Library Basics

With Zotero, you can only have one library on your desktop and one library per online account. Generally, if you want to sync your desktop and online libraries, this will mean that you only have one Zotero library. This differs from some other citation managers, such as EndNote, which allow you to create multiple libraries. However, items in your Zotero library can still be organized on a more granular level; see the Organizing References section of this guide to learn more about how to do this.

You should store your Zotero library on your hardrive, not on the cloud or in a shared drive. Setting up a Zotero account will allow you to sync your library and store the information on Zotero's servers. While your library should not be stored in a cloud storage service such as OneDrive, Google Drive, etc., full-text PDFs associated with items in your library may be. See the Managing PDFs and Maximizing Storage Space with ZotFile section of this guide for more information on storing PDFs separately from your Zotero library.

Adding References

There are several ways to add references to your Zotero library:

Manually

  • This is the most time-consuming option; reserve it for physical items or unusual formats.
  • To add a reference manually, click on the green plus-sign at the top of your library, then choose the source type from the dropdown. If the source type you need does not immediately appear, click on More.
  • Only enter the relevant fields for the item. Not every item will have something for every field! (For example, not every book has a volume number.)

From a file

  • This option is best if you already have a file (e.g., a PDF of a journal article or an exported citation from PubMed) saved on your computer.
  • You can simply drag and drop the file from your file explorer into your Zotero library.
  • Alternatively, you can go to File Import and choose the file from there.

By identifier

  • If an item has an ISBN, DOI, PMID, or arXiv ID, you can add it using just the identifier.
  • Click on the magic wand with the green plus sign at the top of your Zotero library and then enter the identifier into the box provided.

Using Zotero Connector

  • Once you've installed the Zotero Connector plug-in to your browser, you can add references to your library from the web by simply clicking on Zotero Connector while viewing the item.
  • Make sure you already have Zotero open on your computer before using Zotero Connector, or else it won't be able to add the item to your library.

Organizing References

In Zotero, you can only have one library. This differs from some other citation managers--such as EndNote--where you can have different libraries for different projects, classes, etc. While you can only have a single library in Zotero, you can organize that library using collections, subcollections, and tags.

Collections

  • To create a new collection, go to File New Collection or right click on My Library in the left sidebar and choose New Collection from there. 
  • Once you have created your collection(s), you can drag and drop items from your library to a specific collection, you you can add them to the desired collection from the start. 
  • Every item you put in a collection is still in your main library; however, they are not copies, so if you move an item in a collection to the trash, it will remove it from your library entirely, and vice versa. To remove an item from a collection but keep it in your library, right click on the item and choose Remove Item from Collection.
  • The number of collections you create is limited only by your Zotero storage limit (and your computer's storage limit, of course).

Subcollections

  • A subcollection is exactly what it sounds like--a collection below or within another collection.
  • To create a new subcollection, right click on the collection you would like it to be a part of and choose New Subcollection
  • You can create subcollections within subcollections and subcollections within subcollections within subcollections and...well, you get it.

Tags

  • Items that you import from databases or add using a PMID or other identifier may come with tags already attached.
  • You can add, remove, or edit tags by clicking on an item and going to the Tags tab at the top of the right sidebar.
  • Tags are searchable using the search bar above your library.

Adding PDFs

If you have added references to your library without a full-text PDF and you don't already have that PDF saved somewhere, Zotero can sometimes find and attach one. Zotero will not be able to find every PDF you ask it to--and in those cases you will have to find and manually attach one--but it can save you time by finding some of them.

To have Zotero look for PDFs for you, select the item or items for which you want to attach a PDF, right click, and select Find Available PDF. If Zotero can locate a PDF for that reference, it will attach it.

