Today we have a sneak peek at the sacred process of PhD work on writing. This is a story shared by @thoughtsofaphd, a PhD candidate in biomedical science in Canada. He shares how PDF Expert helps him to reduce stress through all the stages, from collecting valuable information in every possible way in the form of a huge number of downloaded books and files to its processing and analysis.
When my friend told me to download PDF Expert, I was hardly excited about downloading an application to read PDFs. We were graduate students (notoriously always behind on reading the hundreds of PDFs we’d downloaded and put in folders called ‘To Read’) and if I’m being honest, I had no plans for actually reading most of them. It’s been 6 years since I first downloaded PDF Expert, and I can’t even imagine doing my PhD without it.
Little Less Chaos around PDF files
There are so many ways that people choose to sort, read, and markup (or not) their PDF files. As a PhD student, I spend a lot of time reading scientific literature. New papers come out in my field every single day, and my e-mail inbox is filled with papers sent to me by colleagues, collaborators, and my supervisor. Keeping up with the literature is no small order. There is a myriad of apps and tools available that notify researchers when new work in their field is available to read, but that’s not where my problem is: I know about the papers, but actually reading them, as well as extracting and storing the important information, is a whole other challenge.
That’s where PDF Expert comes in. Hands down, it is the best PDF markup tool that I’ve used. It’s snappy (quick to load, launch and execute the functions that you ask for), easy-to-use, and has many features that are great for reading literature. In the 6 years since I started using PDF Expert, I’ve developed a system that I use for tracking all of the relevant information about any given paper:
- Where it came from (for example, who sent it to me? Did I download this myself?)
- Why I saved it (did my supervisor send me an e-mail about this paper specifically saying why it was important?
- What was I thinking when I downloaded it?
- The status of the paper (is it read or unread)
- The main points (what are they and where are they in this document?)
Ready, Set, Stamp!
The secret to this system I’ve developed is PDF Expert’s ‘Stamp’ tool. Stamps are like stickers that I can put at the top of the PDF. I have stickers for each of the categories I mentioned, like where the paper came from and the status of the paper (to read or read). As soon as I download a paper, I stamp it with these two stamps so that I quickly know why this paper was downloaded and whether or not I’ve read it.
That’s just the beginning. When I’m ready to read the paper, I prefer to do that on my iPad where I can scribble my thoughts in the margins with my Apple pencil. PDF Expert has seamless integration across devices, allowing me to synchronize folders (I use Google Drive) with PDF Expert on Mac, iPad, and iPhone: this means that any changes I make to a PDF in the synchronized folder will appear on all of my devices. Sometimes months after I download a PDF (graduate students are notoriously behind on reading), I’ll open it on my iPad and the stamps I left at the time of download quickly orient me as to the importance of why I should read this paper.
Color-coding highlights for key information
Then, I start reading. I use the text highlight tool to highlight all of the important information, changing the colors of the highlights for different categories of information (yellow for most things, and orange for particularly important points). When I arrive at critical points of the paper, I have another stamp, called ‘Important Point’ that I place in the margins beside my highlights. This helps me identify during a quick scroll of the PDF where the most pertinent information is. Along the same lines, I have a bunch of other stamps that I use (hypothesis, critique, etc.) to annotate the document.
- Yellow: important information
- Orange: critical information (a particular definition, conclusion, or main argument for example)
- Green: experimental result
- Blue: literature references to read/download
By the time I’ve finished reading a PDF, it’s full of stamps, highlights, and handwritten notes. Sorting through all of that information at a glance is difficult. If I come back to a paper in a year or two (for example, when I start to write my thesis), I want a quick way to know, on the first page, why this paper is significant and what important information it contains.
At the top of the first page, next to the stamps, I summarize the important points in a text box. That way, when I open this PDF in the future, the first thing I’ll see is a text box of the paper’s key points, with the option to scroll down and read through my annotations if I want more context or details. 
Whenever I need to call upon the literature I’ve read to write a research paper or prepare a presentation, the effort I spent marking up PDFs in PDF Expert pays dividends. PDF Expert helps me sort, annotate, and organize information from hundreds of PDF documents in a way that is easy to access, remember, and use for my research. Half the battle is actually reading the papers, and the other half is recalling and being able to use or apply what you’ve read. While PDF Expert can’t help me with the first part, it makes recalling and organizing information from PDFs faster and easier.
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