how to sort research papers

How to Organize Research Papers: A Cheat Sheet for Graduate Students

• August 8, 2022
• PRODUCTIVITY

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.

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).

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.

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

Aruna Kumarasiri

Founder at Proactive Grad, Materials Engineer, Researcher, and turned author. In 2019, he started his professional carrier as a materials engineer with the continuation of his research studies. His exposure to both academic and industrial worlds has provided many opportunities for him to give back to young professionals.

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15 Best Free Web Tools to Organize Your Research

How to stay organized when researching and writing papers

• Emporia State University
• DeveloperWeek 2024: Dates, News, Rumors, and Everything Else to Know

Organizing research is important not only for your own sanity, but because when it comes time to unfold the data and put it to use, you want the process to go as smoothly as possible. This is where research organizers come in.

There are lots of free web-based organizers that you can use for any purpose. Maybe you're collecting interviews for a news story, digging up newspaper archives for a history project, or writing a research paper over a science topic. Research organizers are also helpful for staying productive and preparing for tests.

Regardless of the topic, when you have multiple sources of information and lots to comb through later, optimizing your workflow with a dedicated organizer is essential.

Patrick Tomasso / Unsplash

Many of these tools provide unique features, so you might decide to use multiple resources simultaneously in whatever way suits your particular needs.

Research and Study

You need a place to gather the information you're finding. To avoid a cluttered space when collecting and organizing data, you can use a tool dedicated to research.

• Pocket : Save web pages to your online account to reference them again later. It's much tidier than bookmarks, and it can all be retrieved from the web or the Pocket mobile app .
• Mendeley : Organize papers and references, and generate citations and bibliographies.
• Quizlet : Learn vocabulary with these free online flashcards .
• Wikipedia : Find information on millions of different topics.
• Quora : This is a question and answer website where you can ask the community for help with any question.
• SparkNotes : Free online study guides on a wide variety of subjects, anything from famous literary works of the past century to the present day. 
• Zotero : Collect, manage, and cite your research sources. Lets you organize data into collections and search through them by adding tags to every source. This is a computer program, but there's a browser extension that helps you send data to it.
• Google Scholar : A simple way to search for scholarly literature on any subject.
• Diigo : Collect, share, and interact with information from anywhere on the web. It's all accessible through the browser extension and saved to your online account.
• GoConqr : Create flashcards, mind maps, notes, quizzes, and more to bridge the gap between your research and studying.

Writing Tools

Writing is the other half of a research paper, so you need somewhere useful to go to jot down notes, record information you might use in the final paper, create drafts, track sources, and finalize the paper.

• Web Page Sticky Notes : For Chrome users, this tool lets you place sticky notes on any web page as you do your research. There are tons of settings you can customize, they're backed up to your Google Drive account, and they're visible not only on each page you created them on but also on a single page from the extension's settings.
• Google Docs or Word Online : These are online word processors where you can write the entire research paper, organize lists, paste URLs, store off-hand notes, and more.
• Google Keep : This note-taking app and website catalogs notes within labels that make sense for your research. Access them from the web on any computer or from your mobile device. It supports collaborations, custom colors, images, drawings, and reminders.
• Yahoo Notepad : If you use Yahoo Mail , the notes area of your account is a great place to store text-based snippets for easy recall when you need them.
• Notion : Workflows, notes, and more, in a space where you can collaborate with others.

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• 07 July 2022

How to find, read and organize papers

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Maya Gosztyla is a PhD student in biomedical sciences at the University of California, San Diego.

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“I’ll read that later,” I told myself as I added yet another paper to my 100+ open browser tabs.

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How to Search and Organize Research Articles

• by Tiffany Yue Zhang
• November 01, 2021

Quick Summary

• Organizing research articles using a reference manager and other strategies will make life as a graduate student much easier.

As PhD students, reading is part of our life. There are so many new papers coming out every day, so many research blogs to follow, so many books to read. But, how would you find them and organize them? Certainly, I’ve seen people downloading everything to their desktop and piling up 100 pdfs with no labeling or grouping. To be honest, that was me at one point. When you start to write a report or research paper, it can become a nightmare to organize the reference list. If you are first year graduate student doing research, or if you are just looking for a method to organize your scientific literature, this blog can hopefully help.

Finding Articles

The best resources for starting to build your reading list are your advisor and lab mates.  This is definitely the fastest way to gain background on your research area. Simply ask around the lab about key articles in the research field. The downside of this method is that the pool of articles is limited by what’s already known by your advisor or lab mates. Starting by reading a review paper in your field, then finding and reading the most relevant references listed for the review, is also a good method.

