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.
Once you've gone over the material on this page, try the following exercises to apply your knowledge:
By the end of this section, you should have tried out citing in your chosen text processor.
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.
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.
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.
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).
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.
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, whereas with Mendeley you should find Cite-O-Matic on the References tab on the ribbon), here's what to try.
Check if you have to install it separately:
Try uninstalling and reinstalling the plugin - use the same instructions as above for Mendeley, 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.
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.
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.
If you're using a recent Mac computer that has the new 'M1 processor' and you've installed EndNote, you might get an error message when you try to use the citation add-in in Word, saying "Word wasn't able to load an add-in" or similar. If this is the case, try using this guide from EndNote support to open Word using Rosetta, which should allow you to then use the add-in.
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.
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.
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:
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:
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.
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.
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.
Depending on whether you are using a Master Document or combining chapters by inserting files, the exact process for creating your final reference list using EndNote will be slightly different.
In the Thesis Essentials guide, you will find the guidance on how to create your final reference list for your assembled thesis under Part 3 ~ Assembling your Chapters.
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:
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:
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.
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.
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.
Mendeley has a plugin (Mendeley Cite-O-Matic) that lets you cite as you write using your Mendeley library. It can also create reference lists in your document based upon these in-text citations, which will update as you add more citations to your text.
The Mendeley Cite-O-Matic plugin lets you cite while you write and is compatible with MS Word (including Word for Mac) and LibreOffice. It needs to be installed on both personal and University machines, which can be done by doing to Mendeley Desktop and either following the prompt to install the Citation plugin or going to Tools and then Install MS Word Plugin (Word must be closed before it can be installed).
Once downloaded, the Cite-O-Matic plugin appears in the References tab in Word. If you see a security warning when you open Word, you will need to click Enable Content for the plugin to work.
To insert citations using the plugin, you need to do the following:
If your citation style uses footnotes rather than in-text citations, the Mendeley Cite-O-Matic plugin will automatically create footnotes and put the reference at the bottom of the page. To change formatting style at any point, simply select a new style from the Style dropdown in the Mendeley section of the tab. This will reformat all the citations in your document to this new style.
To generate a list of the references you've cited, place your cursor where you want the bibliography to appear and select Insert Bibliography. This will automatically generate a reference list, which will update as you add more citations to your document.
If you have been writing your thesis using separate documents for your chapters and any other content, you will need to create a final bibliography once you come to assemble your thesis.
Your separate documents containing Mendeley citations may or may not have a reference list at the end, depending on whether you inserted one using 'Insert Bibliography'. If you do, these will need to be removed before inserting the bibliography into the final thesis.
Regardless of whether you are using a Master Document or combining your chapters by inserting files, the process is quite similar. You need to ensure that you leave your citations in the documents when you insert them into your final thesis, and that those references remain in your Mendeley library.
The guide below explains the steps for creating a final bibliography with Mendeley when assembling your thesis, using either method of assembly. It also has guidance on exporting your thesis as a plain text document once this is completed.
If you just want to create a list of particular references to put into another program, rather than cite them into a piece of work, you can do this in Mendeley by copying them as formatted citations.
Firstly, you'll need to select all of the references you want to include - whether by putting them in a group or by using a search to find the right ones, then using Ctrl + A to select them all. Once selected, right click on the references, and choose Copy as... > Formatted Citation. You'll need to ensure you've set Mendeley to use the right referencing style (you can check this under View > Citation Style).
The references are now copied to the clipboard and you can paste them into any other application. It may be useful to paste into a text processing program and save that as your reference list, then if you want to paste those references elsewhere you'll have a copy of the list saved.
Mendeley Desktop can create .bib (BibTeX) files for your Mendeley folders (or for your whole library or single documents) which can then be used with LaTeX. You can also export BibTeX files from Mendeley without this automatic creation, using the Export... option.
Mendeley also has the option to copy specific references as a LaTeX citation or in BibTeX format, which can then be pasted into your document.
To set up the automatic creation of BibTeX files:
By default Mendeley has style definitions for generic referencing styles, which you can see from View > Citation Style. However, the University of York uses versions of these styles that may differ from the generic version, so it is best to install the Univeristy of York versions of these styles (see the box on Using referencing styles if you need to check what style your department uses).
To install the University of York styles, you need to be in Mendeley desktop. Go to the View menu, then Citation Style > More Styles... In the dialogue box, move to the 'Get More Styles' box and search for 'university of york'. Find the style(s) you need for your department, select the style, and click the 'Install' button. This will make the style appear on the 'Installed' tab, and from that tab you can select the style, click 'Use this Style' and then Done to save that change.
Mendeley have brought out a new citation plugin, separate to Cite-O-Matic, which is called Mendeley Cite. It works with Word 365, Word 2016 and more recent, and the Word iPad app, but for older versions of Word you'll need to keep using the previous Mendeley add-in (which is installed from the Tools menu in Mendeley desktop. It doesn't work with footnoted referencing styles like Chicago currently, so if you're using those you'll need to use the other Mendeley Word add-in.
Mendeley Cite is designed so you can insert references without opening the desktop application, unlike the other citation plugin. It appears as a sidebar in Word, unlike other add-ins. You can install it from Mendeley's Cite page.
For full instructions on using Mendeley Cite, see Mendeley's Cite guide.
If you want others to open your Word doc with inserted Mendeley citations on their own device, you'll need to make sure you've removed the link between your citations and your Mendeley library in the version you share with others, as otherwise there could be issues with your citations.
You'll need to use Mendeley's option to Export as > Without Mendeley Fields which you'll find on the Mendeley section of the Word ribbon near when you click to insert citations. This creates a copy of your document that is not linked to Mendeley, as 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.
Sometimes when you do this, it may look like the document has broken. Close both the original and the copied document, then reopen them, and you should see them both. You may also need to check the file format of the new plain text version, as it can be changed from the current Word format .docx to the older Word format .doc. You can change the file type back using the Save As options.
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.
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:
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.
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.
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 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:
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.
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 citationstyles.org.
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.
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.
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.
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.
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.
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 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.
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.
If you're using Google Docs, then from the Zotero menu there is similarly an 'unlink citations' option.
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 and a PDF guide on how to create your thesis in Word.