How to organize research notes

How to Organize Research Notes

[UPDATE: I’ve written a new and expanded post on digital note taking here.]

Your Problem: If you write a lot you most likely read a lot too. To inform your writing projects you gather information from all over the place: a cool blog, a journal article, a newspaper cutting, a PDF, a book chapter, a scrap of paper with an ISBN on it…

If your desk is anything like mine in recent times there are notes-to-self on bits of paper and Post-Its everywhere, and your computer desktop is littered with .txt files with little ideas that you intend to return to later (of course).

How to make sense of it? How do you organize all your research?


Now That’s Organized.

The Importance of Note Taking

We all know it’s good to read widely. Not least because,

Whatever problem you’re struggling with is probably addressed in some book somewhere written by someone a lot smarter than you. – Ryan Holiday

It’s good to have a thought journal to develop your understanding of the facts, ideas, and concepts that you come across and that strike you unexpectedly.

(You might be interested to know that Richard Branson wants you to make more notes.)

Here’s an interesting journal article on the importance of note taking to learning: Note Taking and Learning: A Summary of Research

Note taking, in particular by hand, is an incredibly powerful habit. When you commit your thoughts to paper you process them, distil them, and make more sense of them. Many studies report better recall and better comprehension when handwriting notes is compared to ‘born digital’ notes.

Quite simply, handwriting your notes is better than typing them.

(You can read about the dangers of Going Paperless in another post.)

The key point to consider is that digital note taking encourages shallower processing: it’s too easy.

Copying & Pasting notes, making highlights, and saving-for-later hundreds of PDFs does not count as processing information.

Do not seek shortcuts for your note taking! Do the work to get the rewards.

I’m a techie. I like my iPad. I want my stuff in the cloud. So my solution is a compromise: I work in hand but organize digitally.

This born-physical-stored-digital approach is my attempt to get the best of both worlds. It allows for the cognitive advantages of using a pen and paper and the ease of retrieval and tagging features of digital files.

Here’s my system to create and organise my handwritten notes in order to get the benefits of digitisation but avoid the cognitive costs.

[2017 update – I now use an iPad Pro and Apple Pencil to get the best of both the analogue and digital worlds. Blog post here.]

You need a good notebook:

Make sure you have a notebook that feels special to you. You should want to take it around with you and, most importantly, you should want to write in it.

A notebook with a hard back and a wired spine is my favourite. They don’t get battered in your bag and last as long as you need to fill up the pages. The hard back means there’s always a stable surface – so no wonky words.

A wired spine means you can always flip the page around and write on a smooth, flat page without needing to bend back the spine (which I find really annoying for some reason).

My notebook of choice is the Oxford Black n’ Red A4 Wirebound Hardback Notebook.

Its pages are also perforated, so you can cleanly rip out pages if you need to without ruining the rest of the notebook.

I know there’s a real fashion for Moleskine notebooks these days, and it’s certainly a great brand. But I don’t find their notebooks all that practical.

However, what I think doesn’t matter: it’s important that you have a notebook that you like and want to write in, so just make sure you love your notebook.

Get yourself a good pen:

What’s a good pen? The one you can find that’s a joy to write with.

A good pen might be a crazy-expensive Mont Blanc or a cheap Bic, just make sure it’s one that you like writing with. You want to have an incentive to get those thoughts on the page.

I was recommended the Uni-ball Jetstream recently and have been converted away from Bic Biros. The Jetstream offers a great balance between the ease of writing with a rollerball and the satisfaction of a ‘proper’ ink pen.

Make sure that you, your notebook, and your pen are inseparable:

A confession: I ‘temporarily misplace’ a lot of pens. This is not a good trait if you want to make note taking an easy activity. You can’t make notes without having those tools together at the same time, so why not get a fancy holder?!

Here’s a cool tool to make sure that your notebook and pen are best buddies.

