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

BMC Bioinformatics

Research Article

Piotr Pezik¹  Vivian Lee¹  Dietrich Rebholz-Schuhmann¹  Giulia Venturi²  Monica Monachini²  Riccardo del Gratta²  Simone Marchi²  Valeria Quochi²  Simonetta Montemagni²  Nicoletta Calzolari²  John McNaught³  Paul Thompson³  Sophia Ananiadou³  CJ Rupp³  Yutaka Sasaki⁴ 

[1] European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK;Istituto di Linguistica Computazionale del CNR, Via Moruzzi 1, 56124, Pisa, Italy;School of Computer Science, University of Manchester, Oxford Road, M13 9PL, Manchester, UK;National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK;Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK;School of Computer Science, University of Manchester, Oxford Road, M13 9PL, Manchester, UK;National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK;Toyota Technological Institute, Nagoya, Japan;

关键词: Text Mining;    Semantic Role;    Name Entity Recognition;    Biomedical Domain;    Biomedical Text;   

DOI  :  10.1186/1471-2105-12-397

 received in 2011-02-18, accepted in 2011-10-12,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundDue 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.ResultsThis 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Thompson et al; licensee BioMed Central Ltd. 2011