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Open Access Highly Accessed Research article

The BioLexicon: a large-scale terminological resource for biomedical text mining

Paul Thompson123*, John McNaught123, Simonetta Montemagni4, Nicoletta Calzolari4, Riccardo del Gratta4, Vivian Lee5, Simone Marchi4, Monica Monachini4, Piotr Pezik5, Valeria Quochi4, CJ Rupp123, Yutaka Sasaki126, Giulia Venturi4, Dietrich Rebholz-Schuhmann5 and Sophia Ananiadou123

Author Affiliations

1 School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK

2 National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK

3 Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK

4 Istituto di Linguistica Computazionale del CNR, Via Moruzzi 1, 56124 Pisa, Italy

5 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

6 Toyota Technological Institute, Nagoya, Japan

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BMC Bioinformatics 2011, 12:397  doi:10.1186/1471-2105-12-397

Published: 12 October 2011

Abstract

Background

Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events) involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events.

Results

This article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized) together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is modelled using the Lexical Markup Framework, an ISO standard.

Conclusions

The BioLexicon contains over 2.2 M lexical entries and over 1.8 M terminological variants, as well as over 3.3 M semantic relations, including over 2 M synonymy relations. Its exploitation can benefit both application developers and users. We demonstrate some such benefits by describing integration of the resource into a number of different tools, and evaluating improvements in performance that this can bring.