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Zotero Complete Guide

The MGH IHP's complete guide to using and getting the most out of Zotero

Collections and Tags

Collections and Tags

Zotero logo. The Z is in burgundy, the remaining letters are in black.

Items in Zotero libraries can be organized with collections and tags

Collections allow organization of items into groups and subgroups. The same item can belong to multiple collections and subcollections in your library at the same time. You may want to use collections to help organize by project, course, specific source or specific topic. When you save items in Zotero, you can directly save them into a collection. You can also add previously saved items into collections as well. 

Add a new collection

Tags or "keywords" allow for a detailed characterization of an item. For instance, you can tag items based on topic, methods, status, ratings or your own personal preferences.  Items in your Zotero library can have as many tags as you like.  To add tag to an item, select the item and click "Add Tags" in right hand column. 

Add a tag

You can also filter your library or collection to view items with a specific tag or set of tags. In the heading of Zotero, type your desired search into the "All Fields & Tags" search bar as shown here: 

Zotero search field

 

An important note about Collections & Tags

Tags are portable, but collections are not! 

This means that if you copy items between Zotero libraries, their tags will transfer, but not their collection placements.

The Zotero Collections Model

When using Zotero, it's important to understand the Zotero collections model. Items can belong to multiple collections and sub-collections. Adding an item to multiple collections does not duplicate the item, but rather, single items in a Zotero library can be added to multiple collections. 

Zotero compares this to adding the same song to more than one music playlist, rather than folders in your computer file system. An item is only considered to be a duplicate if it appears in the library "root" (My Library) more than once. Clicking on the root library such as My Library, personal, or group libraries, will show the actual amount of items in the library. 

Ways to Create a New Collection

Start by clicking the New Collection button above the left pane in Zotero. 

New Collection Picture

 

Or, you can right-click on My Library (or other Group library) and choose "New Collection." 

Name a new collection in Zotero

Create a New Subcollection

You can create a new subcollection by dragging and dropping an existing collection onto another collection, or by right-clicking and clicking "New Subcollection

New subcollection

 

To change a subcollection into a main, "top-level" collection, drag it out of the collection and drop it into the empty space in the left Zotero pane, or onto the My Library collection title. 

Adding Items to Collections

  • New items are automatically saved into the collection that is selected at the time of saving. When using the Zotero Save Button from your web browser, select the designated collection in the Zotero app, then click the Zotero save button in your browser. 
  • Existing Items in your library can be added to a collection by selecting them in the center pane, and dragging them onto the desired collection title in the left pane. The item(s) will be added to the new collection, but will not be removed from their original location. 
  • Moving Items between collections is possible by holding down Command (⌘) for Mac or the Shift key for Windows/PC, while simultaneously dragging the item(s) into the new collection. 

*Remember: the My Library view always shows all items in your library, so you cannot move items out of this view. To only see items that do not belong to any collection in your library, open the Unfiled Items special collection. 

Unfiled Items Collection

Renaming Collections

To rename a collection, right click on the collection and choose "Rename Collection." 

Renaming collection

Deleting Collections

To delete a collection from your library, right click on the collection and choose "Delete Collection."  Deleting a collection will also delete its subcollections. 

Delete Collection

Deleting a collection in your library does not delete the items in the collection. Items are still accessible by clicking on "My Library" or the group library name.

To delete both the collection and its items, right-click on the collection and choose Delete Collection and Items.

Delete collection and items

Removing Items from a Collection

To remove items from a collection, select the collection in the left Zotero pane to reveal all items within the collection. Then, in the center pane where items are displayed, select the item you want to remove.   

You can press the "Delete" key to delete, or right-click and choose "Remove Item(s) from collection" 

Remove item from Zotero collection

 

This action will remove the item from the collection, but will not delete the item from your library. To delete an item in a collection, select the item, right-click, and choose "Move Item(s) to Trash."

If you select the "My Library" or group library view, you can also use the delete key to move items to the trash. 

If you select the collection or subcollection, press Command (⌘) + Delete move items directly to the trash.

Searching in Zotero

Searching in Zotero

Quick Search

Quick searches are a way to quickly find items in a library or collection. 

To begin searching click inside the search box at the top-right of the center pane. As you type, only items in the center column that match the search terms will remain.  

Search Bar in Center Pane in Zotero Application

Quick Search can be used in three different modes:  

  • "Title, Year, Creator" - matches to these three fields, as well as publication title.

  • "All Fields & Tags" - matches all fields, tags and text in notes section. 

