My Research Using the Highlights App

A simple and productive workflow system

Photo by Josh Sorenson from Pexels

Over the last five years, I have transitioned to using my iPad as my main computer for note-taking, writing, and research. A big snag in my academic workflow, however, was managing my PDF research documents, notes, and citation information. I believe I have tested every combination of citation manager (e.g., Endnote, Mendeley, Papers, Bookends, Zotero), word processor or text editor, and note-taking app imaginable to create a seamless workflow.

I really dislike citation managers. I want to use them to help manage my research information, but they fall short on the iPad for in-text citations, extraction of highlighted notes, PDF reading, etc. Most of the citation managers also require a subscription fee to house your PDFs and notes on their servers for syncing between devices. In addition, many of the citation managers (e.g., Mendeley, Papers) have been purchased by large academic publishing houses that often restrict access to the academic literature.

When the Highlights app was made available for beta testing on the iPad, I immediately signed up. I had used Highlights on my Mac and really enjoyed its ability to extract highlighted texts and annotations to create markdown style notes for research. Highlights’ also has the unique ability, amongst PDF apps, to extract citation information from the journal article if it contains a digital object identifier (DOI) number. Your research notes, therefore, can also automatically contain the associated journal article’s citation information.

After a few years of development, Highlights is now available for purchase on the App Store, and I would like to share how I have been using Highlights in my research system.

First, I have abandoned citation managers, and have moved all of my research PDF documents into the Highlights folder within iCloud Drive. I really like this setup since all of my PDFs are now on my iCloud Drive, and not managed by another service that I have to pay an additional subscription fee.

My research related reading now takes place within the Highlights app. I highlight the text I want to come back too as well as add my own note annotations as I am reading. Before closing the research article, I typically export the notes into Ulysses, my writing app of choice, for storage and reference. If I need to quickly refer back to the PDF document directly, I simply follow a page URL link embedded within the reference note and it pulls up the original PDF within the Highlights folder.

I currently have over 1500 PDF documents in my Highlights folder. To find a key piece of information from a journal article or book that I can not remember while researching, I use PDF Search. I have set up the PDF Search app to index my Highlights folder. PDF Search uses AI to search through your PDFs for related terms and then ranks the results. PDF Search is an excellent replacement for cataloging your research documents rather than using a clunky citation manager database.

The only thing I am missing from my research system, that citation managers provide, is the ability to insert formatted citations into my document. I have been doing this manually through copy and paste and formatting the citations to fit the journal’s formatting requirements. This is a worthy trade-off for me at this point to have a more flexible and fast research system rather than trying to fit my workflow with a citation manager.

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