Smooth migration from JabRef to Zotero

I wanted to migrate from JabRef to Zotero but I first encountered the following issues:
1) All my Pdf links were lost in the process.
2) The Bibtex field "review" was not transfered. Unfortunately, this field is where I stored all my reading notes for my bibliographic entry.
3) The French diacritical marks were not imported.

Since I am probably not the only one to have these kinds of problems, I describe the fix that I used.
Note that anyone using some customized Bibtex field can modify my JabRef filter (see below) to import the field info as notes in Zotero (or any field you'd like).

The steps:
1- make sure you are using JabRef 2.4 (or later versions: )
2- Install the Jabref plugin called "RIS export format" (this step seems odd since I'm not using this filter, but the command FormatChars of my export filter was not recognized without it). Installation info here:
3- Make a file called Zotero.layout in a text editor including the content at the end of this post.
4- Add your custom-export filter in Jabref: Options --> Manage Custom export
Export name= zotero ; Main layout file= path/to/your/Zotero.layout ; file extension= .txt
5- restart JabRef
6- Use file --> export in JabRef and select "zotero" as the export format
7- Make sure that the export file is in UTF-8 if you care about diacritical marks (open it with a text editor and save it in UTF-8...)
8- Import the file in Zotero. Be patient if the database was large (break it up in smaller part if you feel the need)...

You get the paths to the Pdfs and notes nicely formatted.

I'll now see if the extra functions in Zotero were worth the trouble!

=========Filter Content============
\begin{author} author = {\author},
\end{author}\begin{editor} editor = {\editor},
\end{editor}\begin{title} title = {\format[RemoveBrackets]{\title}},
\end{title}\begin{booktitle} booktitle = {\format[RemoveBrackets]{\booktitle}},
\end{booktitle}\begin{journal} journal = {\journal},
\end{journal} year = {\year},
\begin{volume} volume = {\volume},
\end{volume}\begin{pages} pages = {\pages},
\end{pages}\begin{number} number = {\number},
\end{number}\begin{chapter} chapter = {\chapter},
\end{chapter} \begin{url} url = {\url},
\end{url}\begin{doi} doi = {\doi},
\end{doi}\begin{file} \format[FormatChars,WrapFileLinks(\x = ]{\file} {\format[FormatChars,WrapFileLinks( \p ]{\file}},
\end{file}\begin{address} address = {\address},
\end{address}\begin{publisher} publisher = {\publisher},
\end{publisher}\begin{institution} institution = {\institution},
\end{institution}\begin{howpublished} howpublished = {\howpublished},
\end{howpublished}\begin{issn} issn = {\issn},
\end{issn}\begin{organization} organization = {\organization},
\end{organization}\begin{keywords} keywords = {\keywords},
\end{keywords}\begin{note} note = {\note},
\end{note}\begin{owner} owner = {\owner},
\end{owner}\begin{abstract} abstract = {\format[FormatChars]{\abstract}},
\end{abstract}\begin{comment} comment = {\format[FormatChars]{\comment}},
\end{comment}\begin{review} comment = {\format[FormatChars]{\review}},\end{review}
  • 2) The Bibtex field "review" was not transfered. Unfortunately, this field is where I stored all my reading notes for my bibliographic entry.
    That's supposed to go in the "annote" field.
  • While annote is a standard BibTeX field, it may or may not be the best fit: some BibTeX styles use this for annotations in citations, which may or may not be desirable for one's personal reading notes. Further, Zotero treats 'note' and 'annote' as equivalents on import. It would get stored in the 'extra' field in zotero (rather than an attached note) & would then be dumped into a 'note' on BibTeX export. Given that more styles actually do use the note 'field', I don't think this is desired behavior.

    FClaveau's filter seems to achieve what he want with the way Zotero is designed right now. I don't really know if Zotero's field mapping should be changed or not.
  • But aren't those styles wrong, then (unless they're for annotated bibliographies)? From reading the spec, it's quite clear that "annote" is for user notes, and "note" is for "stuff that goes in the citation."

    But whatever; I trust your judgment, and I'm not a BibTeX user.
  • Sorry--I wasn't clear. Yes, annote is mostly used for only annotated bibliographies. The default styles don't output it & most "popular" non-default styles probably don't output it either.

    My main point is that an 'annote' imported into zotero becomes a 'note' on export, so one must be careful.

    I don't make automated annotated bibliographies much (I'll make a non-annotated bibliography and drag a subset of notes to it); I don't want all of my notes to be dumped by one. I don't know how annotated bibs are handled by Zotero right now.

    If Zotero dumps all attached notes to an annotated bibliography, I suppose consistent behavior would be to:
    1. Import BibTeX 'note' to Zotero's extra
    2. Import BibTex's 'annote' and 'comment' to Zotero's attached notes
    3. Export Zotero's extra to BibTex note
    4. Export Zotero's attached notes to BibTeX's 'annote'
    If Zotero is somehow selective about annotated bibliographies, I'd say 1-3 would stay the same & 4 should be that Zotero's attached notes are exported to 'comment' or some other non-standard field.

    Either way, I think we should change how 'annote' is imported. We may or may not want to change how attached notes are exported.
  • Thanks a lot FClaveau for your tips, it works perfectly fine.
  • @sebayat: Why was BibTeX inadequate for data exchange for you?
  • @noksagt: BibTeX files are in fact what I use at the end (for scientific publication). My problems was not with BibTeX but with JabRef the software that I used so far to manage my BibTeX file. I find Zotero much more convenient.

    @FClaveau: I just have a little complain. If I export the collection in a bibtex format, the bibtexkey are different from the initial bibtex file...
  • My question was why you chose to import JabRef's RIS export rather than BibTeX into Zotero.

    Re. the key:
  • When I import directly from BibTeX to Zotero, all my Pdf links are lost.

    Thanks for the links.
  • FYI: you could have imported the PDFs if you used the old JabRef 'pdf={...}' syntax & I have submitted a patch that supports the file scheme in the current version of JabRef.
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