Cleaning Up Your Research PDF Workflow

One of the many conveniences of the digital world is to be able to have loads of research all on one device, such as a computer, tablet, and even your phone. Personally, I love the fact that I can scan copies of journal articles, book chapters, and other content into PDFs. This allows me to have all my research in one place and I am not scrambling around with hundreds of pieces of paper around my desk when writing a paper. But one of the problems of this (and it is not just limited to digital documents) is how to collate all your highlights and notes in one place. In the past I’ve done this by hand by typing out quotes and notes into Evernote.

Welcome to Highlights for Mac!

*If you just want to checkout my PDF workflow video without reading the post click here


First, one caveat. For the Highlights to work to its full potential the PDF needs to be searchable/OCR’d. Most journal articles that you download from a database are probably already searchable[1]. Articles/book portions you scan to PDF from your library are probably not searchable[2]. There are several gimmicky and “cheap” solutions out there but in my experience there are really only one excellent option: ABBYY FineReader Pro for Mac[3]. At the time of writing this piece you can purchase the app for $83.99 with a student discount. This app also comes packaged with the excellent DevonThink Pro Office for slightly more money. You should really check out this program as it will transform your research[4]. The reason you need a searchable PDF will be explained below.


Ok, now we can actually look at Highlights. At the foundational level Highlights takes your highlights, notes, and images and creates a text file that is connected to the PDF and actually links to it. When you highlight a PDF then Highlights will take the text that is highlighted and copy into into the linked text file in a blockquote. Making a comment on a PDF will result in italics text. And underlining results in a reference.

You can also add notes to the PDF either from the Highlights app or any other PDF reader such as Preview. The text of the note will be added to the text document associated with the PDF.

One other helpful feature is to sort annotations by category. This allows you to set colors as a specific category and the linked noted will sort it accordingly.

There have been other workarounds for this type of functionality but most of them involved using a specific app for highlights and notes. But this will read the highlights and notes from other aps and create the linked text file. After you are all finished you have one PDF with text of your highlights and notes in one PDF without retyping. So as you are reading your PDF you are creating this document without any extra work.

I’ve put together a video below showing a soup to nuts PDF workflow using DevonThink and ABBYY FineReader to OCR, read and highlight on the iPad using PDF Expert 5, opening the PDF to create the linked text file using Highlights, and then finally exporting to Evernote to my notebook for a paper. Perfection.

Apps mentioned:

  1. Highlights for Mac
  2. ABBYY FineReader
  3. PDF Expert 5 (iPad/iPhone)
  4. DevonThink Pro Office

  1. In order to check to see if the PDF is searchable just open up your document and try to highlight the text. If you can then it is searchable if you can’t then it is not searchable.  ↩

  2. Some of you may be one of the lucky ones that the scanner OCRs the document but I would venture to guess that most out there do not.  ↩

  3. There are other OK options. If you are wanting a full-fledged PDF application that rivals Adobe Acrobat Pro I would definitely check out PDFpen Pro 7 from Smile Software. The issue I have found with this program in regards to OCRing PDFs is correctly rendering a scanned PDF that is of facing pages. For example, if you are scanning from a book it does not correctly read the text on both sides of the page. Therefore, you will have issues highlighting and searching. ABBYY FineReader is far superior in this regard. Personally, this constitutes about half my scans so it is a deal breaker for me.  ↩

  4. At some point I will write a blog series on using DevonThink similar to my Evernote for Academics series.  ↩