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International audience; As any resources, ontologies, thesaurus, vocabularies and terminologies need to be described with relevant metadata to facilitate their identification, selection and reuse. For ontologies to be FAIR, there is a need for metadata authoring guidelines and for harmonization of existing metadata vocabularies –taken independently none of them can completely describe an ontology. Ontology libraries and repositories also have to play an important role. Indeed, some metadata properties are intrinsic to the ontology (name, license, description); other information, such as community feedbacks, or relations to other ontologies are typically information that an ontology library shall capture, populate and consolidate to facilitate the processes of identifying and selecting the right ontology(ies) to use. We have studied ontology metadata practices by: (i) analyzing metadata annotations of 805 ontologies; (ii) reviewing the most standard and relevant vocabularies (23 totals) currently available to describe metadata for ontologies (such as Dublin Core, Ontology Metadata Vocabulary, VoID, etc.); (iii) comparing different metadata implementation in multiple ontology libraries or repositories. We have then built a new metadata model for our AgroPortal vocabulary and ontology repository, a platform dedicated to agronomy based on the NCBO BioPortal technology. AgroPortal now recognizes 346 properties from existing metadata vocabularies that could be used to describe different aspects of ontologies: intrinsic descriptions, people, date, relations, content, metrics, community, administration, and access. We use them to populate an internal model of 127 properties implemented in the portal and harmonized for all the ontologies. We –and AgroPortal's users– have spent a significant amount of time to edit and curate the metadata of the ontologies to offer a better synthetized and harmonized information and enable new ontology identification features. Our goal was also to facilitate the comprehension of the agronomical ontology landscape by displaying diagrams and charts about all the ontologies on the portal. We have evaluated our work with a user appreciation survey which confirms the new features are indeed relevant and helpful to ease the processes of identification and selection of ontologies. This paper presents how to harness the potential of a complete and unified metadata model with dedicated features in an ontology repository, however the new AgroPortal's model is not a new vocabulary as it relies on pre-existing ones. A generalization of this work is studied in a community driven standardization effort in the context of the RDA Vocabulary and Semantic Services Interest Group.

International audience; The explosion of the number of ontologies and vocabularies available in the Semantic Web makes ontology libraries and repositories mandatory to find and use them. Their functionalities span from simple on-tology listing with more or less of metada-ta description to portals with advanced on-tology-based services: browse, search, vis-ualization, metrics, annotation, etc. Ontol-ogy libraries and repositories are usually developed to address certain needs and communities. BioPortal, the ontology repository built by the US National Center for Biomedical Ontologies BioPortal relies on a domain independent technology already reused in several projects from bio-medicine to agronomy and earth sciences. In this position paper, we describe six high level challenges for ontology repositories: metadata & selection, multilingualism, alignment, new generic ontology-based services, annotations & linked data, and interoperability & scalability. Then, we present some propositions to address these challenges and point to our previously published work and results obtained within applications –reusing NCBO technology– to biomedicine and agronomy in the context of the NCBO, SIFR and AgroPortal projects.

International audience; Even if multilingual ontologies are now more common, for historical reasons, in the biomedical domain, many ontologies or terminologies have been translated from one natural language to another resulting in two potentially aligned ontologies but with their own specificity (e.g., format, developers, and versions). Most often, there is no formal representation of the translation links between translated ontologies and original ones and those mappings are not formally available as linked data. However, these mappings are very important for the interoperability and the integration of multilingual biomedical data. In this paper, we propose an approach to represent translation mappings between ontologies based on the NCBO BioPortal format. We have reconciled more than 228K mappings between ten English ontologies hosted on NCBO BioPortal and their French translations. Then, we have stored both the translated ontologies and mappings on a French customized version of the platform, called the SIFR BioPortal, making the whole thing available in RDF. Reconciling the mappings turned more complex than expected because the translations are rarely exactly the same than the original ontologies as discussed in this paper.

