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Open Access Methodology article

Mapping biological entities using the longest approximately common prefix method

Alex Rudniy1, Min Song2* and James Geller1

Author Affiliations

1 Computer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA

2 Department of Library and Information Science, Yonsei University, 50 Yonsei-ro, Seoul 120-749, Korea

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BMC Bioinformatics 2014, 15:187  doi:10.1186/1471-2105-15-187

Published: 14 June 2014

Abstract

Background

The significant growth in the volume of electronic biomedical data in recent decades has pointed to the need for approximate string matching algorithms that can expedite tasks such as named entity recognition, duplicate detection, terminology integration, and spelling correction. The task of source integration in the Unified Medical Language System (UMLS) requires considerable expert effort despite the presence of various computational tools. This problem warrants the search for a new method for approximate string matching and its UMLS-based evaluation.

Results

This paper introduces the Longest Approximately Common Prefix (LACP) method as an algorithm for approximate string matching that runs in linear time. We compare the LACP method for performance, precision and speed to nine other well-known string matching algorithms. As test data, we use two multiple-source samples from the Unified Medical Language System (UMLS) and two SNOMED Clinical Terms-based samples. In addition, we present a spell checker based on the LACP method.

Conclusions

The Longest Approximately Common Prefix method completes its string similarity evaluations in less time than all nine string similarity methods used for comparison. The Longest Approximately Common Prefix outperforms these nine approximate string matching methods in its Maximum F1 measure when evaluated on three out of the four datasets, and in its average precision on two of the four datasets.