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Reference Management: a Practical Guide


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

Citing references

Once you have your references collected, you can use reference management software to generate lists of references and to insert citations from your library as you write. This page looks at setting up the right referencing style and how to cite references in your work.

General principles for citing references

Reference managers typically include the ability to insert references from your library directly into a document, using a plugin/add-in for a text processing application.

How do reference managers cite references?

These features work by inserting the citation information for a selected reference in your library in the referencing style you have set it to use. The tools use specific rules to know how to format your citations.

The inserted references may look like normal text, but if you hover over them you'll see they behave a little differently to regular text in a document. That is because these citations are bits of computer code that keep them linked to your reference manager, so they'll update if you update the reference in your library.

Using a 'cite whilst you write' feature to easily insert citations can speed up the process of writing up your work, though it is important to proofread all your citations in your work as sometimes there can be errors in your library or in the referencing style you're using.

Are there other options for citing references?

You can also copy citations from your reference manager and paste them into your document. This can be more time-consuming and requires manually updating the references and creating the bibliography, but allows you to use a wider range of software when pasting your references.

Most tools also allow you to create entire reference lists from selected references in your library, which can be useful for sharing lists of what you've been reading with others or for creating annotated bibligraphies.

Using referencing styles

Referencing styles ensure that all of your references are cited in a consistent and accurate format, making it clear exactly what are your words and where anyone else's words come from.

When using a reference manager, you have to make sure that all your references are accurate and properly formatted in the application, and that you have the right referencing style set up for citing. If your cited references look wrong, it may be that the information is incorrect, or you're using the wrong style.

The link below has details on the styles used by different departments at the University.

On this page in the box for each reference manager you'll find guidance for how to set up the UoY styles and select the right style. Below are links to the styles you'll need, though in many reference managers you can access these without downloading these files by searching for University of York or UoY when accessing more styles (but you will need to download the .zip file for EndNote Desktop).

If you are using a footnoted referencing style like Chicago, you will have to manually insert the footnotes if you're using EndNote to insert citations, meaning it is difficult to swap to a non-footnoted referencing style. However, Zotero automatically inserts the footnotes, meaning you can move between a footnoted and a non-footnoted style automatically.

Citation add-in troubleshooting

Each of the applications has a citation plug-in (or more than one) that you can install in your text processing application (mostly MS Word). These all work slightly differently, but here are some troubleshooting tips if you're having issues with them.

Citation plug-in / add-in won't install?

If you open Word and don't see the citation plugin where you expect (with EndNote, Zotero, and Paperpile, this should be an extra tab on the ribbon), here's what to try.

Check if you have to install it separately:

  • In Zotero, go to Tools > Addins to check which ones you can install and if they're installed
  • Paperpile requires you to download the Word plugin from Paperpile's website.
  • EndNote's Word plugin should install with EndNote desktop, so you shouldn't need to install separately. If you're using EndNote online, you can download the Cite While You Write plugin from EndNote's website to use in Word.

Try uninstalling and reinstalling the plugin - use the same instructions as above for Zotero, and Paperpile. For EndNote desktop, it's easier to uninstall EndNote entirely and reinstall it. This won't delete your data - though we'd recommend making sure you sync your EndNote desktop library with an EndNote account first.

Getting an error message when citing?

If you're getting an error message when you try and insert a citation using a citation plugin in Word, there are a few things you can try.

The first thing to check is whether you have other Word add-ins installed that are interferring with the one you're using. This might happen if you've tried out different reference management applications or if you're working on a University PC.

  • On Windows, open Word then go to File > Options > Add-ins. You'll see a Manage option in that Add-ins dialogue box, and if you use the drop down list to select 'Word add-ins' and then click Go, you'll open a new window with a list of any add-ins installed. Untick any that aren't the one you're trying to use.
  • On a Mac, open Word then go to Tools > Templates and add-ins. This will show you a list of any add-ins you have installed. Untick any that aren't the the one you're trying to use.

If this doesn't work, you might want to try uninstalling and reinstalling the plugin (see the above heading) or uninstalling and reinstalling Word

Alternatively, try searching for the error message online (hint: also include the name of the reference management application to get more relevant results). If that doesn't help, contact IT Support.

