It is crucial to organize research papers so that the literature survey process goes smoothly once the data has been gathered and analyzed. This is where a research organizer is useful.
It may be helpful to plan the structure of your writing before you start writing: organizing your ideas before you begin to write will help you decide what to write and how to write it.
It can be challenging to keep your research organized when writing an essay. The truth is, there’s no one “best” way to get organized, and there’s no one answer. Whatever system you choose, make sure it works for your learning style and writing habits.
As a graduate student, learning how to organize research papers is therefore essential.
This blog post will cover the basics of organizing research papers and the tools I use to organize my research.
Before you start
The importance of organizing research papers
No matter how good your paper management system is, even if you keep all your literature in places that are easy to find, you won’t be able to “create” anything unless you haven’t thought about organizing what you get from them.
The goal of the research is to publish your own work to society for the benefit of everyone in the field and, ultimately, humanity.
In your final year of your PhD, when you see all the papers you’ve stored over the years, imagine the frustration you might experience if you hadn’t gathered the information from those papers in a way that allows you to “create” something with i.
This is why organizing research papers is important when starting your research.
Research with your final product in mind
It is very important to have a clear idea of what your research’s outcome will be to collect the information you really need.
If you don’t yet have all your information, consider what “subheadings” or chunks you could write about.
Write a concept map if you need help identifying your topic chunks. As an introduction to concept mapping, it involves writing down a term or idea and then brainstorming other ideas within it.
To gather information like this, you can use a mind map.
When you find useful information.
Come up with a proper file management system
Sort your literature with a file management system. There’s no need to come up with a very narrow filing system at this point. Try sorting your research into broader areas of your field. When you’re more familiar with your own research, you’ll be able to narrow down your filing system.
Start with these methods:
Don’t waste your time on stuff that’s interesting but not useful:
In your own research, what’s the most important part of a particular paper? You won’t have to pay attention to other sections of that paper if you find that section first.
What is the argument behind your research? Make notes on that information, and then throw everything else away.
Create multiple folders :
Create a file containing related topics if you’re using a computer. Bind the related articles together if you like to print out papers. In other words, keep related things together!
Color code your research papers:
To organize notes and articles, assign different colors to each sub-topic and use highlighters, tabs, or font colors.
Organize your literature chronologically:
Even in a short period of time, you might have missed overarching themes or arguments if you hadn’t read them previously. It’s best to organize your research papers chronologically.
If you want to do all this at once, I suggest using a reference manager like Zotero or Mendeley (more on reference managers later).
File renaming
Make sure you rename your files on your computer according to your own renaming strategy. Taking this step will save you time and confusion as your research progresses.
My usual way of naming a pdf is to use the first author’s last name, followed by the first ten letters of the title and then the year of publication. As an example, For the paper “Temperature-Dependent Infrared Refractive Index of Polymers from a Calibrated Attenuated Total Reflection Infrared Measurement” by Azam et al., I renamed the file as “Azam_Temperature-Dependent_2022.pdf“.
One thing to notice is that I don’t do this manually for all the papers I download. That wouldn’t be as productive, and I’d probably give up after some time renaming every single file. In my reference manager of choice (Zotero), I use a plugin called Zotfile to do this automatically. Zotfile automatically renames files and puts them in the folder I specify every time I add a new paper.
Organizing your research articles by the last names of the lead authors will simplify your citation and referencing process since you have to cite the names of the researchers everywhere. The articles will also be easier to find because they’ll be lined up alphabetically by any researcher’s name you can remember.
Use keywords wisely
Keywords are the most important part of sorting. It’s easy to forget to move a paper to a specific file sometimes because you’re overwhelmed. But you can tag a paper in seconds.
When organizing research papers, don’t forget to develop a better keyword system, especially if you use a reference manager.
My reference manager, for instance, allows me to view all the keywords I have assigned in the main window, making life much easier.
Create annotations
When reading literature, it is very important to create your own annotations, as discussed in the blog post series, “Bulletproof literature management system“.
This is the fourth post of the four-part blog series: The Bulletproof Literature Management System. Follow the links below to read the other posts in the series:
- How to How to find Research Papers
- How to Manage Research Papers
- How to Read Research Papers
- How to Organize Research Papers(You are here)
The best thing to do is to summarize each section of the article/book you are reading that interests you. Don’t forget to include the key parts/arguments/quotes you liked.
Write your own notes
If you decide to read the whole paper, make sure you write your own summary. The reason is that 95% of the things you read will be forgotten after a certain period of time. When that happens, you may have to read the paper all over again if you do not take notes and write your own summary.
By writing your own summary, you will likely memorize the basic idea of the research paper. Additionally, you can link to other similar papers. In this way, you can benefit from the knowledge you gain from reading research papers.
