The following is a guest post from Ben over at Literature Review HQ.
I used a BiBTeX file, with every reference added manually. Possibly not the fastest, but it meant I knew exactly where everything was and what information was included. Anyway, over to Ben…
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What is the best reference manager?
I get asked this a lot. It’s a fair question and I’ve wondered it before. I’ve tested many reference managers and I’ve heard countless opinions from others about a huge array of software. So which is it? Which reference manager beats all the others? If you were starting a writing project today, which reference manager should you choose?
It DOESN’T matter
Sorry if that’s not the answer you wanted but it doesn’t and it shouldn’t matter. Asking the question “which reference manager should I use” is a huge red herring. A definitive answer to this question implies that there is a reference manager out there that will solve all your referencing problems. Frankly, there just isn’t. I don’t think this is necessarily a problem with the reference management software either (or at least they’re not entirely to blame). It’s all about the user. It’s about you and it’s about me.
Reference managers are tools and they are prone to errors, bugs, crashes and the rest. Some are better than others, but you can circumvent all of the problems with some careful usage and a bit of caution.
The reference manager is a tool but YOU are in charge
If you are a chef, the reference manager is your knife. It’s a useful and very important instrument. People surely have their favourites but in reality, there are a great number that will do the job very well. However, what happens if you put a good quality, sharp knife in the hands of someone who doesn’t know how to use it properly? Or someone who hasn’t been safety trained?
The answer is that you end up with a few fingertips in your food (or the literature review equivalent). The knife is important, but it depends how you hold it, how you move it, where you put the food and most importantly where you put your fingers.
Ok so you’re not going to get your fingers chopped of, but reference managers can be dangerous
- They can crash, taking ALL your data with them
- They may not be compatible with your word processor
- They may not format your references in the right way
- They may not be compatible with your literature database
- You can link pdfs to references, but you can only access them via the reference manager. What if you need to change or reset your software? Sorry, you can’t find the pdf’s anymore!
So how do you protect yourself from your reference manager?
A simple measure is to always backup your library in a universal format. I back up my reference library in a .ris format and as a BibTeX file. Together these file types can be used by most reference managers. This means that if something bad happens you can simply transfer your library to a completely new software. Back up your library often and you’ll be ready to switch at the drop of a hat if it is needed.
Another measure is to always save pdf’s of articles with a file name that makes sense and is searchable. I always include the year of publication, the authors name and the journal title. This means that even without the reference manager, you can still tell which pdf is which. Yes this is more time consuming but it also makes you think more carefully about which references to include in you bibliography. A considered approach from the onset is much better than a “reference now, ask questions later” mindset.
Using these two simple methods, I have managed to change between reference managers with practically no disruption. It’s a good exercise even if you don’t want to change. It makes you realise how simple it is to change and how you aren’t reliant on one particular reference manager.
At the end of the day, some people use the same reference manager for their whole career. They look after it. The software works for them and they are happy. Other people like to change, try new technology and see if there is something better out there. Both these approaches are fine. The most important thing is that you always back up your information and keep it safe and accessible independently of the software you currently use. Hopefully the worst will never happen, but if you don’t back up it could cause you a serious headache in the future.
Some good “knives” that I’ve used
- Endnote is pretty good for citations and ubiquitous
- Mendeley for finding new articles
- Papers for finding papers and citations
- Zotero handy browser integration
- Qiqqa useful built in OCR software
- JabRef basic but reliable
What do you use, and why? Leave a comment below…
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I use EndNote because it was free, it does what I need and I don’t backup/access it on the cloud/web but on my desktop PC and a backup stick drive. Until I have a major issue I’d rather not spend too much time learning a new system- and as people have said above the need to edit sometimes helps me remember entries. It’s common enough for most ref systems to allow exporting into it from the web which is handy- even from GoogleScholar which speeds up manual refs. My library is too large for some of the systems above (2-3GB)- caused by my doctorate being an EngD with 15-odd taught modules! (We end up with module specific refs that only sometime get reused in the research project- and I find it better to keep it all in one place).
I think the word processor program and its compatibility can be more of an issue. I have some fun with Word but have found a very useful site that let me manage it and EndNote together; so far enough to get me to the confirmation viva successfully. See for example: http://www.shaunakelly.com/topic/word/numbering
I’m expecting some issues later with the main thesis being larger and more complex, and may switch to Latex for my text as advised by colleagues- so thanks for the backup hints on generic reuseable formats! I don’t know if that works well with EndNote…
I am surprised nobody has mentioned Sente yet. Available for Mac only, it is years ahead of all the other apps out there. It integrates reference management, comments collections, and pdf annotation in one single app which uses mac bundles. plus it has an ipad version and offers sync over their own server.
I’m fairly new to this having only started my lit review a couple of months ago, but I am loving Papers which works brilliantly with my mac. Took me only a short time to learn and I have my Pdf’s backed up on my C drive and separately as well. I tried to download and run endnote initially which my uni provided for free, but had no end of problems with the mac version. The student discount with papers was great value and well worth it.
Hi,
I used Papers for the Mac. I did try Mendeley and even (gasp) Endnote. But I found Papers to be the easiest solution for all in one storage of PDFs, annotation and citations
Kind-of does matter….
1. Do you need to collaborate with others on your research? Share a library?
2. Will you need to use Nvivo or other similar software? Nvivo can only import bibliographic references from some ref software and versions
3. Does your uni subscribe & provide to free to students certain software? Our library offers free workshops in the software- being a master of whatever software is important.
