Skip to Main Content
University of York Library
Library Subject Guides

Reference Management: a Practical Guide


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

Organising references

So you've got references, but how do you sort them out? Reference managers allow you to organise references into folders, check for and delete duplicates, and add notes or add full text PDFs. This page looks at the organisation features in EndNote, Paperpile, and Zotero and how to use them effectively.

Groups, Folders, Labels...

Folder and tag

Reference management applications have ways of sorting your references into categories, but helpfully the names of these vary across each tool.

Though the names vary, there is one important principle to remember. Whether you're using groups, collections, or labels in EndNote, Zotero, or Paperpile, references can be in multiple organisational categories at once. For example, a reference could be in multiple groups in EndNote, or have various labels and be in different folders in Paperpile.

This means that instead of a folder structure like you might be used to in Windows, these groups and folders are suitable for more flexible organisation. A reference that relates to multiple topics or projects can be put in all the relevant groups or folders. If that reference is no longer relevant to that category, it can be deleted from a folder or group without deleting the actual reference.

Am I repeating myself?

When searching databases and catalogues, you may end up finding the same references, and then end up with multiple versions of the same reference in your library when you export the results. Luckily, reference management software has built-in tools to check for duplicates and delete or merge records so you only have one entry for each item in your library.

This helps you keep your library organised, but is also particularly important if you're going to cite using your reference manager's citation tools. If you accidentally cite different versions of the same item at different points in your document, the item will show up multiple times in your bibliography, and each version of the reference may not have the same information. Therefore, it is good to check for duplicates in your library before you start citing in your work.

Accurate references

The reference information you get out of databases and catalogues is only as good as the information put in. Sometimes there might be errors or omitted details, or quirks of the reference that don't make sense (for example, library catalogues may have 'electronic resource' written in the title field, which is very useful when searching for resources, but less useful when that reference is in your library and the item doesn't have 'electronic resource' in its title normally).

Because of this, it is important to check every reference you import into a reference manager. Look to see if the expected fields are filled out and if the details look correct.

If they don't, search on another database or catalogue to find more accurate results. You can then either manually edit the reference, or import the new reference and delete/merge the old one. Some reference managers have options to try and search online for more complete references from within the application, and if the application finds a suitable match it'll update the reference for you.

Organising references with EndNote

EndNote logo

EndNote (both desktop and online) uses Groups to organise references (and with EndNote 21 you can use tags as well). You can also check for duplicates, add research notes, and attach full text PDFs.

Groups and Group Sets

Each reference in EndNote may be assigned to one or more Groups. These work like folders, allowing you to organise references and view all of the items in each group.

To create a new Group, either go to the Groups menu at the top of the screen, or right click on the sidebar on the left of the screen, and choose to create a new Group.

Group Sets are a way of putting groups together, like putting folders all in another folder. This can be a useful way to manage your Groups if you have a lot - for example, you might have a Group Set for each area of research or piece of work, and then Groups within these for particular topics or chapters.

To remove a reference from a Group, select the reference(s) you want to remove, then right click and choose 'Remove references from Group'.

Note: Deleting a reference when viewing a Group deletes it from the Group but does not delete the reference from your library.

Smart Groups

Groups have to be manually organised, but Smart Groups can assign references to that group based on rules you assign. This can allow you to automatically get Endnote to check for references with certain keywords in the title or from a year or journal, or anything else you might need. All of these references will be added to the Smart Group, and any new ones if they come in.

Smart Groups are created the same way as regular groups, but choose the 'Create Smart Group' option. You'll then get to not only name the Smart Group, but choose the rules for inclusion in the group.

Smart Groups can also be put into Group Sets. They'll appear alongside your Groups in EndNote, but have a different icon (a cog).

Checking for duplicates

EndNote has built in functionality to check your library for duplicates so you can ensure you only have one version of each reference saved.

To check for duplicates, go to the Library menu, then Find duplicates.

EndNote will compile a list of duplicates and open a dialogue box to help you decide which to keep. You can also close this dialogue and delete manually from the duplicates list, which is temporarily listed in the Groups panel.

References deleted from the Duplicates list are removed from the whole library.

