OntoSIDES: Ontology-based student progress monitoring on the national evaluation system of French Medical Schools.

We introduce OntoSIDES, the core of an ontology-based learning management system in Medicine, in which the educational content, the traces of students' activities and the correction of exams are linked and related to items of an official reference program in a unified RDF data model. OntoSIDES is an RDF knowledge base comprised of a lightweight domain ontology that serves as a pivot high-level vocabulary of the query interface with users, and of a dataset made of factual statements relating individual entities to classes and properties of the ontology. Thanks to an automatic mapping-based data materialization and rule-based data saturation, OntoSIDES contains around 8 millions triples to date, and provides an integrated access to useful information for student progress monitoring, using a powerful query language (namely SPARQL) allowing users to express their specific needs of data exploration and analysis. Since we do not expect end-users to master the raw syntax of SPARQL and to express directly complex queries in SPARQL, we have designed a set of parametrized queries that users can instantiate through a user-friendly interface.

My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development.

BACKGROUND: Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. RESULTS: In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos. CONCLUSIONS: Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human developmental anatomy. Visualizing embryos with 3D geometric models and their animated deformations perhaps paves the way towards some kind of hypothesis-driven application. These can also be used to assist the learning process of this complex knowledge. AVAILABILITY: http://www.mycorporisfabrica.org/.

My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models.

BACKGROUND: Multiple models of anatomy have been developed independently and for different purposes. In particular, 3D graphical models are specially useful for visualizing the different organs composing the human body, while ontologies such as FMA (Foundational Model of Anatomy) are symbolic models that provide a unified formal description of anatomy. Despite its comprehensive content concerning the anatomical structures, the lack of formal descriptions of anatomical functions in FMA limits its usage in many applications. In addition, the absence of connection between 3D models and anatomical ontologies makes it difficult and time-consuming to set up and access to the anatomical content of complex 3D objects. RESULTS: First, we provide a new ontology of anatomy called My Corporis Fabrica (MyCF), which conforms to FMA but extends it by making explicit how anatomical structures are composed, how they contribute to functions, and also how they can be related to 3D complex objects. Second, we have equipped MyCF with automatic reasoning capabilities that enable model checking and complex queries answering. We illustrate the added-value of such a declarative approach for interactive simulation and visualization as well as for teaching applications. CONCLUSIONS: The novel vision of ontologies that we have developed in this paper enables a declarative assembly of different models to obtain composed models guaranteed to be anatomically valid while capturing the complexity of human anatomy. The main interest of this approach is its declarativity that makes possible for domain experts to enrich the knowledge base at any moment through simple editors without having to change the algorithmic machinery. This provides MyCF software environment a flexibility to process and add semantics on purpose for various applications that incorporate not only symbolic information but also 3D geometric models representing anatomical entities as well as other symbolic information like the anatomical functions.