Zotero includes a pdf view window and annotator. Double click on an item record (that has a pdf attached) to open it.
Centered in the top menu bar are functions that will allow you to annotate the pdf. You can highlight, underline, add a text box, and free draw, as well as add a sticky note to indicate a margin note and draw a box that functions as a screen capture feature.
Click on these icons to use them on the pdf. Below is what the annotations look like in the pdf. They will also show up in the left pane and you can click on them to navigate to where they appear in the document.
You can also add a note to the item separately from the margin-note annotation function. This will show up as an additional child item under the item record, just like the pdf does. In the right pane on the far right, click on the icon towards the bottom that looks like a legal pad, and click on the plus sign by “Item Notes”. You’ll see the drop down menu that allows you to add a blank note or add a note from your annotations.
Adding an 'Item Note From Annotations' will take all of your left pane highlights, boxes, margin notes, etc. and put them into a stand alone item note. Adding an 'Item Note' will make a small, basic text editor appear that allows you to type in text and format it as you go. After creating a note, either from annotations or from scratch (or both), you will see the notes as stand alone child items under the item record, just like the pdf.
Collections and subcollections are the terms Zotero uses to describe folders and subfolders. Use them to organize your Zotero library.
Add Collections to your library by clicking on the manila folder shaped icon in the top left corner of Zotero, adding a name for it, and clicking OK.
Add a Subcollection to this Collection, by right clicking on the Collection and selecting New Subcollection. Name your new Subcollection and it will appear indented underneath your initial Collection. This is a nested folder; a Subcollection within your Collection.
Tags bring items together that you want to be able to bring together across Collections.
Some articles, when uploaded to Zotero, will come with tags. These tags are typically either author keywords, publisher keywords, or subjects assigned to the article when it is indexed. You can find tags on items in the right pane under the tags tab, indicated by a symbol that looks like a gift tag. You can hover over a tag to see its origin.
Add a tag by clicking on the plus sign in the Tags section. It will allow you to type in whatever you like. If you have existing tags that start with whatever you’ve begun typing, it will give you a drop down menu to select the existing tag to add to this item. Click on the existing tag to avoid spelling errors and variations of the same term. When you hover over the tag icon next to a tag you’ve added, it will say that it is a “User-added tag”.
In the bottom of the left pane, you will see all of the tags assigned to items in the collection you're viewing. Left click on a tag to assign a color to it. This both assigns the color to the tag and moves the tag to the top of the list. It also adds a circle icon of the same color to the item record in the middle pane. See the blue tag for glaciation and the blue circle to the left of the article title.
If you read an article and it reminds you of another article you read, or perhaps two papers used the same methodology, or a review paper included another one of your papers you have saved (etc.), you can create connections between these items using the Related feature.
In the right pane, click on the symbol that looks like a chain (two ovals overlapping) to navigate to the Related tab. Click the plus sign to add an item that is related to the item you have selected. A window pops up that allows you to search your library for the item you want to choose to relate to the current item.
When you choose an item to relate to the item you’re on, and click Select, the related item will appear in the Related tab for both items that have been connected. You can add multiple related items to one item. If you click on the item in the Related tab, it will take you to the entry for the other item in your library.