I’ve tried a few ways to marry my note book and pen, from elastic band to a minimalist iPad cover for them both, but this is fairly inexpensive and does the job quite nicely.

Now go forth and take glorious notes! (Some tips here.)

How to digitize your paper notes:

Once you’ve made your notes and you’re ready to organize them and integrate them into your knowledge management system, it’s time to digitize.

You’ll need an Evernote account and the Scannable app from the iTunes Store on your phone / iPad. (If you’re on Android there are alternatives: i.e. GeniusScan)

Scannable is an app from Evernote. It’s great at detecting the edges of documents and then adjusting the lighting to enhance your writing on the page. Here’s an example of a Scannable capture vs. a normal photo using the camera app:


The pdf created by Scannable is on the left, the camera app picture is on the right.

I think the Scannable version is better, don’t you? It’s far easier to read the text, and that’s exactly what we want.

Save the scan and give it an appropriate title, then upload the file to Evernote.

You could stop here: your handwritten notes will now be digitized and available in Evernote. If you’re an Evernote devotee, then you’re good to go!

But I’m a Devonthink person, so there’s one more step to get my handwritten notes into my database software. (You can read more about how I use Devonthink in this post here.)


Importing Evernote notes into Devonthink is straightforward. Make sure you have both Devonthink and Evernote installed on your computer. Then open your database, click [File – Import – Notes from Evernote] and you’re done. Easy.


Now that your written notes are in Devonthink you can tag them, store different notes in different folders within your file structure, or just dump them in an archive folder for reference.

I like this system because the hand-written notes are still available, and the digitised version is in addition to the physical version. Because you can tag and date your digitized notes, the digital copy is easier to retrieve and access, but you’ve also benefited from having made the notes by hand in the first place.

You’ve had your cake and eaten it too.

[UPDATE: I’ve written a new and expanded post on digital note taking here.]


  • Always makes notes in your notebook; buy cool tools that make writing a pleasure
  • Once a week, scan and import; use Evernote and Scannable, import via Devonthink (if you use it)
  • Be awesome – your notes will have a digital home, and still, you’ll benefit from handwriting them

Final Thoughts on Organizing Research notes:

You should always question whether it’s worth adding another task to your workflow (such as digitising your notes). Avoid workflow complexity like the plague, as it creates a disincentive to do creative work.

If you don’t defend simplicity you’ll end up doing loads of busy-work that has no real purpose other than amassing a collection of impressive technology and clever software integrations.

That said: I scared myself with the research I did for my recent post on Going Paperless.

Born-Digital notes are not a shortcut – pen and paper should be what you reach for when doing thinking-work. But the benefits of going digital are real.

The workflow described in this post is my attempt to get the best of both worlds, and the additional effort to use Scannable and import to my research database is worth it.

[UPDATE: I’ve written a new and expanded post on digital note taking here.]

Any thoughts on this? There’s a comment section below ↓

The Benefits of No-Tech Note Taking –

4 Benefits of Writing by Hand –

A Learning Secret: Don’t Take Notes with a Laptop –

The Pen Is Mightier Than the Keyboard: Advantages of Longhand Over Laptop Note Taking –

Marginalia, the Anti-Library, and Other Ways to Master the Lost Art of Reading –

Why Reading On Paper, Scientifically, Makes Us Happier People. –

8 replies
  1. María José Torner says:

    Great article, just what I was looking for! I have lots of handwritten notes, I can´t help it, I tried taking notes on my laptop for a while but doesn´t feel right and now I have a mess. I am like you trying to combine my handwritten thinking process with the practical features of technology for my research, trying to organise my notes digitally as I write them, whoch is a lot of work. I don´t know if Evernote works with tags like Bear (which is only for Mac), I don´t like these type of digital notes, but I would like to try your method, digitalize my handwritten ones and find the way to tag them by topic. Thanks a lot!

  2. Clifford Farris says:

    Your approach is very helpful, but somewhat inadequate for me. However, I don’t have a good solution yet.

