Annabel Bourdé

Université de Rennes

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Marc Cuggia

Université de Rennes

Oussama Zékri

Centre Eugène Marquis

Paolo Besana

Istituto Universitario di Studi Superiori di Pavia

R Duvauferrier

Centre Hospitalier Universitaire de Martinique

Anita Burgun

Institut des Maladies Génétiques Imagine

Carito Guziołowski

École Centrale de Nantes

Bruno Turlin

Hôpital Pontchaillou

François Moreews

Physiologie Environnement et Génétique pour l'Animal et les Systèmes d'Elevage

Anne Siegel

Université de Rennes

Catherine Bohec

Cooperative Institutions

Inserm

Université de Rennes

Centre National de la Recherche Scientifique

Institut national de recherche en informatique et en automatique

Institut de Recherche en Informatique et Systèmes Aléatoires

Centre Hospitalier Universitaire de Rennes

Inria Rennes - Bretagne Atlantique Research Centre

Laboratoire Traitement du Signal et de l'Image

Institut thématique Génétique, génomique et bioinformatique

Université Paris Cité

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OWL Model of Clinical Trial Eligibility Criteria Compatible with Partially-known Information.

SWAT4LS (2012)

Olivier Dameron Paolo Besana Oussama Zékri Annabel Bourdé Anita Burgun

Background Clinical trials are important for patients, for researchers and for companies. One of the major bottlenecks is patient recruitment. This task requires the matching of a large volume of information about the patient with numerous eligibility criteria, in a logically-complex combination. Moreover, some of the patient’s information necessary to determine the status of the eligibility criteria may not be available at the time of pre-screening.

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An Internet supported workflow for the publication process in UMVF (French Virtual Medical University)

International Journal of Medical Informatics (2007)

Jean–Marie Renard Annabel Bourdé Marc Cuggia Nicolas Garcelon Nathalie Souf

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10.1016/j.ijmedinf.2007.01.010

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Using Semantic Web Technologies for Clinical Trial Recruitment

Lecture notes in computer science (2010)

Paolo Besana Marc Cuggia Oussama Zékri Annabel Bourdé Anita Burgun

Patient recruitment

10.1007/978-3-642-17749-1_3

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Ontology driven decision support systems for medical diagnosis - an interactive form for consultation in patients with plasma cell disease.

PubMed (2012)

Valéry Donfack Guefack Valérie Bertaud Gounot R Duvauferrier Annabel Bourdé John N. Morelli

Multiple myeloma (MM) is a malignant disorder characterized by the monoclonal proliferation of B cell derived plasma cells in the bone marrow. The diagnosis depends on the identification of abnormal monoclonal marrow plasma cells, monoclonal protein in the serum or urine, evidence of end-organ damage, and a clinical picture consistent with MM. The distinction between MM stages- monoclonal gammopathy of undetermined significance or indolent myeloma-is critical in guiding therapy. This paper describes how to produce ontology-driven semiological rules base (SRB) and a consultation form to aid in the diagnosis of plasma cells diseases. We have extracted the MM sub-ontology from the NCI Thesaurus. Using Protégé 3.4.2 and owl1, criteria in the literature for the diagnosis and staging of MM have been added to the ontology. All quantitative parameters have been transformed to a qualitative format. A formal description of MM variants and stages has been given. The obtained ontology has been checked by a reasoner and instantiated to obtain a SRB. The form created has been tested and evaluated utilizing 63 clinical medical reports. The likelihood for a disease being the correct diagnosis is determined by computing a ratio. The resulting tool is relevant for MM diagnosis and staging.

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New Results - Systems biology: analysing data and modeling interactions

Michel Le Borgne Jacques Nicolas Ovidiu Radulescu Anne Siegel Carito Guziołowski

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Creating an ontology driven rules base for an expert system for medical diagnosis.

