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 - Dec 1 2011

    Fingerprint

    Genomics
    meta-analysis
    Cluster Analysis
    Meta-Analysis
    Controlled Vocabulary
    genomics
    Intuition
    Semantics
    Ontology
    Motivation
    Experiments
    Technology
    Thesauri
    Throughput
    Datasets

    ASJC Scopus subject areas

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

    Cite this

    Zheng, J., Stoyanovich, J., Manduchi, E., Liu, J., & Stoeckert, C. J. (2011). AnnotCompute: Annotation-based exploration and meta-analysis of genomics experiments. Database, 2011, [bar045]. https://doi.org/10.1093/database/bar045

    AnnotCompute : Annotation-based exploration and meta-analysis of genomics experiments. / Zheng, Jie; Stoyanovich, Julia; Manduchi, Elisabetta; Liu, Junmin; Stoeckert, Christian J.

    In: Database, Vol. 2011, bar045, 01.12.2011.

    Research output: Contribution to journalArticle

    Zheng, J, Stoyanovich, J, Manduchi, E, Liu, J & Stoeckert, CJ 2011, 'AnnotCompute: Annotation-based exploration and meta-analysis of genomics experiments', Database, vol. 2011, bar045. https://doi.org/10.1093/database/bar045
    Zheng, Jie ; Stoyanovich, Julia ; Manduchi, Elisabetta ; Liu, Junmin ; Stoeckert, Christian J. / AnnotCompute : Annotation-based exploration and meta-analysis of genomics experiments. In: Database. 2011 ; Vol. 2011.
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