Mendeley Acquired By Elsevier

First time accepted submitter alexgieg writes "Academic reference manager Mendeley has announced they're joining Elsevier. They say this won't change anything for Mendeley users and that they're still committed to their Open API efforts, all the while acknowledging that Elsevier's reputation hasn't been the best as of late. If you're currently a Mendeley user will you continue using it from now on? Or will this move prompt you to start evaluating alternatives such as the Open Source, Firefox-based Zotero?"

Mendeley Industries

[ArcadeMan]

Mendeley Industries - An Import/Export Company & Purveyor Of Fine Latex Products.

Oh wait, wrong company.

Elsevier are greedy bastards

[Anonymous Coward]

Elsevier are greedy bastards whose existence has a huge negative effect on science and academia.

Re:

[Anonymous Coward]

Same goes with Thomson routers and Springer. All of them are there to make fortune out of open and public work of scientists and graduate students.

In a recent ./ article some were trying to divide journals into fake! and unfake! (i.e. those which belong to Journal cartels and those which belong to smaller companies/countries/universities).

Good alternative: Citavi

[Anonymous Coward]

Personally, I'm sticking with Citavi. It reads all common citation export formats, supports a common library for several people, and works flawlessly :)

Re:

[tehcyder]

I used Endnote for both my thesis (two thesis actually) and papers and it gave me a really hard time. A new bug which has been around for months now freezes MS word if you cut/paste citations or delete them.

Cue the "well don't use MS Word " helpful comments in 3...2...

Re:

[Hatta]

There's always good old BibTeX.

Re:

[digitalvengeance]

I switched from Zotero to Bibtex for my academic work a few months ago. I used Zotero for years and was generally happy with it, but I have really started to enjoy working in latex and bibtex is the obvious choice for that. There is just something really nice about having a plain text document. It can be easily versioned, edited on pretty much any device (including vim from a chromebook I travel with), and being able to manually edit the library file has shown me several errors Zotero made importing sources

Re:

[spasm]

There's a plugin for zotero, autozotbib (http://rtwilson.com/academic/autozotbib) which exports your zotero collection to a bibtex file then keeps the bibtex file synced (ie every time you add a reference to zotero the bibtex file is updated automatically).

Re:

[slartibartfastatp]

Mind if I list some useful stuff that made me use mendeley instead of bibtex:

1) it can export the whole library as bibtex

2) right click over your paper -> "copy citation as tex" -> paste it into your latex file.

3) keep the PDF together with the metadata

4) anotate the PDF

5) search those annotations

6) put DOI, PMID, ARXIVID -> get all metadata from the interwebs

7) organize it with keywords, collections

I can't believe it's better to keep a text file edited by hand than to use an user interface that a

Zotero is a felony

[paulatz]

using Zotero in the USE is probably a federal crime, bearing a liability up to several decades in prison: as they say "Zotero [allows] you to add [content] to your personal library with a single click. [...] a journal article from JSTOR, a news story from the New York Times [...]"

Are we sure that semi-automatically adding an article from JSTOR or NYT to my library is not a violation of their terms of service?

Re:Zotero is a felony

[c0lo]

using Zotero in the USE is probably a federal crime, bearing a liability up to several decades in prison: as they say "Zotero [allows] you to add [content] to your personal library with a single click. [...] a journal article from JSTOR, a news story from the New York Times [...]"

Are we sure that semi-automatically adding an article from JSTOR or NYT to my library is not a violation of their terms of service?

Nope... If it's illegal in your country, that your click is illegal.

Re:

[Anonymous Coward]

Absolutely not. You won't be able to download an article into Zotero if you don't have the credentials to do so in ScienceDirect or JSTOR. I. e. if you don't belong to a University subscribing to their portals.

Re:Zotero is a felony

[Sique]

Absolutely yes. It wasn't forbidden for Aaron Schwartz to download articles from JSTOR (he had the credentials). It was a violation of the ToS to use automated means to robo-download thousands of them. And it was a violation of the IT policies to bring his own equipment there and wire it up to the campus network and hiding its existance.

