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Reference Management: a Practical Guide

Reference Management

This is a practical guide to help you organise your citations and papers using reference management software.

Reference Management: a Practical Guide

Reference management applications allow you collect, organise, and cite material in your work, providing a useful way to keep track of your reading. This practical guide looks at the key processes and features of the reference managers available at the University of York.


How to use this guide

This guide has been designed so you can work through it like an online workbook. Wherever you see a box with the pencil icon, you'll find suggested exercises to complete once you've read over the content on the page. Use the menu at the top of the page to navigate between the different pages.

Each page covers general information as well as specific guides for each of the three main applications supported at York.

This home page is here to provide an introduction to reference management and help you decide if these applications are right for you and which reference manager to use.

Introduction to reference management applications

Why use reference management software?

Reference management software helps you to keep track of your reading and references and makes it easier to find referencing information to cite material in your work.

Using reference management software can save you time compiling and locating your references, and improves consistency and accuracy. However, it isn't a replacement for checking the accuracy of the references you use or for knowing how your references need to be written to comply with guidelines.

What can reference managers do?

Reference management software allows you to:

  • collect references and store them in a library on your desktop or a web account
  • organise references with folders and tags, to sort them by topic/project/author etc.
  • add notes to your references - for example, in order to remind yourself of particular quotes to use
  • store full text PDFs and links to material with references
  • cite your references and create bibliographies in your chosen citation style (e.g. Harvard, APA, Vancouver)
  • share your references with others and create collaborative libraries of references

How does reference management software work?

In short, reference management software collects bibliographic information from other sources and stores it as part of a library shown in the software. You can then use the program to manage these references, including organising them into folders and attaching/viewing PDFs. These references can then be cited in written work, whether through a plugin that works directly from the reference management program to a text processing application or through a copy and pasting method. References and libraries can also be shared with others for collaborative working.

Choosing your reference management process

Reference management is a process that starts whenever you do any kind of reading, research, or exploration of a topic. You need to keep track of what you need to read, what you might read, and what you have already read. This helps you to keep on track of your reading and also means you have the right information ready for when you need to cite material in your work or create a bibliography of what you'd read.

Maybe you've already got a process for keeping track of your reading or maybe you're feeling overwhelmed. Take a moment to reflect on what you do to manage what you read and cite. You could use our suggested Action Plan below which has some prompts to help you consider your own process and if you need to make any changes.

If you decide to use a reference management application (as this practical guide covers), how do you choose one?

The action plan questions will help you reflect on what you need from an application. Maybe you need to be able to easily store full text PDFs, or be able to organise your references into categories. Possibly you're looking for a tool that will cite in Word or Google Docs, or work well across different devices. The summary of each reference management application can then help you consider the key features of each.

Bear in mind you might need to try a few approaches or tools until you find what works for you! You might even want to use different methods for different pieces of work, depending on what suits you. It's all about your own process and what saves you time and effort rather than making things harder. And you can always export your references out of one tool and into another!

Stages of reference management

This guide focuses on four stages of the reference management process: collect, manage, cite, and share.

Reference management is best to get on top of at the start of reading, so you can ensure you keep track of material you read or discover. However, this guide can help at any stage of the process, and you don't have to use reference managers for every part of this process. For example, you may want to use the software to store and manage your references, but manually write your references in your work.


Under Collect you'll find how to gather references in a reference manager from databases, library catalogues, and elsewhere.


The Organise page gives information on sorting your references within the application, putting them into groups and checking for duplicates.


In Cite there is guidance on how to use reference management software with text processors to cite your references when writing.


And finally, Share explains how to collaborate on libraries of references or share certain references with others.

Reference management applications

The University of York supports three different reference management applications: EndNote, Zotero, and Paperpile. All of these can be used on University managed PCs and also installed on your own device (though some are limited to whilst you are at the University).

Each section below goes over the key points about the reference manager. See the box below on this page for links to how to obtain and install the applications.

EndNote logo Paperpile logo Zotero logo


EndNote is a reference manager that has two different versions: EndNote desktop (current version is EndNote 20) and EndNote Online.

EndNote has a full range of features for collecting and organising references, and a plugin that allows you to cite EndNote references in MS Word.

The desktop application allows for sophisticated searches and is useful for systematic reviews as you can customise fields and store a large number of references.

The online version of EndNote is a more limited version and isn't typically recommended to use on its own. However, it is a very useful way of creating a back up of your EndNote desktop library as you can 'sync' your desktop library with an EndNote online account and therefore have it backed up on EndNote's servers. It also means you can access your desktop library remotely from other devices.

Key points:

  • Separate Desktop and Online versions, with the ability to sync the two to back up your library and access it on the go
  • Abiity to organise, customise, and search your reference library with advanced features and 'smart' sorting
  • Can have multiple reference libraries stored on your computer and accessed through EndNote
  • Can cite in MS Word
  • Can only use whilst at the university as EndNote desktop is not a free tool
  • The online version lacks features


Paperpile is an online reference manager that works in the Chrome web browser and cites with Google Docs.

