Mendeley reference manager may be the ultimate roach motel

I was appalled to learn that Mendeley recently began encrypting user’s annotations of their PDFs. This pretty much locks you into using Mendeley, unless you want to go through convoluted hacks that might work (no guarantees).

This is particularly insidious because these annotations that are being locked into Mendeley are more than mere highlights in articles, these are people’s thoughts that they have written down and entrusted to this software. Essentially, it is ransomware.

If I’ve ever suggested Mendeley as a ref manager to look into in a post here, I retract my recommendation.


This is one of the reasons why I store the documents in DevonThink and annotate them there. I personally use Zotero - but would do this even if I were using a different reference manager.


Aye. Like Rose, I don’t trust the layers most of these apps add on. I do my annotations in PDF Expert or DEVONthink, maintain the PDFs in the file system, and then use tools like Skim to automate and interact with my notes. So far it’s working.

I recently got fed up with Zotero’s non-native feel, though, and switched to Bookends. Still getting used to it—importing new finds from the web is particularly counterintuitive compared to the magic button most other reference managers provide—but it’s otherwise really slick.


That is utterly maddening. I wonder how they justify that?

It makes me glad that, though I dabbled a bit in Mendeley years back, I decided not to go with them when they first sold out to Elsevier.

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From the article, they invoke EU privacy, fake news, and conspiracy theories.

Mendeley claimed this was done to comply with European Union data protection laws and to keep data safe. When people asked for specifics and pointed out that encrypting people’s annotations actually seems to contradict the EU regulations’ right to data portability, Mendeley refused to provide further explanation or correction to their statements. Instead they blamed the confusion on fake news and conspiracy theorists.

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I’ve been using it a while (since 6/16, looks like). If I can help with something, let me know and we can start a new thread.


Yes exactly, what I do too and I don’t see why do it any other way now. EndNote used to be a kind of repository like DEVONthink is now, as I thought of it anyway, I never really kept papers in there though! I started using it when everything was still on paper and never got into a new habit on it.

I now use the native bibliography on my LaTeX suite BibDesk I think it is called. I appreciate there is for some a need to import from various sources bibliographies that might be easier to do on EndNote and the others. I don’t find any problem but my use of citiations is quite light now too.

By the way @RosemaryOrchard I am surprised you don’t have “DEVONthink” as a TE snippet! :grinning:

I am inclined really to agree, though the topic is complicated, with that article. There is such a thing as killing the goose that lays the golden egg. I am pretty much for open access now too.

I can appreciate that folks are pushing to dump Mendeley, especially as a citation manger for private databases. Other than rebelling against the near monopoly practices of Elsevier as a reason, better options exist (e.g. Bookends on Mac or Zotero perhaps or JabRef as cross-platform).

One key reason I use Mendeley is to share journal articles and the notes that I make on those journal articles with my research group. They all decidedly do not have (and even prefer to avoid) Macs. Zotero is not well structured for the PDF purists in the hard science/engineering field. Also, as an early adopter to Mendeley, I have 5GB storage rather than its now standard 2GB. I would hold that no other citation management app is close to what Mendeley can offer for cloud based sharing.

I am transitioning out of using Mendeley (to Bookends) to do my own personal libraries. The data encryption is one new reason. Its slow, cumbersome desktop UI and lackadaisical iPad app are the main reasons.

Would that Papers would be further along in its cross platform, non-Web version release. After being enamored some time ago using it on the Mac, I’ve since given up on it. But, I might predict that when they would get their act together and would offer a well-designed cross-platform app, the ReadCube/Papers team could have a gold mine.