The Foundational Model of Anatomy The Foundational Model of Anatomy Cornelius Rosse, M.D., D.Sc. Cornelius Rosse, M.D., D.Sc. Structural Informatics Group Structural Informatics Group University of Washington University of Washington Digital Human Digital Human Open Source Software Framework for Open Source Software Framework for Organ Modeling and Simulation Organ Modeling and Simulation
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The Foundational Model of Anatomy Cornelius Rosse, M.D., D.Sc. Structural Informatics Group
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. Organ Modeling and Simulation. Challenges Interoperability of software - PowerPoint PPT Presentation
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The Foundational Model of AnatomyThe Foundational Model of Anatomy
Cornelius Rosse, M.D., D.Sc.Cornelius Rosse, M.D., D.Sc.
Structural Informatics GroupStructural Informatics GroupUniversity of WashingtonUniversity of Washington
Digital HumanDigital Human
Open Source Software Framework forOpen Source Software Framework forOrgan Modeling and SimulationOrgan Modeling and Simulation
Organ Modeling and SimulationOrgan Modeling and Simulation
ChallengesChallenges
• Interoperability of softwareInteroperability of software
• Representation of biomedical knowledge Representation of biomedical knowledge in machine-processible formin machine-processible form
• Integration and correlation of Integration and correlation of biomedical informationbiomedical information
The Semantic Web: The Semantic Web: A new form of Web content that A new form of Web content that is meaningful to computers will is meaningful to computers will unleash a revolution of new unleash a revolution of new possibilities.possibilities.
By: By: Tim Berners-LeeTim Berners-LeeJames HendlerJames HendlerOra LassilaOra Lassila
Digital Anatomist Information ProjectDigital Anatomist Information ProjectDigital Anatomist Information ProjectDigital Anatomist Information Project
MotivationMotivation
• Manifestations of health and disease are Manifestations of health and disease are attributes of anatomical attributes of anatomical
structures.structures.• Logical and comprehensive representation of Logical and comprehensive representation of
anatomical knowledge can serve as a anatomical knowledge can serve as a foundation for other types of foundation for other types of
biomedical information.biomedical information.
Digital Anatomist ProjectUniversity of Washington
Digital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information SystemDigital Anatomist Information System
What is an Organ?What is an Organ?Organ [L. organum; Gr. organon]Organ [L. organum; Gr. organon]
a somewhat independent part of the body a somewhat independent part of the body that that performs a special function or performs a special function or functions.functions.
Dorland's Medical Dorland's Medical DictionaryDictionary
OrganOrganin animals and plants, a part composed of in animals and plants, a part composed of
several several tissues and adopted to perform a tissues and adopted to perform a specific function or specific function or functions.functions.
Webster’s DictionaryWebster’s DictionaryE.g., liver, heart, lung, kidneyE.g., liver, heart, lung, kidney hand, head of femur, right ventriclehand, head of femur, right ventricle
Organ Modeling and SimulationOrgan Modeling and Simulation
Controlled Medical Terminologies (CMT)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
• 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
Challenges of Anatomical Knowledge RepresentationChallenges of Anatomical Knowledge Representation
ConclusionConclusion
• Inadequacy of Inadequacy of traditional knowledge sourcestraditional knowledge sources
• New need forNew need forcomputer-processable computer-processable anatomical knowledgeanatomical knowledge
Challenges of Anatomical Knowledge RepresentationChallenges of Anatomical Knowledge Representation
Question:Question:
What information should be entered in the What information should be entered in the Foundational Model of AnatomyFoundational Model of Anatomy??
Answer: Answer:
The structure of anatomical structures The structure of anatomical structures that constitute the body.that constitute the body.
Challenges of Anatomical Knowledge RepresentationChallenges of Anatomical Knowledge Representation
““The oesophagus is a muscular tube … The oesophagus is a muscular tube … connecting the pharynx to the stomach. It connecting the pharynx to the stomach. It begins in the neck, level with the lower begins in the neck, level with the lower border of the cricoid cartilage and the sixth border of the cricoid cartilage and the sixth cervical vertebra; descending largely cervical vertebra; descending largely anterior to the vertebral column through the anterior to the vertebral column through the superior and posterior mediastina.”superior and posterior mediastina.”
Gray’s Anatomy, 38th edition, p. Gray’s Anatomy, 38th edition, p. 17511751
What kind of information?
