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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.

Collecting references

With reference management software you can collect the bibliographic information about a source to store in your own library. This page looks at the general principles for collecting references during your search and reading process and how to import references into three applications: EndNote, Paperpile, and Zotero.

General principles for collecting references

What are you collecting?

Bibliographic information usually includes the title, author, date, and other publication details. If you are collecting a reference to a journal you will often be able to collect the abstract and, with some reference managers, the full text PDF (if it is available).

Where do you find references?

References can be collected electronically from a range of different platforms such as Google Scholar, bibliographic databases like Scopus and Web of Science, and library catalogues. Basically, the usual places where you search for information.

When do you collect references?

The best time to collect references to sources is when you are doing your searching. Collect the reference for anything potentially useful - you can always return to it later and decide if it's relevant.

One step or two steps?

When we are collecting references what we are trying to do is copy the selected reference into our reference manager. To do this we first have to select the reference, then extract the bibliographic information and send it to our reference manager.

Some systems can transfer references in one step within your browser, but others will require you to save a small reference file and then import this into the reference management software.

Things to look for:

  • Does your reference manager have a plug in for your browser that you can use to collect the reference?
  • Is there a way to select references, for example with a check box, on your chosen search tool?
  • If you have selected references, is there an option to either send the reference to your reference manager or export a file to import into your reference manager?

Single or multiple references?

On most databases and catalogues, you can pick up multiple references at a time. This can be a much quicker way of getting lots of references into you reference manager rather than sending individual records.

To do this, you'll have to find how that database allows you to select multiple records (usually a check box) and then export the whole list either directly to your reference manager or into a file to import in.

You can tick multiple options on most databases and then choose an export option to export all of the references at once
An example of how to export multiple references in Scopus

What's a RIS?

A RIS (.ris) file is a bibliographic citation file saved in a format developed by Research Information Systems (RIS). RIS files provide information such as title, author, publication date, keywords, and publisher, and contain a series of lines delimited by two-character codes and a corresponding value.

RIS files shown in File Explorer with the extension .ris
RIS files will show up with the extension .ris when you view them.

RIS files were created to standardize the exchange of citation information. When you are exporting references from a database you will often see the option to export in this format - we recommend using RIS to export to any reference manager, especially if you're having issues with another method of collecting references.

Accessing resources

To collect references, you have to find them...

Here are some links to key information and places to search when collecting and accessing resources.

Tips for collecting references from particular sources

You can collect references from most databases and catalogues, but the methods of doing so vary across platforms. Here are a few tips for getting references out of these sources so you can import them into your reference manager.

Bibliographic databases

Most bibliographic databases include the ability to export references, but unfortunately there is no agreed standard, so the precise method varies considerably. Most systems will include the ability to select several references for export and a link/button to begin the export.

If the reference manager you're using has a browser extension to collect references, you can try that first. Often they will pick up the search results and let you choose which to import, but they may not be able to. If not, or you don't have an extension, you can use the export method.

Locate the export option in the database (it could be called 'export' or possibly 'send to' or something else). Look for either RIS / RefMan (for any program) or EndNote (if you're using it). Check which details you're exporting - you'll probably want the full reference and abstract if possible.

Once you've exported the reference, you can import it into your reference manager.

Google Scholar

As with other databases, if you're using a browser extension to collect references, it should be able to 'read' Google Scholar searches to try and collect references, but you may also need to use the export options in Google Scholar. Google Scholar can also be set up so that each reference has a direct link to export into an RIS (or .enw) file.

To set up Google Scholar to include direct export links by each reference, open and click on the Menu (three lines) icon in the top left hand corner. This will open a sidebar, which has 'Settings' at the bottom. Choose 'Settings' and then under 'Bibliography Manager' select 'Show links to import citations into...' and choose 'RefMan'.

Screenshot showing the Settings link on Google Scholar and where to find the RefMan option in Bibliography manager
In the Google Scholar settings you'll find the option to 'Show links to import citations'

This will create a link on each item when you search on Google Scholar that says 'Import into RefMan'. Clicking this link will allow you to download an RIS file for that reference. If you're using EndNote, the EndNote option also works (and downloads a .enw file), but RIS tends to be more reliable.

You can also export multiple references at once using Google Scholar, by adding items to 'My library' using the star icon, then going to 'My library' and selecting all the references you want to export, then using the Export button to get your RIS file.