Searching by key words is another common way to find scientific literature. I use Google Scholar, Web of Science, and Scopus, mostly.  Searches can be done by entering the key words, subject area, document type (e. g. review, articles), and sort by relevance. Start to read from the most cited papers in your field. If you are interested in a specific researcher’s publications, you can follow them on Google Scholar and you’ll get notified when they publish new articles. Lens.org is another good resource for searching, analyzing and managing patent and scholarly data.

Subscribing to RSS feeds is another good way to keep up with recent research. There are a variety of apps that can send notifications when new research papers of interest are coming out, such as Researcher, Feedly and Academia. Pick your favorite topics or journals to follow and get your daily feeds about research topics. You can even track when a paper is cited. These tools are good for scientific literature, but you can also use them for your hobbies, your favorite magazines, etc.

Following blogs can be helpful, as well. As a chemistry student, I follow some of the ACS (American Chemical Society), RSC (The Royal Society of Chemistry) blogs, as well as blogs written by researchers and professors. If you are looking for something interesting to read, follow Retraction Watch. There, you’ll find the research articles that are retracted for fraud, ethical violations, and many other reasons.  Some stories can be quite interesting.

Listening to podcasts can be a good way to broaden your knowledge. Usually, the content in podcasts is less technical and you can learn some basics for topics that you are not familiar with.

Organizing Research Papers

Different people find different ways to organize research articles. Some prefer to print everything out and put them in binders, some prefer to read the digital versions and sort them in folders. Personally, I like to read on a computer screen and sort research papers by project. I usually keep important references in a reference manager. For papers that I want to go over multiple times, I usually print them out and read them carefully. It’s easier to take notes with a printed version and, for some reason, it seems like I can memorize the content longer when I read the printed paper. The main drawback in using hard copies is that it can be difficult to find a specific paper when you have a large pile. With digital versions, it’s much easier to locate specific research articles by keywords.

There are many digital reference managers. This type of software tool can allow you to keep research articles in different folders for each research project. Within the reference manager, you can also take notes, sort by author, year, or topic. Most reference managers also help with searching for research articles. When you write a report or publication, reference managers allow for import of references from these databases directly into Microsoft Word, which is very convenient.  Here are three of the most commonly used reference managers: EndNote, Mendeley  (Figure 1)  and Zotero. All of them can sync between devices and be shared between different people. EndNote is not free, but it is very powerful. It supports many unusual or complex citation formats. Some versions of Mendeley are free. It’s good at dealing with pdfs files and can extract citations from pdfs, as well as searching from pdfs. Zotero is also free and allows for saving snapshots of web pages and annotating them in your library, which is good for web-based publications.

When I read a paper, I usually ask myself the following questions: 1) what’s the purpose of reading this article?; 2) how is the article important or relevant to my work?; and, 3) what’s the take home message?. If the paper is important, I then write down the conclusions and methods. Taking notes makes reading more efficient ( Figure 2).  Notion is a good application to keep track of reading notes and allows for creation of lists of papers for different topics. You can also assign properties to each paper and tag papers with keywords. Notion also supports markdown which makes your notes clean and easy to read. When I read a research article, I usually start with the title and abstract and try to figure out the big picture conclusions or contributions to the research field.  Then, I skim through the figures and the figure captions to get an idea of the key points. If a figure is important, I keep it in my notes. I usually skip the introduction at first if I’m familiar with the author or the research field, instead jumping directly into the results and conclusion sections. From there, I’ll decide if I want to read the paper in detail or not. Different people have different ways of reading papers; find the one that works for you.

I hope you find these methods helpful for finding and organizing research articles and happy reading!

Marcus, Adam, and Ivan Oransky. Retraction Watch , Oct 24 2021, https://retractionwatch.com/. 

“Which Reference Manager? Comparision of Endnote, Medeley and Zotero.” Library Guides , Mar 2 2021, https://aut.ac.nz.libguides.com/managingreferences.

“How to (Seriously) Read a Scientific Paper.” Science , Mar 21 2016, https://www.science.org/content/article/how-seriously-read-scientific-paper.

Getting into the right mindset to read scientific papers quickly:

Before you start anything, you need to isolate your singular goal for reading papers in the first place. Otherwise, you’ll be passively reading every paper that comes up rather than hunting for specific details. Don’t be a forager, consuming anything edible that crosses your path. Be a hunter: have a specific target that keeps you selective, efficient, and guides every step you take.

