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

Chesshire et al. 2023. scientific publication [1] used and referenced  three GBIF mediated occurrence download queries [2,3,4] and associated data. However, in their GBIF records indicate that the data associated with the three download queries are slated for removal at any point after 2021-08-03 . This publication explicitly references the DOIs associated with [2,3,4] and documents the provenance of their associated meta-data records. The provenance was captured using Preston [5,6], a biodiversity dataset tracker. 

The signed citation of this provenance publication can be derived from:

preston history\
 --anchor hash://sha256/9e3ca96d94229e20f47c14efaa59f793845aa37d9f6c698d2dd35876705e9feb\
 --remote https://zenodo.org/record/7849559/files

<hash://sha256/f2d8bdaec7a416a0039e9398cf07c6fa69083f64a6f22de3f252ebb5dd4fd412> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/c457565ea0cec7b0392f1271fcda08440919f03bbf29bb8df1eb926c78a972cc> .
<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/c457565ea0cec7b0392f1271fcda08440919f03bbf29bb8df1eb926c78a972cc> .

And their tracked content include, as obtained via 

preston alias\
 --anchor hash://sha256/9e3ca96d94229e20f47c14efaa59f793845aa37d9f6c698d2dd35876705e9feb\
 --remote https://zenodo.org/record/7849559/files

This data publication, and associated tracked content, can be cloned using:

preston clone https://zenodo.org/record/7849559/files

Note that the original publication dated 2023-04-03 did *not* include the associated tracked data retrieved from https://api.gbif.org/v1/occurrence/download/request/0182006-200613084148143.zip, https://api.gbif.org/v1/occurrence/download/request/0182032-200613084148143.zip, https://api.gbif.org/v1/occurrence/download/request/0182076-200613084148143.zip. However, on 2023-03-17, the data associated with [2], [3], [4] were still marked for deletion in the GBIF ecosystem, two weeks after the respective DOIs were first cited in the v0.1 of this data publication. This 2023-03-17 publication includes tracked content that shows the associated data is marked for deletion, and contains the associated data archives.  

The example below shows a tracked versions of the metadata associated with the download request/query doi:10.15468/dl.w2nndm  [4] indicates that the associated data is scheduled to be "eraseAfter"  "2021-08-03T19:18:46.611+00:00". 

preston cat\
 --remote https://zenodo.org/record/7837572/files\ 
 hash://sha256/6555d581e0ce75c77740811e547da726297d02369b149893faf531f132a2aff0\
 | jq .

{
  "key": "0182076-200613084148143",
  "doi": "10.15468/dl.w2nndm",
  "license": "http://creativecommons.org/licenses/by-nc/4.0/legalcode",
  "request": {
    "predicate": {
      "type": "and",
      "predicates": [
        {
          "type": "equals",
          "key": "DATASET_KEY",
          "value": "e05f6e7d-418e-4407-8e0f-7b8ccf21109e",
          "matchCase": false
        },
        {
          "type": "or",
          "predicates": [
            {
              "type": "equals",
              "key": "TAXON_KEY",
              "value": "4334",
              "matchCase": false
            },
            {
              "type": "equals",
              "key": "TAXON_KEY",
              "value": "4345",
              "matchCase": false
            },
            {
              "type": "equals",
              "key": "TAXON_KEY",
              "value": "7911",
              "matchCase": false
            },
            {
              "type": "equals",
              "key": "TAXON_KEY",
              "value": "7908",
              "matchCase": false
            },
            {
              "type": "equals",
              "key": "TAXON_KEY",
              "value": "7901",
              "matchCase": false
            },
            {
              "type": "equals",
              "key": "TAXON_KEY",
              "value": "7905",
              "matchCase": false
            }
          ]
        }
      ]
    },
    "sendNotification": true,
    "format": "DWCA",
    "type": "OCCURRENCE",
    "verbatimExtensions": []
  },
  "created": "2021-02-03T19:18:46.687+00:00",
  "modified": "2021-02-03T19:20:03.899+00:00",
  "eraseAfter": "2021-08-03T19:18:46.611+00:00",
  "status": "SUCCEEDED",
  "downloadLink": "https://api.gbif.org/v1/occurrence/download/request/0182076-200613084148143.zip",
  "size": 2624689,
  "totalRecords": 11654,
  "numberDatasets": 1
}

Also, on after (re-)running

preston track\
 https://doi.org/10.15468/dl.6cxfsw\
 https://doi.org/10.15468/dl.b9rfa7\
 https://doi.org/10.15468/dl.w2nndm

on 2023-04-20, the download record metadata retrieved from  https://api.gbif.org/v1/occurrence/download/0182006-200613084148143 and associated with https://doi.org/10.15468/dl.6cxfsw appeared to no longer be marked for deletion, as shown by the difference between a pre-2023-04-20 version (i.e. hash://sha256/1c5d8a7399793a634a0dde32f3a94ccf64199f010d7f93baa422c2e1dbb98b2f) with the newly retrieved response on 2023-04-20 (i.e., hash://sha256/2c4c4f4cd1151bc65394466416b066c19422fe22b8eb64c5c144fb7889ea2f16).

The difference is highlighted below using the diff and preston tools via

diff\
 <(preston cat hash://sha256/2c4c4f4cd1151bc65394466416b066c19422fe22b8eb64c5c144fb7889ea2f16 | jq .)\ 
 <(preston cat hash://sha256/1c5d8a7399793a634a0dde32f3a94ccf64199f010d7f93baa422c2e1dbb98b2f | jq .)

yielding:

116c116,117
<   "modified": "2023-04-18T08:09:09.757+00:00",
---
>   "modified": "2021-02-03T18:00:50.416+00:00",
>   "eraseAfter": "2021-08-03T17:50:18.453+00:00",

 This observation is consistent with the 2023-04-18 claim by Daniel Noesgaard [7] that associated download records are no longer marked for deletion.

References 

[1] 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

[2] GBIF.org (3 February 2021) GBIF Occurrence Download https://doi.org/10.15468/dl.6cxfsw

[3] GBIF.org (3 February 2021) GBIF Occurrence Download https://doi.org/10.15468/dl.b9rfa7

[4] GBIF.org (3 February 2021) GBIF Occurrence Download https://doi.org/10.15468/dl.w2nndm

[5] MJ Elliott, JH Poelen, JAB Fortes (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132

[6] Elliott, M. J., Poelen, J. H., & Fortes, J. (2022, August 29, accepted with minor revisions). Signed Citations: Making Persistent and Verifiable Citations of Digital Scientific Content. https://doi.org/10.31222/osf.io/wycjn

[7] Noesgaard, D. 2023. https://discourse.gbif.org/t/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/3915/2 accessed at 2023-04-20 .