request review of 25 records derived from BatLit v0.3

[jhpoelen]

Hi @ajacsherman @myrmoteras ,

Please review the following 25 records from BatLit v0.3 @ hash://md5/350f87ae6b68b96bec135c1d6ebac77d that I've just uploaded to Zenodo's sandbox today.

sandbox record	original zotero metadata
https://sandbox.zenodo.org/records/78986	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b7-2561
https://sandbox.zenodo.org/records/78988	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b10410-12926
https://sandbox.zenodo.org/records/78990	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b16347-18852
https://sandbox.zenodo.org/records/78992	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b22588-25630
https://sandbox.zenodo.org/records/78994	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b36361-38851
https://sandbox.zenodo.org/records/79006	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b52849-55265
https://sandbox.zenodo.org/records/79008	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b57705-60882
https://sandbox.zenodo.org/records/79010	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b67712-70248
https://sandbox.zenodo.org/records/79012	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b74757-77827
https://sandbox.zenodo.org/records/79014	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b86012-88496
https://sandbox.zenodo.org/records/79016	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b91859-94351
https://sandbox.zenodo.org/records/79018	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b104589-107117
https://sandbox.zenodo.org/records/79020	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b107124-109602
https://sandbox.zenodo.org/records/79022	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b114477-117459
https://sandbox.zenodo.org/records/79024	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b122116-124602
https://sandbox.zenodo.org/records/79026	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b136682-139098
https://sandbox.zenodo.org/records/79028	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b144233-146729
https://sandbox.zenodo.org/records/79030	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b146736-149302
https://sandbox.zenodo.org/records/79032	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b167330-170360
https://sandbox.zenodo.org/records/79034	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b174817-177321
https://sandbox.zenodo.org/records/79036	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b177328-179826
https://sandbox.zenodo.org/records/79038	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b189446-191929
https://sandbox.zenodo.org/records/79040	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b191936-194448
https://sandbox.zenodo.org/records/79042	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b198620-201091
https://sandbox.zenodo.org/records/79044	https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b204693-207293

[ajacsherman]

Hi Jorrit, The citations look correct and complete! [...] .

How will we have access to the restricted pdfs? Can we have a practice one? I can't sign in to my Zenodod account through the sandbox. Will that change my access?

Are some records without abstracts because they were not captured in the metadata through Zotero? Will this be an issue down the road? Is there a way to run OCR on the incoming pdfs to extract the ones that are missing? Not a big deal on this end since we can see the abstract in the upload, just curious.

The "Is derived from" link takes me to zotero. Is this what we want? We might get numerous requests for access we will have to field. That is not a platform we can share with the masses. Can we give provenance an alternative way?

What is this link? https://linker.bio/hash://md5/f1c6e7e3c28fc15b6559a44dd4624637 https://linker.bio/hash://md5/f1c6e7e3c28fc15b6559a44dd4624637 Will colleagues have access to the publication on multiple platforms or is this a format for something else?

How were you able to resolve the Rights category? I see some have permission status posted.

Can we include author and date filters here? ->[image: Screenshot (160).png]

On Tue, Jul 2, 2024 at 1:53 PM Jorrit Poelen @.***> wrote:

Hi @ajacsherman https://github.com/ajacsherman @myrmoteras https://github.com/myrmoteras ,

Please review the following 25 records from BatLit v0.3 @ hash://md5/350f87ae6b68b96bec135c1d6ebac77d that I've just uploaded to Zenodo's sandbox today. sandbox record original zotero metadata https://sandbox.zenodo.org/records/78986 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b7-2561 https://sandbox.zenodo.org/records/78988 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b10410-12926 https://sandbox.zenodo.org/records/78990 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b16347-18852 https://sandbox.zenodo.org/records/78992 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b22588-25630 https://sandbox.zenodo.org/records/78994 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b36361-38851 https://sandbox.zenodo.org/records/79006 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b52849-55265 https://sandbox.zenodo.org/records/79008 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b57705-60882 https://sandbox.zenodo.org/records/79010 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b67712-70248 https://sandbox.zenodo.org/records/79012 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b74757-77827 https://sandbox.zenodo.org/records/79014 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b86012-88496 https://sandbox.zenodo.org/records/79016 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b91859-94351 https://sandbox.zenodo.org/records/79018 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b104589-107117 https://sandbox.zenodo.org/records/79020 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b107124-109602 https://sandbox.zenodo.org/records/79022 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b114477-117459 https://sandbox.zenodo.org/records/79024 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b122116-124602 https://sandbox.zenodo.org/records/79026 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b136682-139098 https://sandbox.zenodo.org/records/79028 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b144233-146729 https://sandbox.zenodo.org/records/79030 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b146736-149302 https://sandbox.zenodo.org/records/79032 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b167330-170360 https://sandbox.zenodo.org/records/79034 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b174817-177321 https://sandbox.zenodo.org/records/79036 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b177328-179826 https://sandbox.zenodo.org/records/79038 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b189446-191929 https://sandbox.zenodo.org/records/79040 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b191936-194448 https://sandbox.zenodo.org/records/79042 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b198620-201091 https://sandbox.zenodo.org/records/79044 https://linker.bio/cut:hash://md5/a38fc7cd3f6ee2801909aba9dd8d8cf9!/b204693-207293

— Reply to this email directly, view it on GitHub https://github.com/bat-literature/bat-literature.github.io/issues/14, or unsubscribe https://github.com/notifications/unsubscribe-auth/AXI3CBYRULSZKPMLD4V6WILZKLSIFAVCNFSM6AAAAABKIA45NSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4DMOBTGM4TSMQ . You are receiving this because you were mentioned.Message ID: @.***>

-- Aja Sherman MS Bat Eco-Interactions Database Curator 914-886-8906 @.*** she/her

[jhpoelen]

@ajacsherman thanks for making the time to review the 25 records.

