how to organize printed research papers

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Organizing Papers and References without Losing your Mind

In January, Ulrike Träger wrote a great PLOS ECR post describing how to stay on top of reading during graduate school. If you haven’t read it yet, go take a look, as it’s relevant for people at all career stages. As a follow up, here are a few tips on how to keep track of the papers you want to read without losing your mind.

Choose a reference manager. Sure, you can get by creating a poster or two without a reference manager, but it’s incredibly risky to cite references by hand for manuscripts and grant proposals. Choosing and using a reference manager is also a great way to track papers as you collect them, particularly because reference managers often have powerful search functions. There are many to choose from. Some are free, like Zotero and some versions of Mendeley . Others, like Papers and EndNote , are not, though some paid programs may be free through your institution. Spend some time researching which manager fits your needs, but don’t get bogged down, you can always switch later. Personally, I have transferred references from RefWorks to Zotero to Mendeley to EndNote over the past several years without much trouble.

Choose a place to keep unread papers. Whether it’s a physical folder on your desk or a virtual folder on your desktop, it’s important to have a designated place for unread papers. This folder is more than just a storage space, it should also be a reminder for you to review unread papers. It’s tempting to download papers and forget about them, falling prey to PDF alibi syndrome , wherein you fool yourself into thinking that by downloading a paper you’ve somehow read it. So, set aside some time every few weeks (on your calendar if you need to) to review papers. You won’t necessarily read each paper in detail, but you should complete a quick skim and take a few notes. Try to resist the urge to leave notes like “finish reading later.” However, if needed, consider using notes like “need to read again before citing” for papers that were skimmed particularly quickly.

Choose how to keep track of your notes. It’s a great idea to create a summary of each paper as you read it, but where do you keep this information? Some people write separate documents for each paper (e.g., using the Rhetorical Précis Format ), others write nothing at all, but tag papers (virtually or physically) with key words. The exact components of your system matter less than having a system. Right now, I keep a running document with a few sentences about each paper I read. I also note whether I read it on paper or as a PDF so that I can find notes taken on the paper itself later. If I’m doing a deep read on a specific topic, I might also start another document that has in-depth summaries. I usually keep notes in Word documents, but it’s also possible to store these notes in many reference managers.

Choose how to file read papers. Again, having a system probably matters more than which system you choose. Given the interdisciplinary nature of science, it can be complex to file by topic. Therefore, I find it easiest to file papers by last name of the first author and the publication year. It’s also useful to include a few words in the file name that summarize its content. This will help you differentiate between articles written by authors with similar last names. So, for example, using this method, you might label this blog post as Breland_2017_tracking refs. I keep articles I’ve read in a folder labeled “Articles” that includes a folder for each letter of the alphabet. Therefore, I’d file this blog post in the “B” folder for Breland.

TL;DR. The goal of creating a system to organize papers and references is to be able to easily access them later. If you follow the steps above, it’s relatively easy to keep track of and use what you’ve read – if you want to find a paper, you can search for a key word in your reference manager and/or in your running document of article summaries and then find a copy of the paper in the appropriate alphabetized folder. That said, there is no right way to organize references and I’m curious about how others manage their files. Chime in through the comments and we’ll update the post with any interesting answers!

Pat Thomson (2015) PDF alibi syndrome , Patter blog. Accessed 2/27/17.

Ulrike Träger (2017) Ten tips to stay on top of your reading during grad school , PLoS ECR Community Blog.

Sample Rhetorical Précis: http://oregonstate.edu/instruct/phl201/modules/rhetorical-precis/sample/peirce_sample_precis_click.html

Featured image available through CC0 license.

[…] Organizing Papers And References Without Losing Your Mind – Jessica Breland […]

You have a great organizing skills! I appreciate your tips!

Fantastic tips! Thank you for sharing.

Great tips! It helps me a lot while I’m doing my final diploma project. Thank you.

This is great, very helpful. Nicely written and clearly organized [like your ref lib 😉 ] C

im at the start of my phd and already feeling that i have a lot of literature. i am taking your notes onboard and going to spend some time to organise my files asap. thanks

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System for organising printed papers in folders?

For the people here who do not yet work entirely electronically, and still use printed papers & old school folders to organise their papers, do you guys have a system for organising these papers?

I have bought a few folders today and have made a few rough distinctions, but I am wondering how more advanced academics organise their papers once they've read hundreds to thousands of them (and also roughly on the same very specialised topic).