Most of these tips are designed to help you focus on extracting value efficiently so you won’t give up after two papers! So, what is your goal here? Is it:

• Getting a solid foundation in your field?
• Collecting the newest research for a cutting-edge literature review?
• Finding ideas and inspiration to further your own research?  

I’ll be honest here: The first dozen papers of a new subject will be a grind. But it gets easier, I promise! When you find yourself blasting through the “template” introduction and recognizing citations you’ve already read, you know you’re close to being an expert. At this point, if you’re struggling to understand a new paper in the field, it’s likely the authors’ fault, not yours. 

Keep in mind that academics aren’t exactly known for concise writing. Practice skimming paragraphs for high-value verbs, numerical values and claims. Skip over wordy low-value prose like “We thus appear to have potentially demonstrated a novel and eco-friendly synthesis method for…” It’s easy to fall back to a casual fiction-reading mentality. Try to stay in a high-energy search mode and you’ll be effectively done in half the time.

Later on I’ll reference our journal article notes template , which I used to synthesize notes for my literature review. Go ahead now and open it in Google Drive where you can download and edit it for free. We just ask that you drop your email so that we can stay in touch on new helpful resources and awesome new tools for scientists.

How do you read scientific papers effectively?

Below are my tips for how to read scientific papers most effectively. I used this methodology to write a critical literature review in a brand new field in about 4 months, citing over 150 papers. My first-author paper now has nearly 1000 citations in only six years since publication, making it my advisor’s most highly-cited paper in his 30-year career! You can do this. Just keep reading: 

1. Briefly read the Abstract

The abstract is your most condensed look at the paper. Read it quickly and highlight any claims or phrases that you want more details on. I like to copy the entire abstract text or screenshot into the journal article notes template for later reference. It also helps to copy the keyword text into the template or your citation manager tags so you can search for them later. Things to read for:

• Is the research applicable to what you need right now?
• Are the findings significant enough to help you with your goal?
• What is the most interesting aspect of this paper?

2. Carefully read the Conclusion

Reading the conclusion gives you an instant look at the quality of the paper. Do the authors seem to make claims bigger than appropriate for the scope of the paper? Do they use hyperbole to inflate the importance of the work? Are the results not clearly stated? These could be red flags identifying a poor quality paper. 

Highlight and copy a few of the most important phrases or sentences out of the conclusion into the journal article template in the first bulleted section or into the notes section of your reference manager. Look for:

• What the authors think they accomplished in this work.
• The reasoning behind their results. Any useful insights?
• Ideas for future experiments.  

3. Identify the most important figures and dig through the Results & Discussion for more detail

If you’re still interested after the first two steps, start digging into the results and discussion for more details. Before making the deep dive, write down the specific questions you need to answer in your notes section. Search the paper for those answers, writing down new questions as they come to mind. 

One favorite strategy here is to look at each figure, read the caption and then dig through the text for supporting information (use Ctrl+F for “Fig. 3”, for example). The figures should tell the story as well as (and more quickly than) the text. 

Copy and paste specific claims you may want to quote or paraphrase later. Isolate what the authors think they did from your own commentary and summarize it in your own words.

4. Search the Methods section to answer questions if necessary

The Methods section is usually the most tedious and tiring to read. That’s why we don’t do it first. Only go through it when necessary or you’ll never get to the 100 other papers you just downloaded.

Go back through the Methods when:

• This paper showed a different result than another similar paper, and the methods may have caused the difference. 
• You’re sure you want to include the paper and you want to be critical of the way they conducted their experiments. 
• You may want to replicate their experiment in your own work.

Make sure to note anything unique, odd, or unexpected in their methods. Maybe it will lead to a breakthrough in your own work or help explain a surprise result!

5. Summarize your thoughts and critiques

Re-read your notes so far to check for any missed questions. Go back and extract sentences or paragraphs of the paper that you want to challenge so you can quickly find them verbatim. Write your own thoughts and questions around those topics so you can copy them into your literature review later. Ideas for notes:

• What would you have done differently in the experiment or data analysis?
• Is there an obvious gap or follow-up experiment?
• Does this paper uniquely contribute to the field’s body of knowledge? What is its contribution?

6. Copy important figures into your notes

This is the most important step but many don’t do this. Figures are the anchors of every good journal article and the authors who spend the most time making excellent figures also will get cited the most often in review papers. This leads to even more citations from experimental articles. My secret for getting the most citations of my review paper was to spend more time than typical finding or creating the best possible figures for explaining the content. You can do this too, it just takes time!