4. Can your software “find full text” and attach the PDF automatically from entered references? PDF’s are important for your literature review.
5. Can you make notes? export notes? share notes? Do you need to be able to do this?
I agree it doesn’t matter so much which one- but there are some questions you need to think about before choosing one.
Good point!
Mendeley all the way for me. I love that I can access my library from anywhere so I don’t have to worry about taking papers with me wherever I go.
I think it’s extremely user friendly, which saves time having to learn how to use the software.
I’ve never had any issues with adding references in MS Word for Windows (even on evil Windows 8 which most other software seems behind on).
Has anyone heard of scrivener or activescholar’s reasearchwriter? They seem to be the newest kids on the block for PC-related research collection.
I use citavi since it offers a knowledge management tool. Additional to the storage and structuring of articles, books, etc. it provides the possibility to assigne so called categories to each article or citation I wand to make. So I can concentrate on the reading and notetaking (noting what I want to cite) and subsequently I can concentrate on writing since: Citavi provides a printout of all categories and respectively their assigned citations I want to make. The only thing I need to do then is “filling” text/arguments etc. “around” the listed citations
Qiqqa is comprehensive. Interface is cluttered (but has improved).
Currently I use BibDesk http://bibdesk.sourceforge.net
It’s for MacOS and came in MacTeX.
BibDesk has a nice interface, integrates with spotlight (for search), and also helped me to put some order with the automatic key generation and renaming of a bunch of pdfs, ps and other files that were lying wildly in my disk (it was just a matter of dropping files).
It also has connections to search engines like DBLP and Web of Science, and a bunch of other useful bits, all this without cluttering my bib files nor meshing with my pdfs.
I’ve tried Mendeley and Zotero, but I prefer to have my bibliography offline and just modify a single bib file with another editor if needed. I don’t remember which one was capable of inferring bibliographic data from files, and that is the only feature I want to see in BibDesk, but now my files are tamed so it is not such a deal breaker.
I have been using Mendeley with great results for me PhD
I don’t have to go fetch the references online, I can just save the PDFs wherever I am.
But I most certainly agree about manually checking your references before submitting or even just once a week to make sure that any reference program is inserting them correctly and that the format is correct.
Hi, I see that REFworks is not on you list? It is the one that my university subscribes to, together with “write n cite”. I have had a few errors with it when I try to update references on the document. Have you ever tried it and what is you opinion?
I haven’t used it, anyone else?
I’ve tried RefWorks but one of the things that put me off was the fact that it doesn’t (or at least at the time didn’t) have a ‘Write-N-Cite’ utility for Linux. Incidentally, my university also has a RefWorks subscription. You might be interested in checking out this [1] comparison that the guys at Mendeley put up… they did a pretty good job of comparing five of the most widely used Reference Management application software.
[1] http://goo.gl/DbFYv
I’m a Mac user and I use a combination of Bookends and Mendeley – Mendeley manages my PDFs and it does the file rename trick for me – so if Mendeley dies, my PDFs are all there. Bookends has great integration with MS Word and it scales – I can write documents that are 100s of pages and it will still work!
I agree with the always back-up.
And I agree, the best reference process is the one that you will USE – and that you have to take responsibility for the quality of the data in your system. If you don’t double check spelling and capitalization, then the software can’t help you!
I love Mendeley. It syncs between devices and to the cloud, so I don’t need to worry about backups. I also allows me to create project specific folders and share them with my collaborators.
Cheers,
Julio
I’d be reluctant to rely solely on the cloud for backups… You’ll probably be fine, but I’d always have it backed up somewhere else just in case.
I’ve been bit by Mendeley – it is open source after all – if you find a bug, it can take them a long time to fix it. I love it for managing my PDFs (drag-and-drop and it automatically harvests the information and renames the files for me), but I find it is clunky for integrating citations into a Word document (I use Bookends for that – but I’m on a Mac).
Unfortunately, Mendeley is not open source. They have published the details of their synchronization api, but not the source code of the desktop applications. If it was open source someone would have fixed the following problem (because a lot of people have this problem).
I tried Mendeley for a while, but they fail at bibtex integration. For this reason, I had to choose a different reference manager as I only ever write using Latex + Bibtex (or biblatex).
My current reference manager is CiteULike which does everything I want. It’s fairly simple, but it can collect details of articles from just a doi, or just authors and title. It’s entirely web based as well, so you don’t need to keep syncing. Finally, I can always export the required .bib file for writing my articles.
My money’s on Mendeley. I remember trying out Zotero, Mendeley& RefWorks when I first got into graduate school and eventually settled for Mendeley. I used to be an avid LibreOffice user until I transitioned to LaTeX a few months ago… I loved the LibreOffice Mendeley plugin, but I still find the export to BibTeX feature built within Mendeley quite helpful when preparing manuscripts using LaTeX.
That’s not all though, I can annotate, highlight and add text to items in my library. And above all, I get to have 1GB of free storage space as opposed to the 100MB zotero gives out… I should mention here that my bibliography library is 319MB in size.
James, I think adding references manually to a BibTeX file is actually a great approach. Spending time to physically process references can help you process them mentally and remember what they are about. I always find that the “one-click” solutions make it too easy to build up an unmanageable list of useless references.
It worked fine. I spent a whole day going through a stack of papers and typing the details in… It was incredibly boring, but once done it was easy to use and update.
True it doesn’t matter. But my vote still goes to Zotero.
I like Zotero too. As long as you’re happy with your ref manager and you make backups that’s all that matters.