Annotation of Gene Products in the Literature with Gene Ontology Terms Using Syntactic Dependencies

  • Jung-jae Kim
  • Jong C. Park
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3248)


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.


Gene Ontology Ontological Term Gene Ontology Term Main Clause Subordinate Clause 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Jung-jae Kim
    • 1
  • Jong C. Park
    • 1
  1. 1.Korea Advanced Institute of Science and TechnologyDaejeonSouth Korea

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