Please see my comments to your questions / suggestions below.

How will we have access to the restricted pdfs? Can we have a practice one? I can't sign in to my Zenodod account through the sandbox. Will that change my access?

Zenodo Sandbox is separate from the "real" or "production" Zenodo. To get access to the restricted pubs, please create a sandbox account and let me know what it is by email. Then, I can add you to the batlit sandbox community. After getting added to the batlit sandbox community, you should be able to see the restricted access pubs.

Are some records without abstracts because they were not captured in the metadata through Zotero? Will this be an issue down the road? Is there a way to run OCR on the incoming pdfs to extract the ones that are missing? Not a big deal on this end since we can see the abstract in the upload, just curious.

If the abstract is provided by Zotero, it should appear in Zenodo also. This can be updated if the abstract is added to the associated Zotero records at some later point in time.

The "Is derived from" link takes me to zotero. Is this what we want? We might get numerous requests for access we will have to field. That is not a platform we can share with the masses. Can we give provenance an alternative way?

I think it is important to keep a link to the origin of the record. There's two such links - one pointing to the Zotero platform. Another points to a versioned snapshot of the Zotero metadata records used to generated the Zenodo record.

The reason for keeping both is that the URLs contain information in themselves - for Zotero URL, the record id is referenced, and for the linker.bio URL, the exact version of the Zotero metadata is present.

Please let me know if you continue to have concerns.

What is this link? https://linker.bio/hash://md5/f1c6e7e3c28fc15b6559a44dd4624637 https://linker.bio/hash://md5/f1c6e7e3c28fc15b6559a44dd4624637 Will colleagues have access to the publication on multiple platforms or is this a format for something else?

Great question! Thanks for asking. This link references the exact versioned copy of the pdf associated with the record. This URL provides access to the pdf if credentials are sufficient to see them, otherwise the server should say something like - "I know of the pdf you are asking for, but cannot show you, please contact xyz ." . This feature is still under development, see https://github.com/bio-guoda/preston/issues/290 .

How were you able to resolve the Rights category? I see some have permission status posted.

There's currently not much magic happening in the Zotero -> Zenodo conversion. If the rights information is provided we may be able to populate it, but this is likely a time consuming task due to variation in rights notations. See https://github.com/bat-literature/bat-literature.github.io/issues/2 .

Can we include author and date filters here? ->[image: Screenshot (160).png]

I believe the author / date fields are supported through "Advanced Search" queries. https://sandbox.zenodo.org/help/search . I do like your suggestion to add author / date to the standard search field bar on the batlit community bar.

I'd suggest you contact @myrmoteras to learn more about Zenodo's ability to add advanced search options to the web UI. Perhaps even open an issue at https://github.com/zenodo/zenodo/issues to let the Zenodo engineering team know about your search ui request.

Please let me know if this answered your questions. If not, please send me an invite to discuss in video call.

Thanks again for your detailed questions!

-jorrit

[myrmoteras]

we should add the Biodiversity Literature Repository as a community. This would allow downstream processing without getting a custom permission to do, and we could also easier provide access to all of the BatLit community if we decide at some point.

should we add (Uploaded by Plazi for the Bat Literature Project) as we do in taxodros, not only when we do not have an absteract?

keywords: should we add bats may be also in some other questions?

I think we should not link to Zotero, because this is not a public site, and second because the link will be broken very soon. We should keep the copy of the database, similar that what we did in Taxodros.

is there a way to remove hypertags https://sandbox.zenodo.org/records/79042 https://sandbox.zenodo.org/records/79034

page number missing: This might be book https://sandbox.zenodo.org/records/79036

could we make all publications that include Virus open access? https://sandbox.zenodo.org/records/79030

[myrmoteras]

Questions:

We need to write down the policy what we upload.

• we should avoid having duplicates in the BLR and coviho community.
• do we have examples of book chapters, books, reports, PhD?

[jhpoelen]

@myrmoteras thanks for sharing your questions.

we should avoid having duplicates in the BLR and coviho community.

There's a deduplication workflow outlined in https://batlit.org/#deduplication-workflow . Please review and suggestion additions as needed.

[jhpoelen]

do we have examples of book chapters, books, reports, PhD?

Good point! I can make an effort to include specific samples from book chapters, books, reports and PhD thesis for the next round.

[jhpoelen]

should we add (Uploaded by Plazi for the Bat Literature Project) as we do in taxodros, not only when we do not have an absteract?

The text " (Uploaded by Plazi for the Bat Literature Project) " is always included. If you have an example that does not have the text included, please do share.

[jhpoelen]

I think we should not link to Zotero, because this is not a public site, and second because the link will be broken very soon. We should keep the copy of the database, similar that what we did in Taxodros.

We already have a copy of the record in our database. The main reason I kept the reference is to facilitate maintenance of the records - as a curator, you can directly access the associated records simply by clicking on the link. But yes, the Zotero group is not accessible publicly - you have to be a member.

[jhpoelen]

keywords: should we add bats may be also in some other questions?

thanks for your suggestion @myrmoteras , I've added "bats" and "bat" as a keywords.

[jhpoelen]

we should add the Biodiversity Literature Repository as a community. This would allow downstream processing without getting a custom permission to do, and we could also easier provide access to all of the BatLit community if we decide at some point.

@myrmoteras yes, the batlit submissions would also be submitted to the biosyslit community, just like we did for TaxoDros.

[jhpoelen]

Closing issue - a new review has been requested for BatLit v0.4 hash://md5/b394bdb081f55916b1226b5bc8ba972a at https://github.com/bat-literature/bat-literature.github.io/issues/22 .