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University of Texas University of Texas Libraries

Citation Managers for Research Organization

Organizational Features

Libraries & Collections

Libraries and collections are the primary level of organization. Because the icon for the collection is a folder, you'll find the two terms folder and collection used interchangeably particularly in this tutorial. Creating a hierarchy of folders and sub-folders can be one of the easiest ways to create an organizational scheme to the research in your library. 

Folders will only have the items within that you specifically save to that folder.  This means that items in a sub-folder will not be listed in higher folders in that folder hierarchy. "My Library" on the other hand will contain all of the content within each folder and subfolder in that library. 

Adding a folder/collection:

1.) Right-click on a folder and click "New Subcollection" to add a subfolder under a specific folder.

Add subfolder visual example

2.) Start type to name that subfolder. 

You can always rename folders and subfolders. It's also possible to drag the folders into a hierarchy and then remove them later. In addition, the add folder icon at the top will also add a new folder.


The tagging system is a secondary mechanism for organizing your library. All of the items can have tags and tags can be the same across multiple items and folders. This will allow you to quickly and seamlessly pull together all of the items you have tagged with the same tag. 

The tags window resides in the lower-left pane of the Zotero desktop application. As you navigate through folders and subfolders, note the tags will change. This is because the tags library is reflective of the items contained in the folder that you have open. To see all tags, move up to the "My Library" level. The one exception to this rule is the weighted/colored tags, which will always be at the top of your tags library regardless of whether or not items with the weighted tags are in the specific folders and subfolders you are scanning through. All tags are case sensitive meaning that the tag, "Animal Behavior" will be a separate tag from "animal behavior."

Tags visual example

Adding Tags:

1.) Go to an item in your library and select the tags tab.

Adding tags location visual example

2.) Click the "Add" button. This will prompt a field to appear where you can start typing your tag. Remember, tags are case sensitive. You can add a new tag or start typing a tag that you commonly use and your library of existing tags will pop-up as you type allowing you to select the option you want. 

Add tag visual example

Weighting (Coloring) Tags:

1.) The weighting of tags is completed after the tag is added to the library by adding it to an item. Next to weight (color) that tag, return to the tags library in your left-most pane and right-click on the tag you want to color/weight. 

Weight tags location visual example

2.) This will summon a dialog box allowing you to select the color and order number (1-9) you'd like to assign to the tag. The order number will simply dictate where, in the order of other weighted tags, it appears.

Weight tags visual example

As you only have 9 spaces for colored/weighted tags in each library, it's important to consider how you want to use the weighted tags in your workflow. You can also decolor/unweight a tag that you had previously assigned via the same method of right-clicking on the tag, and selecting "color tag" from the drop-down. 

Tags Imported with Downloads:

Tags can be imported with your downloads. Tags added in this way may represent keywords or subject headings that are assigned in the database you are adding your items from. Some folks like this feature because it enriches each item's metadata and arguably can make it easier to identify items. Some, however, prefer not to use this feature as it adds unstandardized terms into your tags library. 

Turning on/off your automatic tagging:

1.) In the top menu, click Zotero >> Preferences, to open up the preferences window. 

Preferences visual example

2.) Once you have your Preferences window open, navigate to the General tab >> Miscellaneous section. Unchecking or checking this checkbox will turn off/on the function to automatically add tags with downloads for keywords and subject headings. While in this area, I suggest noting the other options available under the General tab. 

Miscellaneous visual example

Related Items

The related items feature allows you to have a third level of organization built into Zotero wherein at the item level another item will be connected to it and vice-versa. Items can have more than 1 related item.

Setting up a related item:

1.) Under a particular item, go to the "related items" tab in the third pane of your Zotero library. 

Related item visual example

2.) This will prompt a dialog box to appear containing your full library allowing you to select any other item in your library.

Related item dialog box visual example

3.) Select the desired item and click "OK" to initiate a relationship between both items. This will create a linking system under the "Related" tab of both items. 

Notes & Attachments

Notes is a feature within Zotero that facilitates managing multiple parts of literature research under one tool. Items can have as many different notes as you want and you can also incorporate standalone notes into folders that are not associated with an item.

Add notes:

1.) To add a note to an item, go to the "Notes" tab under the third pane. 

Add notes visual example

2.) Clicking on the add button will immediately start a new note. The note-taking editor is a basic rich text editor and contains basic functions like hyperlinking linking, highlighting, format alterations, and so on.

3.) You have the option to edit notes within your Zotero desktop application or to pop the editor out of the window to make the window larger and note-taking a little easier particularly while also reading a PDF. It's also possible to tag notes and relate notes to other items.

Notes editor visual example

Extract Annotations from PDFs

This process requires an add-on called ZotFile. ZotFile is free and is a tool that has been available for years. Once Zotfile is installed, this process will allow you to highlight in a PDF reader and transpose those highlights as a Zotero note. The Zotero note will be maintained as a child item in your Zotero library. What's nice about the extractions is that they link back to the page in the text where the annotation was created. 

1.) Open your PDF from the Zotero window and highlight it in your PDF reader. 

2.) Close the reader, saving your PDF.

3.) In your Zotero library, right-click on the PDF you just annotated and click "Extract Annotations" from the drop-down menu. 

Extract Annotations Visual Example

4.) In a few moments, a note containing the annotations will generate as a child item.

Why might this not work? Depending on the PDF reader you use, your annotations in the PDF may be encrypted and not readable by open programs such as Zotero. Additionally, this function will not work if your PDFs are pictures of the text and not actual text that is machine-readable.

List of Zotfile friendly PDF Readers:

  • Adobe Reader
  • Preview

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