Gene name errors: Lessons not learned.

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...

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Autores principales:	Mandhri Abeysooriya, Megan Soria, Mary Sravya Kasu, Mark Ziemann
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/8b429b7b5d454a8c9aeef110207e3418
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id	oai:doaj.org-article:8b429b7b5d454a8c9aeef110207e3418
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spelling	oai:doaj.org-article:8b429b7b5d454a8c9aeef110207e34182021-12-02T19:57:30ZGene name errors: Lessons not learned.1553-734X1553-735810.1371/journal.pcbi.1008984https://doaj.org/article/8b429b7b5d454a8c9aeef110207e34182021-07-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1008984https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Erroneous 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.Mandhri AbeysooriyaMegan SoriaMary Sravya KasuMark ZiemannPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 7, p e1008984 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Mandhri Abeysooriya Megan Soria Mary Sravya Kasu Mark Ziemann Gene name errors: Lessons not learned.
description	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.
format	article
author	Mandhri Abeysooriya Megan Soria Mary Sravya Kasu Mark Ziemann
author_facet	Mandhri Abeysooriya Megan Soria Mary Sravya Kasu Mark Ziemann
author_sort	Mandhri Abeysooriya
title	Gene name errors: Lessons not learned.
title_short	Gene name errors: Lessons not learned.
title_full	Gene name errors: Lessons not learned.
title_fullStr	Gene name errors: Lessons not learned.
title_full_unstemmed	Gene name errors: Lessons not learned.
title_sort	gene name errors: lessons not learned.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/8b429b7b5d454a8c9aeef110207e3418
work_keys_str_mv	AT mandhriabeysooriya genenameerrorslessonsnotlearned AT megansoria genenameerrorslessonsnotlearned AT marysravyakasu genenameerrorslessonsnotlearned AT markziemann genenameerrorslessonsnotlearned
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Gene name errors: Lessons not learned.

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