My definitive guide to manage references in Mac

One big disappointment I have is managing references in Mac. In windows, there are some programs, and Endnote seems to work fine with Word. Also, Mendeley released the new version integrated with word. But, in Mac, there are several problems using Endnote. My word (2004) crashed all the time… specially when I was writing accented characters (á, é, í, ó, ú)… and I am a Chilean guy, and I have to write my thesis, research projects, etc, in spanish.

So, I started to evaluate the options… also online options. These are my thoughts about them:

1. Connotea. It seemed fine to me…but, the problem, as well as many other web-based reference manager tools, is: integration with word. Some developers think that making an “export to word” option will be fine… but I guess these guys never used endnote and they don’t appreciate the “cite while you writing” feature. With just an export option, you have to select, make extensive copy and paste, bla bla bla. But Connotea works well. I didn’t have any problems importing a library created with Papers. And that’s something I cannot say about:

2. 2collab. The biggest disappointment. I couldn’t import any library… either created with Papers, or Endnote, or Connotea, or CiteUlike… It is just useless.

3. CiteUlike. The same as Connotea applies to this app. Also, the interface is very ugly.

And that’s about online tools. I wanted to try Sente, but I am not willing to try som trial-version, to fall in love with it and then to have to spent more than 80 USD. No. I want free applications. I already purchased Papers. There must be an option to use papers and word, at least with a “third-party”.

4. Mendeley: another BIG disappointment. Two things really bothered me.

a) Metadata annotation. I opened my “papers” folder with mendeley… waiting… hours… (while mendeley updated my online library…). And then, voilá! 800 papers… But wait! Just 200, or less, had the right metadata information. The only way to have the 800 papers with the correct metadata, was importing a library from endnote, and all this is to avoid having endnote working because it crashes my word.

b) Absolute no integration with word in the Mac version.

Well… after days surfing the web, I remembered Zotero. I tried Zotero, and bum! Finally the masterpiece missing in my pipeline to work with references in Word.

So, after this long introduction, I will describe:

My definitive Guide to Manage References in Mac

– Software needed: Papers, Zotero, Word.

Step 1: Exporting a RIS library from Papers. You can select a collection, or specific papers… but I recommend to export all your papers. You have to go to File, Export, RIS File.

Step1Export your library as RIS file using Papers.

Step 2: Download Zotero add-on for Firefox, and the Plugin for Word. Follow instructions to install them.

Step 3: You can import several file types into Zotero, to create a libary. For example, a Endnote library. If you have Mendeley (and with God’s help, you have all the metadata as you wish), you can also work with it. But most of the Mac users I know, work with Papers. You have to go to the Actions palette, and press in “Import”.

Step2I apologize… my softwares are in spanish. But you can get the idea

Step 4. Inside Word, insert citations using the button “Zotero Insert citations” in Zoreto toolbar. Once you finished, you can create your bibliography list pressing the “Zotero insert Bibliography” button. And that’s it.

Imagen 4

You can see the Zotero toolbar. And Word run as usually.

That’s it! You have your new system to manage references in Word. I have to do some notes, nonetheless:

– I have Word 2004. I don’t know if this would work with word 2008.

– Also, Zotero works in Firefox. I don’t know if you can use it in another web browser.

– I did not tested this using libraries created with other softwares as Mendeley or even Endnote.

But, it has some advantages:

– Currently, Mendeley does not support viewing pdf files. You have to open acrobat or another reader.. also endnote. But, with Papers, you can view your pdfs as you are working, exporting your selections, getting the right metadata with the fetching tool, printing, searching papers… all in one program! And also, Papers is cheap, compared with similar softwares.

– Also, about Zotero… you ALWAYS have Firefox opened, or not? So, you really don’t have to open a second software. I recommend opening a new window in Firefox, to work with Zotero.

– Finally, Zotero is free. You don’t have to purchase an expensive program.

I hope this can help you. I spent several hours trying to get with something like this. And a disclaimer: I am not part of any Company, or Business… I am just a PhD student trying to make my life (and now yours) easier.

New note added on proof: I had to update Firefox, which I hate… every new version, Firefox gets more heavy, memory-consuming and problematic. Zotero beta release seems to work only with Firefox 3.X version. So, I installed the Zotero version, and the Word plugin that I found in the forums, and I tried creating a new library, and I had problems with special characters (á, ó, ñ, ü, etc). So, I wrote a message in the forum. But, by now, I managed to create a RIS file with endnote, and it worked fine.


