We Need a Better System: Streamlining Academic Digital Workflow from Reading to Writing

We are in an age of unprecedented information access. As academics in the humanities, we all have too much information to handle, too many things to read, and too many files scattered around various folders on our computers. Although we all deal with data, and lots of them in various forms, we are often not trained to organize and process them in a structured and systemized way. It is often assumed that an academic in the humanities would just know how to read, take notes, and write systematically and productively.

The truth is that some (if not most) of us don’t really have a system and may not even have thought about developing one. For example, when it comes to reading and note taking digitally in a PDF file, we’d highlight things within the document via Adobe Acrobat while we read it, add the occasional comments here and there, save them to a folder (often haphazardly named and organized), and then we’d forget about them. As time passes and our memories fade, the highlights and our comments made within the PDF files would become harder and harder to retrieve.

“I think I read that article a couple of years ago. What did it argue again? Ugh, I can’t find it on my computer. I swear I saved it in this folder.”

Sure, you could do an in-text search with a keyword in the PDF, but a “command+F” cannot retrieve the thought processes that you went through while reading that PDF; it can only take you to a decontextualized place in the document. Plus, the in-text search might not even work for a file that has not been OCRed, which means you’d have to scroll down the entire PDF document to find the highlights/comments that you need. This makes it very difficult to review comprehensively what we have annotated in a PDF file later for things like seminar discussions, writing literature reviews, and for our research in general (e.g. writing articles, books, and/or the dissertation).

In other words, in academia, we still tend to read and consume digital sources in an unconnected way. Books and articles are being organized (PDFs saved in badly named folders or even worse, the Downloads folder) and processed (read through Adobe Acrobat or even worse, an internet browser) as isolated entities. Even the highlighted excerpts and notes within a book or article remain isolated and scatted within the document – there is no way to connect them to and with each other unless you write them out in paragraphs in a separate document, as people do in reading reports and literature reviews. But as humanists all know, the books and articles we read are never unconnected; they are all grounded in networks of knowledge production and webs of sources. Academic citation is all about intertextuality. We think while we read in such a networked way, too. But the way that we tend to organize and process digital files, such as reading single PDFs on Adobe Acrobat and then saving them to a folder, prevents us from manifesting the way we think into a digital reality.

As a result, most of us don’t have a coherent and interlinked system that would turn our non-linear reading thought processes into coherently organized and easily retrievable data for academic writing. Having such a system would actually save us a lot of time spent on hunting down old PDFs saved somewhere in our computers and rereading them when writing deadlines approach. Having such a system would also reveal valuable connections between different sources of literature and even synthesis ideas for us that we would not have been able to see otherwise.

This post is thus the first of a series of posts on how I set up such a system for myself, as well as tips on how to set up one for yourself.  

Introducing the Series: Streamlining Your Academic Digital Workflow

In the following months, I will be posting on the following topics on creating a system for digital academic work, which could be roughly categorized into three groups:

Processing Academic Literature:

Reading and annotating PDFs with LiquidText and MarginNote: This post will explore alternative applications to Adobe Acrobat for viewing and annotating PDF files. This post will show how we can export, organize, and share our highlighted excerpts and margin notes, as well as how we can create connections between passages within a single document.

Taking networked notes with RoamResearch, Obsidian, and Logseq: This post will introduce and compare three powerful innovative applications for creating linked notes that could grow into a personal networked database for your research. In this post, I will share a couple of templates I use for taking interconnected literature notes and concept notes inspired by the Zettelkasten method, which could help decrease the friction of writer’s block and smooth out the referencing process of writing.

Managing Academic Data:

Organizing and backing up your data with smart sync: This post will take the opportunity to discuss the art of naming files and folder organization, as well as a few strategies for backing up our precious data. In this post, I will also introduce a couple of backup options for freeing up space on our limited hard drives (be it our laptops or smartphones).

Managing references and Citations with Zotero and Paperpile: Reference managers seem to be one of the most widely used digital tools in academia. Instead of going through the basics, this post will explore the more advanced functions of Zotero (especially within RoamResearch and Logseq) and introduce a lesser-known reference manager, Paperpile.

Producing academic work:

Pre-writing with RoamResearch: This post will introduce some of the tricks I have learned on using RoamResearch (and similar apps) and its functions to do pre-writing, such as drafting conference papers and dissertation chapters. This post will explore how they offer a non-linear approach to writing and have functions that respond to the intertextuality of our research processes that more common applications like Microsoft Word simply don’t.

Translating with RoamResearch: In this post, I will introduce how I utilize the backlinks feature in RoamResearch for translating texts, particularly, how I use the inter-linking system in the app to set up glossaries and notes to ensure consistency.

Please stay tuned.