Troubleshooting Public Data Archiving: Suggestions to Increase Participation

Roche, Dominique G.; Lanfear, Robert; Binning, Sandra A.; Haff, Tonya M.; Schwanz, Lisa E.; Cain, Kristal E.; Kokko, Hanna; Jennions, Michael D.; Kruuk, Loeske E. B.

doi:10.1371/journal.pbio.1001779

Cited by 114 publications

(119 citation statements)

References 38 publications

(78 reference statements)

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“…[35,38] Requesting phylogenetic tree files directly from corresponding authors is successful only about 16% of the time. [35] However, since the above publications, there has been an increased push in the scientific community to make published data more available via publicly available archives.…”

Section: Existing Phylogenetic Data Is Not Availablementioning

confidence: 99%

“…[35] However, since the above publications, there has been an increased push in the scientific community to make published data more available via publicly available archives. [34,[38][39][40][41][42] Nonetheless, deposition rates have not improved (see Box 2). The result of evolutionary estimates not being readily available is that taxonomy is often used as a proxy for evolutionary relatedness (e.g., Tree of Sex Consortium [43] ).…”

Section: Existing Phylogenetic Data Is Not Availablementioning

confidence: 99%

“…[36] Even more concerning, Google Scholar search results are based on citations, so the 100 publications we surveyed were relatively well cited and typically from high impact factor journals, which have a higher tendency to require the deposition of data into a public repository. [38] It is worth considering potential reasons why researchers do not archive their phylogenetic data in an accessible way.…”

Section: Can We Combine Different Phylogenetic Estimates Across the Tmentioning

confidence: 99%

“…One approach to improving data deposition would be for all phylogenetic journals to implement strict data archiving policies and for reviewers and editors to ensure data publication as part of the review process. [39,38] These phylogenetic inferences are not only a result, but also an essential input in future analysis. Mandates by journals and/or funding organizations is one approach that has worked in past to improve data sharing and data deposition.…”

Section: Community Engagement Is Essentialmentioning

confidence: 99%

See 3 more Smart Citations

How and Why to Build a Unified Tree of Life

et al. 2017

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Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow‐up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

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Section: Existing Phylogenetic Data Is Not Availablementioning

confidence: 99%

Section: Existing Phylogenetic Data Is Not Availablementioning

confidence: 99%

Section: Can We Combine Different Phylogenetic Estimates Across the Tmentioning

confidence: 99%

Section: Community Engagement Is Essentialmentioning

confidence: 99%

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How and Why to Build a Unified Tree of Life

et al. 2017

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“…The archival of data in digital repositories and metadata management is the responsibility of the authors (see discussion in Roche et al, 2014). At first inspection, this practice seems to be an altruistic behavior, beneficial to the community with no individual return.…”

Section: Altruistic or Selfish Behavior? Neither One Nor The Othermentioning

confidence: 99%

Forgotten treasures: the fate of data in animal behavior studies

Caetano

Aisenberg

2014

Preprint

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PrePrints AbstractPublished discussions on data stewardship often focus on standardized datasets whose reuse patterns are known. Improvements in stewardship of animal behavior data are virtually absent and lag behind other disciplines such as molecular biology and systematics. In this essay, we discuss best practices of three key aspects related to the collection and archival of behavioral data: data supporting published results; data collected from field observations; and the potential of museum specimens as source of data to animal behavior and ecology. To quantify how much data is shared in publications we reviewed selected journals in animal behavior and behavioral ecology. We found that only an extremely small proportion of the articles published in 2013 made even part of their data available. We discuss about the benefits of making data available, review resources available for data archiving and provide practical guidance for ethologists. We discuss and provide examples of the amount of ethological and ecological data that can be recorded during field observations. To investigate the potential of museum specimens as source of data, we surveyed researchers working in areas related to ecology, animal behavior, and systematics. Both ethologists and systematists agreed that natural history information stored in collections would be a valuable source of data. We make recommendations to enhance data collection and stewardship from the point of view of researchers in animal behavior sciences, considering the special characteristics of the discipline and the type of data that is often produced. We suggest that there is a large amount of crucial data about natural history, ecology and behavior that investigators could glean from collections. Although it is difficult to appreciate the relevance of data for future studies at the time of publication, such data may inspire fruitful opportunities that we cannot afford to lose. PrePrintsData collection is a fundamental step of research and often the most expensive with respect to both time and money, yet the fate of data after publication is often neglected (Heidorn, 2008).Despite willingness to populate digital repositories with data, the fact that many researchers have reservations about doing so (Tenopir et al., 2011;Wolkovich et al., 2012) seems to explain the general lack of data available for publications in the biological sciences (Hartter et al. 2013;Zamir, 2013 -but see Wallis et al., 2013. There are a few exceptions, such as molecular journals that require sequence data archival in publicly accessible repositories among other examples such as the journals Evolution and the Public Library of Science (PLoS). The main reasons why authors opt to avoid storing data in digital repositories are related to concerns about lack of time and appropriate tools to prepare and upload datasets, the potential for data misuse (Whitlock, 2011), and lack of personal benefits (Arzberger et al., 2004). In this essay, we surveyed and evaluated how much data from animal behavior is ...

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Open research data repositories: Practices, norms, and metadata for sharing images

Hansson

Dahlgren

2021

Asso for Info Science & Tech

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Open research data repositories are promoted as one of the cornerstones in the open research paradigm, promoting collaboration, interoperability, and largescale sharing and reuse. There is, however, a lack of research investigating what these sharing platforms actually share and a more critical interface analysis of the norms and practices embedded in this datafication of academic practice is needed. This article takes image data sharing in the humanities as a case study for investigating the possibilities and constraints in 5 open research data repositories. By analyzing the visual and textual content of the interface along with the technical means for metadata, the study shows how the platforms are differentiated in terms of signifiers of research paradigms, but that beneath the rhetoric of the interface, they are designed in a similar way, which does not correspond well with the image researchers' need for detailed metadata. Combined with the problem of copyright limitations, these data-sharing tools are simply not sophisticated enough when it comes to sharing and reusing images. The result also corresponds with previous research showing that these tools are used not so much for sharing research data, but more for promoting researcher personas.

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Troubleshooting Public Data Archiving: Suggestions to Increase Participation

Abstract: Public data archiving has many benefits for society, but some scientists are reluctant to share their data. This Perspective offers some practical solutions to reduce costs and increase benefits for individual researchers.

Cited by 114 publications

References 38 publications

How and Why to Build a Unified Tree of Life

How and Why to Build a Unified Tree of Life

Forgotten treasures: the fate of data in animal behavior studies

Open research data repositories: Practices, norms, and metadata for sharing images

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