BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction

Siddhartha Jonnalagadda, Graciela Gonzalez

    Research output: Contribution to journalArticlepeer-review

    8 Scopus citations

    Abstract

    BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving human readability). The model is based on a "shot-gun" approach that produces many different (simpler) versions of the original sentence by combining variants of its constituent elements. This tool is optimized for processing biomedical scientific literature such as the abstracts indexed in PubMed. We tested our tool on its impact to the task of PPI extraction and it improved the f-score of the PPI tool by around 7%, with an improvement in recall of around 20%. The BioSimplify tool and test corpus can be downloaded from https://biosimplify.sourceforge.net.

    Original languageEnglish (US)
    Pages (from-to)351-355
    Number of pages5
    JournalAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium
    Volume2010
    StatePublished - Jan 1 2010

    ASJC Scopus subject areas

    • Medicine(all)

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