1. The Foundational Model of Anatomy
Digital Human
Open Source Software Framework for
Organ Modeling and Simulation
The Foundational Model of Anatomy
Cornelius Rosse, M.D., D.Sc.
Structural Informatics Group
University of Washington

2. Organ Modeling and Simulation
Challenges
Interoperability of software
Representation of biomedical knowledge in machine-processible form
Integration and correlation of
biomedical information

3. 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

4. Motivation Digital Anatomist Information Project
Manifestations of health and disease are attributes of anatomical structures.
Logical and comprehensive representation of anatomical knowledge can serve as a foundation for other types of biomedical information.

5. Digital Anatomist Project
University of Washington

6. Digital Anatomist Information System
Network
Authoring
Programs
End-User
Programs
Servers
Anatomy Knowledge Sources
Image
Repository
Symbolic
Knowledge
Source

7. Digital Anatomist Information System
Authoring
Programs
End-User
Programs
Network
Servers
2-D
Images
2-D
Annotations
3-D
Model
3-D Image
Volumes
Symbolic
Knowledge
Source
Image Repository

10. Digital Anatomist Information System
Symbolic Authoring Programs
End-User
Programs
Foundational
Model
Builder
Protégé
Network
Servers
Foundational
Model
Meta-
knowledge
Clinical
Info
Image
Repository
Symbolic Knowledge Sources

11. Organ Modeling and Simulation
What is an Organ?
Organ [L. organum; Gr. organon]
a somewhat independent part of the body that performs a special function or functions.
Dorland's Medical Dictionary
E.g., liver, heart, lung, kidney
hand, erythrocyte
Organ
in animals and plants, a part composed of several tissues and adopted to perform a specific function or functions.
Webster’s Dictionary
hand, head of femur, right ventricle

13. Challenges of Anatomical Knowledge Representation
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

14. Challenges of Anatomical Knowledge Representation
Conclusion
Inadequacy of
traditional knowledge sources
New need for
computer-processable
anatomical knowledge

15. Challenges of Anatomical Knowledge Representation
Question:
What information should be entered in the
Foundational Model of Anatomy?
Answer:
The structure of anatomical structures
that constitute the body.
StructureBody = ({SubobjectBody }, {Structural relationship})

16. What kind of information?
“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

17. What kind of information?
“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

18. What kind of information?
“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

19. What kind of information?
Symbolic model,
a conceptualization of a domain of discourse
represented with non-graphical symbols;
in computer-processible (“understandable”) form;
supports inference (reasoning).

20. What is the Foundational Model of Anatomy (FM)?
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.

21. Foundational Model of Anatomy
Fm = (Ao, ASA, ATA, Mk)
where:
Ao = Anatomy ontology
ASA = Anatomical Structural Abstraction
ATA = Anatomical Transformation Abstraction
Mk = Metaknowledge
(principles, rules, axioms)

22. Foundational Model of Anatomy
Anatomical Structural Abstraction
Fm = (Ao, ASA, ATA, Mk) (1)
ASA = (Do, Bn, Pn, SAn) (2)
where:
Do = Dimensional ontology
Bn = Boundary network
Pn = Part-of network
SAn = Spatial Association network

23. 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

24. Networks of ASA
Right
Ventricle

25. Anatomy Ontology Right Ventricle -is a- Anatomical Structure
Cardiac
Chamber
Organ
Subdivision
Organ Part
Anatomical Structure
Anatomy Ontology
-is a-
Right
Ventricle

26. Dimensional Ontology Anatomy Ontology Right Ventricle -is a-
Polyhedron
Volume (3-D)
Dimensional
Ontology
Cardiac
Chamber
Organ
Subdivision
Organ Part
Anatomical Structure
Anatomy Ontology
-is a-
Right
Ventricle

27. Spatial Ontology Anatomy Ontology Boundary Network Right Ventricle
Polyhedron
Volume (3-D)
Spatial Ontology
Cardiac
Chamber
Organ
Subdivision
Organ Part
Anatomical Structure
Anatomy Ontology
-is a-
Sternocostal
Surface
Diaphragmatic
bounded by
boundary of
Anatomical
Surface (2-D)
Right
Coronary
Sulcus
Anterior
Interventricular
Line (1-D)
Inferior margin
of heart
Apex
Boundary Network
-is a-
Posterior
IV Sulcus
Crux of heart
Landmark
Point (1-D)
Right
Ventricle