• research-process

• 2 Use a filing cabinet... –  Solar Mike Commented Feb 26, 2018 at 19:16
• I'm not asking where to put all those folders. I'm asking about how to best structure that collection of papers. –  R. Kohlisch Commented Feb 26, 2018 at 19:27
• 16 I structure them on random piles on random desks and bookshelves across offices, labs and home :-) –  Massimo Ortolano Commented Feb 26, 2018 at 19:28
• 1 One of the huge advantages of using a computerized database for this is that you can use tags to organize your papers- each paper can have several tags and be filed as if it were in several folders at the same time. –  Brian Borchers Commented Feb 26, 2018 at 19:31
• @R.Kohlisch If you are the OP, you might want to merge your accounts. In case, see the Help center here: academia.stackexchange.com/help/merging-accounts –  Massimo Ortolano Commented Feb 26, 2018 at 19:44

3 Answers 3

Separate the semantic ordering from the physical ordering. It keeps your organization flexible, since you can assign each paper to several topics and projects, and change the assignments as you see fit.

This can be achieved by using a filing cabinet or folders on the one hand, and a bibliographic database (be it electronic or in paper) on the other.

Label each paper with some identifier. I recommend the date or month, but also a running number will do. The label doesn't have to carry any meaning. Collect the papers with a certain range of labels in one folder. For example all papers with labels January to March go in one folder called "Jan-March 2018".

In your database, each entry should also carry the corresponding label under which the paper can be retrieved, in addition to the bibliographic data, and any semantic information such as projects and topic keywords. Use the database, not the physical location, for organizing the papers by substance matter.

How the database itself should be organized is another question. I use folders for projects and keywords for topics. Creating a systematic ontology or adopting an existing ontology (e.g. the Dewey system) seems overkill. Instead, I recommend creating keywords on the fly ("tagging") and combing through the keyword list once in a while. This will be more difficult with a paper-based organization than with an electronic database, of course.

• 2 +1, this is how I used to do it. I just kept them in alphabetical order by author surname, sub-ordered by date. This meant I could often skip the database look-up if I had a specific paper in mind or was chasing up a reference from another publication. –  Pont Commented Feb 27, 2018 at 9:46

Personally, I am not keen on organizing printed papers. Even though I prefer to read paper documents, I have never been able to devote enough space for proper organization and have resorted to ad hoc printing of those I really want to analyze in detail (knowing that after a few days after reading I will misplace them somewhere) and on-screen reading of those I really only want to skim through.

As far as I know, he used filling cabbinet-based system for storage of a number of paper fiches, used to organize different ideas: abstracts of books, ideas for papers, etc. I am no aware of him using this method to store full papers, nevertheless you may look into it as an inspiration for your problem solution.

Luhmann's system was subject to a number of studies. Himself, he described the system in the following paper: Kommunikation mit Zettelkästen . This seems to be one description of his system in English.

• 2 thanks. however: Although they were paper document, luhmann did not use his system for the storage of academic papers. –  janus Commented Feb 26, 2018 at 22:44

I sometimes use printed papers in folders too, because it's nice to be able to peruse them without aid of a computer, especially while in a coffee-shop, etc. Others here suggest using a flexible ordering system, but personnally I find that I use the folder to refresh knowledge of a particular research topic for purposes of writing papers in a specific area. Here is what I put in the folder (in order):

One folder of papers per for each broad "area" of research (subject to length considerations).

Cover and spine: Cover page and spine page with clear identification of topic, and my contact details on the folder in case I lose it.

My own papers: My own papers on the topic, in whatever order is most logical, followed by a coloured separator tab.

Bibliography and literature for each topic: For each topic covered by the folder, a cover-page giving full bibliographic information on all the papers for that topic (listed in chronological order of publication), followed by the papers themselves, separated by a coloured page. Sections on different topics separated by a coloured separator tab.

Since I use my folders of printed papers to refresh particular research topics, I don't worry about doubling-up papers across folders (though I might if I started tripling-up, etc.).

The system I use is designed to allow me to review/refresh my knowledge of a particular topic (where I have a research interest) in the order in which the research occurred historically. I can also jump to particular papers of interest easily. The folders are also a useful aid to lend to graduate students if I want to give them some background reading in a research topic.

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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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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.

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