Managing PDFs

EndNote Desktop stores PDFs in your library within a folder on your computer called My EndNote Library.Data. PDFs can be viewed within EndNote Desktop on the right-hand pane (which can be opened into a larger window) or can be opened in your computer's default PDF reader by right-clicking on a reference and choosing File Attachments then Open File (or selecting the reference then pressing Ctrl+Alt+P).

You can attach a PDF to an existing reference in your library by selecting a reference, then using the paperclip icon to choose 'Attach PDF'. This can help you keep track of PDFs you already have by connecting them with the relevant reference information.

EndNote doesn't have functionality to edit or annotate PDFs, but you can open the PDF in a PDF reader of your choice if you want to annotate the PDF. Microsoft Edge (web browser) on a Windows machine or Preview on a Mac are built in tools that allow you to annotate PDFs.

Managing and backing up your EndNote library

EndNote works by having your EndNote library stored as a .enw file and an associated .data folder (e.g. 'MyEndNoteLibrary.enl' and ''). These two items need to have matching file names (with different file extensions) and be stored in the same place on your computer. If one of these is moved or deleted, your EndNote library will stop working.

Unlike other reference management tools, using EndNote desktop doesn't require you to have an account, which means that by default your library is not backed up on EndNote's servers or elsewhere. There are two different options for backing up your EndNote library.

One is to create an EndNote online account (if you haven't already) at and then in EndNote Desktop go to Preferences and choose the Sync tab to set up a sync with your new EndNote online account. This will mean your entire EndNote Desktop library is synced with your online account on EndNote's servers, so if there's issues with your desktop library, you can reset the sync and create a new library based on your online account.

The other option is to create a backup from within EndNote Desktop, by going to File > Compressed library (.enlx) and creating a compressed library. You can then store this somewhere else in case there's any issues with your library or your computer's hard drive. Even if you do this, you may also want to sync with EndNote online for extra peace of mind.

Tags (new to EndNote 21)

EndNote 21 has brought in an additional organisational feature: tags. These are customisable labels that allow you to further organise your references, beyond using groups. You can change the colour and name or tags and add multiple tags to a reference. Anyone you've shared your library with can also view tags you've used. Use the Tags menu on the EndNote toolbar to create tags and then you can right click on a reference and choose Manage tags to add and remove tags from that reference.

All references in a particular tag are viewable on the left hand pane, similarly to groups.

Organising references with Paperpile

Paperpile logo

Paperpile has two different options for organising your items: Folders and Labels. Items can be in multiple folders and also be given various labels to aid with organisation (see the Share page for information on Shared Folders). You can also filter duplicates and access your PDFs through Google Drive.

Labels and Folders

Folders and Labels help keep Paperpile organised and tidy. Items can be in multiple folders and can also have multiple labels as well. There's no set way to use either of them, though it can be useful to use folders to split things into topics or pieces of work, and use labels to mark up particularly categories (e.g. 'to read', 'available online', 'cite in chapter 2').


  • To create a Folder, click on the Add New Folder button (a plus sign next to the Folders header on the left-hand side).
  • To add items to a folder, you can either tick a number of items and click on the Folder icon at the top then select the correct folder, or click on the six squares drag icon that appears when you hover over an item and drag the item into the correct folder on the left-hand side.


  • To create a Label, click on the Add New Label button (a plus sign next to the Labels header on the left-hand side).
  • As with folders, to add items to a label you can either tick items and then click on the Label icon at the top, or click on the six squares drag icon and drag individual items onto a Label.
  • You can change the colour of labels, and you'll see these reflected on each reference wherever you view it - this can be useful for visual categorising

You can rearrange the Folders on the left-hand side by dragging them into the order you want, but Labels are sorted automatically.

Checking for duplicates

If you have any duplicates in your Paperpile library, you'll see that one of the 'Filter' options down the right hand side will be 'duplicates', with a number afterwards. Clicking on this will allow you to view duplicates and then merge or delete them.

Auto-updating references

Sometimes the details you get from bibliographic databases and catalogues aren't the most accurate or complete references. Paperpile has a built-in feature where it can search online to update references with more detailed or accurate information if Paperpile can find it.

On an individual reference, use the arrow icon that will appear on the right hand side of the reference when you hover over it, then select 'Auto-update' to get Paperpile to look for these updates. You can also select multiple references or your entire library (using the Select option, then All) and choose 'Auto-update' from the 'More actions' menu.