20 Responses to “My definitive guide to manage references in Mac”

  1. 1 Ricardo Vidal May 24, 2009 at 10:13 am

    I’m sorry to read that Mendeley hasn’t met your expectations (yet!). However, our next major release will conform to Mac UI standards, will have much improved metadata extraction, will also have a built-in PDF viewer with highlighting/annotation functionality and last but not least, will enable syncing with Zotero.

  2. 2 pabloastudillo May 24, 2009 at 3:58 pm

    Hi, Ricadro!

    Well, I am looking forward for a new release of Mendeley that accomplishes my expectations! I have to say, my expectations are shared by many Mac users. I know that Windows users are happy with the last release of Mendeley (my brother is writing his thesis and a paper and he is happy using his Windows and Mendeley).
    Here in Chile, we have a slow incorporation of these kind of softwares, essentially because ordering a paid program as Endnote costs many more that in US or Europe, because the shipment payments and taxes… that’s why we are so interested in alternatives such as Zotero, Mendeley or web-based toosl. I believe the incorporation of a definitive Word plugin (stable and useful with all office versions starting from 2004, as in Zotero), will make Mendeley the most prominent and convenient software for reference management.

    • 3 Alejandro May 26, 2009 at 10:32 pm

      Hey Pablo,

      You are completely right regarding Mendeley’s “update and sync”… it just takes too long (and I have a FAST inet connection, so there’s no excuse)

      But my main motivation for writing this comment on your post is that…

      Mendeley’s MS Word integration SUCKS.

      I generally support mendeley, but my experience while generating a (customized)reference list, was really terrible.

      For one, you get NO abbreviations (for example, if you want to use the PNAS style…mmm, maybe there is a way and I’m making a fool of myself for ranting with no justification…. anyway, I’ll risk).

      With Endnote you get the “right” formatting with journal names.. correct use of high and low caps, etc, in the different journal’s styles (at least when you import the metadata from NCBI)

      Further (and very importantly), Mendeley kept crashing!

      I will, however, continue to use Mendeley but only as an article (PDF) manager (it’s great-looking!), but definitely Endnote for MS Word integration.

      PS. How’s Zotero better than Endnote for Word integration? (and don’t give me the “it’s free” excuse).

      • 4 pabloastudillo May 26, 2009 at 11:05 pm

        Well… it’s free! jaajja… seriously… in Mac (and I spent days reading posts and forums about this topic), Endnote and Word don’t work at all. For example, if I use Endnote in Word to manage citations, I can’t write accented characters. Every time I write “ó”, or “á”, Word crashes. And usually I lost the changes (even if I set up the autosave every minute, you know that you can write that smart idea in seconds).
        Also, Endnote makes Word slow (even in Mac, which is faster than 90% of the PCs around the world).
        Zotero, works very well with Word, meaning: 1) I can write accented characters; 2) Your computer barely knows that Zotero is on… RAM free for Photoshop, or other softwares; 3) No need for installing RAM and Memory-consuming software… Zotero is a add-on for Firefox.
        Now, I create libraries with Endnote (I still use Endnote because allows me to have these libraries in my Palm), and I import them from Zotero. Works just right. Try it.

  3. 5 Alejandro May 26, 2009 at 11:14 pm

    Does Zotero abbreviate journal titles correctly?
    (shall you chose a journal style that abbreviates titles)

  4. 6 pabloastudillo May 26, 2009 at 11:24 pm

    Yeah, I forgot… So far, I have noticed that Zotero abvreviates journal titles correctly! As in Endnote, you can choose among several styles. And in the Zotero webpage, there are many styles for installing. And, also as in Endnote, if you insert a new citation bewteen previous citations, the bibliography and the citations itself change automatically.

  5. 7 Alejandro May 26, 2009 at 11:28 pm

    Awesome! I’ll play with it and come back with my impressions.

    By the way, you don’t have to ‘re-reply’ in my blog; once you reply to my comments here, I get an alerting email so I know you’ve replied.

  6. 8 Ricardo Vidal May 27, 2009 at 8:49 am

    Hi Alejandro,

    There is an option within Mendeley to allow you to format your references according to a specific citation style. We have a list of citation styles currently available in Mendeley ( Perhaps the style you require is not included in that list. Please let me/us know and we will do our best to include it in our next release.

    If you have any other feedback, feel free to drop us a line at or visit


    • 9 Alejandro June 1, 2009 at 11:43 pm

      Hi Ricardo,

      Thanks for your reply. It’s not an issue of citation style, as much as it is of journal title abbreviation, which is part of a journal’s style. Journals like Nature or PNAS use the journal’s abbreviation name in their reference lists (the “official” abbreviation for each journal title is available at PUBMED, under “journals”). I don’t know if this has been corrected in later releases (I for one, can’t get it to work with the latest build) and this concern (the lack of such a feature) has been raised at the Mendeley’s feedback page (see

      So, ’till now my problem is that even though I select the PNAS style, Mendeley just doesn’t abbreviate the journal’s title in the reference list.