Plain text or Word fields?

When you cite using a reference manager in Word, the citations are not inserted as regular text like you might expect. Instead, they are added as a 'Word field', which means they are actually a clever bit of computer code that links them back to your reference manager. This is why the citations update if you change them in the reference manager, and how the bibliography can update to include all references cited in the document.

To share or submit your document, you should create a plain text copy that is no longer linked to your reference manager. This ensures that the recipient's own reference manager doesn't interfere with your references. There should be an option on the Word add-in you've been using to insert citations to do this - see the box on this page for each application for more on how to remove the Word fields using that tool.

Working with text processors

Not only do you want to cite your references properly, but you want to make sure the rest of your document is suitably set up as well. We have a range of guidance on using text processing tools like Word and Google Docs, including information on using styles for structure and accessibility.

Citing with EndNote

EndNote logo

EndNote allows you to cite references in MS Word using the Cite While You Write plugin, which connects EndNote to Word. You can also export reference lists and import in other referencing styles.

EndNote Cite While You Write plugin in Microsoft Word

The Cite While You Write plugin links MS Word with EndNote. The installation of EndNote Desktop includes the Cite While You Write plugin, which appears as an extra MS Word tab. On EndNote Online, click on the Downloads tab and select the appropriate version for your operating system under the Cite While You Write heading (the plugin is free).

Inserting citations using Cite While You Write can be done via Word or EndNote Desktop:

  • Via Word: Position your cursor where you want the citation to appear. On the EndNote tab in Word, choose Insert Citation. Use the Find control to locate the reference(s), using the CTRL key for multiple selections. Choose Insert for the full citation or the drop-down list if you need to omit the author or year.
  • Via EndNote: In your document, position the cursor where you want the citation to appear. Switch to EndNote and locate the reference you want to insert. Choose Tools, then Cite While You Write, then Insert Selected Citation(s), or you can use the Insert Citation button on the toolbar.

To insert citations as footnotes (as some bibliographic styles require) using EndNote you must first use the MS Word footnote feature. Place the cursor where you want the footnote indicator to go, then go to the References tab and choose Insert Footnote. This adds a footnote and leaves the cursor in the footnote position ready to insert a citation using one of the methods above.

To edit citations, you need to use the EndNote tab and choose Citations, then Edit & Manage Citation(s) rather than edit their content directly, as they are populated using MS Word fields. From the Edit & Manage Citation(s) dialogue box you can add/remove citations, show/hide author or year from a citation, anad add page numbers or other text to a citation. After making changes, chose Bibliography then Update Citations and Bibliography to ensure the reference list is updated.

Troubleshooting tips for Cite While You Write:

  • When using Cite While You Write in Word, you may need to configure it to use the correct EndNote account and application setting, particularly if you are using a University classroom PC. In the EndNote tab in Word, choose Preferences from the Tools group. Switch to the Applications tab and check that the application is the one you are using (EndNote Web for online, just EndNote for desktop). You may need to then add your email address and password connected with your EndNote account.
  • If citations are shown incorrectly, surrounded by a pair of curly braces { } your chosen bibliographic style may not be available (could occur if you edit a document on a computer that does not have access to a style you have previously used).
  • You may also see the curly braces { } if Instant Formatting is turned off. To check this, first select the dialogue launcher at the bottom right of the Bibliography group in the EndNote tab in Word. On the Instant Formatting tab of this dialogue box check the status and turn it on if necessary. Choose OK to confirm this change and then select Update Citations and Bibliography.
  • On University computers, you may also see the curly braces around citations because the Mendeley plug-in is interfering with EndNote Cite While You Write in Word. To fix this, select File > Options, then Add-ins, then at the bottom of that window from the Manage drop-down list select Word Add-ins and then Go... Make sure the add-in labeled Mendeley is unchecked, then select OK.

EndNote Cite While You Write tool in Google Docs

If you have EndNote 21, you can now use EndNote's new Google Docs 'Cite While You Write' tool that allows you to insert EndNote citations in a Google Docs file. It directly integrates with the Premium version of EndNote Online, which can only be obtained with an EndNote 21 licence (for more on this, see the obtaining EndNote information).

