Physical
Anatomical Entity
Anatomical
Structure
Organ
Part
Anatomical
Space
Organ
System
Body
Part
Anatomical
Surface
Anatomical
Line
Human
Body
Semantic Expressivity
Ambiguous part-whole relationships
Right ventricle
Infundibulum
Inflow part
Semantic Expressivity
Ambiguous part-whole relationships
Right ventricle
Outflow part
Inflow part
Foundational Model
Builder
Foundational Model
Builder
Preferred Term: Inflow part of right ventricle
Preferred Term: Outflow part of right ventricle
Semantic Expressivity
Ambiguous part-whole relationships
Right ventricle
Outflow part
Inflow part
Summary
Principled representation of Foundational Model calls for:
• greater specificity and expressivity
than traditional sources
• definition of new classes of anatomical entities
• introduction of new descriptive terms
• modification of existing terms
Conclusions
Conflicts can be solved:
• Establishes an inheritance hierarchy (Ao)
based on inherent structural properties
•
Specifies structural relationships
between anatomical entities
•
Explicitly represents classes and relationships
implied in traditional sources
Continued: Principled Modeling
Prototype problems:
1.
How to reconcile different
naming and classification conventions?
2.
How to assure inheritance?
3.
How to represent different and overlapping
part-whole relationships?
4.
How to represent different kinds of
location attributes?
How Do We Teach Anatomy to the Computer?
Anatomical Relationships
in the
Foundational Model of Anatomy
José L.V. Mejino Jr., M.D.,
Cornelius Rosse M.D., D.Sc.
Structural Informatics Group
University of Washington
Foundational Model of Anatomy
Fm = (Ao, ASA, ATA, Mk)
where:
Ao
ASA
ATA
Mk
= Anatomy ontology
= Anatomical Structural Abstraction
= Anatomical Transformation Abstraction
= Metaknowledge
(principles, rules, axioms)
Anatomical Relationships
Anatomical Structural Abstraction
Fm = (Ao, ASA, ATA, Mk)
ASA = (Do, Bn, Pn, SAn)
where:
Do
Bn
Pn
SAn
(1)
(2)
= Dimensional ontology
= Boundary network
= Part-of network
= Spatial Association network
Dimensional
Ontology
Anatomy Ontology
Anatomical Structure
Volume (3-D)
Organ Part
Polyhedron
Organ
Subdivision
Cardiac
Chamber
-is a-
Right
Ventricle
ASA = ( Do, Pn, Bn, SAn )
Dimensional
Ontology
Anatomy Ontology
Anatomical Structure
Volume (3-D)
Polyhedron
Boundary Network
Line (1-D)
Surface (2-D)
Organ Part
Anterior
Interventricular
Sulcus
Anatomical
Surface
Organ
Subdivision
Cardiac
Chamber
-is a-
-is a-
Sternocostal
Surface
bounded by
bounded by
Right
Ventricle
Right
Coronary
Sulcus
Inferior margin
of heart
boundary of
Diaphragmatic
Surface
bounded by
ASA = ( Do, Bn, Pn, SAn )
Posterior
IV Sulcus
Anatomical
Landmark
-is a-
Point (1-D)
Coronary
Sulcus
Apex
Crux of heart
Dimensional
Ontology
Anatomy Ontology
Anatomical Structure
Volume (3-D)
Polyhedron
-is a-
Boundary Network
Line (1-D)
Surface (2-D)
Organ Part
Anterior
Interventricular
Sulcus
Anatomical
Surface
Organ
Subdivision
-is a-
Heart
Part-of
Network
has
superobject
Wall of RV
-is a-
Sternocostal
Surface
bounded by
bounded by
Infundibulum
Inflow part
of RV
Cardiac
Chamber
has
subobject
Cavity of RV
Right
Ventricle
Right
Coronary
Sulcus
Inferior margin
of heart
boundary of
Diaphragmatic
Surface
bounded by
Cavity of Cavity of
infund. infl.part
ASA = ( Do, Bn, Pn, SAn )
Posterior
IV Sulcus
Anatomical
Landmark
-is aPoint (1-D)
Coronary
Sulcus
Apex
Crux of heart
Dimensional
Ontology
Anatomy Ontology
Anatomical Structure
Volume (3-D)
Line (1-D)
Surface (2-D)
Organ Part
Anterior
Interventricular
Sulcus
Anatomical
Surface
Organ
Subdivision
Polyhedron
-is a-
Boundary Network
-is a-
Heart
Part-of
Network
Cardiac
Chamber
has
superobject
-is a-
Wall of RV
bounded by
Right
Coronary
Sulcus
ASA = ( Do, Bn, Pn, SAn )
bounded by
Infundibulum
Inflow part
of RV
Sternocostal
Surface
has
subobject
Right
Ventricle
Cavity of RV
Cavity of Cavity of
infund. infl.part
Inferior margin
of heart
boundary of
Diaphragmatic
Surface
bounded by
has
adjacency
has
adjacency
to left
anterior
Pericardial
sac
inferior
Left
ventricle
Coronary
Sulcus
Posterior
IV Sulcus
Anatomical
Landmark
inferior
Diaphragm
Spatial Association Network
-is aPoint (1-D)
Apex
Crux of heart
Anatomical Relationships
Anatomical Relationships
Principled Modeling
Prototype problems:
1.
