Not the time or the place: the missing spatio-temporal link in publicly available genetic data
Not the time or the place: the missing spatio-temporal link in publicly available genetic data
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DOI：
10.1111/mec.13254
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发表时间：
2015-08-01
影响因子：
4.9
通讯作者：
Riginos, Cynthia
中科院分区：
文献类型：
--
作者：
Pope, Lisa C.;Liggins, Libby;Riginos, Cynthia
基因数据正在以前所未有的速度产生。许多期刊、机构和资助机构的政策旨在确保将这些数据公开存档，以便发表的结果可重现。此外，公开存档的数据可以被重新利用，以解决未来的新问题。2011年，与生态学和进化论领域的其他领先期刊一起，《分子生态学》实施了强制公共数据存档(联合数据存档政策)。为了评估这一政策的效果，我们评估了从2009年到2013年《分子生态学》杂志上289篇文章的419个数据集的遗传、空间和时间数据。然后，我们确定存档的数据是否可以用于复制手稿中的分析。我们发现，该杂志的强制存档政策产生了实质性的积极影响，将基因数据存档从49%(2011年之前)增加到98%(2011年至今)。然而，31%的公开存档的遗传数据集无法根据手稿或公共档案中提供的信息重新创建，主要原因是数据不完整或将遗传数据与元数据联系在一起的代码不一致。虽然大多数文章确实提供了一些地理信息，但40%的文章没有提供这些信息作为地理坐标。此外，很大一部分文章没有任何关于抽样日期的信息(40%)。尽管纳入时空数据确实需要付出更多的努力，但我们认为，如果这些元数据不与遗传数据一起存档，那么公开可访问的遗传数据对分子生态领域的持久价值就会受到极大影响。
Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be repurposed' to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy, we assessed the genetic, spatial and temporal data archived for 419 data sets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre-2011) to 98% (2011-present). However, 31% of publicly archived genetic data sets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of sampling (40%). Although the inclusion of spatio-temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data.