The Image Data Resource: a bioimage data integration and publication platform

Eleanor Williams, Josh Moore, Simon W. Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Balint Antal, Richard K. Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E. Carzo Salas, Jason R. Swedlow (Lead / Corresponding author)

    Research output: Contribution to journalArticlepeer-review

    165 Citations (Scopus)
    643 Downloads (Pure)

    Abstract

    Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links high-content screening, super-resolution microscopy, time-lapse and digital pathology imaging experiments to public genetic or chemical databases, and to cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable re-analysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open source platform that others can use to publish their own image data. Thus IDR provides both a novel on-line resource and a software infrastructure that promotes and extends publication and re-analysis of scientific image data.
    Original languageEnglish
    Pages (from-to)775-781
    Number of pages7
    JournalNature Methods
    Volume14
    Issue number8
    Early online date19 Jun 2017
    DOIs
    Publication statusPublished - Aug 2017

    Keywords

    • Data integration
    • Protein databases

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