The University library catalogue, YorSearch is very useful for gathering references, especially to physical items you have on loan. You can export single references or pin multiple items to your favourites and export them together.

To export a single reference in the search results, click on the three dots 'more' icon on the right hand side of the item, which should open up additional options at the bottom of the item. Click on the 'Endnote etc (RIS)' option to download an RIS file to import into your reference manager.

Note: if you have an EndNote online account, you can use the 'EndNote online' option to directly import into EndNote. If you're using the desktop version but have an online account synced, you can use this option and then sync your desktop app to see the imported reference.

To export multiple references, use the 'pin' icon on references to add them to 'My Favorites', then from within there select all references and use the three dots 'more' icon again to get the export options.

Can't find the item anywhere?

If you have a physical or online item that you can't find on any databases or catalogues, as a last resort you can manually create the reference in your reference manager. Doing this requires you to be careful about choosing the right reference type and formatting the author names correctly, or your reference will look incorrect when cited.

Already got the references in another reference manager?

If you've already been using a reference management tool and you want to transfer to use another, you don't have to collect all your references again.

All of the major tools have an option to export your entire library, often as an RIS file. This file can then be imported into the reference manager of your choice.

Additionally, if you've used the References tab in Word to collect references, you can export these references to EndNote if you get the Word plug-in for EndNote and use the Export option.

Collecting references with EndNote

EndNote logo

EndNote allows you to import references from RIS and .enw files, as well as some direct import options into EndNote online. There's also a bookmarklet tool that works in a web browser, but it is often easier to use one of the other methods.

Note: This information is specifically for EndNote Desktop, but these methods are very similar for EndNote Online.

Endnote capture reference

EndNote has a bookmarklet tool called 'Capture Reference' that allows you to import references from a page, though it isn't as easy as other reference managers' browser tools.

To use it, you have to save some JavaScript code as a bookmark in your web browser, and then click on that bookmark to open a window to save the reference. EndNote's support page explains the process.

The Capture Reference tool can send a reference to EndNote online, or allow you to export an RIS file to import into EndNote desktop. Using built-in export tools is generally easier, though if you're trying to save web pages as references this tool does allow you to do that.

Importing from a file

Once you've got an RIS or .enw file from a database or catalogue, you'll want to import it into EndNote. You can double click on the downloaded file and it should open in EndNote and import in those references.

If this doesn't work, for example if you have multiple reference management applications installed on your device, then you can go into EndNote, then choose File > Import and select the file you downloaded. You may then have to tell EndNote what kind of file it is before you can import it.

Importing from a PDF

Some PDFs contain metadata that EndNote can read and convert into a reference.

To import a PDF to your EndNote library, choose File then Import... then File... Browse for the PDF you want to import and select PDF under Import Option.

This is not a reliable method as often PDFs do not contain the right information for EndNote to turn them into a reference. You can find the reference online and then attach the PDF to the reference.

Manual entry

If none of the above methods work, you can also add references manually.

  1. In EndNote, choose References, then New Reference.
  2. Make sure to select the correct Reference Type first to ensure the correct fields are shown.
  3. Complete the fields needed to your citation style at a minimum. Authors must be Surname, Forename with multiple authors on separate lines. Do not use the formatting tools - leave this to the bibliographic styles.
  4. Choose File, then Save, or close the reference and choose Save when prompted.

Collecting references with Paperpile

Paperpile logo

The Paperpile browser extension is the easiest way to collect references and PDFs of full text articles with Paperpile, but you can also use other methods if you need.

Paperpile browser extension

Paperpile should always be used in the Chrome web browser and you'll need the Paperpile Chrome extension to quickly collect references and PDFs straight from your browser.

When you sign up with Paperpile (using your University of York email address) you will be prompted to install the Paperpile Chrome Extension. This extension will give you a Paperpile button next to the address bar in your web browser (a small 'P'). When you are on a PDF file, an article page, or a list of search results, you can then add items to Paperpile.

Whenever you are on a supported publishers' website, a green arrow will appear on the Paperpile button. Clicking on this button will give you the option to add the item to Paperpile. If the item has an attached PDF, Paperpile should pull this over to your library as well. This method can also be used when you are viewing a PDF itself.

If you are viewing a list of results, an import button with a plus sign and the name 'Paperpile' should appear next to each result. Clicking on this button will add that item to Paperpile. This method can also find attached PDFs.

