Data queries doi:10.15468/dl.6cxfsw doi:10.15468/dl.b9rfa7 doi:10.15468/dl.w2nndm used in Chesshire et al. 2023 were cited, but remain marked for deletion

[jhpoelen]

Hi!

First, thanks again for opening up this forum to publicly discuss use of biodiversity data.

Second, I was hoping someone could help me understand my observations below:

During the 2023-03-28/30 Native Bee Monitoring RCN [1] Workshop 8 about Data Management, I attended the presentation by Paige Chesshire R scripts for nomenclature cleaning: Paige Chesshire - YouTube . In this presentation, Paige referenced recent work [2] . In this work, they used GBIF mediated data as referenced by [3], [4], and [5].

In reviewing the associated data query DOIs, I noticed that no citation was annotated, and the related data were marked for deletion. So, for some reason the cited DOIs were not picked up.

To help preserve the data associated with the data downloads, I created a data publication [6] on 2023-04-03 and cited the data download DOIs ([3],[4],[5]). And, two weeks later, on 2023-04-17, I tracked the same data download and recorded their associated GBIF metadata.

I found that, despite citing the data download DOIs, no citation had shown up yet. See screenshot below.

What is the procedure to add a citation to GBIF download DOIs and help preserve the data in the GBIF ecosystem ?

Thank you for your hard work in keeping the GBIF community active and their infrastructure up and running.

-jorrit

Jorrit H. Poelen

[1] The National Native Bee Monitoring RCN is funded by the United States Department of Agriculture (USDA NIFA 2020-67014-31865 to S.H.W.)

[2] Chesshire, P.R., Fischer, E.E., Dowdy, N.J., Griswold, T.L., Hughes, A.C., Orr, M.C., Ascher, J.S., Guzman, L.M., Hung, K.-L.J., Cobb, N.S. and McCabe, L.M. (2023), Completeness analysis for over 3000 United States bee species identifies persistent data gap. Ecography e06584. https://doi.org/10.1111/ecog.06584

[3] GBIF.org (3 February 2021) GBIF Occurrence Download Download

[4] GBIF.org (3 February 2021) GBIF Occurrence Download Download

[5] GBIF.org (3 February 2021) GBIF Occurrence Download Download

[6] Poelen, Jorrit H. (2023). Signed Citation of Provenance of GBIF Occurrence Downloads referenced in Chesshire et al. 2023 doi:10.1111/ecog.06584 hash://sha256/f2d8bdaec7a416a0039e9398cf07c6fa69083f64a6f22de3f252ebb5dd4fd412 hash://md5/458490528f55250ef381ba4bb6f81162 (0.2) [Data set]. Zenodo. Signed Citation of Provenance of GBIF Occurrence Downloads referenced in Chesshire et al. 2023 doi:10.1111/ecog.06584 hash://sha256/f2d8bdaec7a416a0039e9398cf07c6fa69083f64a6f22de3f252ebb5dd4fd412 hash://md5/458490528f55250ef381ba4bb6f81162 | Zenodo

[dnoesgaard]

Hi jorrit,

thanks for flagging this. It seems these downlods hadn’t been tagged properly due to a bug that has since been fixed. I’ve retagged the downloads now and they should show up correctly once the index has refreshed.

/Daniel

[jhpoelen]

@dnoesgaard Thanks for your prompt reply and applying a manual fix to add the Chesshire et. al 2023 citation to the respective data download request DOIs.

I was able to independently verify [1] that the associated download requests are no longer marked for deletion.

I have some remaining thoughts on the topic:

1. Wider Impact of Citation Bug
   You said -

It seems these downlods hadn’t been tagged properly due to a bug that has since been fixed.

I was wondering when this bug was introduced / fixed and how it may have affected other (cited) data download requests from being deleted.

2. Do Zenodo Data Publications count as citations for GBIF download records?

I noticed that the Chesshire et al. 2023 is now appearing as a citation in data download request records [2,3,4] . See attached screenshot example of [2] below. Thank you for making this happen!

However, my Zenodo data publication [1] is not listed even though the DOIs are cited in Zenodo description and associated identifier metadata. Can you help me understand how I can make the data publication show up in citations tab?

3. Order of Authors
   For some reason, the GBIF rendered citation for Chesshire et al. 2023 lists Ascher as the first author, even though the publication lists Chesshire as the first (see screenshot below). Given the significance of the author order, I wanted to pass this observation on.
   
   

Thanks again for taking the time to respond to my queries.

-jorrit

Jorrit H. Poelen

References

[1] Poelen, Jorrit H. (2023). Signed Citation of Provenance of GBIF Occurrence Downloads referenced in Chesshire et al. 2023 doi:10.1111/ecog.06584 hash://sha256/9e3ca96d94229e20f47c14efaa59f793845aa37d9f6c698d2dd35876705e9feb hash://md5/43652e3d26989008026e092e3f04b04d (0.3) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7849559

[2] GBIF.org (3 February 2021) GBIF Occurrence Download Download

[3] GBIF.org (3 February 2021) GBIF Occurrence Download Download

[4] GBIF.org (3 February 2021) GBIF Occurrence Download Download

[dnoesgaard]

Hi jorit,

…how it may have affected other (cited) data download requests from being deleted.

After my last reply, I ran a check to see if other entries would have been affected and found a handful. They were also fixed.

Do Zenodo Data Publications count as citations for GBIF download records?

In general, we include all citations of GBIF data, and while a citation graph framework does exist to make this process more or less automatic, some manual curation is still involved. Every citation is added manually, resulting in a lag (days, sometimes weeks even) from when the work is published to when we log the citation.

re. Order of Authors

Thanks for flagging this. We usually rely on metadata from either Crossref or the publisher themselves. Our database doesn’t rank authors, so they just appear in the order in which we get them. I don’t know exactly why this order was used, but upon resynchronizing the metadata from Wiley, the order seems better now. It might take a little while before you’ll be able to see this.

Best,
Daniel

[jhpoelen]

@dnoesgaard thanks again for your prompt reply, and for responding to my queries!