An application of text categorization methods to gene ontology annotation

ABSTRACT

This paper describes an application of IR and text categorization methods to a highly practical problem in biomedicine, specifically, Gene Ontology (GO) annotation. GO annotation is a major activity in most model organism database projects and annotates gene functions using a controlled vocabulary. As a first step toward automatic GO annotation, we aim to assign GO domain codes given a specific gene and an article in which the gene appears, which is one of the task challenges at the TREC 2004 Genomics Track. We approached the task with careful consideration of the specialized terminology and paid special attention to dealing with various forms of gene synonyms, so as to exhaustively locate the occurrences of the target gene. We extracted the words around the gene occurrences and used them to represent the gene for GO domain code annotation. As a classifier, we adopted a variant of k-Nearest Neighbor (kNN) with supervised term weighting schemes to improve the performance, making our method among the top-performing systems in the TREC official evaluation. Moreover, it is demonstrated that our proposed framework is successfully applied to another task of the Genomics Track, showing comparable results to the best performing system.

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INDEX TERMS

Primary Classification:
  H. Information Systems
  H.2 DATABASE MANAGEMENT
      H.2.4 Systems
          Subjects: Textual databases

Additional Classification:
  H. Information Systems
  H.3 INFORMATION STORAGE AND RETRIEVAL
      H.3.1 Content Analysis and Indexing
          Subjects: Abstracting methods; Linguistic processing; Indexing methods

  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

General Terms:
Algorithms, Experimentation, Performance

Keywords:
automatic database curation, genomic IR, text categorization