You install the Cite While You Write plugin for Google Docs via the Google Workspace Marketplace, going to the EndNote 21 Cite While You Write page and clicking Install. You will be asked to select the correct Google account and to allow the tool to access particular parts of your Google account to work. This is to be expected; the plugin is made by Clarivate, EndNote's creator, and you can check their terms and conditions and privacy policy if you wish.

Once installed, if you open a Google Doc you should be able to go to Extensions and see EndNote Cite While You Write listed. Click on it and choose Open to open the sidebar for the tool. You will need to log in to EndNote 21 to access it, using the username and password you use for EndNote online. Once logged in, you should see you references and be able to select and insert them as needed. You can change referencing style using the three dots icon, then Citation Style.

See EndNote's guidance on the Google Docs CWYW for more information on setting up the tool. Note that it currently does not support using footnoted referencing styles.

Exporting a reference list from EndNote

As well as citing in Word, you can also export a reference list/annotated bibliography from EndNote that can be viewed and edited using MS Word and other text processors.

  1. In EndNote Desktop, either view the group or select the references you wish to output as a list, then choose File, then Export...
  2. Enter a suitable file name and change the Save as type to Rich Text Format (rtf).
  3. Select the required reference Output style (the Annotated style includes abstracts) and Save the file.

It is possible to do this in EndNote Online as well, but you choose Format then Bibliography and select the reference group you wish to export from there.

EndNote and assembling your thesis

If you have been writing your thesis using separate documents for chapters and any other content, you need to be aware of some extra points relating to your EndNote references when you come to assemble your final thesis.

If you have inserted citations into your chapters using EndNote, each chapter will end with a reference list. When you combine chapters a new reference list needs to be compiled for the combined chapters. The citations must remain in the chapters and the references need to be present in your EndNote library.

If you are using the Insert > Object > Text from file... method as described on the Creating Documents guidance on assembling your thesis, then the process is:

  1. After inserting a chapter, from the EndNote tab choose Tools > Convert to Unformatted Citations. Converted citations will be in curly braces, e.g. {Dunlop, 2023 #991}.
  2. Check the reference list has been removed from the end of that chapter
  3. Repeat this process for other chapters you add.
  4. Once all chapters have been inserted into the document, on the EndNote tab choose Update Citations and Bibliography. This should recreate the reference list at the end of the entire document.

EndNote, LaTeX and BibTeX

EndNote does not work directly with LaTeX editors, but you can still use reference management features in both EndNote Desktop and EndNote Online and then export groups of references in the BibTeX format.

How to export in BibTeX format in EndNote Desktop:

  1. Ensure that the references you want to export as assigned to one Group.
  2. In the left-hand pane, select the group containing the references.
  3. Choose File, then Export... so the Export dialogue box opens.
  4. Save as Type should be set as Text File (*.txt) and Output style as BibTeX Export. If you've not done this before, you may need to choose Select Another Style... and find BibTeX Export on the list (there is also a 'BibTeX Export using EN label field' option).
  5. Check the Save in location and File Name are suitable and choose Save.

The file will be saved with a .txt extension (so it will open in a plain text editor), but you can manually change this to .bib if you wish.

The export lacks the reference key used for LaTeX citations so this must be generated before use. Reference keys are usually based on the author name and publication year.

To generate a reference key, you can either:

  • Open the reference file in a text editor, invent the keys, and type them in manually.
  • Import them into a BibTeX reference application (such as JabRef, available for free for both Windows and Mac) that will auto-generate the keys.

If you use JabRef to create reference keys for you, you will need to open the reference list in JabRef then choose Edit, then Select all to select all the reference, then select Tools then Autogenerate BibTeX Keys. This will generate keys using the author and year, in the Bibtextkey field in JabRef.

Installing referencing styles in EndNote

EndNote comes with a range of default referencing styles, but the University of York has specific versions of referencing styles that may differ from the generic styles so we recommend that you install the UoY version of the style used by your department.

Additional styles in EndNote desktop are stored in their own folder, and you can check the location of this folder from Edit > Preferences > Folder Locations and then looking under the 'Style Folder' heading. You can change this folder if you want, but if you're using a University managed computer, make sure you choose a location on a networked drive (e.g. on your H: drive) so you'll have the styles available on any University computer.

