Reference management software

tekijä: Liisa Hannele Halttunen-Keyriläinen Viimeisin muutos keskiviikko 02. maaliskuuta 2022, 13.53

We strongly recommend that you use a reference manager tool such as Zotero or Mendeley to manage your references. Among other things, they offer you access to several ready made out-put styles for both in-text citations and bibliographies, so they save time and effort!

Below you can find basic instructions for using Zotero. You can access more complete instructions on the Zotero website: Zotero Documentation.

Zotero is free and open source software. You can download the desktop app from zotero.org.

  • Download the application by choosing Download -> Zotero 5.0 for Windows. The application is available for Windows, macOS, and Linux.
  • University staff can enable Zotero on their work computers from Software Center.
  • In addition to the desktop application, install the following Zotero add-ons: Zotero Connector for your browser and Word or LibreOffice/OpenOffice add-on. If the add-ons do not install automatically along with the desktop application, you can install them via Zotero's desktop application under:
    •  Tools -> Install Browse Connector
    •  Tools -> Add-ons
  • You can also create an account for Zotero. The account copies your reference data to Zotero's servers, allowing you to sync the data to multiple devices. It also allows you to share references with other users. The account can be connected to the desktop application from Edit -> Preferences -> Sync. You can also find there a link to create an account, if you don't already have one.

Adding reference data to Zotero

The easiest way to add reference data to Zotero is through the browser extension Zotero Connector.

  • Install the browser extension through Zotero's desktop application or zotero.org.
  • The browser extension appears as a button in the browser toolbar to the right of the address bar. Zotero's desktop application must be active when you want to migrate reference data.
  • Using your browser, go to the publication, for example in a library database or on the publisher's website. The button changes its shape when it recognizes publication information on webpages. Press the button and the reference data will be transferred to Zotero. You can also select in which folder the data will be added at this point. If you are on a page that provides access to the full text PDF of the publication, the file will also be transferred to Zotero.

Other ways to add reference data to Zotero:

  • .ris or .bib file transfer. Using this method, hundreds or thousands of references can be transferred at once. Use the export function of the database to make the file. In Zotero's desktop app, select "File > Import > A file" and choose the correct file.
  • You can add references completely manually. Use this method if the reference is not available/transferable online. In Zotero's desktop app, select "File > New item" or the button "New Item".
  • You can extract reference data from article full texts in PDF format. Drag the PDF file to the Zotero window. This works best for fairly new articles from international scientific journals.
  • Search for reference data using a publication ID (e.g. doi, ISBN). In Zotero's desktop app, select "Add Item(s) by Identifier".

Organizing and managing references in Zotero

  • You can edit and correct reference information in Zotero's desktop application. Changes are saved automatically. You can also add keywords (Tags), attachments, and notes to references. 
  • You can create folders (Collections) and subfolders. In Zotero's desktop application, use the button "New Collection" or choose "New Subcollection" when right clicking on a folder. You can also rename and delete folders.
  • To move references in folders, drag them over the desired folder. By default, the reference also remains in the old folder when you move it. You can remove a reference from a folder by right clicking it and choosing "Remove Item from Collection".   
  • Deleted references go to the Recycle Bin, where they can be returned from or deleted completely.  
  • Under "Duplicate Items", you can check and combine duplicate references.   
  • You can share reference information with other Zotero users through your Zotero account.

Creating in-text citations and reference lists / bibliographies with Zotero

Zotero can be used to add in-text citations and bibliographies in Word, Libre/OpenOffice, and Google Docs. Word and Libre/OpenOffice add-ons can be installed through Zotero desktop app: "Tools > Add-ons". The Google Doc -tool is part of the Zotero Connector browser extension. In Word, the Zotero add-on appears in the toolbar as its own tab called "Zotero".

  • Word processor add-ons get the reference data from Zotero's desktop app. Therefore you don't sign in separately to the add-on. The desktop application must be installed and active to be able to use the word processor add-ons.
  • You can select a reference style under "Document Preferences". There are about a dozen default styles, but you can add styles to the list through the desktop app. If you change the reference style, in-text citations and bibliography are updated automatically in the new style.
  • The "Add/Edit Citation" button adds and edits in-text citations to the text. You can also add page numbers to citations, and you can hide the author's name if you want the in-text citation to be a year only.
  • The "Add/Edit Bibliography" button makes a bibliography that automatically includes all the sources referenced in the text. The bibliography is updated automatically when you add new in-text citations.
  • Use the "Refresh" button to update with new and modified reference data from the desktop app.
  • With the "Unlink Citations" button, you can unlink the file from Zotero. You should do this only at the moment when you finish writing the text. Unlinked citations cannot be returned. In-text citations and the bibliography are normal text after you unlink the file. After unlinking you can edit the citations and bibliography manually.

If you don't want or can't use one of the word processor add-ons, Zotero can also be used to make copy-pasteable bibliographies. Create a folder for the desired references, select all references in the folder, right click and choose "Create Bibliography from Items". Choose the reference style you want to use. You can save the bibliography as a file or copy it to the clipboard and paste it into the program you want.

A huge number of international reference styles can be used in Zotero. The styles are created in the CSL programming language and are shared with e.g. Mendeley. You can add more styles under Edit -> Preferences -> Cite.

Migrating you references from Refworks to Zotero or Mendeley

It's possible to transfer reference information from your RefWorks account to Zotero or Mendeley using the RIS format. Unfortunately, the pdf full texts attached to the references and the notes made to them do not migrate.

Creating a RIS file in Refworks:

  • First, think about which references you want to transfer. If possible, at this stage it's worth deleting unnecessary references and duplicates from your account. If you want to keep the folder structure of your RefWorks account, you need to move the references folder by folder.
  • Open the All References -view in Refworks, or the folder whose references you want to move. From the Refworks toolbar, select Share > Export references. You can export all references from your account/folder or choose from the list. Select RIS format and press Export.
  • The browser downloads a file called export.ris to your computer. You can find the file in the Downloads folder on your computer. If the folder already had RIS files you have made before, the new files are named export (1) .ris, export (2) .ris, etc. You will be able to transfer your RefWorks account reference data through these files to Zotero, Mendeley, and other reference managers.


Importing the RIS file to Zotero:

  • In the Zotero desktop app, open File > Import from the tool menu. Select import from A file (...) and press Next. Find the right file, for example, in the Downloads folder and open it. You should keep the choice “Place imported collections and items into new collection” and the choice “Copy files to the Zotero storage folder”. Press Next and finish the import.
  • Reference data has been transferred to a Zotero folder (Collection), named after the file, for example “export”. If you are moving references one RefWorks folder at a time, you can name the folder (Collection) accordingly.
  • If possible, it's worth checking whether the data has moved correctly. Any duplicates can be merged with Zotero's Duplicate Items -tool.


Importing the RIS file to Mendeley:

  • In Mendeley's desktop app, open File > Import > RIS... Find the right file, for example in the Downloads folder, open it, and the import will start automatically.
  • References have moved to your Mendeley account, and are selected after the transfer. If you are moving references one RefWorks folder at a time, make a new Mendeley folder for the references.
  • If possible, it's worth checking whether the data has moved correctly. Any duplicates can be merged with Mendeley's Check for Duplicates -tool.
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