Monday, September 19, 2016

20% of Scientific Papers On Genes Contain Conversion Errors Caused By Excel, Says Report

I discovered this in the Sept. 10, 1016 issue of New Scientist.

Aug. 23, 2016

A new report from scientists Mark Ziemann, Yotam Eren, and Assam El-Osta says that 20% of scientific papers on genes contain gene name conversion errors caused by Excel. In the scientific article, titled "Gene name errors are widespread in the scientific literature," article's abstract section, the scientists explain: "The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions."

It's easy to see why Excel might have problems with certain gene names when you see the "gene symbols" that the scientists use as examples: "For example, gene symbols such as SEPT2 (Septin 2) and MARCH1 [Membrane-Associated Ring Finger (C3HC4) 1, E3 Ubiquitin Protein Ligase] are converted by default to '2-Sep' and '1-Mar', respectively. Furthermore, RIKEN identifiers were described to be automatically converted to floating point numbers (i.e. from accession '2310009E13' to '2.31E+13'). Since that report, we have uncovered further instances where gene symbols were converted to dates in supplementary data of recently published papers (e.g. 'SEPT2' converted to '2006/09/02'). This suggests that gene name errors continue to be a problem in supplementary files accompanying articles. Inadvertent gene symbol conversion is problematic because these supplementary files are an important resource in the genomics community that are frequently reused. Our aim here is to raise awareness of the problem."

Autoformatting in Microsoft Excel has caused many a headache—but now, a new study shows that one in five genetics papers in top scientific journals contains errors from the program, The Washington Post reports. The errors often arose when gene names in a spreadsheet were automatically changed to calendar dates or numerical values. For example, one gene called Septin-2 is commonly shortened to SEPT2, but is changed to 2-SEP and stored as the date 2 September 2016 by Excel. The researchers, who published their analysis in Genome Biology, say the issue can be fixed by formatting Excel columns as text and remaining vigilant—or switching to Google Sheets, where gene names are stored exactly as they’re entered.

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