Managing PDFs

PDFs in Paperpile are automatically stored on your Google Drive in a folder entitled Paperpile. These can be easily opened through Paperpile or Drive (though it's easier to find them in Paperpile as they are linked in the reference, whereas in Drive you have to navigate through alphabetical folders by author surname, or search for the author/title in Drive).

Opening PDF files from Paperpile will open with a set PDF viewer, which you can change from Paperpile's Settings, under the Browser Integration options. Paperpile now has a built-in PDF viewer that allows you to annotate PDF files, or alternatively you can choose to open PDFs as Google Drive files or using Chrome's built-in PDF viewer.

You can attach a PDF to a reference in Paperpile, or you can try and get Paperpile to automatically locate and download a full text PDF for any articles you have references for. You can set up Proxy Access in Settings to allow you to access restricted PDFs that you may have institutional access to.

Organising references with Zotero

Zotero logo

Zotero allows you to organise references using Collections and Tags you've defined (see the Share page for how you can also share references with others using Groups). You can also check for and merge duplicate items, manage full text PDFs, add notes and link references together, and view timelines of the references in your library.

Collections and tags

Zotero has two main methods for organising your references: Collections and Tags. Collections work like folders, allowing yout to group together references you want to see together, and one reference can be in multiple collections. Either right click on My Library or click on the New Collection button to create a collection, then drag references to move them in.

Tags are a way of marking up particular themes, categories, or information so you can categorise and find items in your library. Items can have many tags, including automatic ones that may be added from items saved online. To add tags to items, select an item and then on the right hand pane choose the 'Tags' option to view, add, and remove tags from the item. The Tag Selector pane in the bottom left of the Zotero interface allows you to view, select, and filter all of the tags in your library.

Checking for duplicates

In the left hand pane under My Library, you'll find a Duplicate Items heading, where Zotero stores any duplicates in your library. Clicking on this heading will display all duplicate items, and then clicking on an duplicate item will bring up options to merge the duplicates, including allowing you to choose which is the 'master' item, or the one to prioritise in the merge.

Managing PDFs

Zotero allows full text PDFs to be attached to references, either when they are collected or afterwards. To add a PDF or link to full text article to an existing reference in your library, right click on the reference and choose Add Attachment.

Double clicking on an attached PDF will open it in your PDF viewer of choice. If you want to annotate PDFs, Microsoft Edge (web browser) on a Windows machine or Preview on a Mac are built in tools that allow you to annotate PDFs.

Adding notes and related references

Zotero allows you to add your own notes to references, for example key points or quotations you might want to use in your work. Selecting any reference will bring up options on the right hand side of the interface including a 'Notes' option for adding notes.

In the right hand pane you can also add 'Related' references, which can help you build connections between texts and remember which ones have similar material.

Timelines and searches

Zotero has a built in feature that allows you to view the works in your library as a timeline, either by publication date or date you added the reference to the library. This can help you visualise the references in your library and think about the spread of literature you're using. You can find out more on Zotero's support page on timelines.

You can search your Zotero library, and you can also save searches if you don't want to move items into a collection, but do want to see those search results again.

Moving your Zotero library to a different computer

If you need to change devices, e.g. if you get a new computer, then there are two ways of moving your Zotero library to a different computer. You can use Zotero's syncing features to sync your library to your online Zotero account, and then on any new device you just need to use the sync option within the Zotero desktop app.

The other option is to copy and move the data folder to the new device and then move that folder into the right data directory, as found in Zotero preferences in Advanced > Files and Folders and going to Show Data Directory.

For full descriptions of these options, see Zotero's help page on How can I move my Zotero library to a different computer?


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 organise.
  2. Create some relevant groupings for your references (may be Folders, Groups, Labels, etc) and add references to these. If there are multiple options for your reference manager, try setting up different types and seeing how they might be useful for you.
  3. Check your library for duplicates (you might want to purposefully create a copy of a reference so you have a duplicate to find if you don't have a lot of references, so you can see how it works).
  4. If you've not already, scan through your references and check for any obvious errors or omissions. Add any useful notes to references if your reference manager has that feature.
  5. Try opening any full text PDFs you have to see what tool they open in or, if you don't have any, locate a PDF and attach it to a reference.

By the end of this section, you should have created some organisation in your library and tried out some other features!