Semantic annotation is part of the vision for the semantic web. Ontologies are required for this task, and although they are in common use, there is a lack of annotation tools for users that are convenient, simple to use and easily integrated into their processes. This paper presents an ontology-based annotator web service methodology that can annotate a piece of text with ontology concepts and return annotations in OWL. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). The paper also describes an implementation of this service for life sciences and biomedicine. Our biomedical annotator service uses one of the largest available set of publicly available terminologies and ontologies. We used it to create an index of open biomedical resources. Both the deployed web service and a user interface can be accessed at (http://www.bioontology.org/tools.html).