The AnaEE (Analysis and Experimentation on Ecosystems) Research Infrastructure offers experimental facilities for studying ecosystems and biodiversity. A pipeline featuring several applications is developed, based on interoperability of its components and the use of shared semantic artifacts, mainly AnaeeThes thesaurus and OBOE-based AnaeeOnto ontology (to be published). The goal of this pipeline is to generate interoperable datasets and the associated metadata records. The AnaEE semantic workflow consists of 3 steps: At step 1 the observed /measured variable and the acquisition contexts are modeled as a generic graph based on the ontology. At step 2 a dedicated pipeline allows the automation of the annotation process and the production of graph-hosted semantized data. At step 3, a second pipeline is devoted to the exploitation of these semantized data through the generation of standardized metadata records (presently GeoDCAT and ISO) and, data files (presently in NetCDF and csv format) from selected perimeters (acquisition sites, measured variables, experimental factors, years...) (https://hal.inrae.fr/hal-03234155). The semantized data and metadata produced are intended to feed discovery and access portals, data repositories and (Virtual Research Environment) VRE-type platforms.