Importing from a file

Paperpile can read bibliographic information stored in RIS, BibTeX, EndNote, and RefWorks formats. You can export information from databases in these formats and upload them to Paperpile. This is particularly useful when you want to select, export, and then upload a large number of references at once.

  1. Go to Paperpile and click on 'Add Papers', then 'Upload Files'.
  2. Select the file you want to upload to Paperpile. You can also choose a folder. Click 'Start upload' and the references will be added to your Paperpile library.

Importing from other applications

Paperpile has the option to import from other applications directly from the 'Add Papers' button. If you use Mendeley or Zotero, Paperpile can automatically import your library, including attached pdfs and files. If you use EndNote or other software, Paperpile has a migration guide to help you import your library.

If you use Mendeley or Zotero and your library is fully synced online, Paperpile can automatically import your library and attachments. Click on the 'Add Papers' button, choose 'Import from other Programs', and follow the onscreen instructions.

If you use EndNote or other reference management software, you can import your library into Paperpile by following their migration guide. The link to this can be found when click on 'Import from other Programs' as well as below.

Manual entry

If it is not possible to add the reference using any of the above methods, you can add it manually.

  1. Go to 'Add Papers' and click on 'Add Manually'.
  2. Choose 'Enter data by hand'.
  3. Make sure you choose the correct 'type' first, e.g. book, journal article, book chapter etc. This will make sure you are shown the correct fields to fill in.
  4. Complete the fields necessary for your referencing style and any other information you think will be useful.
  5. Click 'Save' and the reference will be added to your library.

Collecting references with Zotero

Zotero logo

Zotero has a web browser extension called Zotero Connector for easily collecting references from web pages, or alternatively you can import references in common formats.

Zotero Connector

To collect references in Zotero straight from your web browser, you will need to install the Zotero Connector (available for Chrome, Firefox, and Safari), which gives you a Zotero button in your web browser that you can click on any page to save even any references in that page or, if there isn't any bibliographic information on the page, save the page as a Web Page in Zotero.

Alternatively, there is a Zotero Bookmarklet tool for anyone using a mobile device or another web browser. Follow Zotero's instructions for how to set it up for your chosen browser.

Add item by identifier (ISBN, DOI, etc)

Zotero has the ability to add items if you know their ISBN, Digital Object Identifier (DOI) or PubMed ID, with Zotero searching for the bibliographic information based on the identifier.

The 'Add item by identifier' button in Zotero (which looks like a magic wand with a plus symbol) allows you to type or paste in a relevant identifier and then press Enter. It is also possible to add multiple identifiers at once (see Zotero's guidance on adding items to Zotero for more.

Importing from a file

To import data from a file like RIS or BibTeX, in Zotero go to File > Import, then select the file you want to import.

Zotero will then ask if you want to copy files to Zotero's storage or link the file. We'd recommend copying the files to Zotero's storage and then deleting the original downloaded file, as this keeps your data organised and allows you to sync your Zotero library with their web version.

Importing from a PDF

If you have PDFs already downloaded and want to see if Zotero can read any metadata stored in them to create a reference for them, you just need to drag the PDF into Zotero. This may not give you a complete reference, however, and Zotero have some more details on their support page on retrieving PDF metadata.

You can also attach PDFs you have downloaded to existing references, so you can locate the reference in a database, add it to Zotero, and then attach the PDF within Zotero.

Manual entry

If it is not possible to acquire a reference through the above means, you can add the information manually.

  1. Use the 'New item' button in Zotero to add a new reference
  2. Choose the appropriate item type from the drop down, or use 'More' for other types of material if the one you need doesn't appear immediately.
  3. Enter as much detail as possible for the item, including following the given format for entering author names.
  4. The new reference saves withyout you needing to do anything.

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

  1. Firstly, set up your reference manager of choice and install any browser plugins or bookmarklet tools they might have (see the homepage if you need to get access to one of the tools).
  2. Next, collect some references. Use the databases and catalogues you typically use when searching for information (or check out your department's Subject Guide for ideas). Use a browser extension or bookmarklet if possible to try and gather references straight from the page into your tool.
  3. Now try exporting some RIS files and importing them into your tool of choice. Go to Yorsearch and gather some references as RIS files from there. Also try Google Scholar if you've not tried it already.
  4. Extension: if you have any PDFs of articles, try importing one into your library and see what happens.

By the end of this section, you should have some references in your library!