PubMed (2011)

Valérie Bertaud Gounot Valéry Donfack J. Lasbleiz Annabel Bourdé R Duvauferrier

Expert systems of the 1980s have failed on the difficulties of maintaining large rule bases. The current work proposes a method to achieve and maintain rule bases grounded on ontologies (like NCIT). The process described here for an expert system on plasma cell disorder encompasses extraction of a sub-ontology and automatic and comprehensive generation of production rules. The creation of rules is not based directly on classes, but on individuals (instances). Instances can be considered as prototypes of diseases formally defined by "destrictions" in the ontology. Thus, it is possible to use this process to make diagnoses of diseases. The perspectives of this work are considered: the process described with an ontology formalized in OWL1 can be extended by using an ontology in OWL2 and allow reasoning about numerical data in addition to symbolic data.

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MyToutatice - Application Notes

Annabel Bourdé

Video presentant : l'installation de l'application Notes la creation de Notes (via l'application et via le drive) le partage d'une note

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BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks

BMC Genomics (2009)

Carito Guziołowski Annabel Bourdé François Moreews Anne Siegel

The method most commonly used to analyse regulatory networks is the in silico simulation of fluctuations in network components when a network is perturbed. Nevertheless, confronting experimental data with a regulatory network entails many difficulties, such as the incomplete state-of-art of regulatory knowledge, the large-scale of regulatory models, heterogeneity in the available data and the sometimes violated assumption that mRNA expression is correlated to protein activity. We have developed a plugin for the Cytoscape environment, designed to facilitate automatic reasoning on regulatory networks. The BioQuali plugin enhances user-friendly conversions of regulatory networks (including reference databases) into signed directed graphs. BioQuali performs automatic global reasoning in order to decide which products in the network need to be up or down regulated (active or inactive) to globally explain experimental data. It highlights incomplete regions in the network, meaning that gene expression levels do not globally correlate with existing knowledge on regulation carried by the topology of the network. The BioQuali plugin facilitates in silico exploration of large-scale regulatory networks by combining the user-friendly tools of the Cytoscape environment with high-performance automatic reasoning algorithms. As a main feature, the plugin guides further investigation regarding a system by highlighting regions in the network that are not accurately described and merit specific study.

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Gene regulatory network

10.1186/1471-2164-10-244

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Automatic Definition of the Oncologic EHR Data Elements from NCIT in OWL

Studies in health technology and informatics (2011)

Marc Cuggia Annabel Bourdé Bruno Turlin S. Vincendeau Valérie Bertaud

Semantic interoperability based on ontologies allows systems to combine their information and process them automatically. The ability to extract meaningful fragments from ontology is a key for the ontology re-use and the construction of a subset will help to structure clinical data entries. The aim of this work is to provide a method for extracting a set of concepts for a specific domain, in order to help to define data elements of an oncologic EHR. Method: a generic extraction algorithm was developed to extract, from the NCIT and for a specific disease (i.e. prostate neoplasm), all the concepts of interest into a sub-ontology. We compared all the concepts extracted to the concepts encoded manually contained into the multi-disciplinary meeting report form (MDMRF). Results: We extracted two sub-ontologies: sub-ontology 1 by using a single key concept and sub-ontology 2 by using 5 additional keywords. The coverage of sub-ontology 2 to the MDMRF concepts was 51%. The low rate of coverage is due to the lack of definition or mis-classification of the NCIT concepts. By providing a subset of concepts focused on a particular domain, this extraction method helps at optimizing the binding process of data elements and at maintaining and enriching a domain ontology.

Web Ontology Language

10.3233/978-1-60750-806-9-517

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From french EHR to NCI ontology via UMLS

International Conference on Ontology Matching (2010)

Paolo Besana Marc Cuggia Oussama Zékri Annabel Bourdé Anita Burgun

Clinical trials are required for evaluating new therapies and diagnostic techniques. We developed a system based on OWL and SWRL aimed at suggesting the clinical trials to which a patient could be enrolled, evaluating on real clinical trials and patients from the University Hospital of Rennes. This paper presents the method employed to map the French expressions from the patient data to terms in the NCI ontology.

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