Guide to Cataloging Research Literature References and Notes
Summary: Immersing in the literature is a crucial component of research, yet cataloging and organizing research papers is not trivial. Here I outline a system for long-term organization of high complexity research literature and corresponding notes designed for ease of use, rapid retrieval of specific papers, and the development of expertise. The system consists of a triple combination of Google Sheets, Google Slides, and Zotero. I discuss why I think this is a particularly robust system, outline how to implement it, and provide an open-access template for anyone to use:
Introduction
Getting involved in research often rapidly brings you face-to-face with a massive amount of literature, as peer-reviewed publications are a major platform for the formal exchange of information and data in science and medicine. You probably have several different uses for such publications, such as taking notes on papers relevant to your field, adding high-quality references to your own papers, learning new or alternative methods used for a particular type of experiment, sending relevant papers to others, preparing for a candidacy exam, and writing a thesis. Furthermore, there are probably several different sub-topics of publications relevant to you.
All of these factors add a lot of complexity to the process of organizing and storing your papers: How do you catalog relevant publications you read, and your corresponding notes, such that in the future you can efficiently retrieve different types of information for different purposes? This is a question I’ve been exploring throughout grad school, and I’ve tried a variety of methods to address it ranging from printing physical copies of publications and annotating them with pen and highlighter to using electronic methods, apps, and softwares. I want to share with you in this blog post a method I’ve found that works best for me, in hopes that this method, or your own variations of it, may be helpful to you. But first, I need to define the variables driving the creation of this system - the things that really matter to me as a grad student (and I suspect to many other researchers) for my literature tracking.
Factors I consider essential for a good literature cataloging strategy:
Backed up on cloud storage so there is minimal risk of catastrophic loss of years of work
Easily visualize the most important information about publications in a format that allows you to scroll through the likely large number of papers you will accumulate
Allows storage of detailed notes that can be collapsed and expanded within the same viewing window mentioned above to facilitate rapid browsing and review.
Easy and automatic referencing of publications in Microsoft Word and Google Drive
Allows grouping of publications by sub-topics
Allows linking directly to the original publication on journal’s website
Allows storage of information-rich (and memory-stimulating) figures from publications in an easily navigable format, and that allows easy recycling of those figures into slides for talks
Direct copying/pasting quotes from publication text into notes
Reliable and rapid syncing across devices
The System Summarized
The system satisfying all of the factors above is actually a 3-part solution consisting of Google Sheets, Google Slides, and Zotero. Although using these three platforms creates a bit of manual work on the front-end when incorporating a new paper into them, I think this is a very worthy time investment that results in enormous payoff when you can efficiently access information and insights from papers you’ve worked hard to understand over years. I also think that regardless of whether you adopt this particular system, at a certain point, if you don’t invest time upfront cataloging the papers you read and the multiple different types of relevant data associated with them (i.e. bibliographic info, your notes, important figures), you will end up spending even more time in the future searching for information you need without remembering where it is.
Figure 1. Visual Summary of Literature Cataloging Strategy
Having given this introduction and overview, I will now discuss in more detail how the different components of this cataloging system work - ideally enough detail that you can replicate this method if you want to try it.
1) Google Sheets
How I use it:
Google sheets is the powerhouse of this whole system. I use a single google sheets file for all of my literature, and every row contains one publication. (I have set every row to be equal length) Additionally, the spreadsheet contains multiple tabs reserved for different literature subtopics. The columns present in each sheet are for each paper’s title, journal, year published, link to the original publication, a checkbox to confirm I’ve uploaded that paper to my Zotero, and a Notes column for taking detailed notes on the paper. I set column names and font sizes based on how important information is to me (i.e., I do not care about actually reading the URL, I just want to be able to click it and go to that URL, so I have made the font size for URL very small, whereas I very much care about seeing the title of the paper, so this font size is large).
