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Turku University Library

Reference Management

General information

Zotero is a free citation management tool that helps you:

  • Save all your references
  • Organise your references into collections, and tag them accordingly
  • Attach PDFs, notes, images, web pages, and other files
  • Cite sources while writing
  • Create bibliographies instantly
  • Share references and bibliographies with colleagues, students, etc.

 

Free version of Zotero gives you:

  • No data or file storage limits when using Zotero on a single computer, without an account.
  • Zotero account allows unlimited data storage, but full text files (e.g. pdfs) are limited to 300 MB.

Getting started:

In order to get the most of Zotero, you will need:

  • The Zotero application: download it from zotero.org or if you are using a university computer, from the Software Center.
  • Create a Zotero account at zotero.org (not necessary if you are only using Zotero on one computer).
  • Download the browser extension: Zotero Connector.

NOTE: If you are running Zotero 5.0 or Zotero Standalone 4.0, the word processor plugins are bundled with Zotero and should install automatically for each installed word processing program when you first start Zotero.

The Turku University Library provides basic assistance in starting to use Zotero.

Zotero gives each user 300MB of free file strage. Citations as such, take up little space. PDFs, videos, photos and other attachments take up quite a bit of space:

Tips for Space management:

Other options to think about:

  • If you do not sync Zotero to the cloud, you won't take up space. But please note! that means that if your computer is stolen, melts down etc, you will lose all y our materials. Remember regular back-ups to an external hard drive, if you do not sync.
  • All you need to know about Zoteros syncing & WebDAV: https://www.zotero.org/support/sync#WebDAV

If you are having problems with Zotero, please contact tietopalvelu@utu.fi.

Building a Zotero library

You can import a single item in multiple ways:

  1. To add a PDF or any other file from your computer, simply drag it to Zotero — you can drag to an existing item to attach the file or drag between items to store as an independent item. Zotero will automatically attempt to retrieve bibliographic metadata for PDFs
  2. You can quickly add items to your library if you already know their ISBN, DOI, PubMed ID, or arXiv ID. To add an item via one of these identifiers, click the “Add Item by Identifier” button (https://www.zotero.org/support/_media/toolbar-lookup.png) at the top of the center column of the Zotero pane, type or paste in the identifier, and press Enter/Return.

The Zotero Connector's save button is a convenient and reliable way to add items with high-quality bibliographic metadata to your Zotero library. As you browse the web, the Zotero Connector will automatically find bibliographic information on webpages you visit and allow you to add them to Zotero with a single click.

  • Download the Zotero Connector from zotero.org.
  • You can use it with Chrome, Firefox, Safari or Edge.
  • You can use the connector with a single item or multiples items from a webpage.

If you are importing a large number of items from scholarly databases, it is better to export the items as a batch in one of the standardised formats (most commonly RIS or BibTex).

Effective use

Organising references in Zotero libraries with Collections and Tags


Collections:

Collections are useful for filing items in meaningful groups (e.g. items for a particular project, from a specific source, on a specific topic, or for a particular course).

  • Create new collections and subcollections on the left side of the Zotero window.
  • Convert a subcollection into a top-level collection by dragging it out of the collection and dropping it into an empty space in the left Zotero pane.
  • To add existing items in your library to a collection, select them in the center pane and drag them onto the collection in the left pane. By default, the items will be added to the new collection but won't be removed from their original location.
  • The same reference can be dragged and dropped to multiple collections.
  • To move items between collections, hold down Shift (Windows/Linux) or Cmd (Mac) when dragging items to a new collection.
  • Rename or delete collections by right-clicking them (control-click on macs) and selecting from the menu.
  • Import items directly to a specific collection or add them to collections after they are already in your library.
  • To only see items that do not belong to any collection in your library, open the Unfiled Items special collection.
Tags:

Tags (or keywords) allow for detailed characterisation of references. You can tag references/items based on their topics, methods, status, ratings, or even based on your own workflow (e.g. “to-read”).

  • The tag selector is located at the bottom of the left Zotero pane.
  • To add a tag to an item, select the item in the center Zotero pane, and open the Tags tab in the right-hand pane. Click the Add button, type the tag name, and click Enter/Return.
  • An individual reference can have as many tags as you like.
  • Drag items to a tag in the tag selector in the bottom left to add the tag to all of them.
  • You can filter your library (or a specific collection) to only show items that have a specific tag or set of tags.
  • To remove a tag from an item, select the item in the items list, click the Tags tab in the right-hand pane, and click the “-” (minus) button next to the tag you want to remove.

 

Coloured tags:
  • Coloured tags appear as small coloured squares next to items' titles in the center pane.
  • Coloured tags are shown at the top of the tag selector and are always visible, even if not assigned to any visible items.
  • Many people use coloured tags for “to read” or “favorite” items. They can even contain emojis (e.g., ⭐️ for favorites).
  • Assign a color to a tag by right-clicking on it and choosing “Assign Color…” In the popup window, select a color from the dropdown menu and click “Set Color”.
  • Remove a color from a tag by right-clicking on it, choosing “Assign Color…”, and clicking “Remove Color”.
  • Up to 9 tags can be assigned colours and numbers.

 

Automatic tags:

Some databases provide keywords for their records, which are saved as Zotero tags. Automatic tags behave the same as manually added tags but are marked by a red icon in the “Tags” tab of the right-hand Zotero pane (versus the blue icon for regular tags).

