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

.
.

And their tracked content include, as obtained via 

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

Tracked content associated with hash://sha256/9e3ca96d94229e20f47c14efaa59f793845aa37d9f6c698d2dd35876705e9feb

content location
content relation
content id

https://doi.org/10.15468/dl.6cxfsw
http://purl.org/pav/hasVersion
hash://sha256/6b8b5f79af53dee98c3654b945389628194c9e9f0ad610852327574b3f99ff7a

https://doi.org/10.15468/dl.b9rfa7
http://purl.org/pav/hasVersion
hash://sha256/a74cfe8a6c6b7d2361f41cc04979c262b5fbba60c0992253ae78fe6d31f414bb

https://doi.org/10.15468/dl.w2nndm
http://purl.org/pav/hasVersion
hash://sha256/6a587a219e78ff2674fbb54d99fed48c21b77bc46608d8f991e79ee06a547fac

https://api.gbif.org/v1/occurrence/download/0182006-200613084148143
http://purl.org/pav/hasVersion
hash://sha256/1c5d8a7399793a634a0dde32f3a94ccf64199f010d7f93baa422c2e1dbb98b2f

https://api.gbif.org/v1/occurrence/download/0182032-200613084148143
http://purl.org/pav/hasVersion
hash://sha256/23d7c875420bea71d24c1ec3ba127f91eff5b368744de14824de0fc4fc090bb2

https://api.gbif.org/v1/occurrence/download/0182076-200613084148143
http://purl.org/pav/hasVersion
hash://sha256/6555d581e0ce75c77740811e547da726297d02369b149893faf531f132a2aff0

https://api.gbif.org/v1/occurrence/download/0182006-200613084148143
http://purl.org/pav/hasVersion
hash://sha256/2c4c4f4cd1151bc65394466416b066c19422fe22b8eb64c5c144fb7889ea2f16

https://api.gbif.org/v1/occurrence/download/0182032-200613084148143
http://purl.org/pav/hasVersion
hash://sha256/e4e9742259e9232c773ab157e34af1cfebfd09050effb49c15db032057fc5750

https://api.gbif.org/v1/occurrence/download/0182076-200613084148143
http://purl.org/pav/hasVersion
hash://sha256/20915d475c63fa6f96ab127ff5efb5554df40208596244349d110432b478168b

https://api.gbif.org/v1/occurrence/download/request/0182006-200613084148143.zip
http://purl.org/pav/hasVersion
hash://sha256/d14a14e549e3caa8965daecad6fcb0cfddd4be12fb78a495b248c380df41db9b

https://api.gbif.org/v1/occurrence/download/request/0182032-200613084148143.zip
http://purl.org/pav/hasVersion
hash://sha256/3fc1b6491813f5d7e2d32b7c6cadb1ae60558f31a4489e23735c43bd74ed4db6

https://api.gbif.org/v1/occurrence/download/request/0182076-200613084148143.zip
http://purl.org/pav/hasVersion
hash://sha256/7ddea84a67329ec8eea389d09798e5b6d60d86c39b975590f117679cdbbe8e20

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 .