How to reconcile different
naming and classification conventions?
2.
How to assure inheritance?
3.
How to represent different and overlapping
part-whole relationships?
4.
How to represent different kinds of
location attributes?
Part_of relationships
Right
Rightventricle
ventricle
Infundibulum
Outflow part
Inflow part
Attributed Part: Shared parts
Tracheobronchial tree
Lungs
Attributed Part: Shared parts
(Netter’s Atlas of Human Anatomy)
Attributed Part: Shared parts
Oculomotor Nerve
(Cranial Nerves: Wilson-Pauwels et al.)
Attributed Part: Shared parts
Attributed Part: Anatomical/Arbitrary
Esophagus
Anterior view
Posterior view
Attributed Part: Anatomical/Arbitrary
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Granularity of parts
Nuclear pore complex
(Alberts et al.: Molecular Biology of the Cell)
Foundational Model of Anatomy
Anatomical Structural Abstraction
Fm = (Ao, ASA, ATA, Mk)
ASA = (Do, Bn, Pn, SAn)
where:
Do
Bn
Pn
SAn
(1)
(2)
= Dimensional ontology
= Boundary network
= Part-of network
= Spatial Association network
Principled Modeling
Prototype problems:
1.
How to reconcile different
naming and classification conventions?
2.
How to assure inheritance?
3.
How to represent different and overlapping
part-whole relationships?
4.
How to represent different kinds of
location attributes?
How
to represent different location relationships?
Spatial Association Network
Fm = (Ao, ASA, ATA, Mk)
(1)
ASA = (Do, Bn, Pn, SAn)
(2)
SAn = (Ln, On, Cn)
(3)
where:
Ln = Location
On = Orientation
Cn = Connectivity
How
to represent different location relationships?
How
to represent different location relationships?
How
to represent different location relationships?
How
to represent different location relationships? Adjacency
Esophagus
Anterior view
Posterior view
Esophagus
T2-3
T8
How
to represent different location relationships? Coordinates
Anterior
Posterior
How
to represent different location relationships? Coordinates
Left
lateral
Anterior
Posterior
Right
lateral
How
to represent different location relationships? Adjacency
Pericardial
sac
How
to represent different location relationships? Coordinates
Left Anterior
Right Anterior
Left Anterolateral
Right Anterolateral
Left
lateral
Left Posterolateral
Left Posterior
Anterior
Posterior
Right
lateral
Right Posterolateral
Right Posterior
T2-3
T8
How
to represent different location relationships? Adjacency
How
to represent part_of and location relationships?
Spatial Association Network
Fm = (Ao, ASA, ATA, Mk)
(1)
ASA = (Do, Bn, Pn, SAn)
(2)
SAn = (Ln, On, Cn)
(3)
How to Teach Anatomy to the Computer?
Why do we need to teach anatomy to the
computer?
What to teach to the computer?
How do we do it?
Conclusions
Summary:
Foundational Model specifies
Anatomy ontology
structure-based classification of
anatomical entities
Structural relationships (ASA)
Conclusions
“The oesophagus is a muscular tube …
connecting the pharynx to the stomach. It
begins in the neck, level with the lower
border of the cricoid cartilage and the sixth
cervical vertebra; descending largely
anterior to the vertebral column through the
superior and posterior mediastina.”
Gray’s Anatomy, 38th edition, p. 1751
Conclusions
Conclusions
Summary:
Foundational Model specifies
Anatomy ontology
structure-based classification of
anatomical entities
Structural relationships (ASA)
Foundational Model omits
function
pathology
clinical cases
Conclusions
Role of Foundational Model of Anatomy
Prototype for symbolic models in other domains
e.g., physiology, pathology, cancer therapy
Core of biomedical knowledge bases
to solve problems in education, research, health care
"Foundational" because
anatomy is fundamental to all
biomedical sciences;
anatomical concepts encompassed by FM
generalize to all biomedical domains.
