BANNER: An executable survey of advances in biomedical named entity recognition

Robert Leaman, Graciela Gonzalez

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    287 Scopus citations

    Abstract

    There has been an increasing amount of research on biomedical named entity recognition, the most basic text extraction problem, resulting in significant progress by different research teams around the world. This has created a need for a freely-available, open source system implementing the advances described in the literature. In this paper we present BANNER, an open-source, executable survey of advances in biomedical named entity recognition, intended to serve as a benchmark for the field. BANNER is implemented in Java as a machine-learning system based on conditional random fields and includes a wide survey of the best techniques recently described in the literature. It is designed to maximize domain independence by not employing brittle semantic features or rule-based processing steps, and achieves significantly better performance than existing baseline systems. It is therefore useful to developers as an extensible NER implementation, to researchers as a standard for comparing innovative techniques, and to biologists requiring the ability to find novel entities in large amounts of text. BANNER is available for download at .

    Original languageEnglish (US)
    Title of host publicationPacific Symposium on Biocomputing 2008, PSB 2008
    Pages652-663
    Number of pages12
    StatePublished - Dec 1 2008
    Event13th Pacific Symposium on Biocomputing, PSB 2008 - Kohala Coast, HI, United States
    Duration: Jan 4 2008Jan 8 2008

    Publication series

    NamePacific Symposium on Biocomputing 2008, PSB 2008

    Other

    Other13th Pacific Symposium on Biocomputing, PSB 2008
    CountryUnited States
    CityKohala Coast, HI
    Period1/4/081/8/08

    ASJC Scopus subject areas

    • Computational Theory and Mathematics
    • Biomedical Engineering
    • Medicine(all)

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  • Cite this

    Leaman, R., & Gonzalez, G. (2008). BANNER: An executable survey of advances in biomedical named entity recognition. In Pacific Symposium on Biocomputing 2008, PSB 2008 (pp. 652-663). (Pacific Symposium on Biocomputing 2008, PSB 2008).