      As I have previously said around here, the greatest thing about Mendeley is it’s continuous consideration for users’ feedback so I’m confident that talking about this can eventually lead to the needed updates.

      Well, maybe this isn’t the place to be having this discussion, so I’ll just go and support the entry at the feedback site.


      • 10 Ricardo Vidal June 2, 2009 at 8:25 am

        Hi again!

        Alejandro, I understand what you mean by citation abbreviations and I’ve mentioned your concerns to the support/programming team and they are aware of it. As you have already stated, there’s an open topic in the feedback forums. We really appreciate your feedback. 🙂

        Keep your eyes open for the next Mendeley release coming out later this month. Hope to read your thoughts on it too!


  7. 11 Dr. EndNote May 27, 2009 at 9:56 am

    There are many discussions on the EndNote User Forums related to fixing Word 2004 crashing. It seems that older Mac profiles often get corrupted and cause the crash:

  8. 12 pabloastudillo June 2, 2009 at 2:15 pm

    I want to thanks to you for the interest in this post and the discussion. Sometimes, reading these kind of discussions in blogs and forums are needed for developers to see that the problems posted by users are not just “isolated cases”. I have a bad experience posting problems in the forum’s pages of some softwares developers, with messages such as “the problem surely is in your Mac configuration”, or “we have no notice of similar cases, then your issue is rare”…
    It seems, in fact, that Mendeley has the best support for users. I hope that Mendeley’s developers can fix the two main problems of this software: “integration with word” and “citation styles”, features in which Zotero is way better. Thanks Ricardo for your comments on this topic!
    To Dr. Endnote: navigating around forums and blogs, it seems that the problem with endnote and Word2004, is not related to “Mac profiles”. The support in the Endnote’s pages is very weak yet, but I guess you can argue why develop a bundle/patch/fix for a suite which is 5 years-old. The reason is the high number of users who still use Office 2004 in Mac.
    We will revisit surely this topic a few months from now, to see the improvements.

  9. 13 Mauro June 3, 2009 at 9:20 am

    I think the problem with managing references as more to do with using M$ Word than using a mac.
    Naive question (not intended to start a troll war). Why are you using M$ Word to write papers?


  10. 14 pabloastudillo June 3, 2009 at 6:03 pm

    A friend is using Latex to write papers. But I think that I don’t need to use another word processor, if I am alrady familiar with Word. Besides, if you don’t have the money for Office, you can download open office, and some reference managers are including integration with this suite.
    I am not in position right now to compare word (or Pages) with Latex, but I guess each program has advantages.

  11. 15 Mauro June 4, 2009 at 4:47 am

    Latex itself is not a word processor, it is a text formatting language (indeed is an application of a broader language: TeX) so working with it is more like writing HTML. There are several WYSIWYG frontends for Latex if you prefer that kind of environment.

    The Latex environment is open so there are many plugins for almost any imaginable scientific publishing nuance: page formats, figure and tables captions and numbers, bibliography styles, and so on. You type the text once and you can produce several ps/pdf versions of the paper with different formats and bibliography styles just changing a couple of instructions in the source file and compiling it.

    There are a lot of free applications to manage references and to produce bibliography files for Latex, for instance: BibDesk.

    Learning curve may be steeper than with word processors but in the long term I think it is worth trying, unless journals you are submitting to accept only word files.

  12. 16 Carla July 15, 2009 at 5:13 am

    1. Me niego a dejar un post en inglé, toy cansá de hablar en inglé
    2. Oye y como le hago con el desastre de papers que ya tengo en el compu?
    esa es mi pregunta.. fin..

  13. 17 Robert Shumake February 3, 2010 at 1:34 am

    Your blog is so informative … ..I just bookmarked you….keep up the good work!!!!

    Hey, I found your blog in a new directory of blogs. I dont know how your blog came up, must have been a typo, anyway cool blog, I bookmarked you. 🙂

    Robert Shumake Paul Nicoletti

  14. 18 Jonathan February 22, 2010 at 1:53 am

    Yup, Mendeley is terrible. It also has problems importing papers with accents in the author’s name. It’s not remotely ready for prime time, yet. They were quite stupid to release poor beta software. Rather than build a customer base, they are basically alienating everybody who might want to use their software before they even release version one.

  15. 20 Anonymous January 13, 2015 at 4:00 am

    it is awesome .i got many informations and it is also nice.☺☺☺☺

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