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Subject Guides

Reference Management: a Practical Guide


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


This is a practical guide to help you get started using reference management software (also known as bibliographic management software). You will find information on these pages detailing the main features of reference management software and specific details on how to use EndNote, Mendeley and Paperpile.

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.

Intro to reference management

Using reference management software can save you many hours of compiling, checking, and correcting your references, and improves consistency and accuracy.

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

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.

Skills Guides

Find videos, interactive tutorials, workbooks and links to specific help for developing your digital and information searching skills:

Reference management software

The University of York supports three reference management applications.

Click the headers below to learn more and to get started with each:


Great for collecting citation information and associated PDFs, and for managing what you've found. Citing works with Google Docs rather than MS Word.


Paperpile is an online reference management program which uses a Chrome extension to quickly collect references and store pdfs. It has lots of options for managing what you've found, and works directly with Google Drive and Google Docs.

  • Buttons appear in the database results for quick transfer

  • Searches for the PDF at the point of collection and very often finds it (especially if you set up the York proxy connector)

  • Auto-update option to correct incomplete records

  • Can generate records from compatible PDFs

  • Two levels of organisation (folders and labels) and a simple user-interface makes managing your references straightforward and visually clear

  • Stores PDFs in Google Drive, giving ample storage (c.10 TB)

  • Cites with Google Docs

  • Importing of records via Paperpile buttons is on an individual level only (or via RIS or BibTeX imports)

  • Only works with Chromium browsers (e.g. Google Chrome)

  • Doesn't cite with MS Word (but you can always transfer your library to a program that does)

To start using Paperpile, take a look at the following links:

We've produced University of York referencing styles for Paperpile.
Always check against the referencing guidance.

Other useful documents:


A good all-rounder that's especially good if you want to make notes directly onto your PDFs. Citing works with MS Word and Libre Office.


Mendeley consists of two components: Mendeley Web and Mendeley Desktop. The former is used to collect references, and the latter is used for advanced management options and for citing. Both are free to use, and Mendeley Desktop is available on all University managed computers.

  • Web Import plugin can find several items on a page and also import PDF

  • Compatible PDFs can be converted into references, and a watch folder can be set up to automatically import any downloaded PDFs

  • Suggests related items based on the contents of your library

  • Has its own PDF reader, allowing you to annotate PDFs and access the annotated versions both locally and online

  • Includes some advanced library management features including filter options

  • Easy-to-use citation plugin for MS Word and Libre Office

  • Web Import tool doesn't always find all the items on a page, and isn't as successful as Paperpile at finding PDFs

  • Imported records are sometimes incomplete (though can be checked against Mendeley's catalogue and updated)

  • Plain-text export in Word is in .doc format so documents may require reformatting prior to submission (though workarounds are available)

  • Free version is limited to 2GB of space

To start using Mendeley, take a look at the following links:

We've produced University of York referencing styles for Mendeley. These can be accessed within Mendeley itself, or you can also access them via the link below. Always check against the referencing guidance.

Other useful documents:


Sophisticated search options for your reference library make this program great for high-end reference management, but if you want to use it on your own computer you'll have to pay (or make do with the online component). Cites with MS Word.


EndNote comes in two versions: EndNote Desktop (available on University computers), and EndNote Online (free to use on any internet connection).

  • Direct import from databases to EndNote Online is possible in some cases (but most importing is done via export files (e.g. RIS, BibTeX etc.))

  • Compatible PDFs can be converted to references

  • EndNote Desktop has advanced management options including two levels of structure (sets and groups), multiple organisation fields, advanced searching, web connections, and smart groups that organise items based on search criteria

  • EndNote Desktop can update incomplete records and search in a number of locations for PDFs

  • EndNote Desktop supports multiple reference libraries

  • Citing via MS Word (including plain-text conversion without loss of formatting)

  • EndNote Desktop is not a free application: if you want to use it on your own computer you will need to buy it (though you can use it for free on University computers)

  • While EndNote Online is free to use, it is not as easy to use as Paperpile or Mendeley and it lacks many of the management features available in those applications

  • Importing of records requires you to know the appropriate import filter for the type of file you're importing (especially in EndNote Online)

  • Syncing between EndNote Desktop and EndNote Online will only work with one EndNote library

To start using EndNote, take a look at the following links:

EndNote Desktop:

EndNote Online:

Other useful documents:

Other programs

While the University supports Paperpile, Mendeley and EndNote, there is no obligation to use any of them, although we may not be able to support you if you're using a different program and need help. You may find another program more to your liking (or you may prefer not to use any program at all).

Mendeley's Cite-O-Matic plugin and EndNote's Cite While You Write plugin are the only two plugins available for use with Microsoft Word on University computers, so if you need to use a University machine you may therefore want to transfer your library to Mendeley or EndNote for the writing-up stage at least.

Forthcoming training sessions

Digital skills training

We run a number of digital skills training sessions each term.
Our digital skills training sessions are open to all members of the University.

To book onto a session, follow its link below (you'll need to log in to the booking system). If a session you're interested in is full, sign up onto the waiting list - if we have enough interest in a session we may repeat it. You'll also find copies of our slides throughout the Skills Guides.

Next digital skills sessions:

Note - What with one thing and another, the following sessions will no-longer be taking part in the advertised locations. We're leaving booking open for now pending decisions on alternate methods of delivery.

Show details & booking for all sessions

Other sessions:

We also run a number of specialised training sessions for staff and research postgraduates: