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I'm using the bibliometrix package in R to do some citation analysis (not biblioshiny) and my Web of Science call was incomplete by about thirty entries, so I downloaded the BibTeX, added it to Zotero, merged it with another collection my Zotero, and then merged the resulting duplicates. Bibliometrix was able to process the BibTeX file straight from Web of Science, but after passing it through and adding the entries I already had in Zotero I now get the following message:

Warning:
In your file, some mandatory metadata are missing. Bibliometrix functions may not work properly!


Missing fields:  AU DE ID C1 CRError in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 0, 131

Does Zotero butcher the BibTeX files? Am I not exporting them from Zotero properly? Thanks.

Phil
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Ben
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1 Answers1

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You can fix this by

  • installing the popular "Better BibTeX" extension for Zotero,
  • restarting Zotero,
  • deleting those bibliography entries that you imported into Zotero where these fields are missing,
  • and then importing them again, now with the extension helping behind the scenes. (I had the same issue with the "collaboration" field provided in bibtex snippets from InspireHEP.)

By default, Zotero does butcher BibTeX files during the import as it discards any fields that don't fit into its own data structure. (It also butchers them in the export, to some degee.) The afforementioned extension uses a line in the "Extra" field of Zotero to store each field that can't be imported into the Zotero structure. It also provides export formats called "Better Bibtex" or "Better Biblatex"; these will then extract those fields from the "Extra" and write them back like they were in the original .bib file or snippet.

It also adds features for handling the citation keys; it'll store the imported ones, let you edit them, show them in a column for sorting, exports them back out to .bib, and provides a configurable format for when you want to generate a key.

user207046
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  • Will it be possible to replicate how Web of Science exports bibtex? Because bibliometrix can process that no problem. – Ben Jul 15 '20 at 09:26
  • I don't know what choices Web of Science makes for export, or what bibliometrix can handle. But BetterBibTex provides many configuration options. There's both the "Export" tab in its settings, and another one beneath "Advanced". You can see for yourself if you can replicate the behaviour you're looking for, or a compatible one. (And if its something simple like writing `Author={Bla}` instead of `author={Bla}`, you can of course use some scripted text processing on the whole exported file.) – user207046 Aug 17 '20 at 07:14