title: BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature.
abstract: BACKGROUND
  To automatically process large quantities of biological literature for knowledge discovery and information curation, text mining tools are becoming essential. Abbreviation recognition is related to NER and can be considered as a pair recognition task of a terminology and its corresponding abbreviation from free text. The successful identification of abbreviation and its corresponding definition is not only a prerequisite to index terms of text databases to produce articles of related interests, but also a building block to improve existing gene mention tagging and gene normalization tools.
  
  
  RESULTS
  Our approach to abbreviation recognition (AR) is based on machine-learning, which exploits a novel set of rich features to learn rules from training data. Tested on the AB3P corpus, our system demonstrated a F-score of 89.90% with 95.86% precision at 84.64% recall, higher than the result achieved by the existing best AR performance system. We also annotated a new corpus of 1200 PubMed abstracts which was derived from BioCreative II gene normalization corpus. On our annotated corpus, our system achieved a F-score of 86.20% with 93.52% precision at 79.95% recall, which also outperforms all tested systems.
  
  
  CONCLUSIONS
  By applying our system to extract all short form-long form pairs from all available PubMed abstracts, we have constructed BIOADI. Mining BIOADI reveals many interesting trends of bio-medical research. Besides, we also provide an off-line AR software in the download section on http://bioagent.iis.sinica.edu.tw/BIOADI/.
authors: Institute of Information Science, Academia Sinica, Taipei 115, Taiwan, Republic of China. clarkkuo@iis.sinica.edu.tw
authors: Cheng-Ju
authors: CJ
authors: Kuo
authors: Maurice H T
authors: MH
authors: Ling
authors: Kuan-Ting
authors: KT
authors: Lin
authors: Chun-Nan
authors: CN
authors: Hsu
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods; D009323:Natural Language Processing; D039781:PubMed; D012984:Software