The AnaEE (Analysis and Experimentation on Ecosystems, ESFRI) Research Infrastructure offers experimental facilities for studying ecosystems and biodiversity. A distributed Information System (IS) is developed, based on semantic interoperability of its components and the use of common vocabularies (AnaeeThes thesaurus and an OBOE-based ontology). Discovery and access portals are fed by information (rdf triples) produced by the semantic annotation of AnaEE distributed resources: relational databases and modeling platforms. A first pipeline is developed for the automation of the annotation process and the production of the semantic data, annotation that may represent a huge conceptual and practical work. A second pipeline is devoted to the exploitation of these semantic data through the generation i) of standardized ISO and GeoDCAT metadata records and ii) of data files (NetCDF format) from selected perimeters (experimental sites, years, experimental factors, measured variables...). Genericity of the tools make them usable in different contexts of ontologies and databases.