American Medical Informatics Association Annual Symposium 2001 The Role of Definitions in Biomedical...

American Medical Informatics Association American Medical Informatics Association Annual Symposium 2001Annual Symposium 2001

The Role of Definitions in Biomedical The Role of Definitions in Biomedical Concept RepresentationConcept Representation

Joshua Michael, José L. V. Mejino Jr., Joshua Michael, José L. V. Mejino Jr., M.D., andM.D., and

Cornelius Rosse, M.D., D.Sc.Cornelius Rosse, M.D., D.Sc.

Structural Informatics GroupStructural Informatics GroupUniversity of WashingtonUniversity of Washington

What is the Digital Anatomist Foundational Model ?

Foundational Model of AnatomyFoundational Model of Anatomyis a is a symbolic modelsymbolic model of the structural organization of the human body; of the structural 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.

Structure of the talk

• The problemThe problemShortcomings of definitions inShortcomings of definitions in

dictionariesdictionariesControlled Medical Terminologies (CMT)Controlled Medical Terminologies (CMT)

• Foundational ModelFoundational ModelRequirements for definitionsRequirements for definitions

support inheritancesupport inheritanceExamplesExamples

• Term rather than concept orientedTerm rather than concept oriented

• Organized alphabeticallyOrganized alphabetically

not according to meaningnot according to meaning

• HomonymsHomonyms

• UnderspecificationUnderspecification

Dictionary DefinitionsDictionary Definitions

““Cerebellum:Cerebellum: The part of the The part of the metencephalon (subdivision of the brain) metencephalon (subdivision of the brain) that occupies the posterior cranial fossa…”that occupies the posterior cranial fossa…”

““Posterior cranial fossa:Posterior cranial fossa: The posterior The posterior subdivision of the floor of the cranial subdivision of the floor of the cranial cavity, lodging the cerebellum…”cavity, lodging the cerebellum…”

Dorland’s Medical Dictionary, 28Dorland’s Medical Dictionary, 28thth Edition Edition

Example of Dictionary DefinitionsExample of Dictionary Definitions

• Often absentOften absent

• When presentWhen presentadopted from dictionariesadopted from dictionaries

implied by hierarchy of termsimplied by hierarchy of terms

CMT DefinitionsCMT Definitions

• Provide the rationale for Provide the rationale for an an inheritance hierarchy (Ao) inheritance hierarchy (Ao) in a structural context;in a structural context;

• Specify the Specify the essenceessence of anatomical entitiesof anatomical entitiesin terms of structural attributes:in terms of structural attributes:

genusgenusdifferentiaedifferentiae

Purpose of Purpose of Foundational Model DefinitionsFoundational Model Definitions

““Aristotelian” hierarchy Aristotelian” hierarchy

constructed on the basis of inheritanceconstructed on the basis of inheritancegenusgenus

subsumes the essential attributes subsumes the essential attributes

shared by all of its descendantsshared by all of its descendants

differentia(e)differentia(e)

distinguish(es) a concept from distinguish(es) a concept from

other concepts of the same other concepts of the same genusgenus

Aristotelian DefinitionsAristotelian Definitions

Esophagus

Leaf conceptLeaf conceptLeaf conceptLeaf concept

Underlying structure

Digital Anatomist Foundational ModelDigital Anatomist Foundational ModelProtégé-2000Protégé-2000

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

Material Physical Anatomical Entity

Material Physical Anatomical Entity -is a--is a-

AnatomicalStructure

AnatomicalStructure

Non-material Physical Anatomical Entity


Physical Anatomical Entity


ConceptualAnatomical Entity


Anatomical EntityAnatomical Entity

OrganOrgan


Material Physical Anatomical Entity -is a--is a-

AnatomicalStructure

AnatomicalStructure








OrganOrgan

BodySubstance

BodySubstance

BloodBloodBloodBlood UrineUrineUrineUrine

Inheritance through Protégé-2000Inheritance through Protégé-2000

• Declare Declare contextcontext of modeling the domain of modeling the domain

• Declare Declare principlesprinciples for for

inheritance hierarchy (ontology)inheritance hierarchy (ontology)

• Explicitly define all classes of the ontologyExplicitly define all classes of the ontology

consistent with context and principlesconsistent with context and principles

Desiderata for DefinitionsDesiderata for Definitions

• Specify concepts by Aristotelian definitionSpecify concepts by Aristotelian definition

genusgenus

differentia(e)differentia(e)

• Essence of concept = Essence of concept =

transitively inherited attributes + differentia(e)transitively inherited attributes + differentia(e)

• Same kind of defining attributes Same kind of defining attributes

should distinguish members of a classshould distinguish members of a class


• To assure transitive inheritanceTo assure transitive inheritance

define classes that have not define classes that have not been been previously identifiedpreviously identified

• Integrate definitions into Integrate definitions into

a machine-interpretable a machine-interpretable

implementation implementation schemescheme







OrganOrganCellCell OrganPart

OrganPart

-is a--is a-

AnatomicalStructure

AnatomicalStructure

BodyPart

BodyPart





HumanBody

HumanBody

OrganSystem

OrganSystem

TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision

Digital Anatomist Foundational ModelDigital Anatomist Foundational ModelProtégé-2000Protégé-2000

Dorland’s Medical Dictionary, 28Dorland’s Medical Dictionary, 28thth Edition Edition ““Cerebellum:Cerebellum: The part of the metencephalon The part of the metencephalon (subdivision of the brain) that occupies the (subdivision of the brain) that occupies the posterior cranial fossa…”posterior cranial fossa…”

Digital Anatomist Foundational ModelDigital Anatomist Foundational Model

““Cerebellum:Cerebellum: subdivision of the metencephalon subdivision of the metencephalon (hind brain) connected to the brainstem by the (hind brain) connected to the brainstem by the cerebellar peduncles.”cerebellar peduncles.”

DefinitionsDefinitions

Dorland’s Medical Dictionary, 28Dorland’s Medical Dictionary, 28thth Edition Edition ““Posterior cranial fossa:Posterior cranial fossa: The posterior subdivision of the The posterior subdivision of the floor of the cranial cavity, lodging the cerebellum…”floor of the cranial cavity, lodging the cerebellum…”

Digital Anatomist Foundational ModelDigital Anatomist Foundational Model

““Posterior cranial fossa:Posterior cranial fossa: subdivision of the cranial subdivision of the cranial cavity demarcated by the plane of the tentorium cavity demarcated by the plane of the tentorium cerebelli from the cranial cavity proper.”cerebelli from the cranial cavity proper.”

DefinitionsDefinitions

Examples from CMT’sExamples from CMT’s

– MeSH has dict. Def’s (Dorlands)MeSH has dict. Def’s (Dorlands)– Snomed (codes terminology according to Snomed (codes terminology according to

meaning, no def’s, only superclass)meaning, no def’s, only superclass)– Galen (computer def’s that do not specify Galen (computer def’s that do not specify

differentia, only genus pure taxonomy)differentia, only genus pure taxonomy)

American Medical Informatics Association Annual Symposium 2001 The Role of Definitions in Biomedical...

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