How I organize papers
Quite a few people have asked me how I organize my literature reading, so here’s a walkthrough of how I do it. This is a method that works for me right now, and I’ve been consistent with doing it this way since I started reading more seriously for my oral qualifying exam.
Paper reading set up:
Printed copy at 85% (for space to write in the margin)
Black pen (for summaries, writing things in my own words, writing things to keep in mind, etc.)
Blue pen (for notes on experiment ideas, how these experiments/findings are relevant to what we study, things to take notes of, things to look up, etc.)
Yellow highlighter for general highlighting
No phone/computer/tablet
Cup of tea/coffee
I used to read on my iPad using Notability. I liked that option because it gives me more colors to work with, but I was also getting too distracted with what colors to use, all the apps on my iPad, and such. These are dry academic papers with a lot to process, and it’s really hard to compete with apps like FB and Reddit with their endless scrolls and easy to understand posts. I find that with my current set up of having just the bare necessity and no distraction means I’m more likely to read my paper and stay reading. Photo above was taken when I was summarizing, so I had both my phone and my laptop and took 2x as long to summarize…
Digital organization set up:
There is a “Paper” section within my OneNote lab notebook
Under this section, each tab has its own topic
Sometimes there are overlaps (interneuron deficit leading to Tourette) would have a main section in Tourette, and that just gets copy/pasted to the Interneuron with a note saying, “duplicate from Tourette”
In each tab has a “Table of Content,” which is a summary table of all the papers I’ve read on that topic
ToC is subdivided into several categories: paper, summary & conclusions, *something specific to this section, and notes & additional questions
Paper: contains title, *first author’s last name* et al., ### (*PI’s last name*)
Summary & Conclusions: things I’ve written in black or highlighted from the paper
*Specific to this section*: I don’t really know how to describe this section besides giving examples. For my Tourette tab, this section is Area Implicated since we’re interested in the regions of the brain associated with Tourette. For my protein of interest (PoI) tab, this section is PoI’s Condition since I want to distinguish the effect seen with heterozygous KO, homozygous KO, conditional KO, and point mutations, to piece out the function of the various domains
Notes & Additional Questions: everything I wrote in blue will go here. This section makes notes of the experiments I came up with while I read, lists questions I have during reading that can guide further reading, etc
This serves as a summary of all the papers I’ve read with enough information to know the paper without having to reread it. In my experience, it’s immensely helpful as I write my qualifying proposal. Having everything about one topic in one place allows me to quickly compare and contrast the different papers and see what has or hasn’t been done before and how to possibly fill the knowledge gap.
Physical organization set up:
My implementation of @cancerbiophd‘s method:
I currently have 1-1.5 inch binders containing 2-3 topics per binder
Each topic is distinguished from the other in the same binder via color coding tags
Each tag is labeled with *first author’s last name* et al., ### (*PI’s last name*)
Papers are stored in plastic sheet protectors to protect all parts of notes from hole punching, and this plastic sheet protector is flagged with the label above
The order of the paper is not really organized. Right now I have it by the order I read it in, but if I come up with a better way of sorting papers, I will adopt that instead
These photos are a bit outdated. I’ve switched my CELSR3/Tourette/Interneuron papers into the 1.5 binder since my research focuses on this particular area, and there’s a lot of papers that I’m reading that pertains to these topics.
Usage
When writing, I have the “table of content” side by side and read through that for a quick summary. If further info is needed, I can go through physical copy for more information, and since it’s organized in a way that makes sense to me, I can find it easily instead of leafing through all of my papers, some with very similar titles and authors.
Hopefully this is helpful to you! If you have any suggestions on how to make this process more efficient or comments on how you personally keep track of your literature reading, please let me know!
Very helpful. Thank you so much for sharing!
