An analysis of metadata reporting in freshwater environmental DNA research calls for the development of best practice guidelines

Version 2.1
An analysis of metadata reporting in freshwater environmental DNA research calls for the development of best practice guidelines
Nicholson, Andrew; McIsaac, Daniel; MacDonald, Caitlin; Gec, Peter; Mason, B. Eric; Rein, William; Wrobel, Jordan; de Boer, Mats; Milián-García, Yoamel; Hanner, Robert H., 2020, "An analysis of metadata reporting in freshwater environmental DNA research calls for the development of best practice guidelines", https://doi.org/10.5683/SP2/VAVKGW, Borealis, V2, UNF:6:YrPsbLJnpyRjMyevOekvNQ== [fileUNF]
Learn about Data Citation Standards.
Dataset Metrics
178 Downloads
Description
As environmental DNA (eDNA) becomes more widely used in research, it becomes increasingly important to have a standard set of reporting guidelines for metadata. The unique properties of eDNA combined with the physical characteristics of the surrounding environment produce highly varied sampling conditions which can influence how an organism is detected. There are also various ways of quantifying and identifying species using eDNA, from sampling and filtering methods to extraction and genetic analysis. It is important to report sufficient metadata to account for this variability and allow for replication of the study. We conducted a systematic review of 160 eDNA studies to determine which data are reported and to assess whether these studies can be replicated. Focusing solely on freshwater studies, we developed a rubric to evaluate each study on 53 criteria based on previous analyses of eDNA research. We found a trend in the data suggesting better reporting at a broad scale, and decreased reporting as categories become more specific. Many of the metrics found to be insufficiently reported are essential to replicability. Our goal is to identify gaps in metadata reporting and develop a framework for developing standard reporting guidelines for eDNA studies.
Subject Medicine, Health and Life Sciences
Keyword environmental DNA, freshwater, metadata, replicability, standardization
Related Publication Nicholson, A, McIsaac, D, MacDonald, C, et al. An analysis of metadata reporting in freshwater environmental DNA research calls for the development of best practice guidelines. Environmental DNA. 2020; 00: 1– 7. doi: 10.1002/edn3.81
Notes

NOTES ON BROWSING:

Click on the "Tree" view to identify folder structure and related files.

NOTES ON PRESERVATION:

The original data files were multi-spreadsheet Excel workbooks. They are presented here as individual spreadsheets. In addition, the content of the workbooks have been exported into preservation-friendly formats and stored in the Preservation Files zip archive.

License/Data Use Agreement

CC BY-NC 4.0

Table
Tree
Filter by
1 to 8 of 8 Files
eDNAArticleList_AddYourFinalData.xlsx
eDNAArticleList/MS Excel Spreadsheet - 48.8 KB
Published Mar 13, 2020
16 Downloads
MD5: e5909d2574919bf0da0e8c7f06accceb
Data
eDNAArticleList_DiscardPapers.xlsx
eDNAArticleList/MS Excel Spreadsheet - 24.2 KB
Published Mar 13, 2020
4 Downloads
MD5: f8b11b6923381a0765124304adc6085b
Data
eDNAArticleList_Explanation.tab
eDNAArticleList/Tabular Data - 742 B
Published Mar 13, 2020
29 Downloads
10 Variables, 15 Observations UNF:6:dKXnJS7ZVV2kKyZizAu+Sg==
Data
eDNAArticleList_FinalArticleList.tab
eDNAArticleList/Tabular Data - 47.4 KB
Published Mar 13, 2020
36 Downloads
27 Variables, 250 Observations UNF:6:/1Nv4QpMgCQpIuhyPq3i2A==
Data
eDNAArticleList_InaccessablePapers.tab
eDNAArticleList/Tabular Data - 1.8 KB
Published Mar 13, 2020
25 Downloads
27 Variables, 22 Observations UNF:6:D1dDcVly71ObU09KbesVEw==
Data
eDNAArticleList_PaperEvaluation.tab
eDNAArticleList/Tabular Data - 6.1 KB
Published Mar 13, 2020
36 Downloads
16 Variables, 84 Observations UNF:6:Z9Y20/14/4Zn0MNdWUhtMA==
Data
NicholsonA_etal_2020_edn381.pdf
NicholsonA_etal_2020_edn381.pdf
Adobe PDF - 751.5 KB
Published Mar 19, 2020
8 Downloads
MD5: 7d5d063ac870e7a2dc9255b0f59f14af
Article
Preview "NicholsonA_etal_2020_edn381.pdf"
PreservationFiles.zip
ZIP Archive - 1.1 MB
Published Mar 13, 2020
24 Downloads
MD5: 852e06e150148279967f44d6aab11175
For preservation purposes, 'flat file' versions of the original data files have been created. Note that for each Excel spreadsheet, a single flat file in comma separated values (*.CSV) format has been created. In addition, if a spreadsheet included formulas, the formulas have been exported into a text (*.TXT) file. If a spreadsheet included charts and figures, this information has been exported into text (*.TXT) and image (*.PNG), files. Finally, there is a visual representation (HTML Snapshot) of each spreadsheet to show the original format including colour coding, graphs, charts and figures.
Data
Preview "PreservationFiles.zip"
Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Enable access request
You must enable request access or add terms of access to restrict file access.
Save Changes
Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.
Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.
Restricted Files Selected

The selected file(s) may not be downloaded because you have not been granted access.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 4.7 GB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Restricted Files Selected

The restricted file(s) selected may not be downloaded because you have not been granted access.

Click Continue to download the files you have access to download.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Private URL

Private URL can only be used with unpublished versions of datasets.

Unpublished Dataset Private URL

Are you sure you want to disable the Private URL? If you have shared the Private URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? The selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? It will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details
 
Version:
Last Updated:
Version:
Last Updated:
Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

  You need to Sign Up or Log In to request access.

Dataset Terms

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

CC BY-NC 4.0

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

https://borealisdata.ca/api/access/datafile/

Request Access

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

Creative Commons Licence
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Compute Batch
Clear Batch
Dataset Persistent Identifier Change Compute Batch
Compute Batch
Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Publish Dataset

This dataset cannot be published until Department of Integrative Biology is published by its administrator.

Publish Dataset

This dataset cannot be published until Department of Integrative Biology and College of Biological Science are published.

Return to Author

Return this dataset to contributor for modification.