Automatic Construction of Biological Abbreviation
Dictionary from Abstracts of Biomedical Papers
Mikio Yoshidamikio@ims.u-tokyo.ac.jp

Kenichiro Fukuda

ichiro@ims.u-tokyo.ac.jp

Toshihisa Takagi

takagi@ims.u-tokyo.ac.jp

Human Genome Center, Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

1 Introduction
Integration of knowledge described in a huge number of biomedical papers is a very important subject in the genome informatics area [1, 2]. Therefore, we need an intelligent information extracting
system to save time. In order to extract information or knowledge from texts and utilize them, it isnecessary to use various kinds of dictionaries, which are helpful in eliminating obscurities contained innatural languages (e.g. ambiguity and polysemy). We sought to develop a protein name abbreviation
dictionary (PNAD) in an automatic way.

2 System
2.1

Approach

The target of our proposed system is extraction of abbreviation de ning expressions. Such expressions are often observed in a typical pattern, in which an original term is followed by a parenthesis
including its abbreviation (e.g. \Thyrotrophin-releasing hormone (TRH)" ). We will call this typeof expression \Parenthetical-Paraphrase", the phrase enclosed in brackets \Inner-Phrase", and thephrase followed by brackets \Outer-Phrase". When a Parenthetical-Paraphrase is used to de ne anabbreviation, we will call it an \Abbreviation-Parenthetical-Paraphrase".

2.2

Abbreviation-Parenthetical-Paraphrase:

Original-Term( Abbreviation )Parenthetical-Paraphrase:

Outer-Phrase( Inner-Phrase )System Architecture

Fig. 1 shows the overall architecture of the PNAD construction system. In this system, we assume
that the Inner-Phrase represents an abbreviation and the Outer-Phrase involves its Original-Term.
Step(1) Extract protein names from machine readable biomedical papers.
Step(2) Extract the Parenthetical-Paraphrase from the protein names extracted in Step (1).
Step(3) Excise Outer-Phrase and Inner-Phrase from the Parenthetical-Paraphrase extracted in
Step (2).
Step(4) Extract a candidate of the Original-Term from the Outer-Phrase, and validate if the InnerPhrase is an abbreviation of the candidate.
Step(5) Register the validated abbreviation and the candidate of its Original-Term into the PNAD.
To extract protein names from machine readable papers, we used the PROPER system [1] that can
extract parenthetical expressions with 94.70% precision and 98.84% recall.

288

Papers

ProteinNames

Protein
Name
Extractor

ParentheticalParaphrases
Extractor
Step (2)

Step (1)

Exciser( Outer-Phrase andInner-Phrase)
Step (3)Outer-Phrase
Inner-Phrase
Step (4)

Step (5)Dictionary
Manager

PNAD

Validation

Figure 1: System Architecture.
Outer-Phrase = “Megestrol acetate”
Inner-Phrase = “megace”

Step(1)

Step(2)
initials and its following ncharacters of each word

Step(3)MaMeacIs the Inner-Phrase
a subsequence ofS1?

Yes

Megestrol acetateNo

Step(4)Hyphenation

A Subsequence (S1)of Outer-Phrase

initials and its following ncharacters of each syllable
Mtae

Meges/trol ac/etate

Step(5)Is the Inner-Phrase
a subsequence ofS1?

Yes

RegisterMetracetNo

Step(6)

Figure 2: A block diagram of the validation method.
2.3

Validation Method

In Fig. 1, the validation block outputs an abbreviation and its original term. Arguments given to thevalidation block are two groups of words which are excised from the Parenthetical-Paraphrase; InnerPhrase and Outer-Phrase. Therefore, it is possible to con rm if the Inner-Phrase is an abbreviationof a candidate of the Original-Term extracted from the Outer-Phrase by checking whether the InnerPhrase is a subsequence of a candidate of the Original-Term or not.
Fig. 2 shows our proposed validation method. The validation process and subsequence extraction
process are done simultaneously. To hyphenate words, we adopted a hyphenation method which had
been used in TEX82 [3].

Acknowledgements
This work was supported in part by a Grant-in-Aid for Scienti c Research on Priority Areas, \GenomeScience", from the Ministry of Education, Science, Sports and Culture in Japan.

References[1] Fukuda, K., Tamura, A., Tsunoda, T. and and Takagi, T., Toward Information Extraction Identifying protein names from biological papers, Proc. of Paci c Symposium on Biocomputing '98,
707{718, 1998.
[2] Ohta, Y., Yamamoto, Y., Okazaki, T., Uchiyama, I. and Takagi, T., Automatic construction ofknowledge base from biological papers, Proc. of ISMB{97, 5:218{225, 1997.
[3] Knuth, D.E., The TEXbook, Addison-Wesley, Massachusetts, 1984.
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