Citation Management Software - Zotero

You can organize your library by creating folders, which are called collections in Zotero. You might find it helpful to organize items by theme/topic or by a specific research project you are working on. You can create a new collection by clicking on the "New Collection" icon or right-clicking on "My Library" and clicking on "New Collection." 

You can also create subfolders by right-clicking on a collection and clicking on "New Subcollection." Right-clicking on a collection will also give you the option to rename or delete a collection.

To put items in a specific collection folder, you can either drag and drop the item into the folder or go to the Libraries and Collections section of the information pane for an item by clicking on the Libraries and Collections icon: In the Libraries and Collections section, you can select the plus sign to add the item to a collection. You can add an item to multiple collections. In this case "Libraries" refers to either your personal library (My Library) or any group libraries that you are a part of.

You can see items that are not in any folder by clicking on "Unfiled Items" underneath all the collections in your library.

You can add tags to items in your Zotero library, which provides another way for you to organize your library. When you are viewing an item in your library, click on the Tags icon  to be taken to the relevant section in the Info pane. You can click the plus sign to add additional tags to your item. You can hover over any tags and click the minus sign to remove a tag.

You can search and filter using your tags by using the bottom left pane that says "Filter Tags". You can search for tags here or browse the list of tags and click on a tag to filter your library to all items with that particular tag.

Some databases will automatically provide tags (or keywords) when you add an item to your library. You can disable automatic tagging by going into your Zotero preferences. 

Zotero has an integrated PDF reader that allows you to read and annotate PDFs within Zotero. To read a PDF, double-click on the item you want to read (an item with a PDF attachment) and it will open in a new tab. From here, you can annotate as you read using the menu options above the PDF. From left to right, these are the options to highlight text, underline text, add sticky notes, add text, select an area, and draw. You can also change the color of your annotations.

If you want to make your annotations searchable, you can add them as a note (either individually or all together). First, click on the Notes icon  in the Info pane on the right-hand side. Here you can see any notes you've added for the item you're looking at (Item Notes). Under "All Notes" you can see the notes you have for all items in your library. Next, click on the plus sign next to "Item Notes" to either create a note that you can then add individual annotations to (by right-clicking on an annotation and selecting "Add to note") or by creating a note containing all of your annotations from the PDF.

Once you've created your note, you can edit the note using the formatting options. If you created a note using your annotations (highlights, underlines, etc.), you can click on the text of your annotation to be taken to the relevant page in the PDF by clicking "Show on Page." There will also be an in-text citation generated for each annotation including the page number.

Sometimes you may add the same item multiple times to your library without realizing it. You can use the Duplicate Items feature to remove any duplicate items from your library by merging them.

You can find duplicates by clicking on "Duplicate Items" underneath all your collection folders in your library. Any duplicate articles will appear here. Click on an article, and all its duplicates will be highlighted. In the right-hand Info pane, you'll see the option to merge however many duplicate items you have as well as the option to choose which version of the item you'd like to use as the master item.

This view also allows you to confirm that the items are actually duplicates before removing them. You can also pick whichever version has the most complete metadata as the master item. Click on "Merge # items" and any duplicate items will be automatically deleted from your library and disappear from the Duplicate Items list.

Note that items can be in more than one collection folder without being considered a duplicate. This feature identifies duplicate items in your top level library.