Re:

[jotaass]

Zotero doesn't allow you to do bulk downloads. It automatically downloads the pdf relating to the article on the current page but only when you add that article to your database (which requires a click). And I don't even think that option is on by default. At most it saves you a few clicks.

Re:

[pesho]

Zotero doesn't allow you to do bulk downloads.

It does to an extent: Do a search or just open a journal at the table of contents page. Then click on the 'add to zotero' icon, which in this case will looks as a folder. You will be presented with a list, that you can download in bulk.

Re:

[interkin3tic]

Call me a cynic, but I'm pretty sure what makes something legal or "send you to prison illegal" is whether some wealthy corporation (and by extension, the government) dislikes you doing it or not.

If you're using zotero in a way someone dislikes enough, they'll find a way to bankrupt you at least for it.

That said, I can't think of how zotero would get you in that much hot water with any of our corporate overlords.

Re:

[mrgunn]

It's hard to imagine what regrettable state of confusion would lead someone to ask such a question. It's absolutely not a crime to store metadata about articles, nor is it a crime to store personal copies of full text. In fact, leading opinion; http://www.infodocket.com/2013/02/15/update-on-proposed-digital-public-library-of-america-dpla-metadata-policy/ [infodocket.com] states that in most cases, metadata isn't subject to copyright. If that's not enough, Thomson Reuters makes such a product themselves.

Not using it anymore from now on

[lbbros]

This announcement is the best way to prevent me from using Mendeley. I will not touch anything that's handled by Elsevier, just as I refuse to review anything that comes from them.

Re:

[damitr]

I agree to this. Slashdot post for Future : More Researchers Moving On To Zotero! It is not just for fun Elsevier have taken up Mendeley, soon your papers will be scrutinized whether they have been downloaded legally or you have an unauthorized copy of the same. And if found using unauthorized copies, you know what they did to Aaron.

Bah.

[Anonymous Coward]

Mendeley was -- and is -- excellent. It's a truly platform independent, sensible, reference manager, arguably only beaten by the closed-source (and pricey) Papers for OS X. I'm really annoyed to hear this; I don't trust Elsevier not to run it into the ground and try and 'monetize' it. At the moment they've got a very effective 'freemium' model going on, one that actually makes sense where you essentially pay more for hosting. It's really convenient having all your papers & citations stored in the cloud.

Re:

[spasm]

I don't use firefox either, so good thing there's been Zotero standalone for several years now (you get offered both the firefox and standalone equally prominently on the download page: http://www.zotero.org/download/ [zotero.org]) along with plugins for chrome and safari. There's also several guides online to setting up either zotero standalone or the firefox version in 'portable' mode on a usb stick, although I haven't tried that myself.

Zotero is good

[staalmannen]

Being a Linux user in the Biomedical field has its issues sometimes, especially with collaborative writing where most colleagues simply out of ignorance work with MS office and Endnote. The combination LibreOffice and Zotero (stand-alone version) has proven the best fit for me to do my work. One disadvantage can be that I need to send my documents with final formatting rather than with the citation tags in the document to ensure that stuff works on the computers of my colleagues.

Re:

[niftydude]

+1 to this. I've been using Zotero for the last 3 years or so - moved to it after lots of frustration trying to run Endnote in wine, and haven't looked back.

Zotero exports the bibtex format quite nicely, so I have very few problems using it with LaTeX either.

Re:

[Monkey-Man2000]

Another happy Zotero user. The fact that it can typically strip citation info directly (and save/store!) pdfs is a killer feature that EndNote doesn't even have I think (at least my old version about 10). And it makes it easy to distribute whole libraries (including pdf docs) to colleagues to boot.

Re:Zotero is good

[miknix]

I've been using Mendeley and I'm quite happy with it. However, I don't use any of the collaborative/social functionalities of Mendeley. What I use and find it very useful is:
1) the autocomplete of bibliographic metadata of papers newly added to the database.
2) generating a single bibtex file for all the papers you have in the Mendeley database.
3) automatic assigning of citation keys for your papers in the database.

