Workshop on anatomical models My Corporis Fabrica: Ontology for - - PowerPoint PPT Presentation

Workshop on anatomical models

My Corporis Fabrica: Ontology for anatomical modeling

Olivier Palombi (MD,PhD)

Guillaume Bousquet Sahar Hassan David Jospin Benjamin Gilles Lionel Revéret Franck Hetroy François Faure

EVASION, INRIA, LJK Grenoble Universities France

History of Anatomy Andreae Vesalii (1543) :

” De humani corporis fabrica libri septem ”

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)

ONTOLOGY

Definition: Is a "formal, explicit specification of a shared conceptualization". An ontology provides a computable representation of the underlying reality.

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.”

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 (is-a): This defines which objects are classified by which class. The meronymy relation ( part_of): Represents how objects combine together to form composite objects.

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

The Open Biomedical Ontologies (OBO) ( http://www.obofoundry.org )

Purpose: ”Creating a suite of orthogonal interoperable reference

• ntologies in the biomedical domain.”

Anatomy in OBO:

• The Foundational Model of Anatomy ontology (FMA)
• The Common Anatomy Reference Ontology (CARO)

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.

• Unified context principle
• Abstraction level principle
• Species specificity principle
• Definition principle
• Organizational unit principle
• Relationship contraint principle
• Coherence principle
• Representation principle

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 XML- formatted results.

( http://sig.biostr.washington.edu/projects/oqafma/ )

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

MySQL implementation in MyCF

www.mycorporisfabrica.org