““The The oesophagusoesophagus is a is a muscular tubemuscular tube … … connecting the connecting the pharynx pharynx to the to the stomachstomach. It . It begins in the begins in the neckneck, level with the , level with the lower lower border of the cricoid cartilageborder of the cricoid cartilage and the and the sixth sixth cervical vertebracervical vertebra; descending largely ; descending largely anterior to the anterior to the vertebral columnvertebral column through the through the superiorsuperior and and posterior mediastinaposterior mediastina.”.”
Gray’s Anatomy, 38th edition, p. Gray’s Anatomy, 38th edition, p. 17511751
What kind of information?
““The The oesophagusoesophagus is ais a muscular tubemuscular tube … … connecting connecting the the pharynx pharynx to to the the stomachstomach. . ItIt beginsbegins inin the the neckneck, , level withlevel with the the lower lower border of the cricoid cartilageborder of the cricoid cartilage and the and the sixth sixth cervical vertebracervical vertebra; ; descendingdescending largely largely anterioranterior toto the the vertebral columnvertebral column through through the the superiorsuperior and and posterior mediastinaposterior mediastina.”.”
Gray’s Anatomy, 38th edition, p. Gray’s Anatomy, 38th edition, p. 17511751
What kind of information?
Symbolic model,Symbolic model,
a conceptualization of a domain of discoursea conceptualization of a domain of discourserepresented with non-graphical symbols;represented with non-graphical symbols;
in computer-processible (“understandable”) form;in computer-processible (“understandable”) form;
Foundational Model of AnatomyFoundational Model of Anatomyis a is a symbolic modelsymbolic model of the physical organization of the human body; of the physical 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.
Spatial Association NetworkSpatial Association NetworkSpatial Association NetworkSpatial Association Network
Anatomical EntityAnatomical Entity
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
-is a--is a-Conceptual
Anatomical Entity
ConceptualAnatomical Entity
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
-is a--is a-Conceptual
Anatomical Entity
ConceptualAnatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
-is a--is a-
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
Anatomical Point
Anatomical Point
Anatomical Line
Anatomical Line
Anatomical Surface
Anatomical Surface
Anatomical Space
Anatomical Space
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
-is a--is a-
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
AnatomicalStructure
AnatomicalStructure
BodySubstance
BodySubstance
BodyPart
BodyPart
HumanBody
HumanBody
OrganSystem
OrganSystemOrganOrganCellCell Organ
Part
OrganPart
TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision
OrganOrganDefinition:Definition:
OrganOrgan
is anis an anatomical structureanatomical structure
• consists ofconsists of maximal sets of organ partsmaximal sets of organ partsconnected toconnected to one another one anotherconstituteconstitute self-contained unit self-contained unitdistinct fromdistinct from other units other units
• connected toconnected to other organsother organs• constitutesconstitutes organ systemorgan system
body partbody part
Anatomical EntityAnatomical Entity
Physical Anatomical Entity
Physical Anatomical Entity
Material Physical Anatomical Entity
Material Physical Anatomical Entity
-is a--is a-
Non-material Physical Anatomical Entity
Non-material Physical Anatomical Entity
ConceptualAnatomical Entity
ConceptualAnatomical Entity
AnatomicalStructure
AnatomicalStructure
BodySubstance
BodySubstance
BodyPart
BodyPart
HumanBody
HumanBody
OrganSystem
OrganSystemOrganOrganCellCell Organ
Part
OrganPart
TissueTissue Organ componentOrgan component Organ subdivisionOrgan subdivision
Foundational Model of AnatomyFoundational Model of Anatomyis a is a symbolic modelsymbolic model of the physical organization of the human body; of the physical 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.
Role of Foundational Model of AnatomyRole of Foundational Model of Anatomy
Prototype for symbolic models in other domainsPrototype for symbolic models in other domainse.g., physiology, pathology, cancer therapye.g., physiology, pathology, cancer therapy
Core of biomedical knowledge basesCore of biomedical knowledge basesto solve problems in to solve problems in education, research, health careeducation, research, health care
"Foundational" "Foundational" becausebecauseanatomy is fundamental to all anatomy is fundamental to all
biomedical sciences;biomedical sciences;anatomical concepts encompassed by FManatomical concepts encompassed by FM
generalize to all biomedical domains.generalize to all biomedical domains.