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ChemEx: information extraction system for chemical data curation
Tharatipyakul, A.; Numnark, S.; Wichadakul, D.; Ingsriswang, S. (2012). ChemEx: information extraction system for chemical data curation. BMC Bioinformatics 13(Suppl 17): S9.
In: BMC Bioinformatics. BioMed Central: London. ISSN 1471-2105, more
Peer reviewed article  

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  • Tharatipyakul, A.
  • Numnark, S.
  • Wichadakul, D.
  • Ingsriswang, S.

    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

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