title: Automatic assignment of biomedical categories: toward a generic approach.
abstract: BACKGROUND
  We report on the development of a generic text categorization system designed to automatically assign biomedical categories to any input text. Unlike usual automatic text categorization systems, which rely on data-intensive models extracted from large sets of training data, our categorizer is largely data-independent.
  
  
  METHODS
  In order to evaluate the robustness of our approach we test the system on two different biomedical terminologies: the Medical Subject Headings (MeSH) and the Gene Ontology (GO). Our lightweight categorizer, based on two ranking modules, combines a pattern matcher and a vector space retrieval engine, and uses both stems and linguistically-motivated indexing units.
  
  
  CONCLUSIONS
  Results show the effectiveness of phrase indexing for both GO and MeSH categorization, but we observe the categorization power of the tool depends on the controlled vocabulary: precision at high ranks ranges from above 90% for MeSH to <20% for GO, establishing a new baseline for categorizers based on retrieval methods.
authors.affiliation: University Hospitals of Geneva, Medical Informatics Service CH-1201, Geneva. Patrick.Ruch@sim.hcuge.ch
authors.forename: Patrick
authors.initials: P
authors.lastname: Ruch
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods*; D000465:Algorithms; D001185:Artificial Intelligence; D004282:Documentation / Q000379:methods*; D016239:MEDLINE; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated / Q000379:methods*; D010506:Periodicals as Topic; D011506:Proteins / Q000145:classification*
chemical_list: D011506:Proteins