Upon finding a new paper I think is worth cataloging, I first decide what literature subtopic it belongs to, then open that tab of my Google spreadsheet and insert a new row there. I then copy/paste the paper’s title, journal, year, and URL into my Google Sheets. I then download the PDF of that paper, drag it to my Zotero (more on that later), and check the ‘Z’ box in my Google spreadhsheet, which tells me that indeed I have a copy of that paper in my Zotero now, so I don’t ever need to download it again. I then double click the cell corresponding to my ’Notes’ column for that paper and boom! I can type in my notes on the paper as needed. Although you cannot do traditional bullet points here, you can type ‘Option’ plus ‘8’ to create one yourself (at least on Mac). When you click a different cell, you’ll notice your ‘Notes’ cell contracts again so that you only see a few lines of it. This is something I love about this format; I can scroll a vast number of literature titles and relevant information, and from the same screen without closing anything or opening a window, I can just double click my ’Notes’ cell for a specific paper, and it will immediately expand my notes section for me to glance through.
Advantages:
Continuously backs up your work to very secure cloud storage; minimal risk of losing your work
Command F: Months and years down the road if you want to quickly retrieve a specific publication you once read or took notes on (*cough cough, such as when you are thesis writing), you can use command F to quickly locate it.
Can store links to the original publication
Allows easily downloading and sending all of your notes in one place
Allows future changes to your organizational layout/updates relatively easily, and will probably be more customizable in the future as Google is very well-developed
Allows you to input papers you haven’t read and indicate this (or am I the only one with this problem?)
Disadvantages:
Does not work well with images. Although you can double click to expand a cell to view an expanded view of your notes for a specific publication, Google Sheets is not well developed for images, and I have not found a good way to include important screenshots from papers within Google Sheets. (This is one of the major reasons why I also use Google Slides in a parallel with Google Sheets which we will get to in a moment)
Some amount of manual effort is required to copy/paste relevant information from each publication you add to your database (~30 seconds per paper)
Bullet points are not as good as in Google docs or Microsoft Word as you have to manually type each one (bullet point is ‘option’ ‘8’)
Can take some getting used to as hitting enter will move you to the next cell rather than start a new line within that cell (hold ‘option’ and hit ‘enter’ to make a new line inside a cell)
2) Google Slides
How I use it:
For a specific paper that has an important figure I care about, I simply copy the information straight from my Google Sheets catalog (title, journal, year, URL), and paste it into the top of a blank Google Slide. This saves you from having to type the same info twice. I then add a screenshot of the figure I care about, and type any notes I have in the ’speaker notes’ section for that slide.
Advantages:
Our brains are wired to interpret information visually, and I think the Google Slides component here really compensates for the lack of images in Google Sheets, making use of our visual learning sides. A lot of the time I become familiar with papers by a distinctive summary figure or data figure, and that’s how I immediately think back to them; this format makes use of that type of memory and allows you to quickly scroll through and remember large amounts of information that is visually encoded. It can also be a high yield format to review material for candidacy, giving talks, etc.
Backed up to cloud
Secure
Syncs across devices
Disadvantages:
It’s an additional platform that makes your life slightly more complicated
3) Zotero
How I use it: Zotero I really use as the platform by which I open the actual publication I’m interested in. When I download a PDF of a publication I want to read, I click and drag that PDF into Zotero, into a folder that corresponds to the sub-topic tabs in my Google Sheets. (I find that clicking and dragging the PDF directly into Zotero works better than the Chrome plugin tool, in which Zotero sometimes cannot automatically pull the full PDF for you. However, if you provide it the full PDF, it is usually very good at creating an accurate citation from that).
Advantages:
Automatic, easy citations, with good plug-ins supporting integration with Google Chrome, Microsoft Word, and Google Drive
Open-source platform and good forum community presence for troubleshooting any issues; very widely used platform that will likely continue improving in the future
Allows you to directly store PDFs of the actual publication, and is a platform you can directly read papers on, whereas the other two Google platforms are for you to catalog your own condensed data
Zotero has an app for ipad/tablet that seems to sync rapidly with desktop zotero, and ipad allows you the option of handwriting notes/marking up publications that way if you prefer using an Apple pencil or stylus
Disadvantages:
It’s an additional platform that makes your life slightly more complicated
Conclusions
The literature cataloging system discussed here requires a little bit of manual work up front (~30 seconds per paper), but in exchange, it forever puts your notes, publication metadata, and knowledge into functionally accessible formats organized by literature subtopic, allowing efficient in-depth review of content, and readily shareable with the rest of the world for a variety of important academic purposes. Even if you don’t adopt this entire system, I hope it helps you generate your own ideas for what will work best for you, and allows you to delve into cool science sooner. Good luck!
Link to Google Sheets Template: Feel free to copy this to your own Google Drive and adapt it for your purposes!
