Reference management software

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

• Download the application by choosing Download -> Zotero 7 for Windows/...  The application is available for Windows, macOS, and Linux.
• University staff can enable Zotero on their work computers from Software Center. If you no longer find Zotero on your work computer, please check the Software Center to see if it needs to be reinstalled.
• You can change the language of the application from Edit > Settings > General.
• In addition to the desktop application, install the following Zotero add-ons: Zotero Connector for your browser and Word or LibreOffice 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 (This installs Zotero Connector to your systems default browser. You can install it to other browsers by going to zotero.org -> Download using that particular browser).
  •  Edit > Settings > Cite > Word Processors
• 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 -> Settings -> Sync. You can also find there a link to create an account, if you don't already have one.
• University of Jyväskylä does not currently have an organisational license for Zotero. Therefore your Zotero account will have a limited space for attached full text files, 300 Mb. When the space is used up, Zotero will put up a notifier about this. It's possible to purchase more space for personal use. You can still save attached files on your computer using the desktop application, only backing up them on your account will stop. Reference data will also always be backed up on your account, even if the attached files aren't.

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".

• 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 search for full texts to attach using the "Locate" -tool.
  • View Online uses the DOI or URL and works best if you're using the university network.
  • Library Lookup requires you to add the JYU library OpenURL resolver to settings:
    • Edit > Settings > General > Locate
    • Resolver: Custom, Base URL: https://libkey.io/libraries/718/openurl
• You can create folders and subfolders (Collections and Subcollections). In Zotero's desktop application, use the button "New Collection" or choose "New Subcollection" when right clicking on a collection. You can also rename and delete collection.
• To move references in collections, drag them over the desired folder. By default, the reference also remains in the old collection when you move it. You can remove a reference from a collection 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.
  • duplicate_detection [Zotero Documentation]
• You can share reference information with other Zotero users by creating "Groups" on your Zotero account. The shared groups also show in the desktop application.
  • groups [Zotero Documentation]

Zotero can be used to add in-text citations and bibliographies in Word, LibreOffice, and Google Docs. Word and LibreOffice add-ons can be installed/reinstalled through Zotero desktop app: "Edit > Settings > Cite > Word Processors". The Google Docs -tool is part of the Zotero Connector browser extension on Google Chrome. In Word, the Zotero add-on appears in the toolbar as its own tab called "Zotero". Help: If the Word plug-in does not install through Zotero despite your best efforts, you can install it by manually copying the Zotero.dotm file to the correct folder.

• 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 Word-file from Zotero. You should do this only when you are finished writing the text. Unlinked citations cannot be returned. In-text citations and the bibliography change to regular 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 get more styles under Edit -> Settings -> Cite -> Get additional styles.

Another way of adding styles is downloading and installing csl-files. Below are some University of Jyväskylä departmental styles available for download.

How to install: Right-click one of the links below and choose "Save link as". You should be able to download a file called "university-of-jyvaskyla-department-of-chemistry-eng.csl" or "tuulatutkija.csl". When you try to open the file, it should install automatically to Zotero. If this doesn't work, go to Zotero and choose Edit -> Settings -> Cite -> +, and add the correct file.

Department of Chemistry -style

Faculty of Sport Sciences -style (Tuula Tutkija)