So basically when I'm writing a paper I just need to go to Mendeley, search for some keywords (the search engine is good), select the relevant paper and copy-paste the citation key into my latex document. That's it!

Does Zotero provide similar functionality?

Re:Zotero is good

[Monkey-Man2000]

I believe all the features you mentioned are included in Zotero, and it can do indexing across pdfs [zotero.org] it stores. You should check it out as they are rather responsive to updates and it is open source [zotero.org] (and free! [zotero.org]) Also, since it is a Firefox plugin, it can detect that you need to be behind a proxy automagically when appropriate, and so it makes adding new citations quite easy. I'm not a developer on it, but just a rather happy user! The only thing I miss from EndNote is an easy way to search Pubmed and pull citations that way, but I suspect they are working on it (or may have added it?) because I've seen other people request this feature in the forums.

Re:

[JanneM]

To automatically generate a single Bibtex file, install the extension here: http://rtwilson.com/academic/autozotbib [rtwilson.com]

Re:

[wmac1]

I used Endnote because of a few cool capabilities.

- You would copy/paste text-citation mix to a new document (from several previous papers/thesis of yours) and it would order the citation numbers (as in IEEE and numbered format) and produce a final reference list.
- You could have multiple types of documents (Journal, Conference paper etc.)
- The numbers were always in the order of usage,
- The formats could be changed and the whole document would be updated immediately.
- The database could be saved on a cloud

Re:

[pesho]

It does have cloud storage.

Re:

[eyeoftheidol]

There's now a Word plug-in for Zotero. I use it for my PhD and find it extremely flexible. I have looked at Mendeley but their user support is pretty poor (maybe it is better if you upgrade to a paid account?) and unless you're running a mainstream OS, you are basically s*rewed.

LaTeX hits most of your criteria.

[girlinatrainingbra]

LaTeX hits your criteria numbers 2, 3, and 4. There's no auto-copy-paste for a mixed text+citation, however you can copy a citation into the bibliography portion of your latex document file and have bibtex handle details for you. Multiple passes of LaTeX automatically take care of the format details for various types of print (article vs. conference proceeding vs. report vs. book chapter), re-ordering and renumbering reference and citation numbers (and chapter numbers and figure numbers and equation numbe

Re:

[pesho]

I used Endnote because of a few cool capabilities.

- You would copy/paste text-citation mix to a new document (from several previous papers/thesis of yours) and it would order the citation numbers (as in IEEE and numbered format) and produce a final reference list. - You could have multiple types of documents (Journal, Conference paper etc.) - The numbers were always in the order of usage, - The formats could be changed and the whole document would be updated immediately. - The database could be saved on a cloud storage (and be available on all PCs) - You could download Endnote files on IEEE, Elsevier (scopus, sciencedirect) and other websites.

How does Zotero fare in the features I mentioned? I used it a few years ago but it lacked integration with MS Word, so I just gave up on it.

It does all of the above, and then some.For starters its has an interface that makes sense, unlike Endnote's which is a random pile of features accrued over the years. Capturing sources takes just one click within your browser. The only exception from your list is that the journals don't provide citation style files (you refer to them as Endnote files) for zotero. However this doesn't matter. You can find pretty much any style you want at http://www.zotero.org/styles [zotero.org]. I think they have the formatting files

Re:

[JanneM]

Been using Zotero with LaTeX for most of my career, and it's been a good fit for my work. I was a bit curious about Mendeley and what it could perhaps do that Zotero can't, but with the earlier rumours and todays news that curiosity is well and truly squashed.

Re:

[BitZtream]

Been using Zotero with LaTeX for most of my career

Its not really a carreer when you've been doing it for just a few years. A career involves a lifelong body of work, which you can not possible have in less than 7 years which is how long Zotero has existed.

The fact that you've only used one product of the type in your 'career' re-enforces my point.

Re:

[JanneM]

I've been using it since shortly after it went public. I've been at my current career for about ten years, so yes, it is "most of my career".

Re:

[serviscope_minor]

The combination LibreOffice and Zotero (stand-alone version) has proven the best fit for me to do my work.

