Bookends vs Zotero vs Mendeley vs Jabref

I have been very dismissive of Mendeley for many years now. For one good reason: the data is always extracted from Google Scholar. I get the worst, most incomplete reference from Mendeley.  Being an early adopter (staring from its beta stage; around 2008), I was left with frustrations with Mendeley. Now, it is time to appreciate one great quality of Mendeley that no other reference manager can emulate: its attempt to do the undo-able. That is, Mendeley tries to get the reference information by reading the PDF file directly. This technology is unique to Mendeley, so far as I can tell. While both Bookends and Zotero can extract some identifiers like DOI and ISBN, they never try to get the Title, the author and the date by directly reading the PDF file.  Mendeley does that. As a result, it is a life saver when you have a lot of junk to clean up.

I recently downloaded more than 3400 pdf files from a linguistic archive. Importing them to any of the references gives not a single relevant reference data–both Zotero and Bookends gave me zero result. I also tried Papers3. Quite interestingly, Papers was able to pick some of them. But, the data it gets was less than 20% success rate.

Then, I dragged them to Mendeley, majority of them get their references filled. Most of them get junk reference, of course, as usual. But, hey, this is technology. We have to do a lot of trial and error. Cleaning the junk library was much better than inserting references, one by one, for 3400 item. For that, I am now grateful of Mendeley.

But, ultimately I cannot live with Mendeley because it gets data from Google Scholar only–always junk data. That is why I have to move back these partially filled references to either Bookends or Zotero.

Completing the incomplete references in Zotero is a nightmare, I learned by the hard way. Zotero excels at getting data from browser (internet) and the attach the PDF over the reference. Having PDFs with incomplete reference or no DOI, however,  Zotero is a huge pain.  I  am a PDF guy. I rarely pick the reference from the web page. I always go to the pdf; and  attempt to fill up the reference when I have some extra time latter. For that, Bookends is much better. BE has a feature called Autocomplete (similar to the Targeted Browsing feature in Sente) which helps me highlight the Title of the book (article) from the pdf and tell it to search it somewhere in the web engines (google scholar, World Cat, or my local library website). That way, I don’t have to write the reference manually.

For Zotero, if you have missed to get the data from the website first, or that the PDF contains no DOI, the only option you have is to manually write the reference. Jabref is even better on that because you can copy and paste references from Google scholar to the existing PDF.

But, I find Zotero  better than Bookends on these two aspects.

  1. Direct syncing of the Bibtex file: using the Better BibTex plugin
  2. Automatically  getting the ISBN of the books. Zotero picks the ISBN of the books almost always correctly. This feature is coming to Bookends as well. But, BE is not really effective at yet.


How about Jabre?

It excels at manipulating references in the bibtex format. Furthermore, it as one unique feature that no other reference manager yet implemented–embedding the XML metadata into the pdf files. There are two good reasons to write metadata into the PDF files.

  • it improves searching: you can search Spotlight by the author or the Title of the book; or order the books by their date of publication. This is specially very useful if you use more advanced searching tools like FoxTrot, or (DTsearch in the windows)
  • you can lose the reference, or share the pdf without losing the reference data about it. If your library is lost or  corrupted, you don’t have to fill the reference data again. You can just drag the pdf and Jabref will populate the reference data for you.

The conclusion is: every reference manager has its own strengths and weakness. Each of them have their own niche users; and niche features. Bookends and Jabref are my all time favorite reference managers. I think I will keep all the 3 reference managers me for now. Some people own three cars, just for sheer fun of it, even if one car is usually enough. I don’t have to chose among these great softwares. I will use Zotero for the books, Bookends for everything else and Jabref for bibtex.

9 thoughts on “Bookends vs Zotero vs Mendeley vs Jabref

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  1. Thanks for the interesting write-up! Papers also attempts to read the XMP metadata embedded in the PDF. This is probably why it got the metadata for some of your PDFs which had no DOI.

    1. I see, it is reading the XML of the files.
      Mendeley reads both the XML and the actual title of the PDF, I think.
      A question: does Papers also write the reference data to metadata of the pdf, or just reading only?

      1. IIRC, Papers 3 only reads the PDF’s XMP metadata on import, but doesn’t write the publication metadata to the PDF on export.

  2. Thanks for this excelente review.

    I’d like to know if you have already tested any of these sofwares to work on multiple devices, for example Mac and iPad. I’d like to know your opinion on cases like these, too. Thanks.

    1. Depends on what you want to do with your iPad. If want to access just your references, all of them have ways of pushing references to the iPad.
      If you want to read the attachments on the iPad, your choices are between Mendeley and Bookends.

      The syncing technology is better in Mendeley–they have their own server. Bookends syncs only via iCloud (which could be crappy at times). But, the annotations made in Mendeley are in proprietary format while Bookends follows the standard PDFkit (adobe). That means: annotations made in Mendeley cannot be viewed or edited in external editors; the ones made in BE could be. BE also supports Wifi sync (non-cloud, computer to ipad sync). The overall experience of reading is better in Bookends. (I admit, I haven’t checked the latest versions of Mendeley). 

  3. I like Jabref most, because of three reasons:

    it is opensource
    it supports the bibtex format natively
    it has a programmable export filter, which makes it easy to export an entry to the Wikipedia-citation-template

    The other (commercial) reference-manager in the OP are outdated, because they are not helping to reducing the costs of creating a paper. The idea of using a software tool for managing the bibliographic references is right, but the next logical step is to use opensource software.

    1. I agree. Jabref is one of the greatest bibtex managers out there. I have always wandered around new reference manager. I always keep Jabref in the background–it is reliable, rich and open.
      In my current setup, I always wondered if I can completely rely on Jabref (get ride of Bookends). The problem is with the file management. Jabref doesn’t give me as much control as Bookends does on that area. The programability of the export template also applies for Bookends.

  4. I’ve just tried to just JabRef, after using mendeley for a while. But i’m not getting the hang of it. I’m importing it into LyX. My problem is that I seem to have to add the info from scratch – I’ve not learnt how to import info from the PDF of elsewhere. And when i import it into LyX, it says ‘bibliography entry not found’
    please could you help? I’m so fed up 😦

    1. I honestly don’t know how Lyx works. I use Texstudio for my latex. Therefore, I cannot say anything about the relationship between Bibtex files and Lyx.
      But, the way it works with your existing Bibtex file exported from Mendeley is by linking the references and the pdf files. It is very easy and fast to link them. There is a feature called Autolink in Jabref. You can check it in the user guide (website; help menu in jabref).
      But, you might be better with Zotero if Lyx is some kind of word process (like MS.word).

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