The Beginner's Guide to Choosing A Reference Manager

This article presents some information on reference management software: what a reference manager does, why it is good to use one, and how to go about finding the right reference management software for you.

This overview is aimed at the novice writer who wants to learn about reference managers in general. I think three groups of people in particular may find this information useful:

  • You are in a situation that requires the production of research-based texts, such as Wikipedia articles, blog posts, term papers, journal articles. Maybe you are starting your higher or further education, or are in a new position that demands the production of reports.
  • You are a novice writer, looking for tools to support you in your writing.
  • You are an experienced writer interested in new tools to facilitate the demands of larger assignments.

If you are an experienced writer and know your workflow already, you might find the more comprehensive guide on choosing a reference manager better suited to your situation.

What is a reference manager, and why should I use one?

A reference management software (also known as citation management software or personal bibliographic management) is an application you can use to

  • store & save,
  • retrieve,
  • organise, and sometimes even
  • search for bibliographic information, i.e. references, quotes, source materials etc.

In addition to functioning as a catalogue for reference materials, most reference manager allow you to annotate those sources, manage their files, and help you import search results from online collections of publications, academic databases and search engines, such as Google Scholar & Google Books, ScienceDirect, JStor, Project Muse, and so forth.

The good news is: there is an abundance of reference management software out there. Never has there been a better time to pick and choose what’s right for you! However, there is no one-size-fits-all solution, as the kind of application you are looking for depends heavily on how you use it and in what contexts you will work with it.

As a novice or inexperienced writer you have to overcome three main hurdles to find the right reference manager for you:

A. You may not realise that / why you need one, i.e. what it can do for you.

B. You don’t know your writing process and workflow yet, so it can be challenging to find a tool to fit the process you’re discovering as you go along.

C. As your don’t know what to expect and don’t know which features you will end up using, the sheer amount of options can paralyse you to the point where you give up on this very helpful tool altogether.

This guide tries to give you all the information you need to get you started to find a good enough reference manager that suits your use case.

Welcome to software (& writing) boot camp

Putting every piece of reading material into a database may appear to be an unnecessary overhead to the wormhole that is writing. Especially when you are at the beginning of your writing life, and all you have to produce are 2,000 word essays or five page term papers.

However, the requirements for your text production are likely to change as you progress. This makes these small scale writing projects a fantastic test field for trying out different approaches, processes and software. While you test, mix and match different styles of working, you will develop your personal best practices. By the time a large new assignment lands on your desk, you will have a trusted workflow, a system and known tools in place. Thus sorted out allows you to focus on the already challenging tasks at hand without worrying about learning a new system or finding the right software.

Advantages of using a reference manager

I will focus on the general aspects that should be covered by all up-to-date reference managing applications. Depending on the software you use, a reference manager can do a lot for you:

  • You can keep track of where you got a source from, which library lent it to you, which friend recommended it, whose gift it was etc.
  • You have one place that stores all your references; they are not buried in several documents.
  • Once stored and captured in the system, the information is re-usable.
  • The data is portable and future-proof. Should the developer cease to maintain or support the software, you can transfer your references to another reference managing application without losing the data.
  • The separation of the text and the sources itself means that you can easily share those references, or any subset of them, with your supervisor, colleagues, class mates etc., instead of maintaining lists of files or nested folder structures manually all over your hard disk.
  • You can organise and annotate your sources, group them freely, thus having an easier time finding it after you forgot the specific title or author.
  • Most software does support file management, so you can associate the reference directly with the corresponding document.
  • You can import reference lists from search engines, such as Google Scholar or ScienceDirect, which often eliminates the dull process of transcribing the data.
  • The manager provides snippets and short codes for each reference, so you don’t have to type the full reference or bibliographic entry every time you want to refer to it. You just use the snippet and the software pulls the correct entry from the database.
  • If you discover a typo or false information in your reference, it is easy to fix it because you store the reference in one place (which serves them to other applications). Fix the entry once and see the correct version displayed in the documents that reference the item.
  • Producing a list of references manually is a tedious and error-prone task: where do all the commas, colons, brackets and full stops go? Was it the title or the publisher that’s supposed to be in italics? What if the professor says MLA style is fine, but decides later on that he wants you to use APA style no matter what? A reference manager can produce any supported style format in less than five mouse clicks.

This is by no means a comprehensive list of the goodness a reference manager can bestow upon you. However, it illustrates that an application handling your references is more than a fancy addition to your application folder. It is an essential app in the writer’s tool box. If nothing else, a reference manager helps you to avoid errors in the process of collecting and referencing correct data.

Finding the candidates

In order to find the software you will take on a test drive during one of your smaller writing projects, you’ll want to know what your needs are. The number of potential reference managing software can be quite daunting. As a novice however, we can assume the following constraints to find a manageable number of test candidates: you are looking for

  • an easy to use, easy to set up software with a friendly user interface
  • a stable application that is developed and maintained on an ongoing basis
  • support for a number of import and export formats
  • support for the bibliographic styles necessary
  • integration with your preferred writing environment, text processor or text editor
  • support for the source types and bibliographic items you’ll need
  • support for open and standardised file formats which allows us to use the data with different software packages
  • a student friendly price tag

In addition to these general assumptions, you have to ask yourself in what kind of environment you are working:

  • Can you ask a friend, who already uses a reference manager, for help?
  • Do you have to share, collaborate on or be particularly portable with your references?
  • Do you use some kind of niche writing environment?
  • Which platforms are you working on? Do you need a platform-agnostic tool, or possibly one that runs on a USB flash-drive anywhere?
  • Do you want to access the data from anywhere or will you only work on your personal computer?
  • Do you need integrated search functionality?