My experience of Zotero/LibreOffice is, to put it politely, a flakey heap of crap. My only other experience of such things is with LaTeX/BiBTeX, which is bullet proof.

Perhaps I'm using it wrong, but it seemed really horrible.

Re:

[ITMagic]

Another very happy user of Zotero here. I have tried Jabref, which I like for it's simplicity, but I find it lacks functionality. There was another on-line collaborative site (beginning with 'C'?) that I tried briefly, and abandoned. I have probably tried several others also - though this is the first time that I have heard of Mendeley...

To be honest, the only downside that I can think of about using Zotero is that it is a Firefox plugin, and we are (supposed to) have a purely MSIE environment on the workst

Re:

[postglock]

What kind of functionality do you feel Jabref lacks? I've only really tried Jabref (and BibDesk and Endnote in my Mac days), and I'm wondering whether I'm missing out on something by not trying Zotero.

Re:

[pesho]

Have you tried Zotero Standalone? You can use it with browsers other than FF.

Worried

[MassiveForces]

I currently subscribe to Mendeley. They have been slowly but surely improving the quality of their software the last three years I have been using it, and I couldn't live without it. There are a few things I would like they've just never bothered to implement, even though many people have requested them, but then again at least they have a good forum and request system. I like to have my library of references synced with me wherever I go, so when I open a word document on any of my computers all the referencing works correctly.

Maybe this will mean they have more support and be able to do things like spend the time on their mobile versions so they actually work. But really I think this is the beginning of the end. Elsevier just doesn't seem to have any incentive to keep Mendeley easy to use with any publisher and have all the sharing capabilities it currently does. What if they don't like the fact I can import any open source format referencing styles for any journals? Maybe they will just make it awfully expensive to keep the current functionality, the price has been going up anyway on storage space. I deal with hundreds of papers in PDF, and Mendeley has the best solution for making notes, highlighting content and organizing PDFs with it's inbuilt viewer which makes it easy to keep up with my research. Zotero lacks these tools I'm not sure what the alternatives would be should Elsevier wreck Mendeley somehow.

Re:

[chooks]

Dammit. We just can't have anything nice around here. I agree with you that this is probably the beginning of the end. The combination of behemoth sized international publishing company and small software company does not appear to favor the small software company.

I'm pissed as I just started using Mendeley last week and really like it. (*sigh*) I've used zotero before but it just wasn't that great/intuitive, but maybe I will have to give it a second shot.

Re:

[tulimulta]

If you're doing annotations on a tablet (which I highly recommend!), try Zotero + Zotfile + Dropbox + an annotation program on your tablet. It works great. Only thing that's missing is Mendeley's handy annotation sharing thing. Well I haven't looked at Mendeley for a couple of years, there's probably more new bells and whistles too.

Re:

[GenieGenieGenie]

For me, these are still early days to comment on the acquisition, but at least one thing you have mentioned has a (complicated and convoluted, but functional) workaround. http://danielcoakley.com/2013/01/setting-up-mendeley-to-sync-to-android-device/ [danielcoakley.com] (I am not affiliated with this site).

Re:

[drinkypoo]

But really I think this is the beginning of the end. Elsevier just doesn't seem to have any incentive to keep Mendeley easy to use with any publisher and have all the sharing capabilities it currently does.

How about the fact that Elsevier had an entire division dedicated to publishing fake journals on behalf of pharmaceutical companies? A person with half a brain and/or the slightest bit of integrity would [slashdot.org] do the right thing [slashdot.org]. Giving money to Elsevier means perverting science.

Re:

[interkin3tic]

Not everyone sees things in such absolutes. For one thing, no one was reading those journals. For another, doing research necessarily means dealing with corporations, all of which have a high chance that they're doing something to leech off of scientific progress.

Open source for mission-critical tools?

