Zotero

"My Library" is the home for all of the items on your individual Zotero account. All items are automatically saved here, unless you manually choose to save them to another folder. You cannot change the name of My Library.

You can use collections in Zotero to sort items. Each item can be placed in multiple collections. To create a new collection on the desktop app, click on the "New Collection" button above "My Library" (it has an icon that looks like a file folder). On the web app, you can create a new collection by hovering over the "My Library" tab, then clicking on the plus sign that appears next to it. 

After clicking this button, you will be prompted to name the new collection and set its location. You can add new collections to My Library, or create a new collection in another collection folder. This means that each collection can contain both individual references as well as other collections. This makes it easy to subdivide references; for example, you could create a collection for your thesis, and then create further sub-collections as part of that collection for different sections of your thesis.

To add an item to a collection, simply drag and drop the item from My Library into the collection folder on the left side of the Zotero interface.

Collections offer a few additional functions. You can add multiple items to a collection by inputting identifiers such as ISBNs, DOIs, PMIDs, arXiv IDs, or ADS Bibcodes. You can also add a file, link to a file, or a note for the entire collection. 

In addition to collections that you create, Zotero automatically creates folders for duplicate items and unfiled items (meaning items that you have not added to a collection but the remain in My Library). Zotero also lists a "My Publications" collection. You can click and drag items from other parts of your library and add them to the My Publications collection. 

You can assign tags to items to further sort them. Zotero will automatically assign tags based on an item's abstract and other information, but you can add additional tags. To add a tag, click on an item, then scroll down to the tags section. Click on the plus sign to add a new tag. You can type in your own term as a tag, or choose from a pre-selected term generated by Zotero. You can also edit the names of any tags, or click on the minus sign next to an individual tag to delete it.

To access all items that have been assigned a given tag, go to the "filter tags" section on the left side of the Zotero interface; this section is accessible from My Library or any collection. This section will list all of the tags assigned to items in the given library or collection. Click on the name of a tag to display all items assigned that tag. If you click on another tag, it will further limit your display to all items that are assigned both tags.