Mendeley sells out; I’m moving to Zotero

“The empire acquires the rebel alliance.” – a very common response in Twitter with the news of Elsevier buying Mendeley.

Yes, this is more on the side of poetic license than reality, but not by far. If you haven’t heard, Techcrunch reported last January on talks between Mendeley and Elsevier. Yesterday, it was confirmed that Elsevier bought Mendeley for an amount between $69-100 million. This announcement opened the floodgates of people denouncing the deal and Mendeley people’s promises that they won’t change. It was sad to see them try to promise something they will have no control over and never talking about any evidence or contractual obligations to protect what Mendeley is from what most people perceive Elsevier is.

Mendeley wasn’t an ideal solution. Mendeley Desktop is heavy and slow and their API was hardly documented. Mendeley admitted their public API is different from the API they used in their application and that the public API sucks. This deal now makes us question Mendeley’s commitment to open science.

This has nothing to do with dealing with for-profit companies or wanting everything for free. This has to do with a company that had become a parasite of research and that doesn’t deserve the benefit of the doubt, as Mendeley’s people seem to claim. They could have waited for Elsevier to show a true commitment to right their wrongs, but not, they want to become part of the rag Elsevier uses to try to clean up their image.

Elsevier has been denounced by editorial boards, libraries, thousands of researchers, and many other groups for their greedy behavior over content that is not generated by them. They bundle titles, forcing libraries to buy access to more than what they want. MIT has opted out of this at a premium. The company also was caught doing some shady business:

“[...] Elsevier put out a total of six publications between 2000 and 2005 that were sponsored by unnamed pharmaceutical companies and looked like peer reviewed medical journals, but did not disclose sponsorship, the company has admitted.” – The Scientist

Elsevier was among the companies that supported the draconian SOPA, until it became too hot to handle. As a reference, check the full MIT fact sheet on Elsevier. Basically, they oppose open access, squeeze the budget of libraries, and make an obscene profit from our work. A former developer, that moved to PeerJ, has written an interesting post on the matter.

Elsevier has also published some open access journals recently, that with the purchase of Mendeley, will be used to try to clean the company’s image. Their efforts for open science have been cosmetic. The question remains, what will happen when they change the current model of Mendeley service to universities to their hated bundles? What will happen when they close access to it to try to squeeze more money from us?

The satirical account @FakeElsevier just published this tweet that summarizes the discussions many have had with some Mendeley people during the last hours:

 

Moving from software to software

I’ve used several reference managers. The first was Endnote 3, but never had a big or important database since I had most of my references in paper. About 6 years ago I moved from Windows to Ubuntu and moved, as much as possible, to open source software. Endnote was not an option. Then, I started using Zotero when it was a Firefox plugin, but I found it limiting. I moved to Aigaion, a system based on Codeigniter that you ran in your own LAMP server. Unfortunately, Aigaion seems to have been abandoned, with their last release two and a half years ago, and their website is dead. I started to look for a new option. I think back then Zotero was available for Linux only as a plugin, so I went with Mendeley.

 

Time to move (hopefully for the last time) to Zotero

So, it was with great pleasure that i saw that Zotero now has a standalone application for my OS (Linux 64bit). They are also available for Windows and Mac and have plugins for Chrome, Firefox, Safari, and LibreOffice/OpenOffice. Moving from Mendeley to Zotero took some time, but reasonable for my large library, and it was easier than I thought. It will still require some cleanup and checking, but it is better than the alternative (staying with an Elsevier company).

I moved about 1600 references, with only around 50 without a file attached, with Mendeley Desktop version 1.8.4 and Zotero version 4.0.4 on Ubuntu 12.04 64-bit. The process should be the same in other platforms, but make a backup just in case. By default Zotero will upload your files to their servers. The free account is limited to 300MB, so if you have more than this, go to “Edit”, “Options”, then in the Sync tab unselect “Sync attachment files in My Library”.

I suggest working in batches if you have a large library. I worked 100 a time to keep it manageable.

  1. Create new folders in Mendeley. You will divide your full library into each folder.
  2. Select a bunch of references from your library and drag-and-drop to an empty folder.
  3. Delete those references from the main library (to avoid duplication). Once the drag-and-drop is done it is as easy as clicking Del on your keyboard.
  4. Go to the new folder, select all the references (Ctrl-A) and hit Ctrl-E.
  5. Save the references in RIS format.
  6. In Zotero, select “Import…” and look for the RIS file. If you have files attached, the RIS file should have the full path to the file in your disk and Zotero will copy it.

That is it. If Zotero works for you, support them by talking about it or getting a subscription. I’ll test it for a while and, if satisfied that it works for me, I’ll get into one of their plans: 2 GB for $20/yr, 6 GB for $60/yr, 10 GB for $100/yr, among other options. Worthwhile for our personal libraries.

If this helps or you find a problem, please feel free to drop a comment below.

 

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  • http://twitter.com/ColditzJB Jason B Colditz

    This is a great commentary and, coming from an Ubuntu novice (12.04 32bit), I appreciate the detailed instructions for transferring to Zotero.  Onward to the next better reference manager!

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  • Hart

    I’ve also just shifted from Mendeley to Zotero. Was just getting used to Mendeley, but had always been a bit miffed by some of their quirks. Thanks for your post.

  • HughPatersonIII

    Thanks this was most helpful discussion and guide.

  • Lorenzo Tlacaelel

    The only info online that helped me to conclusively opt for Zotero over Mendeley. Thank you.

  • stellarjay9

    Your post captures my experience perfectly. Mendeley was promising, so it’s unfortunate. I liked Mendeley’s stand-alone software, which is what induced me to switch from Zotero initially. More recently, I have started to become fed up with bugs and issues with Mendeley (such as losing links to PDFs), and with the Elsevier acquisition, I can leave with good conscience. I, too, will be migrating back to zotero. I just hope they last…like you say, I think we need to support them with the paying plans.

  • http://thestrayworld.com/ Rewarp

    Thanks for the writeup. Your Ubuntu setup mirrors mine nearly exactly so it was really helpful to see another method of migration. I simply exported the bibtex from Mendeley and imported them into Zotero.

  • Roland Gesthuizen

    I just had a go at migrating from Zotero to Mendeley and it seemed rather painless, then I read this blog post and it had me wondering if I should stick with Zotero. I was only interested in the social media aspects of Mendeley when co-authoring on a paper. Any thoughts?