Not the time or the place: the missing spatio-temporal link in publicly available genetic data
Pope, L.C.; Liggins, L.; Keyse, J.; Carvalho, S.B.; Riginos, C. (2015). Not the time or the place: the missing spatio-temporal link in publicly available genetic data. Mol. Ecol. 24(15): 3802-3809. http://dx.doi.org/10.1111/mec.13254
In: Molecular Ecology. Blackwell: Oxford. ISSN 0962-1083; e-ISSN 1365-294X, more
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| Author keywords |
biological ontology;data accessibility;metadata;reproducibility;reuse;standards |
| Authors | | Top |
- Pope, L.C.
- Liggins, L.
- Keyse, J.
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- Carvalho, S.B.
- Riginos, C.
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| Abstract |
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. |
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