  • Automatic tags can be hidden from the tag selector by clicking the multi-color button in the lower-right corner of the tag selector and unchecking “Show Automatic”.
  • You can delete all automatic tags from a library by clicking “Delete Automatic Tags in This Library”.
  • To prevent Zotero from adding automatic tags, uncheck “Automatically tag items with keywords and subject headings” in the General pane of Zotero preferences.

Library lookup in Zotero to find fulltexts through Volter

By adding Volter's OpenURL to Zotero's Library Lookup, you can easily check if the University of Turku has access to the fulltext of the article you are looking for.

Go to Preferences in Zotero (Edit -> Preferences -> Advanced) and add the library's Volter database's OpenURL web address in the box: https://utuvolter.fi/openurl/358FIN_UTUR/358FIN_UTUR:VU1?

Screenshot of Zotero's preferences' advanced tab, OpenURL box with the Volter address circled in red in the middle of the image.

After that when you have a reference open on the right, you can click on the green arrow on top of it, choose Library lookup and you will most of the time move straight through Volter to open the fulltext of the article. If this does not work out, you can always try and look for the fulltext by searching for the journal's name in Volter.

Screenshot of the top right corner of Zotero, with the green arrow dropdown menu activated and library lookup circled in red.

Managing files in Zotero

In addition to item metadata, notes, and tags, Zotero can also be used for managing files.

There are two kinds of files, those attached to a reference and a standalone file. It is a good idea to always use an attached file, because standalone files lack in many Zotero’s features, including citing.

  • If you save a PDF directly to your library, Zotero will attempt to retrieve metadata from it and create a reference automatically.
  • If the item cannot be recognised, you will be left with a standalone attachment.
  • Zotero automatically saves associated web page snapshots and PDFs when you use the Zotero Connector save button in your web browser (option to save associated snapshots and PDFs can be changed in the Zotero preferences).
  • When you have selected a single item in the center pane, you can click the “Add Attachment” paperclip button at the top of the center column.
  • Files in your library can be accessed by double-clicking the item in the center pane. Alternatively, you can right-click the item and select “View PDF” or “View File”.

Deduplicating Items

Clicking on the “Duplicate Items” collection in your library, or right-clicking the library in the left pane and selecting “Show Duplicates” will show the items Zotero thinks are duplicates in the center pane.

  • Zotero currently uses the the title, DOI, and ISBN fields to determine duplicates.
  • You should always resolve duplicate items by merging them, rather than deleting one of the duplicates. Merges will retain all of the collections and tags of the merged items; deleting one item will lose the data.
  • To merge items in the “Duplicate Items” collection, select an item in the center pane. Zotero will automatically co-select the other items that it thinks are duplicates.
  • It may be easier to see which items are selected if you sort the items by Title.

Importing references from RefWorks

University of Turku's subscription to RefWorks is ending on December 31st, 2021.

Below are instructions on how to import your existing references out of RefWorks and into Zotero.

If you want to keep the folder system in the new reference management system, follow these instructions folder by folder. If you want to export the whole reference library without the folder system, export the references from the All References folder. Note: The PDF's you have saved to RefWorks will not be exported with the reference information to the new system!

  1. Go to the folder in you Refworks account where the references you want to export are (All References or a specific folder).
  2. Click on the Share icon and then Export references.
    Top menu of RefWorks where All References folder is active and Share menu is visible.
     
  3. In the Export references menu choose RIS Format from the Format list. Then click on Export.
    Export Reference menu where All references in All References is active with RIS Format in Format menu.
     
  4. Depending on the browser follow either instructions:
    1. If you get a pop-up with an Open with option, you can choose from the menu directly that you want to open the file in Zotero.
      A pop-up window, with Open with Zotero chosen.

      Then a pop-up window will open, where you are asked if you want to save the references into a new collection (corresponds to RefWorks folders).
      An open menu with "Do you want to import the file "export.ris"?" Option checked: Import into new collection.
       
    2. If the file downloads to your computer, go to Zotero, click on File and choose Import from the drop-down menu. Choose A file (BibTex, RIS, Zotero RDF, etc.) from the next menu and click Next.
      Zotero's Import menu, option checked is "A file (BibTex, RIS, Zotero RDF, etc.)". Click Next.
       
  5. Search for the recently downloaded file. Choose from the last pop-up window, if you want the references to be saved into a new collection and if the file will be copied to Zotero's storage folder.
    Option menu where you can choose if you want to "Place imported collections and items into new collection" and if you want to "Copy files to the Zotero storage folder".

If you want to keep the folder system in the new reference management system, follow these instructions folder by folder. If you want to export the whole reference library without the folder system, export the references from the All References folder. Note: You can only export 200 references at a time!

  1. Go to the folder in you Refworks account where the references you want to export are (All References or a specific folder).
  2. In the References menu, click on Export.
  3. Select from the menu that appears next what references you wish to export and select Bibliographic Software from the Select an Export Format dropdown menu.
    Export References window, where All in List and Bibliographic Software from Select an Export Format dropdown menu are selected.
     
  4. When the export has finished, a notification and a link to download the file appears at the bottom of the page.
    A notification letting you know the export was successful: "Export Complete. If you do not receive a file download prompt click here or if you'd like the file emailed to you click here."
     
  5. If the references open in a new browser tab, select all (Ctrl+A) and copy (Ctrl+C).
    1. Go to Zotero.
    2. Open the File menu and select Import from Clipboard to save the copied references into Zotero.
  6. Create a specific folder for the references, if you wish.