International audience; De nos jours, les ontologies sont souvent développées de manière multilingue. Cependant, pour des raisons historiques, dans le domaine biomédical, de nombreuses ontologies ou terminologies ont été traduites d'une langue à une autre ou sont maintenues explicitement dans chaque langue. Cela génère deux ontologies potentiellement alignées mais avec leurs propres spécificités (format, développeurs, versions, etc.). Souvent, il n'existe pas de représentation formelle des liens de traduction reliant les ontologies traduites aux originales et ils ne sont pas accessibles sous forme de linked data. Cependant, ces liens sont très importants pour l'interopérabilité et l'intégration de données biomédicales multilingues. Dans cet article, nous présentons les résultats d'une étude de réconciliation des liens de traduction entre ontologies sous forme d'alignements multilingues. Nous avons réconcilié et représenté à l'aide de vocabulaire du web sémantique, plus de 228K mappings entre dix ontologies anglaises hébergées sur le NCBO BioPortal et leurs traductions françaises. Ensuite, nous avons stocké à la fois les ontologies et les mappings sur une version française de la plate-forme, appelée SIFR BioPortal, pour rendre le tout disponible en RDF (données liées). La réconciliation des alignements s'est avérée plus complexe que ce qu'on pourrait penser car les traductions ne sont que rarement l'exacte copie des originales comme nous le discutons. Mots-clés : Mappings ou alignements multilingues, réconciliations de mappings, web sémantique, données liées, alignement d'ontologies, entrepôt d'ontologies, ontologies biomédicales, BioPortal, interopérabilité et intégration de données, diffusion de données et de connaissances.

International audience; This paper presents a novel background knowledge approach which selects and combines existing mappings from a given biomedical ontology repository to improve ontology alignment. Current background knowledge approaches usually select either manually or automatically a limited number of different ontologies and use them as a whole for background knowledge. Whereas in our approach, we propose to pick up only relevant concepts and relevant existing mappings linking these concepts all together in a specific and customized background knowledge graph. Paths within this graph will help to discover new mappings. We have implemented and evaluated our approach using the content of the NCBO BioPortal repository and the Anatomy benchmark from the Ontology Alignment Evaluation Initiative. We used the mapping gain measure to assess how much our final background knowledge graph improves results of state-of-the-art alignment systems. Furthermore, the evaluation shows that our approach produces a high quality alignment and discovers map-pings that have not been found by state-of-the-art systems.

International audience; Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.

Proceedings of the Fourth Workshop on the Multilingual Semantic Web (MSW4)co-located with 12th Extended Semantic Web Conference (ESWC 2015); International audience; Ontology indexes and repositories are important in the realization of the Semantic Web; however, the need has clearly moved to multilingual capabilities that are hard to offer when dealing with multiple ontologies, originally in different formats and contributed by an open community. In this paper, we present a roadmap for addressing the issues of dealing with multilingual or monolingual ontologies in BioPortal, the reference ontology repository in biomedicine, currently mostly English-oriented. We propose a set of representations to support multilingualism in the portal and to enable a complete use of the functionalities and services for any kind of ontologies and data. While encouraging the community to use the best available specifications to represent multilingual content e.g., Lemon; our objective is to handle multilingualism in a proper semantically rich and consistent manner in the ontology repository. We are currently deploying and implementing these representations in a local instance of BioPortal for French ontologies.

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.

International audience; The field of biomedicine has embraced the Semantic Web probably more than any other field. As a result, there is a large number of biomedical ontologies covering overlapping areas of the field. We have developed BioPortal — an open community-based repository of biomedical ontologies. We analyzed ontologies and terminologies in BioPortal and the Unified Medical Language System (UMLS), creating more than 4 million mappings between concepts in these ontologies and terminologies based on the lexical similarity of concept names and synonyms. We then analyzed the mappings and what they tell us about the ontologies themselves, the structure of the ontology repository, and the ways in which the mappings can help in the process of ontology design and evaluation. For example, we can use the mappings to guide users who are new to a field to the most pertinent ontologies in that field, to identify areas of the domain that are not covered sufficiently by the ontologies in the repository, and to identify which ontologies will serve well as background knowledge in domain-specific tools. While we used a specific (but large) ontology repository for the study, we believe that the lessons we learned about the value of a large-scale set of mappings to ontology users and developers are general and apply in many other domains.