28. Spatial Ontology Anatomy Ontology Boundary Network Right Ventricle
Polyhedron
Volume (3-D)
Spatial Ontology
Cardiac
Chamber
Organ
Subdivision
Organ Part
Anatomical Structure
Anatomy Ontology
-is a-
Sternocostal
Surface
Diaphragmatic
bounded by
boundary of
Anatomical
Surface (2-D)
Right
Coronary
Sulcus
Anterior
Interventricular
Line (1-D)
Inferior margin
of heart
Apex
Boundary Network
-is a-
Posterior
IV Sulcus
Crux of heart
Landmark
Point (1-D)
Part-of
Network
Heart
super-
object
Inflow part
of RV
Infundibulum
Wall of RV
Cavity of RV
subobject
-is a-
has
Cavity of
infund.
infl.part
Right
Ventricle

29. Spatial Association Network
Polyhedron
Volume (3-D)
Spatial Ontology
Cardiac
Chamber
Organ
Subdivision
Organ Part
Anatomical Structure
Anatomy Ontology
-is a-
Sternocostal
Surface
Diaphragmatic
bounded by
boundary of
Anatomical
Surface (2-D)
Right
Coronary
Sulcus
Anterior
Interventricular
Line (1-D)
Inferior margin
of heart
Apex
Boundary Network
-is a-
Posterior
IV Sulcus
Crux of heart
Landmark
Point (1-D)
Part-of
Network
Heart
super-
object
Inflow part
of RV
Infundibulum
Wall of RV
Cavity of RV
subobject
-is a-
has
Cavity of
infund.
infl.part
Right
Ventricle
has
adjacency
anterior
inferior
to left
Left
ventricle
Pericardial
sac
Diaphragm
Spatial Association Network

30. Anatomical Entity

31. Anatomical Entity
Physical
Anatomical Entity
-is a-
Conceptual

32. Non-material Physical
Anatomical Entity
-is a-
Physical
Anatomical Entity
Conceptual
Anatomical Entity
Material Physical
Anatomical Entity
Non-material Physical

33. Non-material Physical
Anatomical Entity
-is a-
Physical
Anatomical Entity
Conceptual
Anatomical Entity
Material Physical
Anatomical Entity
Non-material Physical
Anatomical Entity
Anatomical
Space
Anatomical
Surface
Anatomical
Line
Anatomical
Point

34. Non-material Physical
Anatomical Entity
-is a-
Physical
Anatomical Entity
Conceptual
Anatomical Entity
Material Physical
Anatomical Entity
Non-material Physical
Anatomical Entity
Body
Substance
Anatomical
Structure
Cell
Body
Part
Human
Organ
System
Organ
Organ
Part
Tissue
Organ component
Organ subdivision

35. Organ Organ Definition: 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 other organs
constitutes organ system
body part

36. Non-material Physical
Anatomical Entity
-is a-
Physical
Anatomical Entity
Conceptual
Anatomical Entity
Material Physical
Anatomical Entity
Non-material Physical
Anatomical Entity
Body
Substance
Anatomical
Structure
Cell
Body
Part
Human
Organ
System
Organ
Organ
Part
Tissue
Organ component
Organ subdivision

37. Protégé 2000

38. Foundational Model of Anatomy
Anatomical Structural Abstraction
Fm = (Ao, ASA, ATA, Mk) (1)
ASA = (Do, Bn, Pn, SAn) (2)
where:
Do = Dimensional ontology
Bn = Boundary network
Pn = Part-of network
SAn = Spatial Association network

39. Protégé 2000

40. ASA: Part of Network

41. ASA: Part of Network

42. ASA: Part of Network

43. ASA: Part of Network

44. ASA: Part of Network

45. ASA: Part of Network

46. Foundational Model of Anatomy
Fm = (Ao, ASA, ATA, Mk)
FmBODY = {FmANATOMICAL_ENTITY}

47. Conclusions 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.

48. 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.