[mwexler]

For those wondering, here's what I gathered as some context.

Zotero = Your personal research assistant. Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research. https://www.zotero.org/

Mendeley = Reference Management Software, produced by Elsevier who also happens to be the publisher of many peer-reviewed journals. Elsevier come under fire for it's high costs and gateway actions to restrict access to information they've published in journals and host in archives. This most recent action of making the database of references in Mendeley difficult to export is a continuation of their attempt to protect what they, and some legal systems, would see as their IP. Others disagree.

The battle continues...

[zwaps]

Let me try to explain.

Mendeley and Zotero basically do the same thing, which is categorizing literature - specifically research papers. Mendeley offers a built-in PDF viewer with annotations tools, Zotero relies on external viewers for that. Both offer cloud storage.

Researchers usually have to categorize and scan over huge amount of prior literature. If you are working on a project, you usually want to have a good library or folder structure detailing relevant literature. When writing your paper, you also want to be able to cite from this library quickly, via BibTex for example.

Researchers maintain a personal library with literature they read, plan to read or have cited. When researchers collaborate, they need to merge these libraries. Since tools differ, the lowest common demoninator is often a dropbox somewhere. Sometimes everyone works on Zotero or Mendeley, such that files can be shared within the system. Usually not.

Mendeley and Zotero used to be equally open to sharing and collaborating. Mendeley was in a sense superior as it was polished, had great tools to annotate and great tools to work with Meta-data. Zotero, while FOSS, was always behind.

Then, Mendeley was bought by Elsevier, the largest publisher. Elsevier does not want people to share PDFs, because Elsevier wants everyone to pay for the priviledge to download those pdfs. Thus, Mendeley started to make it more and more difficult to collaborate. Now it is even difficult to share files within the Mendeley eco-system!

Perhaps you are using Calibre for you Ebooks. Now imagine Calibre would deactivate any way for you to view, send, export or use your files (the files that YOU put into it) outside of the Calibre Ebook viewer, and it would encrypt its database so that you would not even try. That's what happened.

Sharing research is the lifeblood of science, and Elsevier wants to destroy it.

Elsevier has done many other things that has harmed scientific progress - the majority of this undertaking you fund with you tax dollars! The way this is done is almost comically blatant. Elsevier acts like a comicbook villain. They are literally evil.

[fantasticfears]

Do you try tools like Scholia building bib file which is using Wikidta? https://tools.wmflabs.org/scholia/about

[ramraj07]

Mendeley was originally a startup. Precisely why people even started embracing it (though I didn't, something always felt fishy for me) and then they got acquired by Elseiver.

I have nothing but good things to say about about Papers for Mac though.

[biomcgary]

I've never used Papers, but have had colleagues that swear by it. However, it is not open source, so you still run the risk of the developers selling out just like Mendeley.

[kaitai]

The nice thing about Papers is that you download every pdf and have a local copy. Of course the developers could change how it's done.

[carbocation]

Good idea re: giving context as to what these programs are. For most of us who do research, these programs are essentially interchangeable "reference managers." Here's what I mean:

I read a scientific paper or look up a citation. I add that with a click or two to my reference manager. It also stores the PDF for me.

In the future, I can easily re-read the PDF. I can annotate it and the annotations will be stored.

Critically, when writing my own paper, I can import those citations and trivially change the format to whatever the publisher wants without any effort.

To me, across most features, these two programs do exactly the same thing. When picking a citation manager, it's more about which one I trust will be around for the long haul and will not interfere with my research.

[zwaps]

The only difference is that Mendeley has a built-in PDF viewer with annotation. Of course since you can no longer share these annotations, nor export the pdf, that's all pointless.

Mendeley opens PDFs externally, but many PDF readers can create and save annotations.

[carbocation]

In your second paragraph I think you mean to lead with "Zotero" instead of "Mendeley." And yes, I agree with that distinction. In practice, it hasn't been much of a problem (even though I do my work across OS X and Linux).

[henriquemaia]

On your second paragraph you meant Zotero. I just added this comment to make yours more clear.

[boyband6666]

I think you meant to say "when my paper is rejected, I can trivially change the format of references to whatever the publisher of my second choice journal wants without any effort" ;-)

[carbocation]

Ha! Actually, I use this so that while I write my papers, I can use a format where I can see the first author's name and the publication year (which is meaningful when I glance at it). Then, when I submit, I can quickly put it into the format that the publisher wants, which seems to generally be numeric (and meaningless). But, hey, I won't complain about anything that lessens the pain of rejection :)