bat-literature / bat-literature.github.io

The Bat Literature Project aims to facilitate discovery of scientific literature on bats (Chiroptera)
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suggest to annotate open-access literature references for reference published on or after 2000 #2

Open jhpoelen opened 1 month ago

jhpoelen commented 1 month ago

Currently, some open access publication references in Bat Lit v0.1 published on/after 2000 are do not include the "rights" field.

This means that work is needed to mark related Zenodo records related as "open access" so that folks can access the pdf without restrictions.

For instance, sandbox pub https://sandbox.zenodo.org/records/53942 is an open access publication, but was marked as "restricted" because the associated Zotero record https://zotero.org/groups/5435545/items/DP629R8S does not include the "rights" field (see attached screenshot).

@ajacsherman @myrmoteras curious to hear your thoughts on how to annotate access rights for pubs published on/after 2000. . .

image

ajacsherman commented 1 month ago

Let's discuss this more. Currently, I am following a protocol that reduces the amount of manual metadata input. If I need to monitor/edit one or more fields for all of our citations, we will not meet our goal of 20,000 publications anytime in the near future. Most of the pdfs I drop into zotero have metadata automatically indexed.

jhpoelen commented 1 month ago

OpenAlex (see https://openalex.org) keeps records of scientific publications. These records include information about their DOI as well as whether they are open access (according to Open Alex).

Suggest generate a list of all DOIs associated to works published on or after 2000 that OpenAlex knows about, and include their open access status.

jhpoelen commented 1 month ago

See associated gist - https://gist.github.com/jhpoelen/8b263027ff13c7b788fa24866ce73bfb .

jhpoelen commented 1 month ago

unfortunately, it appears that the OpenAlex claims about open access may not be as accurate as hoped -

For instance, here's a list of open access claims related to the journal "Mammalia" states that https://doi.org/10.1515/mamm.1991.55.3.397 is an open access publication. However, the html landing page for the publication mentioned "Requires Authentication." See screenshot below.

is open access pub date doi url
false 2021-11-19 https://doi.org/10.1515/mammalia-2021-0025
false 2022-01-31 https://doi.org/10.1515/mammalia-2021-0121
true 1991-01-01 https://doi.org/10.1515/mamm.1991.55.3.397
false 1952-01-01 https://doi.org/10.1515/mamm.1952.16.1.37
false 1971-01-01 https://doi.org/10.1515/mamm.1971.35.4.648
false 1942-01-01 https://doi.org/10.1515/mamm.1942.6.2.74
false 1947-01-01 https://doi.org/10.1515/mamm.1947.11.3.160
true 2014-01-05 https://doi.org/10.1515/mammalia-2013-0113
false 1946-01-01 https://doi.org/10.1515/mamm.1946.10.2.92
false 1968-01-01 https://doi.org/10.1515/mamm.1968.32.2.204
false 1952-01-01 https://doi.org/10.1515/mamm.1952.16.1.24
false 1950-01-01 https://doi.org/10.1515/mamm.1950.14.1.29
true 1955-01-01 https://doi.org/10.1515/mamm.1955.19.2.302
false 1962-01-01 https://doi.org/10.1515/mamm-1962-0414
false 2014-01-07 https://doi.org/10.1515/mammalia-2013-0102
false 1983-01-01 https://doi.org/10.1515/mamm-1983-0314

image

jhpoelen commented 1 month ago

Let's discuss this more. Currently, I am following a protocol that reduces the amount of manual metadata input. If I need to monitor/edit one or more fields for all of our citations, we will not meet our goal of 20,000 publications anytime in the near future. Most of the pdfs I drop into zotero have metadata automatically indexed.

I'd be up for meeting in person, or discussion in this thread. I was hoping to document your protocol and include it in https://bat-literature.github.io , so that we can define roles (e.g., Aja is the curator, Jorrit helps to translate the Bat Lit corpus to Zenodo and GitHub).

ajacsherman commented 1 month ago

Can you elaborate on the purpose of role definitions? Or point me to an example (taxadros?)? We agreed to not list contributors for each pub since there is a lot of overlap. Is that what you mean?

jhpoelen commented 1 month ago

@ajacsherman thanks for your prompt reply!

I was thinking that the purpose of the role definition is that folks (including ourselves) understand who does what in context of the Bat Lit project.

I've added a proposal to our google docs bat lit note document for your review at https://docs.google.com/document/d/1IiQt0Xg92HdFB4Snu3e4M5K1sUPi29OgT7jn_PK0Q8c/edit#heading=h.3f2nztoq6qyg

Curious to hear your thoughts.

ajacsherman commented 1 month ago

Currently, I am not curating the "rights" field while adding literature. I will defer to Donat for how to proceed since he is more familiar with the Zenodo access requirements. My understanding is that the pdfs that we share will be available to our community regardless of the access level.

ajacsherman commented 1 month ago

I would like to add that for each field I curate, my process will take longer. If we as a group decide to curate more fields, I suggest moving our 20,000 paper deadline.

jhpoelen commented 1 month ago

My understanding is that the pdfs that we share will be available to our community regardless of the access level.

If you are an admin / member of the Bat Literature Repository community on Zenodo or on Zotero, you have access to copies of publications dated before 2000 and on/after 2000.

