[Esip-sample-curation] Sample list tool?

Mon Feb 27 16:53:32 EST 2023

Hi Lesley,

Thanks for the info! Yes, we're talking about the same thing, except your version seems to be much better developed. I would be interested in working on the sample and geochemistry use cases in whatever capacity would be useful.

Adam
________________________________
From: Lesley Wyborn <Lesley.Wyborn at anu.edu.au>
Sent: Monday, February 27, 2023 1:21 PM
To: Mansur, Adam <MansurA at si.edu>; esip-sample-curation at lists.esipfed.org <esip-sample-curation at lists.esipfed.org>; Shelley Stall <SStall at agu.org>; Martina Stockhause <stockhause at dkrz.de>; Deborah Agarwal <daagarwal at lbl.gov>; Kristina Vrouwenvelder <kvrouwenvelder at agu.org>
Subject: Re: Sample list tool?

External Email - Exercise Caution

HI Adam

Thanks for this suggestion.

I would draw your attention to the newly formed Research Data Alliance Complex Citation Working Group<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rd-alliance.org%2Fgroups%2Fcomplex-citations-working-group&data=05%7C01%7CMansurA%40si.edu%7Cc1b06bf3a3a54556165608db1908a916%7C989b5e2a14e44efe93b78cdd5fc5d11c%7C0%7C0%7C638131297226170614%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wSbJMlFemGQjyUTMv9OCsIxcGv8x%2F96t%2BHod19yWnWg%3D&reserved=0>. I have cc’ed on my email my group co- chairs (Shelley, Martina, Deb)

The physical samples use case is listed in the  Complex Citation WG Case Statement<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rd-alliance.org%2Fgroup%2Fearth-space-and-environmental-science-complex-citations-working-group%2Fcase-statement%2Fearth&data=05%7C01%7CMansurA%40si.edu%7Cc1b06bf3a3a54556165608db1908a916%7C989b5e2a14e44efe93b78cdd5fc5d11c%7C0%7C0%7C638131297226170614%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9M3q1pZUv1U4EmwrkWrTZb%2BEd7aZdNWf0BQLVg9audM%3D&reserved=0> and will also be discussed in the upcoming RDA P20 Session - Complex Citation WG Session<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rd-alliance.org%2Fplenaries%2Frda-20th-plenary-meeting-gothenburg-hybrid%2Fcomplex-citations-earth-and-space-sciences&data=05%7C01%7CMansurA%40si.edu%7Cc1b06bf3a3a54556165608db1908a916%7C989b5e2a14e44efe93b78cdd5fc5d11c%7C0%7C0%7C638131297226170614%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SBjowXNx5rm6fN1gRjxj%2BHv%2FoLjbBIRfXS6iKdmJA48%3D&reserved=0>.

I have been the one that put forward a use case for physical samples –  that is, we need to create a ‘reliquary’ that references say hundreds of samples each with their own DOI/PID.  A reliquary itself has a DOI/PID, but all samples within the reliquary can be found, referenced and cited so that the collector of the sample, the curator of the sample and the funder of any part of the samples life cycle (including from the field to the museum/sample repository) can be credited and both funders and researchers can measure the use and impact of their research

I think we are talking about the same thing.

We have quite a community behind this Complex Citation WG (see list at end of case statement) and it would be great if someone would be prepared to drive this use case for physical samples who is actively working on sample collection and/or preservation.

Please let me know if you or anyone else would like to work on this samples use case with this newly formed RDA group for Complex Citation. Currently I am listed against the Geophysics, Geochemistry and Samples use cases and I don’t have the bandwidth to do all three!!!

Take care

Lesley

From: Esip-sample-curation <esip-sample-curation-bounces at lists.esipfed.org> on behalf of Mansur, Adam via Esip-sample-curation <esip-sample-curation at lists.esipfed.org>
Date: Tuesday, 28 February 2023 at 5:02 am
To: esip-sample-curation at lists.esipfed.org <esip-sample-curation at lists.esipfed.org>
Subject: [Esip-sample-curation] Sample list tool?

Hi all,

I was reading over the sample citation guidance and had a comment that was way too long for the Google Doc. The current draft gives the following guidance for documenting long lists of samples:

If your study uses many samples and would result in a prohibitively long list: create this table as a separate file, archive the table in an appropriate repository (such as Figshare, Zenodo, Dryad; or through institution- or domain-specific repositories), and link to the table.

These lists would ideally be machine-readable so that interested parties could easily find a sample or track sample usage, but it's not clear to me that the current guidance will allow this. The main drawbacks that I see are:

  *   Lists will use different formats and will not be validated, making it annoying to extract information from them
  *   List citations will use different formats and DOIs, potentially making them difficult to pick out of a paper
  *   Lists will be static and will not reflect changes in ownership or availability over time
  *   Lists will not be used consistently across papers

I'd like to think about building a tool to generate, store, and create DOIs for specimen lists instead. Lists would consist of only the most basic sample and ownership information (something like the DOI of the related publication plus the original sample identifiers, sample GUIDs, and owner information.) Where GUIDs with appropriate metadata are available (like at least some implementation of IGSNs), ownership information could be pulled in and updated. Since the data would all be in one place and linked to but not formally associated with a publication, it would also be possible to create and search sample lists for already published papers (for example, if an institution that has absorbed a collection would like to tag previously published papers that include those samples.) As with the current guidance, lists could be linked as references in new papers and the tool could supply a preferred citation to make them easier to find.

I know this would be one more thing to build and maintain in perpetuity, and I'm sure I'm underestimating the difficulty of implementing it, but I do think this kind of tool could be helpful for research collections especially.

Best,

Adam

Adam Mansur (he/him)

IT Specialist

Department of Mineral Sciences

w 202.633.1828  mansura at si.edu<mailto:mansura at si.edu>

SMITHSONIAN INSTITUTION

NATIONAL MUSEUM OF NATURAL HISTORY

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