  • "Everything" - matches all fields, tags, text in notes, and indexed text in PDF (if PDF indexing is enabled)

Click the arrow in the Quick Search field to choose your preferred search mode: 

Modes for Quick Search

Zotero suggests using quotation marks at the start of your search when searching through large collections. This prevents searches from running until you type Enter/Return or a second quotation mark. 

Advanced Search

Advanced searches offer more and finer control than quick searches, and allow you to make saved searches. Click on the magnifying glass icon to open up the Advanced search window. 

advanced search

In the Advanced Search window, you can filter items by the content of specific fields or properties, like item or collection type. 

Advanced Search Window

Multiple filters can be selected at once by clicking the (+) icon to add more filters, or (-) to delete filters.  

Multiple Filters - Advanced Search

To search through a specific library, select it at the top of the window where it says "Search in library."

It is not possible to search multiple libraries simultaneously, at this time. 

By default, items only show up in search results if they satisfy all search criteria. To change this, so that all items matching at least one criterion are returned in the search, change the "Match" option to "any" as shown below: 

Advanced Search - Match search to any criterion

You can filter items by the collection or saved searches they belong to.

To include items in subcollections in your search results, check the "Search subcollections" box. 

Search subcollections - Advanced Search Zotero

To hide non-matching parent items with child items that do match the search criteria, and to collapse matching parent items with matching child items, check "Show only top-level items." 

To match search criteria against both parent items and their children, check "Include parent and child items of matching items."

If this option is selected and "Match" is set to all, parent/child items will still show up if just part of the criteria is met by the parent item and the other part by a child item. 

Wild Cards 

The % percent sign character acts as a wild card in advanced searches, substituting for zero or more characters. For example, the search term "W%Shakespeare" will match "W Shakespeare" ; "W. Shakespeare" and "William Shakespeare"

To search for items where a field contains any content at all, search for the % percent sign character alone. 

Saved Searches

When you save an Advanced Search, it will appear as a collection in your library, with a Saved Search icon:

Saved Search Icon 

Instead of the normal Collection icon: 

Collection icon

Saved searches only store the search criteria that you set, not the search results. Your saved searches are consistently updated after you add new items. For example, if you created a Saved Search with criteria for "Date Added" set to the "last 7 days", your search results will always display items that have been added in the last 7 days. 

To save a search, click the "Save Search" button in the Advanced Search window.

Save Search Zotero

Enter a name for your saved search. 

New Saved Search window

You can also create a saved search by right-clicking on a library and selecting "New Saved Search": 

New Saved Search from Library

To edit or delete a saved search, right-click on the saved search and select "Edit Saved Search" or "Delete Saved Search": 

Edit Saved Search Zotero

Using Complex Search Criteria

It is possible to run complex Boolean searches by using multiple Saved Searches. 

For example: To run (a OR b) AND (c OR d)

1. First, make a Saved Search called "Condition 1" for (a OR b) 

2. Then make a Saved Search called "Condition 2" for (c or d) 

3. Finally, run a third Advanced Search and search for "Collection" "is" "Condition 1" AND "Condition 2

See an example of this in Zotero below: 

Advanced Search window

PDF Full-Text Indexing

Full-Text PDF Indexing allows embedded text within PDFs to be searched with:

- Quick Search (via the "Everything" option)

- Advanced Search (via the "Attachment Content" option) 

You can control how much text in a PDF is indexed in the "Search pane" of Zotero preferences.

The default is 500,000 characters, 100 pages. 

Zotero searching preferences

Indexing happens automatically in the background when Zotero is idle. You can remove indexed text with the “Clear Index…” button or re-create the index from scratch using the “Rebuild Index…” button. You can check the index status of any PDF attachment by selecting the attachment item in the Zotero library and looking at the “Indexed:” field in the right pane.

If an item isn't being indexed (e.g., if it is not showing up not showing up an 'Everything' Quick Search), verify that the item has searchable text and that the text is properly stored in the PDF (e.g., try to copy text out of the document and ensure that it is high quality). If the PDF has valid text, rebuild the item's index by right-clicking on it and choosing “Reindex Item”. If you are still having issues, please ask a question on the Zotero forums.

Note: At this time, only PDF full-text content (and plain text files) can be indexed by Zotero. Other document types (e.g., .docx, .odt, .epub) cannot be indexed by Zotero.

Sorting Items in Zotero

Sorting Items in Zotero

Items in the center pane can be sorted by various properties:

  • Title
  • Creators
  • The date they were added to your library

Sorting items

To change the way items are sorted, click on any of the column headers at the top of the center pane.

For example, if you click on “Title”, all your items will be sorted alphabetically by title.

Clicking a header multiple times will sort the items in ascending or descending directions (the header will show an upward and downward arrow). 