However, for the general public, only publications dated before 2000 will be available. This means that, with currently metadata provided, open access publications dated on/after 2000 will be restricted to the general public and only available to a select few.

I leave it up to Cullen and Donat @myrmoteras to figure out quality/ quantity priorities.

Thanks again for sharing your notes.

ajacsherman commented 1 month ago

So then won't the publication year demark which are open access? Let's ask the group if they know a tool we can use to idetify open access status from a citations list of those publications occuring in/after 2000. This could streamline our processing and get you that datapoint.

jhpoelen commented 1 month ago

So then won't the publication year demark which are open access?

The <2000 >=2000 rule was provided by Plazi. This rule does not determine the license of the publication: there are closed access publication published prior to 2000, and there are open access publications published after 2000.

jhpoelen commented 1 month ago

For context, the v0.2 of batlit corpus contains the following distinct license values for related publications items. Note that the majority of items have no rights information (2775), followed by 165 entries with a cc-by 3.0 url.

So, in order to make decisions based on the rights text of Zotero entries, we'd need to align the available right fields, in addition to populating those without any information.

   2775 
    165 http://creativecommons.org/licenses/by/3.0/
     27 http://www.springer.com/tdm
     24 http://onlinelibrary.wiley.com/termsAndConditions#vor
     14 https://www.cambridge.org/core/terms
     14 2021 The Author(s)
     12 https://www.elsevier.com/tdm/userlicense/1.0/
     11 https://creativecommons.org/licenses/by/4.0/
      9 http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining
      8 2020 The Author(s)
      7 2019 The Author(s)
      6 http://creativecommons.org/licenses/by/4.0/
      6 2022 The Author(s)
      6 2021 Springer Nature Limited
      5 http://doi.wiley.com/10.1002/tdm_license_1.1
      5 http://doi.wiley.com/10.1002/tdm_license_1
      5 2018 The Author(s)
      4 https://www.liebertpub.com/nv/resources-tools/text-and-data-mining-policy/121/
      4 2020 The Author(s), under exclusive licence to Springer Nature Limited
      3 Copyright © 2020, American Association for the Advancement of Science. http://www.sciencemag.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.
      3 American Association for the Advancement of Science
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jhpoelen commented 1 month ago

Note that OpenAlex marked a publication as open access, even thought the publisher DOI requires access.

https://doi.org/10.1515/mammalia-2013-0113

vs.

https://openalex.org/works/w2052756318

vs.

https://hal.science/hal-01114386/document

image

image

image

jhpoelen commented 1 month ago

as shared by @myrmoteras

From: Ross Mounce [...] Sent: Thursday, June 6, 2024 10:54:51 PM To: Donat Agosti[ <[...]) Subject: RE: list of open access journals / articles

EXTERNAL SENDER

Hi Donat,

[...] I’d recommend https://github.com/ropensci/roadoi or the Unpaywall Simple Query Tool which can check upto 1000 articles at a time: https://unpaywall.org/products/simple-query-tool

Ultimately, Unpaywall/OpenAlex are always going to have false positives and false negatives because the publishers do like to change the status of their articles – they turn the paywall OFF & ON at whim sometimes 🤷‍♀️ Unpaywall/OpenAlex do the best they can and are considered the gold standard at doing this.

Kind regards,

Ross

Dr Ross Mounce Director of Open Access Programmes

ARCADIA

Fifth Floor | 40 Villiers Street | London WC2N 6NJ

[...]

www.arcadiafund.org.uk

Arcadia is a charitable foundation that works to protect nature, preserve cultural heritage and promote open access to knowledge. Since 2002 Arcadia has awarded more than $1.2 billion to organizations around the world.

jhpoelen commented 1 week ago

See also OpenAlex R package: https://docs.ropensci.org/openalexR/ as shared by @n8upham

jhpoelen commented 1 week ago

@arw36 noted that

Fleming_etal_1998 https://academic.oup.com/jmammal/article/79/1/147/841906

was marked as open, but somehow that annotation did not get marked in BatLit .

jhpoelen commented 1 week ago

Here's the record -

cat refs.csv\
 | grep Fleming\
 | grep 1998
"https://www.zotero.org/groups/bat_literature_project/items/P3XN369Z","Fleming | Nelson | Dalton","1998","Roosting Behavior of the Lesser Long-Nosed Bat, Leptonycteris curasoae","Journal of Mammalogy","10.2307/1382849"

image

arw36 commented 1 week ago

would/could it be under notes or tag if not a set field in Zotero?

jhpoelen commented 1 week ago

@arw36 which column in the bat co-roosting database are you referring to?

arw36 commented 1 week ago

access_right. There are others that are standardly used in Plazi, but have not been completed (e.g., "license")

jhpoelen commented 1 week ago

@arw36 got it . . . thanks!

via https://docs.google.com/spreadsheets/d/1y5uBKvyzDQgQUtyRHvn5f20IOA7LoMho/edit?gid=307351258#gid=307351258

I noticed

image

jhpoelen commented 1 week ago

@arw36 as far as I know, @ajacsherman is not using the sheet to populate the metadata . The associated pdfs are dropped into Zotero, and Zotero takes care of the metadata extraction. @ajacsherman can you confirm?