Even if Zotero doesn't find a PDF for you, it can still help you see if our library provides access to it! The first time you want Zotero to check the library's collection and subscriptions for an item, go to Edit Preferences > Advanced. Under "OpenURL," paste the following link into the field labeled "Resolver": https://pitt.primo.exlibrisgroup.com/openurl/01PITT_INST/01PITT_INST:01PITT_INST?sid=

Now, whenever you want to look an item up in Pitt's library system, you can elect the item in your library that you wish to find full-text for, and then click on the green arrow near the top right of the Zotero window. From the drop-down menu that appears, select Library Look-Up. If we provide access to that item, you will be taken to a listing for that item in PittCat, and from there you can see where the full-text is available. If the library doesn't provide access to that item, then you may need to use Document Delivery to get it.

Managing PDFs and Maximizing Storage Space with ZotFile

The Zotero community has developed a number of plugins that can enhance your workflow or integrate Zotero with other programs. One plugin that you may find very useful is ZotFile.

ZotFile is a third-party plugin that can help you manage your attachments. If you are using the free version of Zotero, which limits your storage within Zotero to 300MB, ZotFile may be very useful to you. You can set ZotFile up to automatically link full-text PDFs of articles to references in your library while storing the PDFs separately; this way, the PDFs will not be taking up any of your 300MB of storage. References on their own take up very little space, so 300MB becomes a reasonable storage limit once there are not PDFs using up the storage space. You can still access these PDFs from your Zotero library, but instead of opening within Zotero, the PDFs will open in your default PDF-reader.

The first step is to install Zotfile from zotfile.com, following the directions provided by the developers of the plugin.

Next, you will need to choose a cloud storage service with which you would like to store your PDFs. Using a cloud storage service ensures that you will be able to access full-texts of items in your Zotero library from anywhere.

  • Google Drive, Dropbox, MEGA, Sync, Box, and OneDrive will all work for this purpose.
  • If you do not already have the the desktop sync app (e.g., OneDrive sync app) for whatever service you choose, download it now.

Then you need to create a new folder within the app's syncing folder on your desktop. Your PDFs for your Zotero library will live here, so name it accordingly.

Now, go to Zotero and open Tools > ZotFile Preferences. Under the General Settings tab, there will be an empty bar labeled as "Source Folder for Attaching New Files." You will most likely want to choose your downloads folder for this (e.g., C:\Users\name\Downloads).

Below that, there are options for "Location of Files." Select the radio button by "Custom Location." Then, choose the folder that you created in the syncing app for your Zotero PDFs. 

ZotFile Preferences window, General Settings tab, showing source folder for attaching new files and location of files.

You're almost done! But, first you need to adjust your sync settings in Zotero so that the PDFs are not automatically added to your Zotero online library (because if they are then they will count towards your 300MB of free storage). To do this, go to Edit > Preferences > Sync. Then deselect "Sync attachment files in My Library using Zotero." This way, your references will still sync with your Zotero web library, but your full-text PDFs will sync with the cloud service you have selected.

Zotero preferences window, Sync tab, the option to sync attachment files in my library using Zotero has been deselected

If you download an app on your mobile phone or tablet for the cloud storage service that you chose above, you will also be able to access your PDFs on that device. 

An important thing to note about this method is that when you are using your Zotero Web Library, you will not be able to directly access your full-text documents from there. You will need to go to the website for your cloud storage provider (Box, OneDrive, etc.) to view them. 

ZotFile can do other things as well, from automatically renaming PDFs according to rules of your choosing to extracting highlighted text from PDFs. Other ZotFile tutorials include:

Retraction Watch Integration

Zotero automatically checks your library for items that have been retracted through an integration with Retraction Watch. Retraction Watch maintains a database of retracted articles, so if you add an item to your library that has already been retracted or an item already in your library gets retracted, you will receive a notification in Zotero. 

Retraction Watch is a nonprofit organization (just like Zotero!), and there may be some time between an item being retracted and its addition to the Retraction Watch database. Therefore, you might not be notified in Zotero to an item's retraction until several weeks after the item has been retracted.