3 Chapter 2: Building A Smart Note Taking System

“I hear and I forget, I see and I remember, I do and I understand.”  Chinese proverb

Note-taking is a fundamental, though often underestimated, part of academic life. It’s the quiet, behind-the-scenes work that takes place while we read, listen, reflect, and think. Long before a sentence is written or an argument is shaped, it’s the accumulation of notes that silently scaffolds our intellectual endeavors.

As Ahrens (2017) aptly observes, “every intellectual endeavour starts with a note” (p. 1). These are raw materials, the seeds from which ideas grow. And these seeds are not planted in front of a blank page; they’re sown during the learning process itself.

Ahrens further reminds us that “the process of writing starts much, much earlier than that blank screen and that the actual writing of the argument is the smallest part of its development” (p. 1). In other words, effective writing doesn’t begin with typing, it begins with deliberate, purposeful note-taking.

Nachiappan (2022) refers to note-taking as an “art,” but we prefer to see it as a skill, one that can be learned, refined, and applied by anyone invested in deep learning. The cognitive benefits are enormous. When you take notes, you’re engaging in a mental process that forces you to identify key ideas, synthesize information, and make personal connections.

Boch and Piolat (2005) explain that note-taking reduces cognitive load by externally storing information, freeing up mental resources for higher-order thinking. Similarly, Kobayashi (2006) found that combining note-taking with regular review leads to significantly better learning outcomes. Active note-taking during lectures or readings, especially when followed by review, has also been shown to enhance both memory retention and long-term recall (Kiewra et al., 1995).

Understanding the cognitive value of note-taking is one thing, implementing it is another. Without a clear system, even the best insights can vanish into the void of scattered notebooks and forgotten files. That’s why structured, intentional systems are key. One of the most influential is Niklas Luhmann’s slip-box method, a system that organizes information and  also fosters the generation of new ideas over time.

To help you bring this system to life, we also introduce a curated selection of AI-powered tools designed to enhance how you capture, organize, and work with your notes; tools that align perfectly with the slip-box approach and make it easier to build a sustainable, evolving knowledge base. We’ve intentionally placed this chapter at the beginning of the book because note-taking forms the foundation of everything that follows. Before diving into how AI can support various stages of the research process, it’s essential to first decide on the system you’ll use to manage your ideas. This chapter lays that groundwork.

1. Building Your Note-Taking System

In the 1960s, German public servant and legal scholar Niklas Luhmann reimagined the process of note-taking through what became known as the slip-box, or Zettelkasten, method (Ahrens, 2017). Dissatisfied with conventional approaches, he began writing each idea on a small slip of paper, assigning it a number, and linking it contextually rather than by strict topical categories.

This practice allowed him to revisit and build upon ideas easily, creating a continuous internal dialogue that led to novel insights (Ahrens, 2017). Over three decades, Luhmann published 58 books and hundreds of articles across fields such as law, politics, and education; an intellectual output many attribute directly to his note-taking method (Ahrens, 2017, pp. 11–14).

In How to Take Smart Notes, Sönke Ahrens expands on Luhmann’s method, showing how it can serve as a “second brain,” a dynamic space outside your mind where knowledge is stored, nurtured, and interconnected. As Ahrens notes, the power of this system lies in its structure. It liberates your memory from the burden of recall and frees your mind to do its best work: making connections, generating ideas, and thinking deeply.

Ahrens categorizes notes into three types:

Fleeting notes (quick, temporary jottings), permanent notes (refined, long-term insights), and project-specific notes (organized by the context of an ongoing task). For us, the note taking process is simplified into two categories: fleeting and permanent. We store permanent notes in project-specific folders, keeping our workflow focused and our research accessible. For this book, for example, we’ve created a main folder in Obsidian titled AI in Academic Research, with subfolders for each chapter.

For capturing fleeting notes, those sparks of insight that strike while jogging, driving, or waiting at the doctor’s office, we use the voice memo and Notes apps on ours iPhonea. Ahrens recommends having something portable at hand, whether it’s a napkin or a digital tool, and we’ve found these simple apps indispensable for catching ideas in motion.

