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This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Bioinformatics

Open Access Proceedings

ChemEx: information extraction system for chemical data curation

Atima Tharatipyakul, Somrak Numnark, Duangdao Wichadakul and Supawadee Ingsriswang*

Author Affiliations

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

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BMC Bioinformatics 2012, 13(Suppl 17):S9  doi:10.1186/1471-2105-13-S17-S9

Published: 13 December 2012

Abstract

Background

Manual 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.

Results

We 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.

Conclusions

ChemEx 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 webcite.