    First for books, I actually dictate my reactions relevant page by relevant page into Dragon 15 and transcribe them. This is much faster than typing them.

    Second, I look over hundreds of web pages, reference material, and so on in text, photo, and scanned ancient materials form. There right now are saved electronically with a little attention to saved titles to organize them. For example, anything related to Norsemen is started with Viking . . .. Photos of San Francisco in 1849 are started with San Francisco . . ., and so on. I generally do not rate them – a big mistake.

    Third, I have browser bookmarks for about five hundred web sites also.

    This amounts to perhaps a million and a half words or so and several thousand images. I keep them stored on my hard drive, but have an archive hard drive as back up. I keep a third copy on USB drives, but they tend to run out of space.

    Thanks for your article. I have not addressed how to make a bibliography of my stuff since I am writing historical fiction, but need to face that some day.


  3. Eelco says:

    Hi Nick,
    normally the first page in a Google search yields the most helpful articles. But this post appeared on the second or third page, and it is just what I needed! I have been reading a lot of books on personal development, psychology, religion, spirituality, sports, nutrition, etc. I read these books on paper, underlining interesting sentences. I then wrote the sentences I underlined in Word. I also take notes from YouTube video’s and seminars. Now I have a lot of word documents and even Excel documents with quotations.
    I reached the point now that I combine knowledge from different books and even field. So, I plan to write a blog, give workshops and presentations, or maybe even a book. So, the problem is; how to find all the quotations (ideas) on a specific topic from different books in different word documents. They are all over the laptop. Without categorization or tagging.
    Thank you very much for the tip on Devonthink. I will try this out from now. And also, thanks for the note taking by pen. I am considering buying an iPad and pen. Great idea. You are right; when you write you retain the information better.
    I still wonder how to organize al the Word documents and categorize them. I suppose Devonthink will help me out?

    • Nick Blackbourn says:

      Hi Eelco,

      I’m glad you came across the article and found it helpful!

      It does sound like Devonthink might work well for you. I find that it helps make connections between notes/article I hadn’t considered, and that can only strengthen your research and writing.

      With certain documents, you might find it easier to ‘index’ the external folder rather than import them to Devonthink. That means you can find them and tag them in DT, but also be able to use the files in external applications (like Word).

      Good luck getting all your material organised — it might take some time but it will be worth it!


  4. Kee Warner says:

    I was searching this morning for good systems for filing information for research projects. I am surprised that there is so little guidance on how to set up and use filing systems for various purposes. I have been doing this for many years, but I still seem to make it up as I go along. Your system for notetaking has some appeal, but I will have to give it some thought. The Ipad/Iphone/Icloud have been a great boon for my creative writing as I always have drafts with me and can tinker whenever I want. I am not sure they work as well for organizing larger projects. Perhaps that is where the Notebook could come in. Thanks for sharing.

  5. Elizabeth says:

    Great article, great advice. I’m in way over my head with my ocean of notes dating back to the 2000’s. I’ve got at least six ‘master notebooks’, more purse-sized notebooks than I’ve even bothered to count, and hundreds of scraps of paper with quickly scribbled notes. I’ve got an avalanche of ideas that I keep adding every day. Yikes. I’ve entered a lot of the info into Word files, and the drive folders are just as confusing and frightening. Any more great advice for organizing computerized notes? I don’t seem to be using the folder and file system in the most effective way. Any suggestions would be gratefully received :)

    • Nick Blackbourn says:

      Hi Elizabeth,
      I think it really comes down to how your brain works and the type of projects you take on. You might want to organise a file system by date and then tag by topic. Or vice versa. Or, if you are willing to digitise all your notebooks, your could just throw everything into a Devonthink database, index the files, and then rest on the search function.
      There are many systems you *could* adopt but the starting point really has to be what you’re hoping to get out of the database, then work back from there.


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