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You can organize your references into collections and subcollections. Here you can arrange what you have found and keep like items together. To create a collection, click on the Folder icon on the far left of the tool bar. You can make subcollections to further subdivide the collection, just right click on the collection. You can create as many collections and subcollections as you like. Your collections will appear in the far left column in the Zotero pane.
You can tag individual items or references with keywords to categorize your findings and search for them later. You can see your tags below your collections.
To see these features in action check out these videos, for more detailed information please see this same page.
One of Zotero's nicest features is the ability to take notes on the items you have created! You can create a child note that is attached to an item or standalone notes which are not attached. So you can actually take notes on the item within Zotero!
You can add a child note when viewing an item and clicking on the notes tab in the far right pane. Or you can click on the icon in the Tool Bar to choose either type of note.
For more information see Zotero's help.
You can attach files to your items including pdfs of articles, etc. Please check out all these features.
Please note: When you download Zotero you will be asked to create an account. You will be given 300mg of storage space. This can be used up quickly and if you don't want to buy more storage space from Zotero, you can use the "Attach link to file" option to point to where it is stored on your computer. If you take many snapshots of websites, these won't take up that much space, but eventually you may need to be more storage space.
If you do attach your pdfs, you might want to add Zotfile as an add-on to manage your attachments. This will not work if you link to your files on your computer!
You can search your Zotero collections with either the quick search or the advanced search. Click on the magnifier icon for an advanced search or type in the box to its right for an quick search.
For more detailed information see Zotero's help.
You can sort your items in the center colunm by author/creator, titles, dated, etc.