title: Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora.
abstract: BioC is a recently created XML format to share text data and annotations, and an accompanying input/output library to promote interoperability of data and tools for natural language processing of biomedical text. This article reports the use of BioC to address a common challenge in processing biomedical text information-that of frequent entity name abbreviation. We selected three different abbreviation definition identification modules, and used the publicly available BioC code to convert these independent modules into BioC-compatible components that interact seamlessly with BioC-formatted data, and other BioC-compatible modules. In addition, we consider four manually annotated corpora of abbreviations in biomedical text: the Ab3P corpus of 1250 PubMed abstracts, the BIOADI corpus of 1201 PubMed abstracts, the old MEDSTRACT corpus of 199 PubMed(®) citations and the Schwartz and Hearst corpus of 1000 PubMed abstracts. Annotations in these corpora have been re-evaluated by four annotators and their consistency and quality levels have been improved. We converted them to BioC-format and described the representation of the annotations. These corpora are used to measure the three abbreviation-finding algorithms and the results are given. The BioC-compatible modules, when compared with their original form, have no difference in their efficiency, running time or any other comparable aspects. They can be conveniently used as a common pre-processing step for larger multi-layered text-mining endeavors. Database URL: Code and data are available for download at the BioC site: http://bioc.sourceforge.net.
authors.affiliation: National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA Rezarta.Islamaj@nih.gov.
authors.forename: Rezarta
authors.initials: R
authors.lastname: Islamaj Doğan
authors.affiliation: National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Donald C
authors.initials: DC
authors.lastname: Comeau
authors.affiliation: National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Lana
authors.initials: L
authors.lastname: Yeganova
authors.affiliation: National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: W John
authors.initials: WJ
authors.lastname: Wilbur
mesh_terms: D000004:Abbreviations as Topic; D000465:Algorithms; D064229:Biological Ontologies; D057225:Data Mining; D009323:Natural Language Processing