Conclusions
Evolving knowledge-based application for
Anatomy education:
“Intelligent” Digital Anatomist
Digital Anatomist Information System
Authoring
Programs
End-User
Programs
Network
Servers
Image
Repository
Foundational
Model
Metaknowledge
Clinical
Info
Symbolic Knowledge Sources
Digital Anatomist Information System
“Intelligent” applications
Authoring
Programs
Anatomy
Tutor
Anatomy
Consultant
Network
Servers
2-D
Images
2-D
Annotations
3-D
Model
Image Repository
3-D Image
Volumes
Foundational
Model
Clinical data
Symbolic Info
Digital Anatomist Information System
“Intelligent” applications
Authoring
Programs
Anatomy
Tutor
Anatomy
Consultant
Network
Graphics
Server
2-D
Images
2-D
Annotations
3-D
Model
Image Repository
Image
Server
Data
Server
3-D Image
Volumes
Knowledge
Server
Foundational
Model
Clinical data
Symbolic Info
Digital Anatomist Information System
“Intelligent” applications
Authoring
Programs
Anatomy
Tutor
Anatomy
Consultant
Network
Metaknowledge
DIGITAL ANATOMIST
Graphics
Server
2-D
Images
2-D
Annotations
3-D
Model
Image Repository
Image
Server
Data
Server
3-D Image
Volumes
Knowledge
Server
Foundational
Model
Clinical data
Symbolic Info
Foundational Model of Anatomy
Fm = (Ao, ASA, ATA, Mk)
where:
Ao
ASA
ATA
Mk
= Anatomy ontology
= Anatomical Structural Abstraction
= Anatomical Transformation Abstraction
= Metaknowledge
(principles, rules, axioms)
Conclusions
Evaluation of FM by
Anatomists
Clinicians
Researchers
Conclusions
Fm = (Ao, ASA, ATA, Mk)
where:
Ao
ASA
ATA
Mk
= Anatomy ontology
= Anatomical Structural Abstraction
= Anatomical Transformation Abstraction
= Metaknowledge
(principles, rules, axioms)
How do we teach
Anatomy to the Computer?
"We are made wise not by the recollection on our past,
but by the responsibility to our future."
George Bernard Shaw
Spare slides
Portal Venous Tree
Vena Caval Tree
Systemic Arterial Tree
Interactive Radiology Exercises
Pericardial Effusion
3-D Structure Primitives
•296 models of thoracic viscera
•17 models of coronary arteries
FM Server
FM
rcorartconus
3-D
Primitives
lcorartatrial
Data Server
Conus branch of right coronary artery-> rcorartconus
Atrial branch of circumflex coronary artery->lcorartatrial
FM Server
FM
“Data Server”
3-D
Primitives
Correspondences
Semantic Specificity: synonyms
Authoring program: Protégé
Semantic Specificity: synonyms
Semantic Specificity: synonyms
Semantic Specificity: synonyms
What is the Foundational Model of Anatomy (FM)?
A symbolic model of anatomy (science)
represents the physical organization (structure)
of biological organisms;
currently limited to the human body.
"Foundational" because
anatomy is fundamental to all
biomedical sciences;
anatomical concepts encompassed by FM
generalize to all biomedical domains.
What is a foundational model?
Foundational Model
is a symbolic model;
declares the principles
for including concepts and relationships
that are implicitly assumed
when knowledge of the domain
is applied in different contexts;
explicitly defines
concepts and relationships
necessary and sufficient for consistently
modeling the structure of the
coherent knowledge domain.
Evolving knowledge-based application
Dynamic 3-D Scene Generator
Digital Anatomist Information System
“Intelligent” applications
Authoring
Programs
Anatomy
Tutor
Anatomy
Consultant
Network
Metaknowledge
DIGITAL ANATOMIST
Graphics
Server
2-D
Images
2-D
Annotations
3-D
Model
Image Repository
Image
Server
Data
Server
3-D Image
Volumes
Knowledge
Server
Foundational
Model
Clinical data
Symbolic Info
Web Browser
CGI Script
Graphics Server
FM Server
FM
“Data Server”
3-D
Primitives
Correspondences
Digital Anatomist Information System
“Intelligent” applications
Authoring
Programs
Anatomy
Tutor
Anatomy
Consultant
Network
Metaknowledge
DIGITAL ANATOMIST
Graphics
Server
2-D
Images
2-D
Annotations
3-D
Model
Image Repository
Image
Server
Data
Server
3-D Image
Volumes
Knowledge
Server
Foundational
Model
Clinical data
Symbolic Info
Pleural Cavity