We present a method for automatically annotating gene products in the literature with the terms of Gene Ontology (GO), which provides a dynamic but controlled vocabulary. Although GO is well-organized with such lexical relations as synonymy, ‘is-a’, and ‘part-of’ relations among its terms, GO terms show quite a high degree of morphological and syntactic variations in the literature. As opposed to the previous approaches that considered only restricted kinds of term variations, our method uncovers the syntactic dependencies between gene product names and ontological terms as well in order to deal with real-world syntactic variations, based on the observation that the component words in an ontological term usually appear in a sentence with established patterns of syntactic dependencies.