Once you've located the style folder, you only need to move or copy the style files into that folder. You can download the .zip file of the UoY styles for EndNote Desktop or if you're on a University managed PC, go to T:\IT Training\EndNote\Styles and copy that folder.

EndNote also allows you to edit styles and save a version with your edits, though this can be tricky. Only do this if you know that the issue is due to the referencing style, not your references.

Note: If you're using EndNote online only, then you just need to check you've got an enhanced account and then you should be able to see the University of York styles in the full list of styles under Format > Bibliography.

Removing EndNote-linked fields to share your Word doc with others

If you want others to open your Word doc with inserted EndNote citations on their own device, you'll need to make sure you've removed the link between your citations and your EndNote library in the version you share with others, as otherwise there could be issues with your citations.

What you'll need to do is use EndNote's Convert to Plain Text option which will create a new copy of your document in which the citations are just regular text and are not linked to EndNote. You still want to keep the original version that is linked to EndNote, in case you need to keep working on the document or ever need to change anything, so the converted version is a copy.

You can find the option in Word on the EndNote tab in the ribbon. On Windows you'll see a 'Convert Citations and Bibliography' button, which you can click to bring up the 'Convert to Plain Text' option to select. On Mac you may need to go to the Tools option on the EndNote tab, then choose 'Convert to Plain Text' from there.

Screenshot of using the Convert Citations and Bibliography button in Word and then choosing 'Convert to Plain Text'

Citing with Paperpile

Paperpile logo

Paperpile could previously only cite in Google Docs using the Google Docs add-on that should install when you install Paperpile. However, there is now a public beta for the Word plugin, allowing you to cite in Word using your Paperpile library (note: this is in beta so features may change or be withdrawn). You can also copy and paste Paperpile citations, including multiple citations at once.

Citing with the Paperpile Google Docs add-on

To use the citation features with Paperpile and Google Docs, you need to be using the Chrome web browser and have the Paperpile Chrome extension installed. As long as you have these and are logged into Paperpile, the Google Docs Paperpile plugin will automatically load when you open Docs. The first time you format a document, the Paperpile plugin must be authorised to allow it to scan and modify your document to insert citations.

To insert a citation:

  1. Position the cursor where you want the citation to go in the document.
  2. Click on the Paperpile menu in the toolbar and choose Insert Citation, or use the shortcut CTRL+ALT+P (on Windows) / Shift+Command+P (on Mac) to open the citation window.
  3. Type to search within your Paperpile library. Choose a result to add it to the citation.
  4. Clicking on the citation tag opens up a panel with details and advanced options such as adding page numbers or text to go before or after the citation, or suppressing the author.

The citation is inserted into the Google document as a link with placeholder text. Paperpile can reformat your document and generate the bibliography by choosing Paperpile then Format Citations. You will need to give permission to the plugin the first time you format a document.

To choose a different citation style, choose Paperpile then Citation style... to open the citation style window.

Note:You can only use the Google Docs plugin with the same Google account from which you signed up to Paperpile. If you have documents owned by your non-Paperpile Google account, you'll need to share and edit them with your Paperpile-linked account.

Citing with the Word plugin (beta)

Previously, Paperpile only allows you to cite in Google Docs, and you had to export your library to cite using Word. However, there is now a public beta version of a Paperpile Word plugin available, which does allow you to cite in Word. As this is a beta, it could be withdrawn at any time and features may change, so be warned if you are using it.

Note: As this is a beta, you can install it on your own device, but it is not available in Word on University PCs.

To use the beta, go to Paperpile's Word plugin page and download the right version depending on if you're using Windows or Mac. On Windows run the file to install the plugin (you may then need to run that application to install in Word). On a Mac, open the file, copy to Applications, and then open that application to install the plugin in Word.

Once installed, it will show as a tab in Word. You can then put your cursor wherever you need to add a citation and use the add citation button to insert these. If you select an existing citation and click that button, you can edit your citations.

