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Universiteitsbibliotheek – LibGuides

Reference management: Introduction


The information in this libguide will be updated coming August 2021.


In this LibGuide you will find extensive information about managing your literature, which methods and programmes are available and which suit your purpose best.

What is reference management?

Reference management is systematically collecting, organising and using references to sources. How to do so in the most efficient way depends on the type of sources you use most frequently and also on your personal workflow and preferences.

Why reference management?

Good reference management is an enormous help in retracing  what you have seen and read. It also helps you to reuse, add annotations to and share your references. Moreover, it leads to accurate citations. In short: good reference  management enables you to work more effectively and efficiently. 

Ways to manage references

There are many ways to save and organise (references to) sources/literature:

  1. To save print/hardcopy versions of papers and books
  2. To download full text publications and saving them in folders on your hard disk or in the cloud
  3. Just save favorites/bookmarks in your browser
  4. Just save favorites/bookmarks in a social bookmarking tool such as CiteULike
  5. To make simple lists in a text document, spreadsheet or using general database software
  6. To use a dedicated reference management tool such as EndNote, RefWorks, MendeleyZotero or one of many others

Tools for reference management

There are dozens of dedicated reference management tools. The best known and most widely used are:

  • Mendeley, a free tool primarily built around a full text workflow, with good synchronisation between the desktop application and web interface, with a built in PDF-reader and strong social functions.
  • Zotero, a free, independent and open source tool, with very good ability to recognise and capture bibliographical data on webpages.
  • RefWorks, a complete tool, licensed by Utrecht University, supported by many search engines and databases with fast and reliable direct export options, but, being a pure web service, sometimes a bit slower and without a good full text workflow.
  • EndNote, also very complete and professional, and with almost unlimited sharing functions; there is a UU-license.

To help you choose the tool that best suits your needs, take a look at our comparison tables.

Whatever tool you choose, it is always relatively easy to switch at a later stage and import your references in another tool.

What to consider when choosing a reference tool?

  1. How accurate does it have to be? If completeness and accuracy of your references is important, the best choice is a system that either supports direct export by many search engines (RefWorks, EndNote), or a tool with accurate scraping (Zotero, and to a lesser degree Mendeley) or a tool that allows importing PDFs and extracting the data from those search engines (e.g. Mendeley, Papers, Flow, Zotero stand alone). When these options are not available, the most reliable way to import bibliographic data is to travel the long route ( first saving data in a file and then importing that file).
  2. What scholarly search engines do you use regularly? Check whether the tool supports easy and reliable importing from your favorite search engines and databases. You can use our comparison tables or check for yourself.
  3. Do you often work in groups or write papers together? Most tools support some sort of sharing of references or files, open or in groups. However: here the details really matter: do you want to share with people using the same tool, or also with people using other tools? Do you want to be able to share annotations added to your PDFs? Do you want to share with large groups? Do you want to be able to share with several groups? If sharing, working together in groups or co-authoring is important to you, these functionalities should be checked carefully. Also the options you have here depend on the type of plan/license you have.
  4. Are you a PDF-collecting type of person? Are you someone who always downloads full text PDFs, just to make sure you do not lose track of  them or because you can add annotations to  those PDFs? Or are you someone who just saves links/references because you know you can always retrace and download them later on? The first method is better supported by Mendeley or Zotero, the latter by RefWorks (also considering that RefWorks supports the UBU-link). Please also consider that often you lose access to paywalled literature when you leave (this) university. Having you own full text library of favorite papers can be asset.
  5. Do you write systematic reviews? If so, you probably download lots of references from various databases and search engines and may want to deduplicate them. Deduplication with purely web-based tools may be cumbersome and sometimes produces time out messages. Also the exact deduplication algorithm and options for fine-tuning may be important.
  6. Do you often use grey literature / reports or do yo often use niche literature databases? The web is a great source for reports and other grey literature. However for this type of literature standard options to import the bibliographical data are often lacking. The same holds for some of the smaller literature databases. In those cases it is nice to be able to rely on good web page scraping functionality. Zotero is leading here.
  7. Do you expect to be an intensive user of the tool? Hardcore users benefit from tools that are available as desktop application (with optionally also a web interface). That type of software has the edge in speed. You can choose either Mendeley, Zotero stand alone, Colwiz, Papers or Endnote.
  8. Do you work on many different computers/devices? Then either a pure web based tool such as RefWorks or a tool with good synchronization of locally installed software (e.g. Mendeley) may the best choice.

To comparison of tools

How reference management tools can help you

With reference management tools you can:

  • Collect bibliographic data from search engines and databases
  • Save and store full text files such as PDFs
  • Organise references in (smart) folders, use tags etc.
  • Annotate references or full text files
  • Share references or files publicly or privately with a group
  • Cite references

Additionally you may sometimes:

  • Profit from (topical) communities
  • Work on the same document with co-authors
  • Share accounts or make multiple accounts
  • Perform advanced tasks such as deduplication

Three tips to work more effectively

These tips will often speed up your work:

  1. Invest in using a dedicated reference management tool if you use more than a handful of references and expect to write more than just one paper.
  2. Use a tool that also supports citing references in your text editor, especially if you write a lot.
  3. Always check and see if the reference data your tool has imported are complete and correct. For some databases and tools there are instances when you have to correct or complete the data.