The best reference manager Zotero doesn’t have an “add image” button in the “Notes” section but you can actually screenshot the image with the Snipping Tool then Ctrl+v paste it into the notes section! Now when you come back to the paper you’ll get an instant look at the most significant figures. If you know you want to use one of these figures in your review, add a tag to the paper like “Figure Rev. Paper 1”.

7. Pick important references (especially review papers) out of the Introduction and Discussion

Now that you have a good understanding of the paper, it’s time to start tidying things up and thinking of where to go next. Skim the introduction for helpful references or check the first 5-10 listed in the References section to find mostly review papers you can use for new leads. Go and download these into an “Unread review papers” folder in your citation manager for when you get stuck later. 

Then, go to the journal/library website and check for new papers that have cited this paper. This will help you follow the trail of a specific research topic to see how it’s developing. Download the interesting ones and put them in an “unread” folder for this very specific research topic. In Zotero, you can even tag the paper as “related” to the current paper for quick access later.  

8. Clean up the metadata if you plan on citing this paper later

If there’s a chance you’ll cite this paper later, make sure to clean up the metadata so your word processor citation plugin creates a clean reference section. Author initials may be backward, special characters in the title may be corrupted, the year or issue of the journal could be missing or the “type” of citation could be wrong (listed as a book instead of journal article) which would change the format.

Fully tag the paper using whatever system you’ve come up with. Keywords, chemicals, characterization methods or annotation tags like “Best” can all be useful. One other trick I used was to come up with an acronym for the paper I was about to write - “NMOBH” for example - and use that as a tag in any paper that I planned to cite later.

Being methodical in your post-read organization will save you many hours and endless frustration later on. Follow these tips on how to organize your research papers and you’ll be a pro in no time. You’re almost done, but don’t skip this part!

9. Take a break, then repeat!

This methodology makes it a little easier to get through a paper quickly once you get some practice at it. But what about 10 papers? 100?! You can’t do all of your reading in a week. I set a habit for myself over the summer to read two papers a day for 2 months. If I missed a day, I made it up the next day. This keeps you fresh for each paper and less likely to miss important points because you’re falling asleep!

Get comfortable. I preferred to kick back on a couch or outside in a chair using my laptop in tablet mode so I had a long vertical screen and a stylus to highlight or circle things. Reading 2-column scientific articles on a 13 inch 16:9 laptop screen at a desk for hours on end is a special kind of torture that I just couldn’t endure. Change scenery often, try different beverages, take breaks, and move around!

Here are some bonus tips for breaking the monotony between papers:

• Pick your top few most controversial, confusing, or interesting papers and ask a colleague or advisor for their thoughts. Bring them some coffee to discuss it with you for another perspective. 
• Email the authors to ask a question or thank them for their contribution. This is a great way to make a connection. Don’t ask for too much on the first email or they may not respond - they are busy!  
• Reward yourself for every paper read. Maybe a small snack or a short walk around the block. Physically cross this paper off your to-do list so you internalize the good feeling of the accomplishment!

How do you choose which papers to read next?

So you’re downloading 15 new papers for every 1 paper you read? This could get out of control quickly! How do you keep up? Here are some tips for prioritization:

Google Scholar is an excellent tool for tracking citation trees and metrics that show the “importance” of each paper. Library portals or the journal websites can also be good for this.

• If you’re starting a search on a new topic, begin with a relevant review paper if one exists. Beware of reading too many review papers in a row! You’ll end up with an intimidating pile of citations to track down and it will be difficult to know where to start after a few-day break. 
• Prioritize experimental papers with high citation numbers, in journals with high impact factors and by authors with a high h-index (30+) published within the last 5 years. These papers will set the bar for every paper you read after. You can check the journal’s rank in your field by using Scimago . 
• Identify the most prominent authors in this field and find their most recent papers that may not have many citations (yet). This indicates where the field is heading and what the top experts are prioritizing. 
• After you’ve covered a lot of ground above, start taking more chances on less-established authors who may be taking new approaches or exploring new topics. By now you’ll be well-equipped to identify deficiencies in methods, hyperbolic claims, and arguments that are not well-supported by data. 

Final takeaways for how to read a scientific paper:

• Don't be a passive word-for-word reader. Be actively hunting and searching for info.
• Read in this order: Abstract, Conclusion, Figures, Results/Discussion, Methods.
• The figures are the anchors. Save the best ones to reproduce in your article and spend extra time to create your own summary figures to supercharge your chances of citation.
• Clean up the metadata and use a good tagging system to save time later. 
• Set your daily goal, reward yourself for finishing, and take breaks to avoid burnout!

