 Welcome to the 4th module in our unit on reading and annotating content in Zotero. Now that we've covered the basics of using notes in Zotero, including how to generate reports, we can start to dig into some more advanced tips. In this module, I'm going to show you how you can work with your favorite PDF viewer to create highlights and annotations that Zotero can import and use. To do this, I'll be introducing a terrific Zotero add-on called ZotFile, which is one of my all-time favorite Zotero tools. This module covers highlighting and annotating PDFs, installing and configuring the ZotFile add-on, extracting a table of contents from PDFs, and extracting annotations from PDFs. To follow along in this module, you need to have Zotero installed on your computer. You can get the software at Zotero.org. And for more information on the basics of using Zotero, see our online guide or check out the mastering Zotero guide on GitHub. This module also uses examples from a sample Zotero library. You can use your own Zotero library to try out the features I cover, but I've also made the sample items for this course available for you to import into your own Zotero library. That way you can see exactly what I see and follow along click by click. To learn how to get and import these sample items, see the course setup module and come back to this one when you're ready. Let's get started. So part of this unit is about how Zotero can be used to combine and organize all your research notes and other information. One popular method students and researchers use to create notes is to annotate PDF files directly. Now most PDF viewers can do this in some way. I won't go into PDF annotation tools in detail, but as an example, here's the free Adobe Acrobat Reader with two examples open. Both of these PDFs are in the Halifax Explosion Collection. This is what I refer to as a clean or modern PDF because it was created as a digital document instead of being scanned from a paper copy. In Adobe Acrobat Reader, you'll see that I can choose this highlighter and highlight text. I can also use this tool to add a note or a comment in the margins. Some tools will let you highlight in different colors or add images or other elements. Now this example is a different kind of PDF. You can see it's been scanned from a physical journal and so each page is actually an image instead of text that I can highlight or edit. It's not easy to highlight or copy text in articles like these and I refer to these kinds of documents as dirty PDFs. For a PDF file like this, you'll see that if I try to highlight things, it might not work or it might be inconsistent or I might only be able to draw a box. The software can't always interpret the text because it's an image. I can usually still add comments though. The nice thing about doing annotations and highlighting with PDF attachments in Zotero is that if I save the PDF, my notes and highlights are actually saved along with the file. This is great because I can reopen the PDF file later and I can see all my highlights and my notes but unfortunately I can't search them alongside my other notes and highlights the ones earlier in Zotero unless I open a bunch of files or I print them all. Thankfully, there's a solution for that and it involves extending Zotero's features using an add-on. I'm going to show you the Zot file add-on in this module. It can do several things with PDF files in Zotero but one of its best features is that it can extract your highlights and annotations from a PDF file and create them as notes in Zotero. Not only that but it will try to create a hyperlink for each snippet that links directly to that point in your PDF file. There's more too. Some PDFs contain a table of contents that you can use to locate sections of the document. For these files, Zot file can extract the table of contents and store it as text, hyperlinked of course, which could be a big help for large PDF files such as book chapters or complete ebooks. Like all Zotero notes, these extracted annotations can be tagged and related to other items. The contents of the notes are searchable and every extracted annotation includes a location reference like a page number that makes it even easier to create proper citations. All of this makes it easy to incorporate PDF annotations and notes into your research workflow. I think Zot file is a terrific tool, so let's get it. As I mentioned, Zot file is an add-on, a plugin that adds new features to Zotero. Just like the Zutilo add-on I talked about in Unit 1, Zot file is open source and available for free. The add-on is currently maintained by Joshua Legowe. Add-ons like Zot file are all listed in a directory of add-ons or plugins that you can find on the Zotero website. Zot file is listed here, among many other add-ons, but it also has its own website at ZotFile.com. This site is pretty simple, but there's full documentation for the add-on here. Most importantly though, there is a download link at the top left at this page, so we want to grab that. Just one warning here, the XPI format used by Zotero is the same format used by Firefox for their web browser extensions. So make sure you right-click and save instead