Title: Mining the botulinum research literature

Authors: Regina Z. Cer, Uma Mudunuri, Robert M. Stephens, Frank J. Lebeda

Addresses: Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA. ' Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA. ' Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA. ' Research Area Directorate 2, US Army Medical Research and Materiel Command, 504 Scott Street, Ft. Detrick, MD 20702-5012, USA

Abstract: The literature search section (botXminer) in the botulinum resource database (BotDB; http://botdb.abcc.ncifcrf.gov) contains a new query tool – |Batch Search|. In basic mode, a user can submit a list of words or phrases that are used to conduct a sequential search of the titles, abstracts and MEDLINE contents of clostridial neurotoxin citations. A table of results is returned that contains the numbers of citations found for each query term that are, in turn, linked to information from PubMed and MEDLINE for each citation. In matrix mode, a user can join two lists of user-defined terms in which all of the results from the combinatorial pairs are returned in a matrix. Each matrix element is linked to a citation list. In both modes, searches can be refined by selecting a range of publication years. Examples of |Batch Search| matrices are statistically analysed for their quality by calculating their recall and precision values.

Keywords: batch searches; batch queries; information retrieval; recall; precision; F1-measure; biomedical literature; literature search; botulinum resource database; combinatorial query; controlled vocabulary; database searching; clostridial neurotoxins; botulinum research.

DOI: 10.1504/TBJ.2009.031679

The Botulinum Journal, 2009 Vol.1 No.3, pp.270 - 280

Published online: 17 Feb 2010 *

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