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Gene name errors: Lessons not learned

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journal contribution
posted on 2024-06-19, 04:39 authored by M Abeysooriya, M Soria, MS Kasu, Mark ZiemannMark Ziemann
Erroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. To assess this, we performed a scan of supplementary files published in PubMed Central from 2014 to 2020. Overall, gene name errors continued to accumulate unabated in the period after 2016. An improved scanning software we developed identified gene name errors in 30.9% (3,436/11,117) of articles with supplementary Excel gene lists; a figure significantly higher than previously estimated. This is due to gene names being converted not just to dates and floating-point numbers, but also to internal date format (five-digit numbers). These findings further reinforce that spreadsheets are ill-suited to use with large genomic data.

History

Journal

PLoS Computational Biology

Volume

17

Article number

ARTN e1008984

Pagination

1 - 13

Location

United States

Open access

  • Yes

ISSN

1553-734X

eISSN

1553-7358

Language

English

Publication classification

C1 Refereed article in a scholarly journal

Issue

7

Publisher

PUBLIC LIBRARY SCIENCE