workshop on anatomical models - inriaworkshop on anatomical models my corporis fabrica: ontology for...
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Workshop on anatomical models
My Corporis Fabrica: Ontology for anatomical modeling
Olivier Palombi (MD,PhD)
Guillaume BousquetSahar HassanDavid JospinBenjamin GillesLionel RevéretFranck HetroyFrançois Faure
EVASION, INRIA, LJKGrenoble UniversitiesFrance
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History of Anatomy
Andreae Vesalii (1543) : ” De humani corporis fabrica libri
septem ”
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Terminologia Anatomica (TA)
1903: Internationnal Federation of Association of Anatomists (IFAA) is created
1961: ‘Nomina Anatomica’ (NA)
1980: Federative Committee on Anatomical Terminology (FCAT) is created
1989: ‘Terminologia Anatomica’ (TA)
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ONTOLOGY
Definition: Is a "formal, explicit specification of a shared conceptualization".
An ontology provides a computable representation of the underlying reality.
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ONTOLOGY COMPONENTS
Instances: The general purposes of an ontology is to provide a means of classifying individuals. , even if those individuals are not explicitly part of the ontology.
Classes: Abstract objects.
Attributes: Properties.
Relations: ways in which classes can be related to one another.
“The patella is a part of the knee and is a bone organ.”
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ONTOLOGY RELATIONS
The set of relations describes the semantics of the domain.
“The patella is a part of the knee and is a bone organ.”
The subsumption relation (isa):This defines which objects are classified by which class.
The meronymy relation ( part_of): Represents how objects combine together to form composite objects.
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A FORMAL ONTOLOGY
Definition: A Formal ontology is an ontology with a structure that is guided and defined through axioms. = Foundational Ontologies
● indefinite expandability.● content and context independence.● accommodate different levels of granularity.
Basic formal Ontology (BFO) ( http://www.ifomis.org/bfo ).
In biomedicine within the framework of the OBO Foundry
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The Open Biomedical Ontologies (OBO) ( http://www.obofoundry.org )
Purpose: ”Creating a suite of orthogonal interoperable reference ontologies in the biomedical domain.”
Anatomy in OBO: ● The Foundational Model of Anatomy ontology (FMA)● The Common Anatomy Reference Ontology (CARO)
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The Foundational Model of Anatomy ontology (FMA)( http://sig.biostr.washington.edu/projects/fm )
FMA contains 75 000 classes and over 120 000 terms; over 2.1 million relationship instances from over 168 relationship types.
● Protégé : Framebased system developed by members of Stanford Center for Biomedical Informatics Research. Protégé is an authoring and editing environment for ontologies.Protégé is used to enter and modify data in a MySQL database with a specific relational database schema.
● Querying Agent for the Foundational Model of Anatomy (OQAFMA): is a database querying tool that provides access to FMA. Takes StruQL queries as input and returns XMLformatted results. ( http://sig.biostr.washington.edu/projects/oqafma/ )
● Unified context principle● Abstraction level principle● Species specificity principle● Definition principle● Organizational unit principle● Relationship contraint principle
● Coherence principle● Representation principle
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The Foundational Model of Anatomy ontology (FMA)( http://sig.biostr.washington.edu/projects/fm )
● Protégé is an authoring and editing environment for ontologies.
● Querying Agent for the Foundational Model of Anatomy (OQAFMA): is a database querying tool that provides access to FMA. Takes StruQL queries as input and returns XMLformatted results. ( http://sig.biostr.washington.edu/projects/oqafma/ )
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www.mycorporisfabrica.org
Anatomical ontology for mechanical modeling.
Based on FMA Extensions:
mechanical parameters geometric informations functions and process
A new relational database A specifc GUI
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MySQL implementation in MyCF
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www.mycorporisfabrica.org