Lastly, remember that this blog is sponsored by BioBox Analytics ! BioBox is a data analytics platform designed for scientists and clinicians working with next-generation-sequencing data. Design and run bioinformatic pipelines on demand, generate publication-ready plots, and discover insights using popular public databases. Get on the waitlist and be the first to access a free account at biobox.io !

What sections of a research paper should you read first?

The Abstract and Conclusion sections of a research paper give you a quick sense if you should continue spending time on the paper. Assess the quality of the research and whether the results are significant to your goals. If so, move to the most important Figures and find additional details in the Results and Discussion when necessary. 

What is the fastest way to read a research article?

Skim the Abstract and highlight anything of interest. Skip to the Conclusions and do the same. Write questions that pop up. Examine each Figure and find the in-line reference text for further details if needed for understanding. Then search the Results and Discussion for answers to your pre-written questions.  

What is the best citation manager software to use for my scientific papers?

I used Mendeley through grad school but recently Zotero seems to be more popular. Both are free and have all the features you need! EndNote is excellent but expensive, and if you lose your institutional license you’ll have a hard time transferring to one of the free offerings. Zotero is your best bet for long-term organizational success!

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How to Organize Research in 2025 [Notes, PDFs, Docs, Tabs]

Let's dive in and get right to the point. Here's what you stand to gain by reading.

My personal journey with research: quick background

When I am forced to describe myself for whatever reason, one of the things I default to saying is "I'm an information junky" or "I'm a serial creator."

Throughout my life, I've been tinkering and searching for the perfect system to organize the research that I inevitably find myself doing on an ongoing basis.

I've come to the realization hoarding information and creating content is just in my nature.

I'm always researching for fun, thinking about new ideas, jotting down notes, and connecting the dots between existing and future content in my brain.

There are a couple of things that I've tweaked to get my current setup down and now my process has made me hyper-efficient.

When I went on a journey to refine my process of organizing research, there were a few things I was looking for: simplicity, robustness, and versatility.

My goal was to reduce the amount of time spent on administrative tasks like managing files and documents, and minutia like clicking between files.

In a nutshell, I wanted to maximize my capacity for doing deep work and stay in creative flow as long as possible.

So, without further ado, let's dive into the article!

Organizing research: I was a cluttered mess

In the past, I would do research and have things minimized at the bottom of my screen or have multiple documents open.

So this is solving a problem that I had for a long time, which was, I would always take notes on multiple resources, and then I would copy and paste the link of the resource if available.

Specifically, if I was working with a PDF or a word doc, I would have no way of being able to tie that original source to the note that I was making.

My environment would inevitably become cluttered.

I usually ended up positioning all my materials in a split-screen view anyways, except I would have to "hide" individual tabs and windows behind each other and stack them in order to click them when I needed them.

Kahana: a life-saving app to organize research

One of the unique aspects and benefits of using Kahana for note-taking is that you can have all of your documents, and files linked in one hub AKA one window so you don't have multiple tabs open.

Over everything else, it's simple.

This allows me to have all of my PDFs, word documents, and tabs that I've saved in one singular place.

Now, I don't feel like information is slipping through the cracks.

It's not rocket science or life-changing - but when I'm dealing with hundreds ( and thousands ) of files across my research projects, it becomes a time suck to have to toggle back and forth between Word documents, PDFs, tabs, and notes.

Kahana makes it easy to analyze everything in one place.

Kahana - farewell floating doc chaos

When it comes to organizing research notes, PDFs, docs, and tabs, Kahana is a software that simply gets the job done.

For reference, here is a list of benefits of Kahana as a software platform for organizing research:

• Dynamic interface
• Split-screen view (side-by-side)
• Bulk upload content and files
• Supports large PDFs up to 100 MB
• Supports Word documents
• Supports images (PNG, JPG)
• Embed YouTube videos
• Clip articles & web pages (Chrome browser extension)
• Smart Linking (internal linking of files and notes)
• Folders & Subfolders
• Works across all devices (web-based)
• Unlimited collaboration
• Works with Notion
• Works with Grammarly
• Flow Streak 🔥
• Add metadata/tags for organizing content
• It's 100% free - not a free trial, just free (here's the pricing page for reference)

When it comes to organizing research, Kahana is simple yet powerful by design. While some platforms pack a lot of features and have a steep learning curve, Kahana is easy to use and integrates well with many processes.

