title: Building a high-quality sense inventory for improved abbreviation disambiguation.
abstract: BACKGROUND
  The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation.
  
  
  RESULTS
  A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts.
  
  
  BACKGROUND
  The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/.
authors.affiliation: Graduate School of Information Science and Technology, University of Tokyo, Tokyo, Japan. okazaki@chokkan.org
authors.forename: Naoaki
authors.initials: N
authors.lastname: Okazaki
authors.forename: Sophia
authors.initials: S
authors.lastname: Ananiadou
authors.forename: Jun'ichi
authors.initials: J
authors.lastname: Tsujii
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D016206:Databases, Bibliographic; D004014:Dictionaries as Topic; D016239:MEDLINE; D015233:Models, Statistical; D009323:Natural Language Processing; D016133:Polymerase Chain Reaction / Q000379:methods; D015203:Reproducibility of Results; D012984:Software; D014057:Tomography, X-Ray Computed / Q000379:methods