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