AnnotCompute: Annotation-based exploration and meta-analysis of genomics experiments

Jie Zheng, Julia Stoyanovich, Elisabetta Manduchi, Junmin Liu, Christian J. Stoeckert

    Research output: Contribution to journalArticle

    Abstract

    The ever-increasing scale of biological data sets, particularly those arising in the context of high-throughput technologies, requires the development of rich data exploration tools. In this article, we present AnnotCompute, an information discovery platform for repositories of functional genomics experiments such as ArrayExpress. Our system leverages semantic annotations of functional genomics experiments with controlled vocabulary and ontology terms, such as those from the MGED Ontology, to compute conceptual dissimilarities between pairs of experiments. These dissimilarities are then used to support two types of exploratory analysis-clustering and query-by-example. We show that our proposed dissimilarity measures correspond to a user's intuition about conceptual dissimilarity, and can be used to support effective query-by-example. We also evaluate the quality of clustering based on these measures. While AnnotCompute can support a richer data exploration experience, its effectiveness is limited in some cases, due to the quality of available annotations. Nonetheless, tools such as AnnotCompute may provide an incentive for richer annotations of experiments. Code is available for download at http://www.cbil.upenn.edu/downloads/AnnotCompute.

    Original languageEnglish (US)
    Article numberbar045
    JournalDatabase
    Volume2011
    DOIs
    StatePublished - 2011

    ASJC Scopus subject areas

    • Information Systems
    • Biochemistry, Genetics and Molecular Biology(all)
    • Agricultural and Biological Sciences(all)

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