My Corporis Fabrica (MyCF): Ontology for Physical Anatomical Modeling

Olivier Palombi (MD, PhD)François FaureAli DickoJean-Claude

David JospinMaxime Favier

Marie-Paule Cani

Anatomy Laboratory (LADAF)UJF, Grenoble 1LJK, IMAGINE, INRIAFrance

World Wide Web Consortium (W3C)

Semantic Web

Terminology of Anatomy

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 of Anatomy

The Foundational Model of Anatomy ontology

Protégé is an authoring and editing environment for ontologies.

FMA

FMA (3.1) contains 83 281 classes over 120 000 termsover 2.1 million relationsover 186 propertiesonly 150 definitions !

Bioportal : National Center for Biomedical Ontologyis.

My Corporis Fabrica

MyCF www.mycorporisfabrica.org

Ontolgy-based physical modeling of musculo-skeletal system

From Generic to Specic Musculoskeletal Simulations using an Ontology-based Modeling PipelineAli Hamadi Dicko, Benjamin Gilles, François Faure , Olivier PalombiINTELLIGENT COMPUTER GRAPHICS (ICG) 2012

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(c)

(a)

rigid bones

articulated frame

rigid mapping

joint spring

(b)

pelvis

femur

patella

tibia

Calcaneus, talus, toes

Ontolgy-based physical modeling of musculo-skeletal system

Result: Articulated body system

VIDEO

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Tendon TendonMuscle Fiber

Muscle model

Thelen muscle model [Thelen 2003]

Controlled musculoskeletal system

Controlled musculoskeletal system by MyCF

MyCF : Ontology of anatomy functions

Using functions to manage anatomical complexity

MyCF Browser

Rigid bones

Articulated body system

Musculoskeletal system Deformation model

Complete model

Pipeline : musculoskeletal model

Real-time physics engines : the knee flexion

Real-time physics engines : the hip rotations

Real-time physics engines : the hip adduction & abduction

From Generic to Specific Musculoskeletal Simulations using an Ontology-based Modeling Pipeline

Registration of the reference model to the subject-specific data.

Videos

Real-time physics engines : specific knee flexion

Open questions and futur works

• FMA• Limited to anatomical structures• Genes expressions (phenotypes) • No used in practice (why?)

• MyCF• Focused on functions• Made to build physical 3D models • Take into account the finality of the models

New software architecture for MyCF - Representational state transfer (RST) from Roy Fielding (2000) - Web Service