of trying to download the file by clicking on it. In Firefox, if I just click the link, you'll see that it thinks I'm trying to add a plugin to Firefox instead of Zotero, and that's not what we want. So make sure you right-click and save. Next, we want to install the ZotFile add-on. In Zotero, go to Tools and then Add-ons. Click the gear icon and select Install add-on from file. Browse to the location of the add-on in your downloads folder and add it. Some add-ons require you to restart Zotero before they're activated, and ZotFile is one of those. So I'll click this Restart Now link, and Zotero will close and reopen for me. Configuring ZotFile is pretty straightforward. ZotFile will do everything we want without having to do any special setup, but there's a configuration menu you can use to set options. It's under Tools, ZotFile Preferences. The only thing we're going to check here now is on the Advanced tab, where the PDF extraction settings are. Now the default settings should work, but make sure that these two checkboxes add full in-text citation and use actual article book chapter page are selected. Now let's close this window and see what ZotFile can do. First, let's use ZotFile to extract annotations from a PDF file. This is the PDF file I annotated at the beginning of this video. You can see that I have a couple of sentences highlighted and have added a comment as an annotation. To extract these things into notes in Zotero, I select the PDF file in Zotero. Then I right-click, go to Manage Attachments, and select Extract Annotations. You can see that the add-on is working from the pop-up at the lower right. If there's a problem with this process, you'll see a red X and an error message there. After a moment, you'll see that I have a note with the title Extracted Annotations, including the date. When I open the note, you'll see that it has extracted my comment as a note and mentioned the page number that it's on. And you'll also see the text I highlighted, verbatim, including an in-text citation with the year and page number. This is the best part. If I click the citation link, Zotero will open the PDF attachment and take me directly to that point in the text. Now, the other thing I can quickly do is extract a table of contents if the PDF file has one. Now, you won't always have a PDF file with a table of contents in it, but there is a way to tell. For example, using the free Adobe Acrobat Reader, if I open the menu bar on the left, a PDF file with a table of contents will have this bookmarks icon. If you don't see the icon, then the PDF file you're looking at doesn't have one. This e-book, Histories of Indigenous Peoples and Canada in the Literature Review Collection, has a table of contents in it. So I'll just close this file and show you how to extract the table of contents information into Zotero. You just right-click on the PDF attachment, go to Manage Attachments, and then choose Get Table of Contents. You'll see that when I select the PDF file now, I see a hyperlinked table of contents in the note area of the item pane. Now, since the items in the table of contents are in this text area, they're searchable, and, of course, I can use the links to open the PDF file and jump directly to the corresponding section. This is a great feature for working with large PDFs, assuming, of course, they actually have a table of contents that you can extract. Now, in the previous module, we talked about generating reports based on Zotero items. And as you might guess, annotations that we extract using ZotFile will also be visible in those reports. Here's an example. If I generate a report from this e-book, which also has an extracted annotations in it, you'll see that the report shows all of the info about the book, plus all of the extracted highlights and annotations, including the page reference links. And since we extracted the table of contents for the book, the contents appear in the report as well. These page reference links are my favorite part. If I decide to use these quotations in a paper later, I don't have to go back to the paper to look them up. I already have them in my note or my report, including the page reference that I need for my citation. Now, ZotFile can actually do more for you. It can rename your PDF file so that the file names are all consistent. It can also automatically attach the most recently downloaded file on your computer to a Zotero item, which saves a couple of steps when you're importing items into Zotero. And these features are beyond the scope of this module, but you'll find information and instructions for those options on the ZotFile webpage. So those are the basics of working with ZotFile. The next and final module in this unit is for people who prefer to highlight and annotate PDF files on a tablet or iPad. I'll be showing you how you can use Zotero to export files to your tablet and then automatically import the highlights and annotations when you're finished working with them. It's a great feature, but it's an optional module. If you don't use a tablet for your readings and research, you can move on to Unit 3, where we'll be talking about using Zotero to support your research workflow.