Wednesday, January 5, 2011

Long delayed Mendeley review

Way back in August, I started playing around with Mendeley after getting annoyed with Endnote. I said that I would write up a review after I had been using it a while, and I think I have enough experience with it to compare it to Endnote.

There are many things I really like about Mendeley. I really like reading papers in it, since I can save notes about the paper that I can search and share if so desired. Searching inside pdf files also works very well, and it is much, much easier for me to use Mendeley than to try to remember which paper I was thinking of and then open it in Adobe Reader. I never really got into Endnote's pdf features--the pdf search and import features were buggy and irritating when first introduced, so I never got into the habit of using them.

The pdf import feature in Mendeley works very well for me. I was able to convert over most of my library directly from my pdf files. This also works well with my new literature review system. Now that I am trying to use RSS to keep up, it is very easy for me to download pdfs into a directory that Mendeley watches. I also use Web of Science for searches and download pdfs through there. This is a huge improvement from my old system of exporting Endnote data, then importing the reference, since bibliographic imports happen automagically. Correcting errors in imported files is really easy, and can be done manually or via Google Scholar search. I spent a bunch of time initially correcting entries, but now I don't really have to. There is a pretty decent time investment in importing hundreds of pdf files at once, especially if you want to be able to properly search by author (since the author names MUST be imported properly for this to work). I did not try importing my Endnote library, but that is another option.

There are a few downsides I've found to Mendeley. I find the cite while you write interface a little clunky. It is not unusably so, and it is really easy to find the paper I want to cite using Mendeley's search functions. I thought the same about Endnote's interface, so this wasn't a major downgrade for me. One minor quibble--it is not possible to do unrestricted edits in the bibliography generated by Mendeley. This is something I have only just started playing with, so I am not sure what exactly I did to cause Mendeley to complain about it.

One big issue I discovered is that Mendeley and Endnote DID NOT play well together in one document I was working with. The references got corrupted and I had to strip out all the references and redo it all using just Endnote (since that is what my collaborator uses), which was really annoying. This is hopefully just a minor glitch for me, but may become a problem when I am writing with collaborators who still use Endnote. I haven't had this problem in some of my own documents (updating old proposals, for example). I plan to avoid on using two reference management systems in the same document as much as possible, but be careful if you do!

Mendeley was very disappointing in one area, and that is in keeping a library synced between two computers. I used to use a laptop and a desktop, and I tried to use Mendeley to sync my library between them, but this caused me lots of grief. I had lots of duplicates in my library, and Mendeley sometimes lost track of where the pdf files were on my laptop. I have solved this problem for myself by switching to using one computer (a laptop with a dock), but this seems like a feature in Mendeley that needs a lot of work, but could be very useful.

I don't really use the online features of Mendeley much, but in theory, you can grab citations while surfing and also have access to pdfs through the Web interface. I am not sure how well this works, since I always download pdfs when I want to cite and/or read something, but this is something that might be useful to people who use Google Scholar for searching and/or don't always work on the computer where their pdf library resides.

In short, I am keeping Mendeley. That it is free is only icing on the cake!

UPDATE: Thoughts on the latest update here.


Bashir said...

I've been using Mendeley for a a while now. The desktop works well for what I need, general article cataloging. I think the online part has potential, particularly the groups.

Mr. Gunn said...

Hi Prodigal! Glad to hear you're getting along well with Mendeley. I'm a little worried that you had such problems with the sync, though. That isn't a part of the service that many people have trouble with. I feel certain that support could sort things out for you in a hurry if you'd drop them a quick email describing your setup, what you did, and what didn't happen that was supposed to.

It's unfortunate that Endnote and Mendeley can't work together on one document very well. They both expect that they're the only one being used, and there's currently really no way for one program looking at a document to know that the other one may be used in the future. A common citation insertion format would help, but I expect that Google will get there first by adding some hooks to the Google Doc API, so programs can work peacefully together.

Thanks again for the nice review and let me know if I can help with anything else!

GamesWithWords said...

Hi Prodigal. After reading this, I tried out Mendeley. I have to say it didn't work as well for me as for you. The PDF library part was ok. The lack of smart collections and the buggy searching was mildly annoying, but it has some other good features. So compared with Papers on that count, I'd say it's a wash. But when it comes to citations, it can't handle APA format *at all*, so I still have to use Endnote anyway. Perhaps they'll fix it eventually. I don't know what kind of citation format you use, but I take it that works better.
Full review here.

prodigal academic said...

That is too bad--Mendeley has all the bibliographical formats I need, so I didn't even consider that issue. To be honest, if I could switch to a Mac for everything, I would probaly use Papers and Endnote too. Mendeley is much better than Endnote for me, and replaces most of the functionality of Papers, but Papers is more polished.

Candid Engineer said...

I recently switched to a Mac, and have had so many problems with Endnote crashing Word documents in the past, I just wanted to switch. Also the fact that they release a new version of their software every 5 weeks, which really pisses me off.

I can't seem to get Papers without straight up paying for it (the sellers oddly do not take Purchase Order #s for single-site usage). So I decided to try out Mendeley. I haven't had any real problems with it so far, but I haven't tried the Cite&Write because they haven't yet made Mendeley compatible with Office 2011 for Mac. So I'm waiting on that one.

Anonymous said...

I had the same problems with Word/EndNote. I made the switch to LaTeX a year or two ago in part so that I could use BibTex for references. I have been very happy withthis approach for citations, but keeping track of pdfs and notes is still a struggle.