Quick video of Kahana for organizing research notes

How to Organize Research for Beginners

To get started, you can just drag and drop files and docs to a hub or click the upload button.

When you want to settle in for deep work, you can use the Zen Mode feature, which allows you to blow up your screen, and then you can also get rid of menus and just minimize them without having to click all of them one by one.

All this gives you an ideal situation for analyzing your content while you read: just a great environment for actually focusing on the material.

And then meanwhile, whenever you happen to see information that you want to capture, you can just make a quick note in the same application or plop in the material.

One of my best practices is to attach a Smart Link ( see blue link in the screenshot above ), which is a feature unique to Kahana, which allows me to actually "tie" or "associate" the original source of the note back to the note itself.

If you're just combing through you don't have to go and like open up some minimized folder or a minimized file anymore to check your references: you can just do it, do it with a Smart Link.

Claim My Free Research Organizing Templates

No need to start from scratch! To help you get started organizing research, we've created multiple free templates that are ready out-of-the-box and formatted with folders and subfolders.

The best way to organize research notes, projects, sources, papers, files, articles, findings

I started using the process that I described above in 2021, and I haven't looked back since.

When it came to researching dense topics like life sciences, clinical trials, and patient centricity as a college student and later as a management consultant, I used to be a cluttered mess, unable to organize anything neatly.

But now with my new techniques and the ability to use Kahana across all of my different projects, I'm saving so much time because I don't really have to re-upload or reopen everything one by one anymore.

I've basically eliminated duplicate work across all my research and writing processes.

After a long journey, I finally feel at peace with my process for organizing research.

I am always trying to improve as a creator and make content that is genuinely helpful.

So, if you have constructive feedback and/or questions, please voice them in the comments down below!

I hope you found this article to be helpful!

Talk with a Kahana representative

Fill out your information and a Kahana team representative will reach out to you. Have a simple question?  Search our library of articles

• Library Home
• Research Guides

Writing a Research Paper

• Organize Your Information

Library Research Guide

• Choose Your Topic
• Evaluate Sources
• Draft Your Paper
• Revise, Review, Refine

How Will This Help Me?

Organizing will help you:

• Simplify citing sources
• Avoid plagiarism
• Make the works cited page easy

Links for More Help

These links help with organization.

• Quoting, Paraphrasing, & Summarizing From the OWL at Purdue, this link can help you summarize, paraphrase, and quote effectively.
• Honor System - Tips for students The site for K-State's Honor and Integrity System can help you make wise choices about your research.
• Avoiding Plagiarism This resource from the OWL at Purdue can help you understand plagiarism and how to avoid it.
• Taking Notes EasyBib takes a look at four popular note-taking systems and the differences between them.

Create a Working Bibliography

A working bibliography, or list of potential sources, helps you track your information.

• Keep a list and add sources as you find them.
• Include sources from your background reading, Search It, library databases, or the web.
• Include all citation information for sources.
• Record URLs and dates of access for online sources.

Read Sources and Take Notes

Read sources you didn't get to yet and re-read sources if needed.

Taking notes helps you manage your sources and identify information you want to use in the paper. Use the system that works best for you. 

The system you choose for taking notes is critical to help you track your use of sources and avoid plagiarism. Even professional writers have run into problems in this step of the process, so be careful. Remember these tips:

• Note clearly whether you quoted, paraphrased, or summarized the source
• Track the page numbers for the information in the source

Adjust Your Thesis

After studying your sources in detail, your original thesis statement may work fine, and that is super. However, you may find you need to adjust the focus of your paper and, as a result, your thesis statement. This is OK! It means you learned something from your research!

If you adjust your thesis, some of your research material may no longer be relevant. This is OK too. This is a good time to eliminate those sources from your working bibliography (unless your assignment requires you to cite all consulted sources). 

Identify Support for Main Ideas

Now that you've read your sources and, if needed, adjusted the focus of your paper, you're ready to identify how you will support the main ideas of your paper. 

• Synthesize (combine parts to make a whole) the information from your sources.
• Add to the information or draw conclusions from the information to make your own contribution to the conversation about this topic.
• Resist the temptation to use one source exclusively to support each main idea of your paper. 

The amount of support your main ideas need depends on the length of your paper and how new or controversial a stance your paper is taking. In general, each idea should have at least a few pieces of evidence to support it.

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• Next: Draft Your Paper >>
• Last Updated: Feb 27, 2024 1:56 PM
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