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Comparison of resources is a frequent task in different bio-informatics applications, including drug-target interaction, drug repositioning and mechanism of action understanding, among others. This paper proposes a general method for the logical comparison of resources modeled in Resource Description Framework and shows its distinguishing features with reference to the comparison of drugs. In particular, the method returns a description of the commonalities between resources, rather than a numerical value estimating their similarity and/or relatedness. The approach is domain-independent and may be flexibly adapted to heterogeneous use cases, according to a process for setting parameters which is completely explicit. The paper also presents an experiment using the dataset Bioportal as knowledge source; the experiment is fully reproducible, thanks to the elicitation of criteria and values for parameter customization.

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; Semantically analyze patient-generated text from a biomedical perspective is challenging because of the vocabulary gap between patients and health professionals. The medical expertise and vocabulary is well formalized in standards terminologies and ontologies, which enable semantic analysis of expert-generated text; however resources which formalize the vocabulary of health consumers (patients and their family, laypersons in general) remain scarce. The situation is even worse if one is interested in another language than English. In previous studies, we attempted to produce a French preliminary Consumer Health Vocabulary (CHV) by mining the language used within online public forums & Facebook groups about breast cancer. In this work, we show our effort to concretely align the vocabulary produced to standard terminologies and to represent its content (terms & mappings) using semantic web languages such as RDF and SKOS. We used a sample of 173 relations built around 64 expert concepts which have been automatically (89%) or manually (11%) aligned to standard biomedical terminologies, in our case: MeSH, MedDRA and SNOMEDint. The resulting vocabulary, called MuEVo (Multi-Expertise Vocabulary) and the mappings are publicly available in the SIFR BioPortal French biomedical ontology repository.

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.

As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. To help manage these vast and disparate data sources, researchers have turned to the Semantic Web. Specifically, ontologies are used in data annotation, natural language processing, information retrieval, clinical decision support, and data integration tasks. The development of software applications to perform these tasks requires the integration of Web services to incorporate the wide variety of ontologies used in the health care and life sciences. The National Center for Biomedical Ontology, a National Center for Biomedical Computing created under the NIH Roadmap, developed BioPortal, which provides access to one of the largest repositories of biomedical ontologies. The NCBO Web services provide programmtic access to these ontologies and can be grouped into four categories; Ontology, Mapping, Annotation, and Data Access. The Ontology Web services provide access to ontologies, their metadata, ontology versions, downloads, navigation of the class hierarchy (parents, children, siblings) and details of each term. The Mapping Web services provide access to the millions of ontology mappings published in BioPortal. The NCBO Annotator Web service “tags” text automatically with terms from ontologies in BioPortal, and the NCBO Resource Ind ex Web services provides access to an ontology-based index of public, online data resources. The NCBO Widgets package the Ontology Web services for use directly in Web sites. The functionality of the NCBO Web services and widgets are incorporated into semantically aware applications for ontology development and visualization, data annotation, and data integration. This overview will describe these classes of applications, discuss a few examples of each type, and which NCBO Web services are used by these applications.