The search box at the top of the center pane, at the far right edge of the pane, is useful for running simple searches of your library.
The drop-down menu lets you select from a few different search options. You can really only search a single word or phrase effectively using Quick Search.
Under "Edit," select "Advanced Search."
In this box, you have much more control over where you search, you can create complex searches (such as a word in the title, plus an author's last name, plus a tag). You can also use the % (percent) sign as a wildcard in Advanced Search.
In Advanced Search, you can save a search, which will then appear as an option in your collections are in the left-hand pane. Click on the saved search name to run it at any time.
Collections are folders in which to organize your references. All your references will always display in the main "My Library" folder, but you can also group them into named collections and subcollections. This is less like the folder organization of your computer and more like creating playlists: My Library is your library of music, and each folder is a playlist you create from items in your library.
To add a collection:
Other useful things to know about collections:
Tags are descriptive keywords you can add to items in your library. They appear in the Tag Selector box at the bottom of the left-hand Zotero pane. Clicking on one will only show you references with that tag.
Zotero sometimes adds tags automatically, pulling in data like subject headings when you import a reference from a database. To avoid this, go to Edit → Preferences → General tab and uncheck the box for "Automatically tag items with keywords and subject headings."
Automatic tags can be hidden by opening the Tag Selector's Actions menu (the multi-colored dots in the bottom right of the box) and unchecking "Show Automatic." You can also delete existing automatic tags by choosing that option in the same menu.
To tag a reference, select it in the center pane and click on the "Tags" tab in the right-hand pane.
Click "Add" and type your tag. If you start typing and there's already a tag in your collection similar to that, it will show up as a suggestion.
To tag anything else (a file, link, or note, for example), select it in the center pane. Just as with a normal reference, look to the right-hand pane but near the bottom.
An easier way to add tags, so you don't have to remember the ones you've already created, is to select something in the center column and drag it onto the tag in the Tag Selector. This works for anything in your library.
To remove tags, select the tagged item and click the minus sign next to the tag in the right-hand pane.
To rename or delete tags from your library, look at the tag box at the bottom of the left-hand pane. Right-click the tag you want to modify.
To merge tags, for example because you accidentally created both "teenagers" and "teenager," simply rename one to match the other.
Searching Using Tags
You can search for items using tags in the search box at the top of the center pane, in the "Advanced Search" under the "Edit," or by simply clicking on a tag in the Tag Selector box.
You can search your existing tags using the search box at the bottom of the tag box, too. Keep in mind that selecting more than one tag in that box is an AND search: an item must have ALL of the tags in order to appear in the center pane.
Coloring Your Tags
You can assign colors to up to nine of your tags, which will change both the color of the tag text and add a colored box next to tagged items.
Colored tags take priority in the Tag Selector box and appear at the top of the tag list for an item.
Right-click a tag in the Tag Selector to add or remove a color.
You can create a relationship between items in your library using the Related feature.
To do this:
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.
If you find relating items helpful, you may want to install the plugin Zutilo, which allows you to select several references in the center pane, right click, and relate them all at the same time.