American Medical Informatics Association
Annual Symposium 2001
The Role of Definitions in Biomedical
Concept Representation
Joshua Michael, José L. V. Mejino Jr., M.D.,
and
Cornelius Rosse, M.D., D.Sc.
Structural Informatics Group
University of Washington
What is the Digital Anatomist Foundational Model ?
Foundational Model of Anatomy
is a symbolic model of the structural 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.
Structure of the talk
• The problem
Shortcomings of definitions in
dictionaries
Controlled Medical Terminologies (CMT)
• Foundational Model
Requirements for definitions
support inheritance
Examples
Dictionary Definitions
•
Term rather than concept oriented
• Organized alphabetically
not according to meaning
• Homonyms
• Underspecification
Example of Dictionary Definitions
“Cerebellum: The part of the
metencephalon (subdivision of the brain)
that occupies the posterior cranial fossa…”
“Posterior cranial fossa: The posterior
subdivision of the floor of the cranial cavity,
lodging the cerebellum…”
Dorland’s Medical Dictionary, 28th Edition
CMT Definitions
• Often absent
• When present
adopted from dictionaries
implied by hierarchy of terms
Purpose of
Foundational Model Definitions
• Provide the rationale for
an inheritance hierarchy (Ao)
in a structural context;
• Specify the essence of anatomical entities
in terms of structural attributes:
genus
differentiae
Aristotelian Definitions
“Aristotelian” hierarchy
constructed on the basis of inheritance
genus
subsumes the essential attributes
shared by all of its descendants
differentia(e)
distinguish(es) a concept from
other concepts of the same genus
Leaf concept
Esophagus
Underlying
structure
Digital Anatomist Foundational Model
Protégé-2000
Digital Anatomist Foundational Model
Protégé-2000
Digital Anatomist Foundational Model
Protégé-2000
Digital Anatomist Foundational Model
Protégé-2000
Anatomy Ontology
Organ
-is aSolid Organ
Cavitated Organ
Organ with cavitated
organ part
Heart
Organ with
organ cavity
-is a-
Esophagus
Anatomical Entity
Physical
Anatomical Entity
Material Physical
Anatomical Entity
Conceptual
Anatomical Entity
-is a-
Non-material Physical
Anatomical Entity
Anatomical
Structure
Organ
Anatomical Entity
Physical
Anatomical Entity
Material Physical
Anatomical Entity
Body
Substance
Blood
Urine
Conceptual
Anatomical Entity
-is a-
Non-material Physical
Anatomical Entity
Anatomical
Structure
Organ
Inheritance through Protégé-2000
Inheritance through Protégé-2000
Inheritance through Protégé-2000
Inheritance through Protégé-2000
Inheritance through Protégé-2000
Inheritance through Protégé-2000
Inheritance through Protégé-2000
Inheritance through Protégé-2000
Desiderata for Definitions
• Declare context of modeling the domain
• Declare principles for
inheritance hierarchy (ontology)
• Explicitly define all classes of the ontology
consistent with context and principles
Desiderata for Definitions
• Specify concepts by Aristotelian definition
genus
differentia(e)
• Essence of concept =
transitively inherited attributes + differentia(e)
• Same kind of defining attributes
should distinguish members of a class
Desiderata for Definitions
• To assure transitive inheritance
define classes that have not been
previously identified
• Integrate definitions into
a machine-interpretable
implementation scheme
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
Digital Anatomist Foundational Model
Protégé-2000
Definitions
Dorland’s Medical Dictionary, 28th Edition
“Cerebellum: The part of the
metencephalon (subdivision of the brain)
that occupies the posterior cranial fossa…”
Digital Anatomist Foundational Model
“Cerebellum: subdivision of the
metencephalon (hind brain) connected to
the brainstem by the cerebellar peduncles.”
Definitions
Dorland’s Medical Dictionary, 28th Edition
“Posterior cranial fossa: The posterior
subdivision of the floor of the cranial cavity,
lodging the cerebellum…”
Digital Anatomist Foundational Model
“Posterior cranial fossa: subdivision of the
cranial cavity demarcated by the plane of
the tentorium cerebelli from the cranial
cavity proper.”
Examples from CMT’s
– MeSH has dict. Def’s (Dorlands)
– Snomed (codes terminology according to
meaning, no def’s, only superclass)
– Galen (computer def’s that do not specify
differentia, only genus pure taxonomy)