The volume of data in biomedicine is constantly increasing. Despite a large adoption of English in science, a significant quantity of these data uses the French language. Biomedical data integration and semantic interoperability is necessary to enable new scientific discoveries that could be made by merging different available data. The community has turned to ontologies and terminologies to design semantic indexes of data that leverage the medical knowledge. However, besides the existence of various English tools, there are considerably less ontologies available in French and there is a strong lack of related tools and services to exploit them. This lack does not match the huge amount of biomedical data produced in French, especially in the clinical world (e.g., electronic health records). SIFR investigates the scientific and technical challenges in building ontology-based services to leverage biomedical ontologies and terminologies in indexing, mining and retrieval of French biomedical data (Figure 1). Within the project, we work on several research questions from semantic indexing, text mining, terminology extraction, ontology enrichment, disambiguation, ontology alignment, multilingualism in ontologies and semantic annotation in order to offer the community with services and applications capable of leveraging the use of biomedical ontologies in their data workflows.