SIFR BioPortal : Un portail ouvert et générique d’ontologies et de terminologies biomédicales françaises au service de l’annotation sémantique

National audienceContexte – Le volume de données en biomédecine ne cesse de croître. En dépit d'une large adoption de l'anglais, une quantité significative de ces données est en français. Dans le do-maine de l’intégration de données, les terminologies et les ontologies jouent un rôle central pour structurer les données biomédicales et les rendre interopérables. Cependant, outre l'existence de nombreuses ressources en anglais, il y a beaucoup moins d'ontologies en français et il manque crucialement d'outils et de services pour les exploiter. Cette lacune contraste avec le montant considérable de données biomédicales produites en français, par-ticulièrement dans le monde clinique (e.g., dossiers médicaux électroniques). Methode & Résultats – Dans cet article, nous présentons certains résultats du projet In-dexation sémantique de ressources biomédicales francophones (SIFR), en particulier le SIFR BioPortal, une plateforme ouverte et générique pour l’hébergement d’ontologies et de terminologies biomédicales françaises, basée sur la technologie du National Center for Biomedical Ontology. Le portail facilite l’usage et la diffusion des ontologies du domaine en offrant un ensemble de services (recherche, alignements, métadonnées, versionnement, vi-sualisation, recommandation) y inclus pour l’annotation sémantique. En effet, le SIFR An-notator est un outil d’annotation basé sur les ontologies pour traiter des données textuelles en français. Une évaluation préliminaire, montre que le service web obtient des résultats équivalents à ceux reportés précedement, tout en étant public, fonctionnel et tourné vers les standards du web sémantique. Nous présentons également de nouvelles fonctionnalités pour les services à base d’ontologies pour l’anglais et le français

Critères de comparaison des plateformes d’ontologies biomédicales NCBO BioPortal et CISMeF: RAPPORT DE STAGE MASTER 2 INFORMATIQUE - Spécialité DECOL

Du 01 Mars 2013 au 31 aout 2013, j'ai effectué mon stage de Master 2 DECOL au sein du LIRMM, à Montpellier. Ce stage de Master 2 fut l'occasion de mettre en application les nombreuses connaissances enseignées en Master DECOL. Ce stage s'inscrit dans le cadre du projet SIFR financé par l'Agence Nationale de la Recherche (ANR) 3.Dans ce chapitre nous allons présenter le projet dans lequel s'inscrit ce stage et les différents partenaires du stage. Nous détaillerons également les objectifs et les technologies utilisées

An Approach to Compare Bio-Ontologies Portals

International audienceBackground: main biomedical information retrieval systems are based on controlled vocabularies and most specifically on terminologies or ontologies (T/O). These classification structures allow indexing, coding, annotating different kind of documents. Many T/O have been created for different purposes and it became a problem for finding specific concepts in the multitude of existing nomenclatures. The NCBO (National Center for Biomedical Ontologies) BioPortal2 and the CISMeF (Catalogue et Index des SitesM'edicaux de langue Franc¸aise) HeTOP3 projects have been developed to tackle this issue. Objective: the present work consists in comparing both portals. Methods: we hereby are proposing a set of criteria to compare bio-ontologies portals in terms of goals, features, technologies and usability. Results: BioPortal and HeTOP have been compared based on the given criteira. While both portals are designed to store and make T/O available to the community and are sharing many basic features, they are also very different mainly because of their basic purposes. Conclusion: thanks to the comparison criteria, we can assume that a merge between BioPortal and HeTOP is possible in terms of functionnalities. The main difficulties will be about merging the data repositories and applying different policies on T/O content

Comparing BioPortal and HeTOP: towards a unique biomedical ontology portal?

International audienceThe volume of data in the biomedical field constantly grows. The vast majority of information retrieval systems are based on controlled vocabularies and most specifically on terminologies or ontologies (T/O). These classification structures allow indexing, coding, annotating various types of documents. In Health, many T/O have been created for different purposes and it became a problem to find specific concepts in the multitude of nomenclatures. The NCBO (National Center for Biomedical Ontologies, Stanford University) BioPortal project and the CISMeF (Catalogue et Index des Sites M'edicaux de langue Franc¸aise, Rouen University Hospital) HeTOP portals have been developed to tackle this issue. While both portals are designed to store and make T/O available to the community, they are also very different mainly because of their basic purposes. The present work consists in comparing both portals and in answering the following question: is it possible to merge BioPortal and HeTOP into one unique solution to manage T/O

An Approach to Compare Bio-Ontologies Portals

International audienceBackground: main biomedical information retrieval systems are based on controlled vocabularies and most specifically on terminologies or ontologies (T/O). These classification structures allow indexing, coding, annotating different kind of documents. Many T/O have been created for different purposes and it became a problem for finding specific concepts in the multitude of existing nomenclatures. The NCBO (National Center for Biomedical Ontologies) BioPortal2 and the CISMeF (Catalogue et Index des SitesM'edicaux de langue Franc¸aise) HeTOP3 projects have been developed to tackle this issue. Objective: the present work consists in comparing both portals. Methods: we hereby are proposing a set of criteria to compare bio-ontologies portals in terms of goals, features, technologies and usability. Results: BioPortal and HeTOP have been compared based on the given criteira. While both portals are designed to store and make T/O available to the community and are sharing many basic features, they are also very different mainly because of their basic purposes. Conclusion: thanks to the comparison criteria, we can assume that a merge between BioPortal and HeTOP is possible in terms of functionnalities. The main difficulties will be about merging the data repositories and applying different policies on T/O content

Comparing BioPortal and HeTOP: towards a unique biomedical ontology portal?

International audienceThe volume of data in the biomedical field constantly grows. The vast majority of information retrieval systems are based on controlled vocabularies and most specifically on terminologies or ontologies (T/O). These classification structures allow indexing, coding, annotating various types of documents. In Health, many T/O have been created for different purposes and it became a problem to find specific concepts in the multitude of nomenclatures. The NCBO (National Center for Biomedical Ontologies, Stanford University) BioPortal project and the CISMeF (Catalogue et Index des Sites M'edicaux de langue Franc¸aise, Rouen University Hospital) HeTOP portals have been developed to tackle this issue. While both portals are designed to store and make T/O available to the community, they are also very different mainly because of their basic purposes. The present work consists in comparing both portals and in answering the following question: is it possible to merge BioPortal and HeTOP into one unique solution to manage T/O