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This article is part of the supplement: Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2011: Genomics

Open Access Proceedings

Discriminative application of string similarity methods to chemical and non-chemical names for biomedical abbreviation clustering

Atsuko Yamaguchi1*, Yasunori Yamamoto1, Jin-Dong Kim1, Toshihisa Takagi2 and Akinori Yonezawa1

Author Affiliations

1 Database Center for Life Science, Bunkyo-ku, Tokyo, Japan

2 Department of Computational Biology, The University of Tokyo, Kashiwa, Chiba, Japan

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BMC Genomics 2012, 13(Suppl 3):S8  doi:10.1186/1471-2164-13-S3-S8

Published: 11 June 2012

Abstract

Background

Term clustering, by measuring the string similarities between terms, is known within the natural language processing community to be an effective method for improving the quality of texts and dictionaries. However, we have observed that chemical names are difficult to cluster using string similarity measures. In order to clearly demonstrate this difficulty, we compared the string similarities determined using the edit distance, the Monge-Elkan score, SoftTFIDF, and the bigram Dice coefficient for chemical names with those for non-chemical names.

Results

Our experimental results revealed the following: (1) The edit distance had the best performance in the matching of full forms, whereas Cohen et al. reported that SoftTFIDF with the Jaro-Winkler distance would yield the best measure for matching pairs of terms for their experiments. (2) For each of the string similarity measures above, the best threshold for term matching differs for chemical names and for non-chemical names; the difference is especially large for the edit distance. (3) Although the matching results obtained for chemical names using the edit distance, Monge-Elkan scores, or the bigram Dice coefficients are better than the result obtained for non-chemical names, the results were contrary when using SoftTFIDF. (4) A suitable weight for chemical names varies substantially from one for non-chemical names. In particular, a weight vector that has been optimized for non-chemical names is not suitable for chemical names. (5) The matching results using the edit distances improve further by dividing a set of full forms into two subsets, according to whether a full form is a chemical name or not. These results show that our hypothesis is acceptable, and that we can significantly improve the performance of abbreviation-full form clustering by computing chemical names and non-chemical names separately.

Conclusions

In conclusion, the discriminative application of string similarity methods to chemical and non-chemical names may be a simple yet effective way to improve the performance of term clustering.