Run bibliography through zotero #160

BeastyBlacksmith · 2023-10-27T13:38:36Z

I imported and then exported our bibliography into zotero + better bibtex.

This way its sorted by citation key and fields are standardised, I don't know whether that is breaking anyones workflow though, so I'll open this for discussion.

CaptainSifff · 2023-10-27T13:58:07Z

You should talk to @jngrad since he introduced a lot of them.

jngrad · 2023-10-27T14:12:28Z

bibliography.bib

-@TechReport{Alibay2022,
-  author      = {Alibay, Irfan and Barnoud, Jonathan and Beckstein, Oliver and Gowers, Richard J. and Naughton, Fiona and Wang, Lily},
-  title       = {{MDAK}its: Supporting and promoting the development of community packages leveraging the {MDA}nalysis library [v0.1.0]},


I have no experience with Zotero, so maybe my questions will sound naive, but:

is changing from @TechReport to @Report safe? I know that some bibtex styles don't implement all resource types, or only implement them partially, in which case the generated reference will be incomplete.

is there a reason for changing Supporting to {{Supporting}}? If I'm not mistaken, some BibTeX styles enforce their own capitalization rules (e.g. title case, or all lowercase except after a period).

The reason I'm asking is that we will publish in different outlets, which will likely use different BibTeX styles. I used resource types like @TechReport which are supported on modern BibLaTeX processors as well as on the deprecated BibTeX processor (which is still used by some scientific publishers).

jngrad · 2023-10-27T14:15:42Z

bibliography.bib

-  author    = {Astigarraga, Julen and Cruz-Alonso, Ver{\'{o}}nica},
-  title     = {{\textexclamdown}Se puede entender c{\'{o}}mo funcionan {G}it y {G}it{H}ub!},
-  journal   = {Ecosistemas},
-  year      = {2022},
-  volume    = {31},
-  number    = {1},
-  pages     = {2332},
-  month     = apr,
-  issn      = {1697-2473},
-  doi       = {10.7818/ecos.2332},
-  publisher = {Asociacion Espanola de Ecologia Terrestre ({AEET})},
+@online{AcademicProgrammesHPC,
+  title = {Academic Programmes},
+  author = {{High-Performance Computing in Europe}},
+  url = {https://hpc-portal.eu/academic-programmes},
+  urldate = {2023-08-25}
+}
+
+@article{Ahn2014,
+  title = {Open Badges for Education: What Are the Implications at the Intersection of Open Systems and Badging?},
+  author = {Ahn, June and Pellicone, Anthony and Butler, Brian S.},
+  date = {2014-08},
+  journaltitle = {Research in Learning Technology},
+  volume = {22},
+  publisher = {{Association for Learning Technology}},
+  issn = {2156-7077},
+  doi = {10.3402/rlt.v22.23563}
+}
+
+@article{Ahsan2023,
+  title = {Implementation of Micro-Credentials in Higher Education: {{A}} Systematic Literature Review},
+  author = {Ahsan, Kamrul and Akbar, Suraiyah and Kam, Booi and Abdulrahman, Muhammad Dan-Asabe},
+  date = {2023-03},
+  journaltitle = {Education and Information Technologies},
+  publisher = {{Springer Science and Business Media LLC}},
+  doi = {10.1007/s10639-023-11739-z}
+}
+
+@inproceedings{Akoh2017,
+  title = {Determinants of Mobile Learning in {{Indigenous}}/{{Cultural}} Contexts: {{The}} Phenomenon in {{Canadian First Nations}}},
+  booktitle = {Tomorrow's Learning: {{Involving}} Everyone},
+  author = {Akoh, Ben},
+  editor = {Tatnall, Arthur and Webb, Mary},
+  date = {2017},
+  series = {{{IFIP}} Advances in Information and Communication Technology},
+  volume = {515},
+  pages = {24--34},
+  publisher = {{Springer International Publishing}},
+  location = {{Cham, Switzerland}},
+  issn = {1868-422X},
+  doi = {10.1007/978-3-319-74310-3_4},
+  booksubtitle = {Learning with and about {{Technologies}} and {{Computing}}},
+  eventdate = {2017-07-03/2017-07-06},
+  isbn = {978-3-319-74310-3},
+  lccn = {2018930742},
+  venue = {Dublin, Ireland}
+}
+
+@inproceedings{Alghamdi2017,
+  title = {Game-Play: {{Effects}} of Online Gamified and Game-Based Learning on Dispositions, Abilities and Behaviours of Primary Learners},
+  booktitle = {Tomorrow's Learning: {{Involving}} Everyone},
+  author = {Alghamdi, Jawaher and Holland, Charlotte},
+  editor = {Tatnall, Arthur and Webb, Mary},
+  date = {2017},
+  series = {{{IFIP}} Advances in Information and Communication Technology},
+  volume = {515},
+  pages = {55--63},
+  publisher = {{Springer International Publishing}},
+  location = {{Cham, Switzerland}},
+  issn = {1868-422X},
+  doi = {10.1007/978-3-319-74310-3_7},
+  booksubtitle = {Learning with and about {{Technologies}} and {{Computing}}},
+  eventdate = {2017-07-03/2017-07-06},
+  isbn = {978-3-319-74310-3},
+  lccn = {2018930742},
+  venue = {Dublin, Ireland}
+}
+
+@online{AlgorithmicBattle,
+  title = {Algorithmic Battle},
+  author = {{RWTH Aachen University}},
+  url = {https://tcs.rwth-aachen.de/lehre/algobattle/WS2023/},
+  urldate = {2023-07-03}
+}
+
+@report{Alibay2022,
+  type = {White paper},
+  title = {{{MDAKits}}: {{Supporting}} and Promoting the Development of Community Packages Leveraging the {{MDAnalysis}} Library [v0.1.0]},
+  author = {Alibay, Irfan and Barnoud, Jonathan and Beckstein, Oliver and Gowers, Richard J. and Naughton, Fiona and Wang, Lily},
+  date = {2022-08},
+  institution = {{MDAnalysis}},
+  doi = {10.6084/m9.figshare.20520726.v1}
+}
+
+@report{AllDigital2022,
+  type = {White paper},
+  title = {Strategies to Address the Digital Skills Gap in the {{EU}}},
+  author = {{ALL DIGITAL} and {HUAWEI} and {EY}},
+  date = {2022-04},
+  institution = {{Huawei Technologies Co., Ltd / Europeandigitalskills.eu}},