The last set of questions is looking at your personal preferences. This is where you definitely have to test and see for yourself how you interact with the software and whether it supports your habits.

With some of the features one may have to accept a compromise; you should definitely separate must-have-features from nice-to-have functionality. Maybe sharing a database with your team is an absolute must-have, whilst support for document management is not.

The application should, however, be comfortable for you to use. If the software gives you headaches, or if it feels like an assault on your design sensitive eyes to even look at the interface, you will end up not using it.

I won't say the application has to be fun to use, but you should try to find a software that does not feel like another hassle on your journey to the written text.

Testing the candidates

As a rule of thumb you’ll want to test everything you’d want to use the application for, plus all the functions that are potential life savers. For instance, if you plan on managing all your references with the software, producing your bibliography and citing your sources, you’ll test

  • data entry: Does it support all the source types you’ll encounter, such as Web pages / electronic sources, reports, papers, books… ?
  • data import: Does it import properly from the catalogues you use?
  • data management: Can you tag or group your references as you like? Is the search functionality good enough?
  • bibliography export: Does it support the style format(s) you need for your list of references (e.g., APA, MLA,…)?
  • cite functions: Does it give you all the types of citations you’ll need (e.g., full cites, short references,…)? Does the software integrate well with your favourite writing application, text processor or text editor?

The life saving functions you want to test before you’ll ever need them, are:

  • any backup features: Some applications have an integrated backup feature. Try it and find out what kind of backup it generates. What can you do with this backup? Is it a standalone thing or will you need the precise software it was created with to use the backup?
  • data export: Which export formats are supported? Is the export usable and easy to import into another application? How big is the export file?
  • import: If this is your plan B, second-in-line, go-to-alternative-software in case your reference manager explodes on you: test the import features. Is the import clean? Do you have to manually adjust a lot of stuff, or can you import and just run with it?

This is not a comprehensive list; the features you'll want to test are the ones you’ll plan on using later, so be sure to try first before you trust!

Where to start?

I found the following applications to be a great starting point for further explorations of the reference manager landscape. The list of suggestions is skewed toward Mac OS X apps, simply because I am a Mac user and haven’t had the opportunity to test a lot of Windows or Linux software in that space recently.

Wikipedia has a full list of applications as well as a feature based comparison.

  • JabRef — cross-platform, runs from a USB flash-drive; offers a functional user interface and is quite actively translated into languages other than English.
  • Mendeley — great community with a reference manager, cross-platform; one of the fastest growing science and research communities online.
  • Papers — fantastic manager for Mac OS X / iOS; great for search, import and working with PDFs.
  • Sente — «iTunes for references» for Mac OS X / iOS.
  • BibDesk — powerful & friendly BibTeX editor / interface; I’ve been using it in combination with LaTeX / TeXShop for over 7 years now and it never let me down. Actively developed since 2001.
  • Bookends — Mac OS X; integrates well with Mellel, Scrivener, DevonThink & OmniOutliner; the user interface is functional.
  • EndNote — for Windows & Mac.
  • Citavi — for Windows; free up to 100 references; this is not enough for larger projects (thesis or dissertation scale), though.

In addition to stand-alone software, there are several online communities and Web application that help you organise your references.

  • BibSonomy
  • CiteULike
  • Connotea
  • Zotero — is a tool of its own: the fully fledged reference manager is a Firefox extension; it provides a lot of features but depends on the Firefox browser. They are currently developing a standalone version for the major platforms. You can have a look at the alpha version; be aware that alpha software is not save to use in a production environment!

I have not tried any of them, except Zotero, but again, this is no testament to their usefulness. I just never had a need for that sort of thing.


How do you go about finding the right reference manager for you? There are three steps you can take, to find the right application:

Step 1

Ask yourself questions about your writing environment, the necessary functionality and the resources (both time and money) you are prepared to invest:

  • Find out what you need: What are the must-have functions you need to cover? What are the most important features for you?
  • What are your constraints (e.g., budget, are you a Mac, Windows or Linux user…)?
  • What are your personal preferences: What nice-to-have features would you like to see?

Step 2

Rally up the candidates and prepare a small set of test data. Dedicate a certain amount of time to get to know the likely candidates. Don't go overboard here! You do not need to know or test every single function the application provides.

Have a look at the preferences to see how easy it would be to adapt or adjust functions or the user interface. Are the default preferences straightforward and fit for your purposes?

Explore the user interface. Find out whether you can work with it. Does it behave as expected, are you comfortable using it? If so, have a look at all the tasks you'd want to perform with the software; try and test the standard use cases. If this goes well, have a look at export and import features as well as backup functionality.

Step 3

If an application proves itself functional up to this point, consider the nice-to-have features. Compare the applications you played with. Is there a clear winner or loser?

In case you end up with several worthy candidates, use each one on small real-world projects. The day-to-day use cases reveal usability issues that may not arise in your test session.

For instance, if there is one task you have to accomplish frequently and this function is hidden in the third subsection of a tiny menu within a bloated and obscure context menu… it may take you some time and five clicks or more to reach the menu item and perform the task. This complicated interaction may not seem to be an issue whilst testing on a small set of sample data. But be assured that this sort of thing will drive you crazy pretty soon once you realised its implications for larger sets of data.

The lesson to take away is: It is ok to adjust some of your working habits; it is absolutely normal to learn new tasks or workflows as you adopt a new software. But your focus should always be on how this supports your writing, not: how do I get out of this programme ASAP? If that is the case, you better find another software that suits your scenario.

I hope this introduction gives you enough information to go out on your own and find a suitable reference manager for your needs. If you are up to digest even more information about this subject, have a look at the comprehensive guide on choosing a reference manager which is intended for advanced users of such applications.

Details & meta

Fri, 17/06/2011 - 14:39