You can read, highlight, and annotate a PDF within Zotero using Zotero’s built in PDF reader.

You can tell if a PDF is attached to an item in your library by looking for this little icon on the right or by scrolling down to the ‘attachments’ section in the right-hand sidebar. If I double click the item, my PDF will open in a new tab and I can start reading and annotating.

PDF Reader: Overview Let’s start with an overview of the PDF reader’s interface. You can toggle between your library and your open PDFs using the tabs at the top. In the central section we have the PDF itself. On the left we have the annotations sidebar, where any annotations we make to the text will be displayed. You can open and close this using the toggle sidebar option in the top left. On the right, we have another sidebar with the referencing information and other details for this item. We can use this ‘Toggle Context Pane’ item to minimise this sidebar for now.

Over on the left, in this menu bar, we have some reading and navigation options. We can use these buttons to zoom in and out of the PDF. We can jump to a particular page of the document by typing a page number in here and pressing enter. You can also use the magnifying glass icon on the right to search for a particular keyword in the document. And then use the arrows to navigate through the various mentions of this term.

Annotating your PDFs In the centre we have the annotations toolbar. We can use this to highlight text, underline text, add a sticky note, add text to the document, screenshot an area, draw on the document or select a colour for our annotations. You can highlight the text using the toolbar highlight button, like so. This will highlight the text in the selected colour. Alternatively, you can highlight the text as normal, and a pop-up will appear, allowing you to select the highlight colour. Any text you’ve highlighted will automatically appear in the annotation’s sidebar, with the page number as a heading. In some cases, you may only see a preview of the text you highlighted. Click the text twice to see all of it. Underlining text works in the same way.

You can click this annotation and select ‘Add Comment’ to add notes relating to this highlighted/underlined text. This is great for paraphrasing a point in your own words or adding your own ideas. Just make sure to clearly distinguish between your own thoughts and the content of the text. There’s also an option to add tags to an annotation. Type in your desired tag and click add. To remove a tag, click on it and press the minus icon. Tags are a useful way to organise your notes and references.

Have you highlighted too much text? Remove highlights by right clicking on them and selecting delete. Be aware that this will also delete any comments you added to this highlighted text. You can highlight or underline the text using different colours for different themes, topics or tasks in your workflow. For example, you could use green for anything related to climate or orange for any citations you want to follow up. Whatever works for you.

Once you’ve highlighted or underlined different sections with different colours, these coloured squares will appear in the bottom left. These act a bit like filters. Click a coloured square to see only the highlights of that colour. Unclick the square to reverse this.

Now let’s look at some of the other annotation options.

To add a sticky note, select the Add Note button from the toolbar. Then click on the page wherever you’d like the sticky note to appear. As with highlights, your sticky note will appear in the annotation’s sidebar with the page number as a heading. Type any notes in the comments section and add tags if you want to. Sticky notes will be added in the colour you have currently selected in your toolbar. You can easily change the colour of your sticky note or any other annotation by clicking the three dots to see more options and selecting a different colour. Alternatively, you can right click the sticky note and change the colour there.

You can use sticky notes however you want. But we find them useful for summaries. For example, you could add a sticky note at the beginning of the PDF with a summary of the whole text, or with a reminder of how the text relates to your research. This will save you a lot of time rereading things when you come back to this text later, as you can see how they relate to your research at a glance.

The select area tool is a bit more situational. It allows you to take screenshots of the PDF, which you can then add comments and tags to. It’s particularly useful for capturing diagrams, tables, graphs, or images within a text. To use the Select Area tool click the Select Area toolbar button, and then click and drag around the section of the text you want to screenshot. A snapshot will appear in the left-hand side in the annotations sidebar. And once again, you can click this to add comments and tags.

You can also use the add text button to add your own text directly to the document or use the draw tool to annotate the text more freely. Anything you write or draw will appear in the annotations sidebar, but you can’t add comments to these, only tags.

Annotating Web Snapshots With Zotero version 7, you can annotate web snapshots as well as PDFs. Zotero will often take a snapshot automatically when you save a source to your library with the Zotero connector, particularly if it can’t grab a pdf. This icon indicates there is a snapshot attached to your reference. You can see this more clearly by opening that item’s drop-down menu. The process for annotating snapshots is the same as with PDFs, just double-click to open the snapshot and annotate it using the toolbar. Snapshots won’t have all the annotation options, but you can highlight and underline text and add sticky notes, and then add comments and tags to these annotations.

Creating Notes Now we’ve covered the main ways to annotate in Zotero, let’s focus on the notes function. If I open the right-hand sidebar again, then click the yellow notes icon, this opens the notes menu. There are two main sections. All notes gives a list of all the notes I’ve created using Zotero previously, and then the item notes section refers to any notes I’ve already made in connection to this PDF. I can use this plus button to add an item note. This opens a notepad which works a lot like a word document where you can type freely.

You can use this notes toolbar to format and search your notes just like a word document. You can also click the three dots to see more options. This gives you the option to edit in a separate window, allowing you to full-screen your notes document. At the bottom of your note, you also have the option to add relations and tags.

The note we’ve just created is called an item note because it’s attached to this specific item/reference. You can also create standalone notes which aren’t attached to any specific items in your Zotero library. These are useful for more general notes that relate to multiple sources stored in your library. To create a stand alone note, go back to your library tab and click the add note icon, then select ‘New Standalone Note’. This creates a note in the folder you currently have selected. You can also use this button to create a ‘New Item Note’ for any item you have selected.

Notes vs. Annotations It’s important to remember that annotations and notes are distinct in Zotero. They’re kept in separate sections, and your note documents are visible in your Zotero library. For example, if I expand this item reference in my library, you can see that my example note is attached to the reference. But I can only see the annotations by going into my PDF. The key difference is only notes can be imported into a word document. But you can easily add your annotations to a note so you can import them into word.

There are a few ways to do this. To bring over select annotations, simply drag and drop them over your item note. Alternatively, you can right click an annotation and select Add to Note. This pulls over any highlighted or underlined text as quotes, or any screenshots, along with your attached comments. It also creates a citation which includes the relevant page number.

You can also create a note from your annotations to bring all of them over at once. Head back to the notes list page using this arrow. Click the plus button again and select ‘Add Item Note from annotations.’ This will create a note with all your annotations. Zotero will automatically title this note ‘Annotations’ and add the date and time. With any note Zotero will automatically use the first line or sentence as the title. We recommend adding an intuitive title to your notes so they’re easy to find. Once you’ve brought your annotations over, you can continue to edit and add to this note.

By default, Zotero brings annotations over without their colours. If you prefer to see the colour coding in your notes, select more options and click Show Annotation Colours. Just keep in mind that if you import your notes to word, they will have these colours if you selected this option. If you prefer them to be plain text, import them without the annotation colours. You can do that by selecting more options again and selecting Hide Annotation colours.

Adding your notes into Word You can import your Zotero notes into your word document with a simple click of a button, much like you would add a citation. To do this, open a word document and go to the Zotero tab at the top. Click insert note. Select your desired style. A yellow search bar will appear. Use this to search for and select a note you want to insert. Your most recently edited notes will appear in a list below the search bar, so you can add these more easily. Once you’ve picked a note, Zotero will add all the content from your note into word, including citations for the text your notes relate to. What’s useful is these citations are linked to Zotero, so when you add a bibliography or if you already have one, Zotero will add a corresponding reference. Place your cursor where you’d like your bibliography and select the Add or Edit Bibliography button. You can see Zotero’s generated a reference for the text I was taking notes on.