If you're trying to easily collect citations and full text PDFs from web pages or cite web pages themselves, then Paperpile is very useful. It stores all PDFs in Google Drive too, which makes them easy to find and access.

Previously, Paperpile could only cite in Google Docs, meaning you had to export to another reference manager to cite in MS Word. However, there is now a public beta for the Paperpile Word citation plugin so you can now cite in Word with your Paperpile library (note: as this a beta, features may change or be withdrawn).

The University of York pays for a licence for Paperpile so you can use it whilst at the University. When you leave, you can export your references into another reference management application if you want.

Key points:

  • Searches for and saves PDF as references are collected
  • Stores PDFs in Google Drive so plenty of storage
  • Cites with Google Docs (and Word in beta)
  • Only works in Chrome web browser
  • Has mobile apps to view and edit library on the go


Zotero is a free, open source reference manager that offers flexibility due to the fact it can cite in MS Word, Libre Office, and Google Docs.

Zotero is a good general reference manager that offers a range of features for collecting, organsing, and citing. If you're looking for something you can use when you leave the University and which is a free open source tool rather than being owned by a major publisher, then Zotero is a good option. It also works well with the OSCOLA referencing style, so if you use that it can often be the best reference manager to use.

Key points:

  • Free and open source so you can use beyond your time at the university
  • Has a browser extension for collecting references from web pages or web pages themselves
  • Can cite in MS Word, Google Docs, and Libre Office
  • Doesn't have built-in PDF annotation

Installing reference management applications

At the University of York you can get access to all four of the supported reference management applications in various ways - we recommend you follow the instructions linked below for the application in question to ensure you have the right account and are installing it from the right location.

Obtaining EndNote

You can obtain EndNote desktop whilst a member of the University to use on unmanaged and personal devices. The IT Services web pages have information on obtaining EndNote.

EndNote is also already installed on University classroom PCs, and you can install EndNote on managed PCs through Software Centre.

Note: If you are installing Endnote on a recent Mac computer that has the new 'M1 processor', you may also need to follow steps on this guide from Endnote support to ensure that Endnote can open.

For EndNote online, you have to register on EndNote's website. To ensure you have a University enhanced account (which gives you access to the University styles), you will need to do this on a campus PC or using the Virtual Desktop Service. The IT Services page on EndNote online has full details.

Obtaining Paperpile

Paperpile works within the Chrome web browser, so as long as you already have that on your device, you don't need to download anything to use Paperpile. University PCs already have Chrome installed.

The University of York pays for a licence for Paperpile so you can use it whilst at the University. To sign up for Paperpile, follow the steps on the IT Services Paperpile page.

Paperpile also has mobile apps available for iOS and Android, which you sign into using your Paperpile account once signed up as above. Search in the respective app store for 'paperpile' to find and install the free app.

Obtaining Zotero

Zotero is installed on University classroom PCs and can be installed from Software Centre on managed devices. The IT Services web pages have information on obtaining Zotero.

As Zotero is not connected to your University account, you can continue to use it after you leave the University as long as you ensure you change your email address or sign up with a non-University one.

Reference management training session

We regularly run a Reference Management training session, which covers the key principles of all of the four areas of reference management and discusses the different applications supported at the University of York.

Below are the slides for the session, and a recording of a virtual run of the session. To support these materials, we recommend working through this practical guide and doing the suggested exercises on each page.

Full Reference Management slides on Google Slides

Note for Mendeley users

This guide previously had content for Mendeley Desktop, which was also found on University computers. However, Mendeley have retired Mendeley Desktop and from 1st September 2022 it will no longer be possible to download Mendeley Desktop. Mendeley's replacement, Mendeley Reference Manager, will not be supported by the University, as it lacks functionality compared to other reference managers and the previous version of Mendeley.

Moving from Mendeley to another reference manager

If you want to use a reference manager with more functionality, or you use a footnoted referencing style like Chicago, you can easily move your entire Mendeley library into another reference management application like those listed on this guide. For people using footnoted styles, we'd recommend moving your library to Zotero, which also allows you to insert references in a footnoted style and have the footnotes added.

You can export an RIS file of your Mendeley library and then import this file into another reference manager using the guidance found on the Collect page. For further guidance, see:

Continuing to use Mendeley

If you want to continue to use Mendeley, you will need to move to Mendeley Reference Manager, as Mendeley Desktop will no longer be supported or updated. For help using Mendeley Reference Manager, please contact Mendeley Support.

Further resources

This guide covers all of the key areas of reference management and we recommend you work through it first, but you may also want to check out other resources, including our PDF guides, the reference management applications' own help pages, and our Skills Guides on finding and working with resources.

Below are links to other material we think you might find useful.

Resources for specific reference management applications

Resources for literature searching and writing

Forthcoming training sessions

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