[Esip-sample-curation] Sample list tool?

Mon Feb 27 19:13:14 EST 2023

Yes, I am also interested in working through samples use cases for complex
citations.

Joan

On Mon, Feb 27, 2023 at 3:35 PM Lesley Wyborn via Esip-sample-curation <
esip-sample-curation at lists.esipfed.org> wrote:

> Hi Adam
>
>
>
> I see you are already a member of the mailing list for the RDA Complex
> Citation Group. <https://www.rd-alliance.org/node/74222/members>
>
>
>
> If you would like to progress the Physical Samples Use case that would be
> great – is anyone else in the ESIP samples cluster interested in doing
> this.  Is anyone from iSamples on this mailing list?
>
>
>
> At the moment, as you can see in the  Complex Citation WG Case Statement
> <https://aus01.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%7CLesley.Wyborn%40anu.edu.au%7Cb5b839df478b4919521c08db190d1586%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C638131316222225143%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UbJ732tGbfJ8V119799W9%2FRkp7gmOVI91HNjwldxCpE%3D&reserved=0>,
> the physical samples use case is woefully under developed relative to the
> three main ones, so we would need to start to develop something to match
> these.
>
>
>
> As the geochemistry use case is not really a topic for this samples list,
> I will email you separately – is anyone else interested in the geochemistry
> use case we are trying to develop as part of this RDA Complex Citation
> Group?
>
>
>
> Take care
>
>
>
>
>
>
>
> Lesley
>
>
>
>
>
> *From: *Mansur, Adam <MansurA at si.edu>
> *Date: *Tuesday, 28 February 2023 at 8:53 am
> *To: *Lesley Wyborn <Lesley.Wyborn at anu.edu.au>,
> 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?
>
> 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://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rd-alliance.org%2Fgroups%2Fcomplex-citations-working-group&data=05%7C01%7CLesley.Wyborn%40anu.edu.au%7Cb5b839df478b4919521c08db190d1586%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C638131316222068920%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1ks3iJp2wFa%2BWj0UyuBnkTtA5ka5Q0bZrHIpJiO99fU%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://aus01.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%7CLesley.Wyborn%40anu.edu.au%7Cb5b839df478b4919521c08db190d1586%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C638131316222225143%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UbJ732tGbfJ8V119799W9%2FRkp7gmOVI91HNjwldxCpE%3D&reserved=0>
> and will also be discussed in the upcoming RDA P20 Session - Complex
> Citation WG Session
> <https://aus01.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%7CLesley.Wyborn%40anu.edu.au%7Cb5b839df478b4919521c08db190d1586%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C638131316222225143%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=a33%2FalYSGx8t5yPR0YUK7pMAx%2FVe1%2B8E0VwhQyQZOgc%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
>
>
>
> SMITHSONIAN INSTITUTION
>
> NATIONAL MUSEUM OF NATURAL HISTORY
>
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