How to Create, Extract, and Manage PDF Annotations and Highlights

An efficient workflow for annotating PDFs, extracting highlights and comments, and filing them is essential for research, writing, and studying. Ideally highlights and comments should contain back-links that take you right back to the correct page in the PDF source document.Extracted-PDF-Annotations

Adobe’s Acrobat Reader DC, PDF-XChange Editor, and various other PDF readers allow you to annotate PDF files. But, you don’t want these annotations to remain “imprisoned” in your PDF. Your highlights and comments become a lot more useful if you can extract them, aggregate markups from several documents, and re-find them when you need them. Unsurprisingly, the free version of Acrobat Reader doesn’t allow the export of annotations as a word or text file.

To accomplish this in an elegant way, I recommend that you manage your PDF documents in Zotero, a free, open-source research document management system created and maintained by the Roy Rosenzweig Center for History and New Media     (George Mason University). With Zotero, you can collect and organize a large variety of document types, including PDF documents and web pages with the click of a few buttons.
To extract and manage PDF annotations in Zotero, you additionally need the free add-on Zotfile from Zotfile was created by Joscha Legewie, a professor at New York University. A big thank you to Dr. Legewie for programming and maintaining this excellent cannot-live-without add-on!

Read moreHow to Create, Extract, and Manage PDF Annotations and Highlights

Managing Kindle Highlights and Notes in Zotero, Evernote, and OneNote

Zotero-Kindle-highlights-Evernote-OneNoteAmazon’s Kindle allows you to highlight passages in books and take notes. Do you want to export and organize these highlights and notes, so that you can archive, review, search, and share them? Then this post is for you.

Let me put forward some suggestions on how you can save and manage a Kindle book’s annotations together with its bibliographic information in your Zotero library. We are also going to look at saving Kindle annotations in Evernote and OneNote and linking these notes to a Zotero library.  The exported annotations will allow us to jump directly to the corresponding locations in the book. For more info on Zotero, please check this post.

In the following, I use Spark!: How exercise will improve the performance of your brain, by John J. Ratey and Eric Hagerman to illustrate the procedure.

Let’s get started by saving the book’s bibliographic information to Zotero

  1. Find the book’s sales page on Amazon.
  2. Open your Zotero library, open the collection (here Brain Improvement) in which you want to save the book’s information and Kindle annotations, and click the book symbol:

Zotero-Amazon-Kindle-save-bibliographic-entry-1This will save the book’s bibliographic entry as an item in your Zotero library.

Next, we are going to retrieve the highlights and notes for the book

Read moreManaging Kindle Highlights and Notes in Zotero, Evernote, and OneNote

Syncing Zotero with Dropbox and Between Several Computers

Zotero-Dropbox-Sync-Remember-Everything-OrgIn this post I want to shed some light on how you can sync your Zotero library between different computers, and between your computer and Dropbox, a popular cloud storage service. Due to the nature of the matter, what follows is somewhat technical, but don’t let that deter you. Once setup, the synchronization works automatically in the background, without any further effort.

In a previous post, I introduced Zotero, a popular free research tool by the Roy Rosenberg Center for History and New Media of George Mason University. As a brief recap: Zotero allows you to organize all your research sources and create a complete digital library with the click of a few buttons. To learn more about this fantastic tool and why every knowledge worker should consider using it, please check this post.

Recommended approach for syncing Zotero between different computers.

Zotero allows you to synchronize everything via its own cloud storage service, Zotero Storage. “Everything” includes:

  1. the Zotero data (i.e., the database with all bibliographic information, tags, and notes)
  2. the Zotero files (i.e. attachments, such as PDF documents, videos, books, and webpage snapshots)

The basic plan (upto 300 MB) is free. 2GB will cost you $1.67 per month ($20 per year), and 6 GB set you back $5 per month ($60 per year). IMO, Zotero Storage should be your first consideration as it is very easy to setup and manage, it is affordable, and your payments support the up-keeping of the infrastructure.

There are, however, some good reasons why you might want to employ a different method to sync your Zotero files:

  1. You have a very large number of attachments or some very large attachments.
  2. You have already subscribed to a service like the popular Dropbox, and would rather avoid paying for an additional cloud storage service.
  3. You have a very slow or expensive internet connection, but have your computers connected via a local area network.
  4. You are looking for a solution to create a local backup for your files (and database).

(The database is usually below the free storage limit and should always be synchronized via Zotero’s cloud service.)

Here then are some alternative solutions you can employ:

Read moreSyncing Zotero with Dropbox and Between Several Computers

Zotero – Create Your Digital Library for Knowledge, Research, and Citation Management

Zotero-Research-Management-SoftwareIntroducing Zotero, free, open-source research software to collect, organize, manage, and share all kinds of information. This includes web pages, articles, research papers, videos, PDF documents and annotations, complete books, and your own notes. Zotero takes the pain out of managing citations and creating bibliographies. It features a Word plugin that works seamlessly with Word and formats citations in all common citation styles.

Read moreZotero – Create Your Digital Library for Knowledge, Research, and Citation Management


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