Semantic interoperability, i.e., the ability to automatically interpret the shared information in a meaningful way, is one of the most important requirements for data analysis of different sources. In the area of clinical and epidemiological studies, the target of the National Research Data Infrastructure for Personal Health Data (NFDI4Health), interoperability of data collection instruments such as case report forms (CRFs), data dictionaries and questionnaires is critical. Retrospective integration of semantic codes into study metadata at item-level is important, as ongoing or completed studies contain valuable information, which should be preserved. We present a first version of a Metadata Annotation Workbench to support annotators in dealing with a variety of complex terminologies and ontologies. User-driven development with users from the fields of nutritional epidemiology and chronic diseases ensured that the service fulfills the basic requirements for a semantic metadata annotation software for these NFDI4Health use cases. The web application can be accessed using a web browser and the source code of the software is available with an open-source MIT license.