Sunday, February 22, 2015

Moving to Zotero (from Mendeley)

Mendeley is proprietary, closed-source software. It also requires the user to store citation data on its servers, and was bought by Elsevier back in 2013. In contrast, Zotero provides similar functionality, and is free and open-source (GNU Affero licence).

Although Zotero can be operated as a standalone application, it works best as a Firefox plug-in. It seems to be a pretty good system, but importing from Mendeley, particularly if you want to keep your PDFs attached, is tricky. Here's how to do it:
  1. Make sure you have installed both the Zotero and the ZotFile plugins to Firefox. 
  2. Under Zotero configuration (the 'cog' menu), search tab, make sure PDF Indexing software has been installed.
  3. Export all references from Mendeley using .bib format. 
  4. Move your .bib file into the same directory as the attached PDFs.
  5. Use search and replace to change the file links in the bib file (see example below).
  6. Don't try to import more than about 500 references at a time. If necessary, split the file made in step 3 into multiple parts, and import one at a time.
  7. Use the import function in zotero (under the "+" menu).
  8. If you have standard options set in Zotero and ZotFile, the PDFs will have been sensibly renamed and copied into the zotero directory which is inside your Firefox profile). So, presuming you have a backup, you should delete the directory from which you imported the PDFs.

Changing file attribute
Basically, you need to remove the path, and just leave the filename. You also need to remove the ":pdf" ending. So, from this:

file = {:Users/andywills/Documents/Research/0 - Paper archive/Abeles-M0-1995-001.pdf:pdf}

to this:

file = {Abeles-M0-1995-001.pdf}

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