The DIEGO Lab graph based gene normalization system

Ryan Sullivan, Robert Leaman, Graciela Gonzalez

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

    Abstract

    Gene entity normalization, the mapping of a gene mention in free text to a unique identifier, is one of the primary subtasks in the biomedical information extraction pipeline. Gene entity normalization provides many challenges, specifically with the high ambiguity of gene names and the many-to-many relationship between gene names and identifiers. Drawing inspiration from recent work in word sense disambiguation, this paper presents a gene entity normalization system based on entity relationship graphs. This system creates a concept graph from the possible entities and their relationships within a full-text document, and takes advantage of a node ranking algorithm to rank and score each potential candidate entity. This system is a prototype to represent a specific approach to gene normalization, and the results reflect this. However, this system demonstrates that the relationship graph-based approach, an approach grounded in a theoretical basis, can potentially be useful for gene normalization and possibly for the normalization of various biomedical entities.

    Original languageEnglish (US)
    Title of host publicationProceedings - 10th International Conference on Machine Learning and Applications, ICMLA 2011
    Pages78-83
    Number of pages6
    DOIs
    StatePublished - Dec 1 2011
    Event10th International Conference on Machine Learning and Applications, ICMLA 2011 - Honolulu, HI, United States
    Duration: Dec 18 2011Dec 21 2011

    Publication series

    NameProceedings - 10th International Conference on Machine Learning and Applications, ICMLA 2011
    Volume2

    Other

    Other10th International Conference on Machine Learning and Applications, ICMLA 2011
    CountryUnited States
    CityHonolulu, HI
    Period12/18/1112/21/11

    ASJC Scopus subject areas

    • Computer Science Applications
    • Human-Computer Interaction

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  • Cite this

    Sullivan, R., Leaman, R., & Gonzalez, G. (2011). The DIEGO Lab graph based gene normalization system. In Proceedings - 10th International Conference on Machine Learning and Applications, ICMLA 2011 (pp. 78-83). [6147052] (Proceedings - 10th International Conference on Machine Learning and Applications, ICMLA 2011; Vol. 2). https://doi.org/10.1109/ICMLA.2011.140