After reading a paper, make sure to ask these questions:
- Why is this source helpful for your essay?
- How does it support your thesis?
Keep all the relevant information in one place so that you can refer to it when writing your own thesis.
Use an app like Obsidian to link your thinking if you keep all your files on a computer, making things much easier.
When you are ready to write
Write out of order
Once you have all the necessary information, you can use your filing system, PDF renaming strategy, and keywords to draw the annotations and notes you need.
Now that you’re all set to write, don’t worry about writing the perfect paper or thesis right away.
Your introduction doesn’t have to come first.
If necessary, you can change your introduction at the end – sometimes, your essay takes a different direction. Nothing to worry about!
Write down ideas as they come to you
As you complete your research, many full-sentence paragraphs will come to your mind. Do not forget to write these down – even in your notes or annotations. Keep a notebook or your phone handy to jot down ideas as you get them. You can then find the information and revise it again to develop a better version if you’re working on the same project for a few days/weeks.
My toolbox to organize research papers
Stick with the free stuff
Trying to be a productive grease monkey, I’ve tried many apps over the years. Here’s what I learned.
- The simplest solution is always the best solution (the Occam razor principle always wins!).
- The free solution is always the best (because they have the best communities to help you out and are more customizable).
As someone who used to believe that if something is free, you’re the product, I’ve learned that statement isn’t always true.
Ironically, open-source software tends to get better support than proprietary stuff. It’s better to have millions of enthusiasts working for free than ten paid support staff.
There are a lot of reviews out there, and EndNote usually comes out at the bottom. I used EndNote for five years – it worked fine, but other software improved faster. Now I use Zotero, which I like for its web integration.
Obsidian, my note-taking app of choice, is also free software. Furthermore, you own your files; also, you’ve got a thriving community.
There are a lot of similarities between the software as they adopt each other’s features, and it’s just a matter of preference.
Zotero
In any researcher’s toolbox, a reference manager is an essential tool.
A reference manager has two important features: the ability to get citation data into the app and the ability to use the citation data in your writing tool.
It should also work on Windows just as well as macOS or Linux, be free, and allow you to manage PDFs of papers or scanned book chapters.
Zotero, in my opinion, gives you all of this and more.
Zotero is one of the best free reference managers for collecting citation data. It includes a browser plugin that lets you save citation information on Google Scholar, journal pages, YouTube, Amazon, and many other websites, including news articles. It automatically downloads a PDF of the associated source when available for news articles, which is very convenient.
One of the things I really like about Zotero is that it has so many third-party plugins that we have almost complete control over how we use it.
With Zotero 6, you can also read and annotate PDFs, which is perfect for your needs.
My Research paper organizing workflow in Zotero:
- Get References and PDF papers into Zotero: I use Zotero’s web plugin to import PDFs directly
- Filing and sorting: I save files from the web plugin into the file system I already have created in Zotero and assign tags as I do so.
- File renaming: When I save the file, the Zotero plugin (Zotfile) automatically renames it and stores the pdf where I specified.
- Extracting Annotations and taking notes: I use Zotero in the build pdf reader to take notes and annotate, and then I extract them and link them in Obsidian (next section).
Obsidian
You need to keep your notes organized and accessible once you’ve established a strong reading habit. For this purpose, I use Obsidian. I use Obsidian to manage everything related to my graduate studies, including notes, projects, and tasks.
Using a plugin called mdnotes, Obsidian can also sync up with my reference manager of choice, Zotero. It automatically adds new papers to my Obsidian database whenever I add them to Zotero.
Obsidian may have a steep learning curve for those unfamiliar with bi-directional linking, but using similar software will make things much easier. Thus, you may be better off investing your time in devising a note-taking system that works for you.
You can also use a spreadsheet! Make a table with all the papers you read, whatever tool you choose. Include the paper’s status (e.g., whether you’ve read it) and any relevant projects. This is what mine looks like.
I keep all my notes on an associated page for each paper. In a spreadsheet, you can write your notes directly in the row or link to a Google document for each row. Zotero, for example, allows you to attach notes directly to reference files.
Conclusion
While it might seem like a lot of work, keeping a database of papers you’ve read helps with literature reviews, funding applications, and more. I can filter by keywords or relevant projects, so I don’t have to re-read anything.
The habit of reading papers and learning how to organize research papers has made me a better researcher. It takes me much less time to read now, and I use it to improve my experiments. I used this system a lot when putting together my PhD fellowship application and my candidacy exam. In the future, I will thank myself for having the foresight to take these steps today before starting to write my dissertation.
I am curious to know how others organize their research papers since there is no “right” way. Feel free to comment, and we will update the post with any interesting responses!
Images courtesy: Classified vector created by storyset – www.freepik.com
