The study of ecosystem functioning requires multidisciplinary approaches and mobilises numerous research teams. The data produced are very abundant but their reuse and integration is often difficult due to their low level of standardisation. The development of semantic interoperability is a major challenge for the sharing and reuse of these data. This objective is implemented within the framework of the AnaEE research infrastructure dedicated to experimentation on ecosystems. The modelling of the experimental system is based on the OBOE ontology extended for disciplinary needs. It covers the measured variables, the different components of the experimental context, from sensor and plot to network, by the atomic decomposition of the observed entities, their characteristics and their qualification, the units and naming standards. This modelling allows the semantic annotation of relational databases and flat files for the production of graph databases. Carried out on all the data generated by the experimental platforms, this practice produces semantically interoperable data that meets the linked opendata standards. The work carried out contributes to the development and use of semantic vocabularies within the ecology research community.