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 problemThe problem Shortcomings of definitions in dictionaries Controlled Medical Terminologies (CMT) Foundational ModelFoundational Model Requirements for definitions support inheritance Examples

Term rather than concept oriented Term rather than concept oriented Organized alphabetically Organized alphabetically not according to meaning Homonyms Homonyms Underspecification Underspecification 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, 28 th Edition Example of Dictionary Definitions

Often absentOften absent When presentWhen present adopted from dictionaries implied by hierarchy of terms CMT Definitions

Provide the rationale forProvide the rationale for an inheritance hierarchy (Ao) in a structural context; Specify the essence of anatomical entitiesSpecify the essence of anatomical entities in terms of structural attributes: genusdifferentiae Purpose of Foundational Model 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 Aristotelian Definitions

Esophagus Leaf concept

Underlying structure

Digital Anatomist Foundational Model Protégé-2000

OrganOrgan Solid Organ Cavitated Organ Organ with cavitated organ part Organ with cavitated organ part Organ with organ cavity Organ with organ cavity HeartHeartEsophagusEsophagus -is a- Anatomy Ontology

Material Physical Anatomical Entity Material Physical Anatomical Entity -is a- Anatomical Structure Anatomical Structure Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Conceptual Anatomical Entity Conceptual Anatomical Entity Organ

Material Physical Anatomical Entity Material Physical Anatomical Entity -is a- Anatomical Structure Anatomical Structure Non-material Physical Anatomical Entity Non-material Physical Anatomical Entity Physical Anatomical Entity Physical Anatomical Entity Conceptual Anatomical Entity Conceptual Anatomical Entity Organ Body Substance Body Substance BloodBloodUrineUrine

Inheritance through Protégé-2000

Declare context of modeling the domainDeclare context of modeling the domain Declare principles forDeclare principles for inheritance hierarchy (ontology) Explicitly define all classes of the ontologyExplicitly define all classes of the ontology consistent with context and principles Desiderata for Definitions

Specify concepts by Aristotelian definitionSpecify concepts by Aristotelian definitiongenusdifferentia(e) Essence of concept =Essence of concept = transitively inherited attributes + differentia(e) Same kind of defining attributesSame kind of defining attributes should distinguish members of a class Desiderata for Definitions

To assure transitive inheritanceTo assure transitive inheritance define classes that have not been previously identified Integrate definitions intoIntegrate definitions into a machine-interpretable implementation scheme Desiderata for Definitions

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

Digital Anatomist Foundational Model Protégé-2000

Dorland’s Medical Dictionary, 28 th 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, 28 th 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.” Definitions

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)