The huge amount of the available information in the Web creates the need of effective information extraction systems that are able to produce metadata that satisfy users information needs. The development of such systems, in the majority of cases, depends on the availability of an appropriately annotated corpus in order to learn extraction models. The production of such corpora can be significantly facilitated by annotation tools that are able to annotate, according to a defined ontology, not only named entities but most importantly relations between them. This paper describes the BOEMIE ontology-based annotation tool which is able to locate blocks of text that correspond to specific types of named entities, fill tables corresponding to ontology concepts with those named entities and link the filled tables based on relations defined in the domain ontology. Additionally, it can perform annotation of blocks of text that refer to the same topic. The tool has a user-friendly interface, supports automatic pre-annotation, annotation comparison as well as customization to other annotation schemata. The annotation tool has been used in a large scale annotation task involving 3,000 web pages regarding athletics. It has also been used in another annotation task involving 503 web pages with medical information, in different languages.