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Sunday, December 28, 2008

Call for OA to raw microarray datasets

Maxine Clarke, Call for authors to deposit microarrays in public databases, Nautilus, December 8, 2008.  Excerpt:

In a Correspondence to Nature Methods (5, 991; December 2008) responding to an Editorial in the March 2008 issue of the journal (Nat. Meth. 5, 209; 2008), Scott A Ochsner, David L Steffen, Christian J Stoeckert, Jr and Neil J McKenna report a study showing that researchers are not routinely depositing supporting raw microarray datasets into a public database.

The Correspondence authors surveyed papers from the 2007 issues of 20 journals, searching the text for reference to deposition of a microarray dataset. They find that the rate of deposition of datasets was less than 50 per cent. The authors note the effort required by authors to deposit these complex data in public microarray repositories, even though repositories are simplifying submissions while encouraging compliance with MIAME (minimum information about a microarray experiment) standards. They write: "Although microarray datasets are most useful to bioinformaticians in their raw, unnormalized forms, which facilitate cross-comparison with other datasets, processed datasets are more useful to the bench scientist. Moreover, unless a description of the experimental details is available, neither form of the data are biologically interpretable." They urge repositories to require deposition by authors and propose journals require a statement in the manuscript identifying a repository and accession number at the time of submission, with the record embargoed until acceptance of the paper. (Of the 16 Nature journal papers that were part of the survey, such accession numbers were provided in 15 cases.) They conclude: "Seven years after the elaboration of the MIAME principles, the emerging discipline of microarray meta-analysis, exemplified by the cancer gene expression resource Oncomine, continues to be hobbled by the mundane, time-consuming and often fruitless exercise of tracking down annotated full datasets. We call for a renewed collective effort from researchers, publishers and funding organizations to redress this situation and secure these data-rich research resources for posterity."

The full text of the Nature Methods Correspondence, with supporting data, is here.

Policy note: the Nature journals have for some years required authors to submit MIAME-compliant microarray data to the GEO or Arrayexpress public repository. Details of the journals' polices can be found here.

PS:  Thanks to Heather Piwowar for the alert, and thanks to Maxine Clarke, the Publishing Executive Editor of Nature, for excerpting this TA correspondence to Nature's OA blog.