Should the institution and publisher fields be merged together? Publishers cannot be held responsible for the views expressed by institutions. For publishers like Zenodo or ArXiv, this might look very odd.

It's not visible in this diff (I used "hide whitespace" mode), so here is the original content:

institution = {Europeandigitalskills.eu}, publisher = {Huawei Technologies Co., Ltd},

here is the new content:

institution = {{Huawei Technologies Co., Ltd / Europeandigitalskills.eu}},

Seems publisher fields are missing altogether : / zotero/zotero-bits#16

jngrad · 2023-10-27T14:18:31Z

bibliography.bib

-
-@Misc{Alves2021,
-  author       = {Alves, Daniel and Isasi, Jennifer},
-  title        = {Publica{\c{c}}{\~a}o do {P}rogramming {H}istorian em portugu{\^e}s},


Same point as earlier: this file now contains UTF-8 characters, making it impossible to submit the manuscript to a journal that still uses e.g. natbib.

bibliography.bib

jngrad · 2023-10-27T16:38:08Z

@BeastyBlacksmith After rebasing your work on top of a resorted bibliography to make the diff more readable (jngrad/zotero), I noticed that Zotero changed the titlecase without taking into account that non-English text needs to follow different capitalization rules. For example:

old: Software-Engineering-Empfehlungen des DLR
new: Software-Engineering-Empfehlungen Des DLR
errors:                                ^

old: Note d'opportunité sur la valorisation des logiciels issus de la recherche
new: Note d'opportunité Sur La Valorisation Des Logiciels Issus de La Recherche
errors:     ^               ^               ^                      ^

I have the impression that Zotero assumed all title fields were given as lowercase, and that all words starting with an uppercase were proper nouns. This would explain why there are so many words inside double curly braces, and why all titles were reprocessed into Harvard-style title case.

If we want to proceed with this PR, I would suggest we go through all non-English titles to manually correct capitalization with curly braces, and retouch all tech report institution fields which have been merged with the publisher field. The easiest way would probably be to start from the original BibTeX, remove all publisher fields from @TechReport records (since it doesn't exist in Zotero), manually protect the ~15 non-English records, and then pass it through Zotero.

BeastyBlacksmith · 2023-10-30T12:57:59Z

@BeastyBlacksmith After rebasing your work on top of a resorted bibliography to make the diff more readable (jngrad/zotero), I noticed that Zotero changed the titlecase without taking into account that non-English text needs to follow different capitalization rules. For example:
old: Software-Engineering-Empfehlungen des DLR
new: Software-Engineering-Empfehlungen Des DLR
errors:                                ^

old: Note d'opportunité sur la valorisation des logiciels issus de la recherche
new: Note d'opportunité Sur La Valorisation Des Logiciels Issus de La Recherche
errors:     ^               ^               ^                      ^
I have the impression that Zotero assumed all title fields were given as lowercase, and that all words starting with an uppercase were proper nouns. This would explain why there are so many words inside double curly braces, and why all titles were reprocessed into Harvard-style title case.

If we want to proceed with this PR, I would suggest we go through all non-English titles to manually correct capitalization with curly braces, and retouch all tech report institution fields which have been merged with the publisher field. The easiest way would probably be to start from the original BibTeX, remove all publisher fields from @TechReport records (since it doesn't exist in Zotero), manually protect the ~15 non-English records, and then pass it through Zotero.

Thanks for investigation. I figure that the gains don't outweight the work here and we leave things as is.

jngrad · 2023-11-08T17:25:26Z

bibliography.bib

+@report{Centeno2022,
+  type = {Conference and workshop report},
+  title = {European Digital Skills Certificate Feasibility Study. {{Report}} of the 1ˢᵗ Stakeholders' Consultation (24ᵗʰ {{February}} – 12ᵗʰ {{March}} 2021)},


wow 😮 Zotero replaced text inside \textsuperscript{} by vaguely similar-looking letters from unicode blocks "Phonetic Extensions" and "Spacing Modifier Letters". Took me a while to figure out why LaTeX was complaining about glyphs not existing in most font families, including lmodern. Some of these glyphs are actually replaced by crossed rectangles in generated PDF files.

import/export add pain

c4233c0

jngrad reviewed Oct 27, 2023

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BeastyBlacksmith marked this pull request as draft October 27, 2023 15:16

jngrad reviewed Nov 8, 2023

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Run bibliography through zotero #160

Run bibliography through zotero #160

BeastyBlacksmith commented Oct 27, 2023 •

edited

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Run bibliography through zotero #160

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Run bibliography through zotero #160

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BeastyBlacksmith commented Oct 27, 2023 •

edited