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Parachute approach to evidence based medicine: Arguments are easily refuted

Authors
Publisher
BMJ Publishing Group Ltd.
Publication Date
Source
PMC
Keywords
  • Letters
Disciplines
  • Computer Science
  • Design

Abstract

NCBI GEO standards and services for microarray data Ron Edgar and Tanya Barrett National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 45 Center Drive, Bethesda, MD 20892-6511, Email: [email protected] The Minimum Information About a Microarray Experiment (MIAME) guidelines are a data content document developed by the Microarray Gene Expression Data (MGED) Society that outlines the information that should be provided when describing a microarray experiment1. Many journals and funding agencies have adopted the guidelines, with the aim of facilitating access to the elements of a study that would enable independent evaluation of results. However, the MIAME requirements have been criticized recently2, 3. The criticism stems, in part, from different interpretations of the level of detail required to adequately report a microarray experiment, and debates as to whether there is a genuine benefit to making microarray data public. The Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (NCBI)4 and ArrayExpress at the European Bioinformatics Institute (EBI)5 are the two major public databases of microarray data. Although they have different designs, both databases support capture of all data elements defined by MIAME. Figure 1 presents a timeline of major landmarks in the evolution of the GEO database, together with concomitant growth in submissions. GEO was launched in 2000, more than a year before the MIAME guidelines were proposed. Because there was not yet a consensus on reporting standards for microarray data, or even an obligation to make microarray data public, GEO initially allowed a minimal level of experimental detail to be supplied. Over the ensuing years we continually monitored the needs and requests of end-users, and gauged the level of effort submitters were realistically willing to invest in making their data public. We responded with incremental improvements to databa

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