Normalizing biomedical terms by minimizing ambiguity and variability.

BMC Bioinformatics
Yoshimasa TsuruokaSophia Ananiadou

Abstract

One of the difficulties in mapping biomedical named entities, e.g. genes, proteins, chemicals and diseases, to their concept identifiers stems from the potential variability of the terms. Soft string matching is a possible solution to the problem, but its inherent heavy computational cost discourages its use when the dictionaries are large or when real time processing is required. A less computationally demanding approach is to normalize the terms by using heuristic rules, which enables us to look up a dictionary in a constant time regardless of its size. The development of good heuristic rules, however, requires extensive knowledge of the terminology in question and thus is the bottleneck of the normalization approach. We present a novel framework for discovering a list of normalization rules from a dictionary in a fully automated manner. The rules are discovered in such a way that they minimize the ambiguity and variability of the terms in the dictionary. We evaluated our algorithm using two large dictionaries: a human gene/protein name dictionary built from BioThesaurus and a disease name dictionary built from UMLS. The experimental results showed that automatically discovered rules can perform comparably to carefully crafte...Continue Reading

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Citations

Oct 9, 2012·Journal of the American Medical Informatics Association : JAMIA·Ning KangJan A Kors
Sep 26, 2009·BMC Bioinformatics·Kevin NagelDietrich Rebholz-Schuhmann
Feb 26, 2010·BMC Bioinformatics·J Lynn FinkPhilip E Bourne
Oct 14, 2011·BMC Bioinformatics·Paul ThompsonSophia Ananiadou
Oct 15, 2013·PloS One·Dietrich Rebholz-SchuhmannIan Lewin
Jun 24, 2010·Trends in Biotechnology·Sophia AnaniadouDouglas B Kell
Dec 21, 2010·Journal of Traumatic Stress·Brett TruskoTheodore Speroff
Feb 23, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Kyle H Ambert, Aaron M Cohen
Dec 10, 2013·Journal of Biomedical Informatics·Glenn T GobbelMichael E Matheny
Oct 23, 2013·Journal of Biomedical Informatics·Suresh SubramaniJeyakumar Natarajan
Jan 16, 2010·Journal of Biomedical Informatics·Xuezhong ZhouBaoyan Liu
Apr 22, 2011·BMC Bioinformatics·David Martinez, Timothy Baldwin
Sep 26, 2014·PLoS Computational Biology·David R BlairAndrey Rzhetsky
Jan 7, 2016·PloS One·Paul ThompsonSophia Ananiadou
May 28, 2010·Nucleic Acids Research·Janez Konc, Dusanka Janezic
Oct 30, 2008·Nucleic Acids Research·Daniel BarrellRolf Apweiler
May 26, 2009·Nucleic Acids Research·Stefano AngaranConcettina Guerra
Jan 1, 2021·Bioinformatics·Salvador Casaní-GaldónAna Conesa

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Software Mentioned

BioThesaurus
UMLS

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