By default, Zotero will show columns for the Title, Creators, and Attachments properties in the center pane. You can change which properties are shown by clicking the sort icon (), found to the right of the column headers. Checking properties in the dropdown menu adds them to the center column, and unchecking removes them.

Edit sorting columns

For each column, you can also choose the Secondary Sort field (which field is used to break ties when sorting). Make sure to select the column first, before selecting the Secondary Sort function. See below: 

Secondary sort function

By default, properties in the center pane are arranged from left to right in the order in which they are shown in the dropdown menu. You can rearrange them by dragging and dropping the headers.

Manually switch column order

To reset the order, select “Restore Column Order” in the dropdown menu.

Restore column order

Creating and Storing Notes in Zotero

Creating and Storing Notes in Zotero

Child Notes

To create a child note, select an item in the center pane.

Then, either click the “New Note” button at the top of the center pane () and select “Add Child Note”, or go to the “Notes” tab in the right-hand pane and click the “Add” button.

Child Note - with Icon

You can also right-click an item and select “Add Note”

Right click - Add note

Standalone Notes

Standalone notes are not directly attached to any item in your library.

Standalone notes will appear alongside any other items in your library or collection.

To create a standalone note, click the “New Note” () button and select “New Standalone Note”.

Standalone note

Tagging and Relating

As with any other item in Zotero, notes can be tagged and related to other items. Both features can be accessed via the bottom of the note editor.

Searching Notes

Notes can be searched via the general Zotero search. You can search text within a note using the note editor's “Find and Replace” button or Ctrl/Cmd-F.

Images in Notes

You can embed images into Zotero notes by dragging them from your filesystem. Note, however, that embedded images are not officially supported and will not sync (and may potentially cause other syncing problems). If you need images to sync in Zotero, you should add them as separate attachment files. Additional support for embedded images in notes will be added in a future version.

Related Items

Related Items

In addition to Collections and Tagsanother way to express relationships between items is by setting up "Relations."  Relations can set up between any pair of items in a library (it is not possible to relate items from different libraries).

To create a relation, select an item in the center pane and go to the “Related” tab of the right pane.

Going to the Related Tab on a Zotero Item

Click the “Add” button, and select one or more items from the same library in the pop-up window (hold down Ctrl or Shift [Windows/Linux] or Cmd or Shift [Mac] to select multiple items) and click “OK”.

Add related items in Zotero library

The selected items will now show up as related items in the “Related” tab, and clicking an item will take you straight to that item.

With the Zutilo plugin, you can also select multiple items in the center pane, then right-click and choose “Related selected items” to related all selected items to each other in one click.

Note that when you relate item A to B, B will be automatically related to A.

But relations are not transitive: relating A to B, and B to C, will not automatically relate A to C.

Some suggestions of how you could use this feature:

  • connect book chapters to their parent volume

  • connect book reviews to the book reviewed

  • connect different versions of a work (e.g., connecting a conference presentation that eventually became an article that eventually became a book)

  • link associated items from different collections

  • link items that form parts of a single work (e.g., articles in a series)

  • connect standalone notes to the items they discuss

  • link one item to another discussed in the Abstract or Notes fields

  • link items that have similar comments in the Abstract or Notes fields

Duplicate Detection

Duplicate Detection

As you build your Zotero library, you may add duplicated items. For example, you could have saved the same item twice from a webpage, or imported an item that you have already saved in your library.

Zotero can help you identify possible duplicates and allow you to merge them.

How to Find Duplicates

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 Duplicate Items Folder

 

Zotero currently uses the title, DOI, and ISBN fields to determine duplicates. If these fields match (or have no information entered), Zotero will also compare the years of publication and author/creator lists (if at least one author last name plus first initial matches) to determine duplicates. 

Duplicate detection only works within a library. Items in different group libraries are separate items. They won't show up in the “Duplicate Items” collection of any one of the libraries.

Merging 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 these data. Merges are also automatically recognized by the word processor plugins and don't affect your automatically generated citations and bibliographies.

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. Click the “Merge <number> Items” button in the right pane to merge the items. If the item fields don't match completely, you can select one item to be the “master” from the list at the top of the right pane, then select alternative versions of mismatched fields using the icons to the right of each field.

Video coming Soon

It may be easier to see which items are selected if you sort the items by Title. You can select a single item in the “Duplicate Items” view by holding down Alt/Option while clicking. You can de-select an item from a set of duplicates by holding down Ctrl (Windows/Linux) or Cmd (Mac) while clicking.

You can also select a group of two or more items of the same item type anywhere in your Zotero library, right-click, and select “Merge Items…” from the context menu