The plugin also allows you to export your file to a Google Doc (preserving Paperpile citations), or to import either Word docs with Zotero or Mendeley citations, or a Google Doc with Paperpile citations, into Word, converting any citations to Paperpile ones if needed. These citations won't be added to your Paperpile library by default, though if you edit the citation and then edit the reference, it is possible to 'update' that citation in your Paperpile library, which adds it.

For further updates on the Paperpile Word citation features, keep an eye on their Help Centre.

Creating a reference list

You can use Paperpile to copy and paste a reference list into another application without having to cite all of the references in Google Docs to do so. Select the references you want in your list in Paperpile (can be easiest to put them all into the group, then use the Select > All feature at the top of Paperpile), then click on the Cite menu, then 'Citation'.

From that menu there's also an option to change your citation style, if you're not copying the references in the right style.

Paperpile and LaTeX

Paperpile has options for citing using LaTeX editors, including the ability to export in BibTeX format and a method for copying a LaTeX citation to the clipboard.

You can export references from Paperpile in BibTeX, which can then be used with LaTeX editors. To do this, you can either:

  • Export your Paperpile to BibTeX by going to the gear icon in the top right-hand corner, then choosing Settings. Select the Export tab and then Export to BibTeX.
  • Select one or more references then choose the drop-down menu from the Cite button at the top of the page. Select BibTeX to copy the reference(s) to your clipboard (you can also use the shortcut Ctrl+B).

In the drop-down menu from the Cite button, you can also copy a LaTeX citation straight to the clipboard. Again, you need to select the reference(s) to cite first. You can also use the shortcut Ctrl+Shift+K.

Installing referencing styles

You can set Paperpile to use the citation style you need both for citing in Google Docs and when copying citations from within Paperpile. You can tell Paperpile to use the University of York version of the style your department uses, or any other style found on

To check your citation style and change it, click on your name or the gear icon in the top right hand corner of Paperpile, then choose Settings from the menu. In the Settings dialogue box, choose 'Citation Styles'.

You'll see the default style currently set in Paperpile. Click 'Change style' to get a dialogue box that allows you to search for other styles - search for 'university of york' to see the UoY specific styles. Once you've found the right one, select it and then click 'Set citation style'.

You can also access the Paperpile Choose citation style box from the Paperpile menu in Google Docs.

Removing Paperpile-linked fields to share your document with others

If you want others to open your Word doc with inserted Paperpile citations on their own device, you'll need to make sure you've removed the link between your citations and your Paperpile library in the version you share with others, as otherwise there could be issues with your citations. You can also remove the links from a Google Doc, but this is a more complex process as it isn't achieved in the same way as Word fields.

If you're using the Word add-in for Paperpile, then you can create a version without the 'citation codes' to remove the link to Paperpile. First, make sure your document is saved (ideally, do this on a copy of your actual document). On the Paperpile tab in Word, go to Settings and Tools, then Remove Citation Codes. You'll see a warning dialogue that you'll want to save a backup, and it will offer to save a backup file (with the links to Paperpile kept) at the same time. At this stage make sure you do have a copy still linked to Paperpile, then you can choose to remove the citation codes.

Screenshot of using the Paperpile tab to choose Remove Citation Codes'

If you're using Google Docs and want to remove the links to Paperpile, the options are more complex as Google Docs works differently. See Paperpile's support forum post on removing citation URLs from Google Docs for the options Paperpile suggest.

Citing with Zotero

Zotero logo

Zotero has plugins to allow you to cite within Word, Google Docs, and LibreOffice, and also has features to generate bibliographies and copy individual citations.

Citing with Zotero in text processors

Zotero has various plugins available to automatically add citations from your Zotero library into a text processing application. Zotero's help page on word processor plugins lists the ones available, with guidance for how to install and use the ones for Word, LibreOffice, and Google Docs.

To cite with a Zotero plugin, place your cursor in your document where you want the citation to go, then use the menu or toolbar plugin provided to choose 'Add/edit Citation'. This will bring up a citation dialogue box that allows you to search for and select the relevant citation(s) from your Zotero library. Once these are selected in the diaglogue box, hit the Enter key to insert the reference.

The 'Add/Edit Bibliography' button inserts a bibliography into the document at that location, based on the references already cited in the document using Zotero. This will update whenever you add a new citation to that document.

