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May 28, 2012 research, ubuntu, zotero

How to mindmap your zotero items

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I love zotero as a reference manager. And I love mindmaps. In particular I love docear, which is built on best-of-breed opensource mindmapper called Freeplane. I usually mindmap at the start of the process of developing a project or an article, but sometimes in the later stages too. Now what docear does is it also builds in jabref, which is another great reference manager. This gives me the following cool functionality:

  • Drag a document reference from the jabref window in docear to add the reference to your map
  • If the reference contains a pdf file which you have annotated, you can automatically import all your annotations (and the document’s bookmarks) as child nodes. This is very useful! You can double-click on the parent node and the document opens; in some cases you can click on the child node and go straight to your comment in the pdf.

But it has taken me about a week to work out how to manage this process in detail. My requirements were these:

  • I use both academic references and pdfs but also (often large numbers of) plain unpublished pdfs and other documents related to projects I am working on. I need to be able to reorganise them from time to time into different subfolders and also import any annotations I have made in them.
  • If I reorganise my pdfs in different folders, the links in docear musn’t break.
  • I want to have access to the same bunch of references both from zotero and from docear.
  • I am on ubuntu linux.

How I did it:

  1. Installed Foxit reader under Wine as my pdf reader. This is great for annotating, and also supports opening the pdf at the correct page when you double-click on an imported annotation in docear. Unfortunately, docear can’t import highlightsmade in foxit.
  2. Agreed with myself that my primary way of making notes on a doc is with pdf annotations.
  3. Agreed with myself that in the case of unpublished project pdfs, I won’t keep separate copies in the filesystem at all. I just import them straight into zotero e.g. by dragging and dropping, and delete the originals. I use folders and subfolders in zotero to keep them organised. Zotero doesn’t change the location of the actual file when you do this, so links in docear stay pure.
  4. Installed autozotbibwhich instantly saves an updated bibtext export of the Zotero database as soon as you change it. (This will be slow with a big database though). Then I set it to export straight to the docear.bib database which is displayed inside docear. This is the trick which keeps Zotero and docear in step. It does mean there is no point in editing the jabref database inside docear because any such changes will be overwritten.
  5. (This was the hardest part) Ignored all the other promising potential building blocks like the “incoming” folder in docear, zotfile, auto linking of pdfs with matching bibtex keys in jabref, etc. etc. These were the red herrings!
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