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Overview of how I keep bib records in Zotero and notes in DEVONthink

Mike Hucka edited this page Jan 10, 2022 · 8 revisions

The development of Zowie was motivated by the goal to use Zotero to collect papers and maintain all bibliographic info, and use DEVONthink for everything else: search, PDF annotation, note-taking, and classification. This separation makes it possible to use Zotero for what it does best – acquiring papers and maintaining bibliographic information – and DEVONthink for what it does best, and avoid having to duplicate and synchronize metadata between them. The overall approach involves the following:

  • Use DEVONthink to index the PDFs stored in the Zotero database on my computer;
  • Use Zowie to write Zotero select links into the DEVONthink metadata of the PDF files so that the PDF files themselves contain references to their parent records in Zotero; and
  • Use DEVONthink's "launch url" command (u) to make it easy to jump from DEVONthink to the Zotero entry for any given PDF, by virtue of the fact that the PDF file contains the Zotero select link pointing to the bib record in Zotero.

The Zowie configuration described elsewhere in this wiki makes the URL a PDF in DEVONthink be the entry in my (local) Zotero database, and thus the DEVONthink "launch url" keystroke (^u) immediately switches to Zotero and shows the entry there. This link is called the Zotero select link – it has a form like zotero://select/library/items/XHASHQER.

Using DEVONthink for everything else makes it possible for me to mark up the PDFs using DEVONthink's PDF tools (which I like very much, especially on an iPad). It also makes it possible to keep notes as documents in DEVONthink that reference the PDFs in DEVONthink.

In Zotero, to copy reference information or a citation, I created some keyboard shortcuts for copying citations and references in different formats. The shortcuts are a mix of using Zutilo and Keyboard Maestro.

Disadvantages of the current scheme:

  • This approach only works when using local storage in Zotero, and not when using the Zotero "linked attachments" approach.
  • DEVONthink's "launch url" command doesn't work on iOS, so you can't use this approach to jump from DEVONthink to Zotero entries on an iPad. I don't have a good solution for this at the moment.