Some days ago we started here a discussion about which program could be the best to organise a researchers library, papers after papers, issues after issues.. Let’s try to summarise,
On the other hand, Zotero and Mendeley have presented themselves as two very useful tools for library organisation. Both are free and run on every system, so to speak. Summarising their characteristics;
Zotero is an add-on for Firefox, while this works very nice when you are searching and adding papers directly it might became something not so comfortable when you are just surfing on the web or when you just want to read with documents and leave the browser alone. Firefox still consumes some valuable resources of the computer, for those using old computers that might be a problem. Mendeley instead, works as a separate tool, independent from any other program. And however, both have the possibility to add to the library directly with one click.
Mendeley is able to, if you add the PDF directly to the Library, retrieve all the information about it, as long it is text readable PDF and not just a PDF made up from pictures, i.e., old scanned papers. You can do the same just specifying the DOI or the PMID.
Personally speaking, once in your library I found much more comfortable and easy to find what I am looking for in Mendeley than in Zotero.
Both programs have large community online, and both allow you to synchronise with the server. Comparing, Zotero gives you only 100 MB free at the beginning and Mendeley 500 MB + 500 MB shared. However, Zotero is cheaper in the upgrade, in case you want to have extra space.
In terms of group synchronisation, Zotero has some several conflicts when dealing with version of different languages. I never tested this option in Mendeley.
Zotero can’t open the PDFs by it self, depending always on your PDF reader. And because is dependent on Firefox it will often be necessary to change the way Firefox open PDFs… On the other hand, Mendeley cames with an outstanding characteristic, in my point of view. Not only it allows you to open PDFs directly on the program itself, being completely independent from external program, but also it allows you to underline and add notes. For linux users that is undoubtedly gold! Finally we can forget about trying to run Adobe Professional in our systems and use a native program. One can argue that Okular already did the job. Yes, but no so well done as Mendeley. Actually, Okular was imperfect enough to become unusable, at least last time I used, around 6 month ago. This characteristic for me puts Mendeley far above Zotero.
Telling a bit more, Zotero stores the data in your computer in a non-human readable way. That is, you cannot find you paper if you go just surfing in or File Browser. Mendeley do much better the job by creating a tree of files according to your preferences.
Citation and Word Plug-ins: I have already used both programs to do the citation and references task. As far as my knowledge (yes, as a good researcher I didn’t want to investigate more into the issue :D) Zotero plug-ins can reach more programs than Mendeley, p.e., Mendeley plug-in do not work with Microsoft Office under 2003, while Zotero does.
Zotero is much more powerful in citation and references because it allows you to surf freely on your library while adding each paper at a time, when adding multiple references. Mendeley still doesn’t allow you such thing, you have to select all the papers without changing the Library folders, that is, you have to found your paper in the list of “All Documents”, which when dealing with hundreds or thousands of papers might be a little painful. Moreover, Mendeley does not allow you to edit multiple references, say (1-4), you have always to redo it, you can’t just add the (1-6) later without selecting again the 1-4.
Regarding references styles, Zotero is a bit more evolved, however, Mendeley can retrieve the citation styles from Zotero.
So, how to decide, should one use Zotero or Mendeley?
If you don’t care about PDF annotation and you are okay with the search engine of Zotero and the fact that it is and add-on, I would recommend Zotero, without any doubts.
However, if you really appreciate PDF annotation and easy search, Mendeley is your solution. However, by now, one cannot rely only on Mendeley, it is still a bit painful to do the citation work.
Therefore I come across with the solution of using both simultaneously :). By now I am keeping in Zotero just the information about the papers (without the PDFs), synchronised with the server, 100 MB are enough for the task. And I will use Zotero plug-ins for the citation work. While keeping Mendeley with the PDFs along with all the other information, and by now 500 MB are enough for my Library.
So, you can argue that at the end I am using more resources and more confusing strategy. Yes, but my computer is powerful enough to deal with the task and for my strategy of work it is painful, in one way or another, to use just one of the programs. However, in my opinion, Mendeley has much more possibilities to develop and to become much better than Zotero, simply because their bases differ. Do not forget that Zotero is already at version 2 and Mendeley stills in 0.9.
Whatever the case, I really appreciate the community for developing such tools! Both are excellent, and without them.. life as a researcher would be even more painful :D
Remember that this post is just my opinion about the issue, was my intention to share with you this idea, might it also be useful for you.
Looking forward for your answer