Mark Lynam said...

Hello hello. I've been using EndNote, dabbled with Mendeley and Zotero, and am now using Citavi. I'd love to hear from you and others if you decide to give Citavi a whirl. It's been around awhile, it seems, though this their first release in English. I really like the ability to make notes, extract quotes and tag my research literature. More info at citavi*dot*com.

chasjonesaz said...

I have been using Mendeley for about 1 year now and I really like parts of it, and really don't like other aspects of it. I haven't been able to successfully sync with my online databases for at least 4 months. I emailed Mendeley and they got back to me very quickly once asking for more info. When I sent it to them the next day, I never heard back. Emailed them again later and never heard back. I really wish that we could make custom citation formats, but I've been able to find similar formats to the ones that I want to use. Its a pain to figure out, although they are getting more and more citation styles over time. I should also be able to edit my citations or bibliography in MSWord after inserting them, but I just copy and paste as unformatted text when I need to make my edits. That's unfortunate too. I really like the same features that the blogger notes. Mendeley also has a major fail in that you cannot copy your entire database to a file to synchronize your database onto a new computer. If you get a new computer, you can bring over all of your citations, but your PDF's are no longer linked to those records. I think that most of my PDF's were automatically linked up when I got a new computer, but it definitely was not without a lot of angst.

Anonymous said...

I have just started using Mendeley and I found your blog. Just wondered if you are still using Mendeley or not - how did it go? Do you have any tips or suggestions?

Anonymous said...

I use Bibtex for myself but with colleages we started to use Mendeley to store our production. What I haven't found out yet is how to search the bibliography and select references according to specific criteria. Basic data base things... Mendeley really only has the free Find command? Anyone know?

Anonymous said...

Never got the hang of Endnote, it feels like a massively illogical programme to me, but I've used Qiqqa and Mendeley and tried Citavi a little.

Qiqqa has interesting features, like the automatic OCR and the filling of metadata through google scholar, but it's mainly aimed at the humanities and IMO is not ready for primetime yet (e.g. it can not handle ä, ñ and similar characters). Qiqqa also does a *very* bad thing in that it adds its logo to all PDF's, causing image degradation.
Mendeley is more stable and good at most things but its syncing is bugged (dupes multiply), it can not import metadata via google scholar, and the monthly payment thing is annoying.
Citavi is the possibly most stable and definitely prettiest of them, but it is very basic and lacks a lot of features.

If one could mash these three together one could create the ideal PDF & citation manager, but as of right now they're all missing or bugged on important features.

Maybe things will improve when they've had a year or two more to mature.

Anonymous said...

Hi All, I am about to choose one of the programmes which have been reviewed here. Great help. I was wondering whether you know if Mendeley can be synced now with Mac Microsoft 2011? I am inclined to download Papers, I had a trial version and had a glimpse, but I a don't know it well enough. Which on is better for Humanities? Does Papers work on more than two computers?
Thanks lot!@martarabikowska

Anonymous said...

It's alright but nothing special. It doesn't convert to MLA format properly. It doesn't record articles from sites such as JSTOR correctly. It omits the website name and lists it as 'Print' instead of 'Web." It also messes up the author names.

For example its version: Author, Gradgrind et al. “A Plea for Gradgrind.” 3.1973 (2008): 196–205. Print.

Correct version is Author, Sadrin Anny. “A Plea for Gradgrind.” The Yearbook of English Studies, Vol. 3 (1973): 196–205. JSTOR. Web. 18 May 2012.

So not that great really.

Imtiaz Habib said...

The comment above that "Citavi is very basic and lacks a lot of features" is inaccurate and uniformed. I have been using it and find it to be far more capapble and flawlessly desgined than ANY of the other programs, including Mendeley and Qiqqa which are its closest competitors although it is the priciest (worth it I think, am about to buy it).

Anonymous said...

Struggling with Mendeley daily and need to vent.

Mendeley is the only reference management software I've tried. In theory, it has a lot of awesome capabilities. I wanted something that does more than just organize citations, but also manages my actual document library. Mendeley does this with some very convenient features (automatically sorting documents into folders on your computer, etc.)

In practice, though, it is irritating to use because it is incredibly slow and crashes constantly. The Word reference plug-in is glitchy and often causes Word to freeze, resulting in lost work unless you're very diligent about saving frequently. In general, I feel like I spend half my time waiting for Mendeley to process something or other.

It was also quite difficult to create a workflow that involves Dropbox and iAnnotate on my iPad. I don't use the Mendeley not taking and annotating stuff because iAnnotate is so much better. This is how I do all my reading and annotating, and I wanted a system that allowed those annotations to be automatically saved in the documents in the Mendeley library on Dropbox so that they'd be accessible from any device. However, opening a document on iAnnotate through the Mendeley iPad app automatically downloads a duplicate to the iPad, meaning that accessing my library through the app is pointless. I have to make a note of the author, go into the actual Mendeley library folder on Dropbox, and open the file from there. A detour, but doable. Took me a while to figure out, though. However, I'm left wondering what the point of the app is. You can't get it in a flow with Dropbox and iAnnotate, and it provides only a fraction of the organizational capabilities of the Mendeley desktop on my PC.

Also, I too always download PDFs, and grabbing JUST the citation from the internet while browsing is kind of pointless for me. I don't use those functions anymore.

Overall, functional but annoying. Then again, Mendeley is trying to do it all, so I guess I should try to be more generous.