[tulimulta]

I considered a couple of years ago moving to Mendeley from Zotero, they had a nice PDF annotation feature for research teams on the desktop software, this was pretty cool before the age of annotating articles on tablets. My prime reason for not moving was that Mendeley's monetarization logic was not clear. Along with it not being open source, it was easy to stay with Zotero: made by a not-for-profit institution, and open source. Now I'm really glad I stuck with Zotero!

Zotero + Zotfile + a tablet is all I

Re:

[girlinatrainingbra]

re: I guess it always pays off to be always suspicious of shiny new applications, when it is not immediately clear why is it free (as in beer)?
:>)
Very good point. I'm adding that criterion to my list of things to consider as I try out new things for my software considerations for university. When it's not clear what the "monetization strategy" is, they could also be trying to get "first mover" advantage with a cool idea, or they could possibly be hiding their monetization strategy because revealing i

Any good alternatives other than zotero?

[Anonymous Coward]

What alternatives do people recommend? I tried zotero, admittedly this was quite a while ago, but it was so unbelievably awful that I vowed not to go back. I also don't really like being tied into firefox extensions...

Re:

[Anonymous Coward]

Zotero has a standalone version now - I use that with a Chrome extension.

Other (non-free, pricey) options include EndNote and RefWorks.

The only other free option I've tried is Qiqqa, which has some cool features, but was a little too buggy for daily use when I last tried it. It is being actively developed, though, and it might be better now.

Wikipedia has a comparison of reference management software [wikipedia.org] that lists a bunch.

Just be a real scientist...

[aaaaaaargh!]

... and use BibTeX! There are good front-ends like JabRef if you don't like editing test files.

Re:

[jrminter]

I use JabRef and am quite satisfied. I also prefer LaTeX to Word etc and with Sweave can include chunks of R code to produce figures. RStudio is a decent IDE for all of this and

Sweave/LaTeX/BibTeX files are all text files and work efficiently with git for version control. Having everything under version control has saved my bacon more than once. An added benefit of git is that it is easy to keep work synched across multiple computers with different operating systems.

I find support from these Open Source co

Re:

[vajorie]

Used with JabRef as the front end (and Ubuntu One as the cloud storage), Bibtex provides me with a very convenient and non-binary (and OS-independent) way to store interlinked articles, the references to which I can easily plug in if using Latex (and some other software like LibreOffice) for a paper.

Haven't used either yet, but...

[Shag]

I now know which one I won't be trying.

I'm on Academia, though. A bit silly, given my lack of peer-reviewed publications...

3..2..1

[Stirling Newberry]

Converting everything today. The content mafia is a racket.

How to close your Mendeley account

[slashdotmsiriv]

http://support.mendeley.com/customer/portal/questions/699525-how-to-close-an-account [mendeley.com]

Seems like a consolidation in citation apps

[Master Of Ninja]

This is quite interesting seeing that my citing app of choice Papers was recently taken over by Springer [papersapp.com] another big research publisher. I wonder if all these big publishers are wanting to take over the low cost and mass marker reference/citation managers, especially as some of them have social features. Nothing beats having loyal customers who you can data mine nowadays - even Google is in the game with Google Scholar. The older style reference managers are fairly expensive, and by having a low end product which is free, I think Elsevier will go someway to restore some of their reputation, especially as their ScienceDirect resource is actually quite good.

Of course you hate Elsevier BUT ..

[fygment]

... note this interesting /. article: http://science.slashdot.org/story/13/04/08/2325234/fake-academic-journals-are-a-very-real-problem [slashdot.org]

So really, you need big-publishing if only to keep it all real.

Re:Of course you hate Elsevier BUT ..

[drosboro]

... except, of course, that Elsevier has apparently been publishing some of those fake academic journals themselves. See, for example, this comment [slashdot.org].

It may actually benefit Zoytero

[pesho]

Papers was picked up by Springer and now Mendelay is becoming part of Elsevier. This may have a silver lining for zotero. Papers, Mendeley and Zotero use CSL for formatting the references in the text. This means that the publishers now will have a very strong incentive to provides the CSL files for their publication, as they have done all along with the EndNote styles. Of course they can just be redirect their users to Zotero for styles or lock the export of CSL files to their preferred reference manager,