You can customise what information is shown in the citation, for example adding page numbers or removing the author name if needed. For more information, see Zotero's help for the Word plugin, LibreOffice plugin, or Google Docs connector.

Creating a reference list and copying citations

Zotero has built in features to easily copy formatted references into other applications, either formatted as in-text citations or as part of the bibliography. The easiest way to do this is using the keyboard shortcuts when one or multiple references are selected - Ctrl-Shift-C for formatted as bibliography and Ctrl-Shift-A for formatted as in-text citations (Mac users should substitute Ctrl for Cmd in those shortcuts).

You can also select one or multiple references and then right click and choose 'Create Bibliography from Selected Item(s)' to export a list of these references (or a single reference). You can choose the referencing style and whether this is formatted as a bibliography or as in-text citations, and then choose to either export as RTF (a text file), HTML (for viewing in a web browser), copy to clipboard (to paste anywhere), or print.

For more on these options see Zotero's guidance on creating bibliographies

Zotero and LaTeX

You can export references or your entire Zotero library as a BibTeX file, which allows you to then put these references into a LaTeX editor if you are using one. If you collect together all of your references to go into the bibliography of your LaTeX document, you can then export those references in the BibTeX format, giving you a .bib file you should store in the same location as your LaTeX document. Searching online will offer more guidance on how to cite within LaTeX.

Users of Overleaf with a subscription can also link their Zotero and Overleaf accounts. University of York staff and students can request a free Overleaf Pro account.

Installing referencing styles

Zotero can cite in a range of referencing styles, with some generic versions built in and any other styles needing to be obtained from within Zotero. The University of York has specific versions of referencing styles that may differ from the generic styles so we recommend that you install the UoY version of the style used by your department.

To install the University of York styles, or any other styles you may need, go to Preference (Edit > Preferences, or Zotero > Preferences on a Mac), then click on the Cite header to see which styles are installed. By default these will be generic versions of major styles. Click on 'Get additional styles...' to search for and install other styles - to find the York styles, search for 'university of york' and click on the style you need. This will add it to the list you can select from.

Removing Zotero-linked fields to share your document with others

If you want others to open your Word doc with inserted Zotero citations on their own device, you'll need to make sure you've removed the link between your citations and your Paperpile library in the version you share with others, as otherwise there could be issues with your citations. You can also do this if you've used Google Docs and want to unlink your citations from your Zotero library.

If you're using Word, you first need to make sure that you've made a copy of your document that contains Zotero citations, and make sure you're working in the copy, not the original document. This will mean you still have a version that is linked to Zotero that you can update as needed. Once you've done this and you're in the copy in Word, go to the Zotero tab in Word and click on 'Unlink Citations'. You'll see a dialogue box that warns you the links to Zotero will be broken, and once you choose OK, your citations will be unlinked.

Screenshot of using the Zotero tab to choose Unlink citations'

If you're using Google Docs, then from the Zotero menu there is similarly an 'unlink citations' option.


Once you've gone over the material on this page, try the following exercises to apply your knowledge:

  1. Firstly, make sure you have some references in your library (if not, see the Collect page that you can cite.
  2. Check which referencing style you need to be using and install the University of York version (if relevant).
  3. Make sure you've installed the citation plugin for your text processor.
  4. Open a blank document in your text processor, write some text, and then insert a citation using the plugin. If it doesn't done automatically, insert a bibliography at the end of your document. Then add more text to the body of your document, then add a second citation using the plugin. See how the bibliography updates (you may need to hit a 'refresh' button).
  5. Open a new blank document in your text processor. In your chosen reference manager, try copying a formatted reference or a selection of references, and then paste them into this new blank document.
  6. If you've done both 4 and 5, click on the references in each document to see the difference - the ones inserted using a plugin should highlight in a light grey with just one click (because they are still linked to your reference manager), whereas the copied text ones won't.
  7. Extension: Check your references match how you expect your referencing style to look. At this stage, you might want to try adding more referencing using the method you'll be likely to use in the future, or try working out how to export a plain text version of your document (if you used a plugin).

By the end of this section, you should have tried out citing in your chosen text processor.