ChemEx: information extraction system for chemical data curation

BMC Bioinformatics

Proceedings

Supawadee Ingsriswang¹  Duangdao Wichadakul¹  Atima Tharatipyakul¹  Somrak Numnark¹ 

[1] Information Systems Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Klong 1, Pathumthani, Klong Luang, Thailand;

关键词: Information Extraction;    Partial Match;    Machine Readable Format;    Compound Entity;    Information Viewer;   

DOI  :  10.1186/1471-2105-13-S17-S9

来源: Springer

【 摘 要 】

BackgroundManual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure image recognition and text mining together.ResultsWe have developed ChemEx, a chemical information extraction system. ChemEx processes both text and images in publications. Text annotator is able to extract compound, organism, and assay entities from text content while structure image recognition enables translation of chemical raster images to machine readable format. A user can view annotated text along with summarized information of compounds, organism that produces those compounds, and assay tests.ConclusionsChemEx facilitates and speeds up chemical data curation by extracting compounds, organisms, and assays from a large collection of publications. The software and corpus can be downloaded from http://www.biotec.or.th/isl/ChemEx.

【 授权许可】

Unknown   
© Tharatipyakul et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.