Before we explore the tools that can support a personalized note-taking system, let us first share some practical tips drawn from decades of research and expert advice. Consider these your guiding principles as you shape your own process:

• Keep it concise and structured: Focus on key points rather than writing everything verbatim. A clear structure will help your future self navigate your notes (Suritsky & Hughes, 1991).
• Use your own words: Rephrasing in your own language promotes understanding, not just transcription (Nachiappan, 2022).
• Visuals help: Tables, flowcharts, mind maps, even doodles, can clarify complex ideas and reveal connections (Makany, Kemp, & Dror, 2009).
• Color-code wisely: Strategic highlighting and color use can enhance memory. But don’t stop there, summarize what you’ve highlighted to deepen retention (Kiewra et al., 1995).
• Abbreviate and symbol-use: Save time and maintain focus on comprehension rather than transcription (Suritsky & Hughes, 1991).
• Create a framework: Use headings, lists, and bullet points to give shape and flow to your notes (Nachiappan, 2022).
• Review quickly: Revisit your notes soon after capturing them to clarify, elaborate, and fill in any missing thoughts (Suritsky & Hughes, 1991).
• Review deeply: Don’t just reread, restructure, rephrase, and rework your notes. This active engagement leads to deeper learning (Suritsky & Hughes, 1991).

2. AI Note Taking Tools

After years of exploring educational technology, we’ve tested more note-taking platforms than we can count, some exceptional, others forgettable. When it comes to academic research, especially if you’re aiming to build a sustainable slip-box system, not all tools are created equal. In this section, we’ll introduce you to platforms that do more than just help you jot things down. These tools support deeper thinking, reveal meaningful connections, and help you develop long-term knowledge over time.

For us, Obsidian and Notion rise above the rest. These two offer robust environments for creating and maintaining a digital slip-box, places where our permanent notes live, evolve, and interconnect. Both allow you to link notes together, visualize relationships between ideas, and resurface older insights in ways that deepen your research. That said, we’ve also included other tools worth exploring based on your individual workflow and note-taking style.

It’s worth noting that most of these platforms now include built-in AI. These features can summarize long articles, extract key points, or even suggest links between ideas. And while impressive, let’s be clear: AI is a support system, not a replacement for your own thinking. If you want to truly benefit from your notes, you have to wrestle with them, rephrase, question, connect. The tools can guide the process, but the value lies in your engagement!

2.1. Obsidian

Obsidian is a note taking platform that provides you with the tools to build a living, thinking archive of your ideas. Obsidian is a full-on thinking environment designed to help you link, organize, and evolve your ideas over time. Obsidian offers a wide variety of practical features that enhance the quality of your note taking.

First, there is the bi-directional linking system that allows you to create connections between concepts, topics, sources, and insights. And those connections are where the real magic happens. Rather than keeping everything trapped in isolated folders, Obsidian allows you to build a network of knowledge that grows with you and reflects how your thinking develops.

Here’s how it works in practice: let’s say you come across a great stat or quote in a paper, just enclose it in double brackets like this [[ ]] and Obsidian will either create a new note or link to an existing one. You don’t need to stop what you’re doing or interrupt your train of thought. Over time, as your notes accumulate, you’ll start to see links you didn’t expect, connections between studies, overlapping ideas, recurring themes.

Another powerful feature especially for those of you who love non-linear formats is the graph view. Graph view lets you actually see how your notes are connected, each one represented by a little dot, with lines tracing out the relationships. You can zoom in on a local view to see what’s linked to the note you’re working on, or zoom out to get a global sense of your entire vault. The visual layout helps you spot patterns, gaps, and clusters of knowledge you might otherwise overlook.

Another thing we love about Obsidian is that everything is stored in plain-text Markdown files. That means your notes are future-proof, you can open them in any editor, move them around, back them up, and you’re not locked into a proprietary format. Plus, Markdown gives you just enough structure (headings, lists, bold, italics) without getting in your way. It’s fast and lightweight, and perfect for academic writing.

And if you use a third-party reference system such as Zotero you can easily integrate it into your Obsidian workflow. You can also install community plugins to take things even further. There are plugins for spaced repetition, citation management, outlining, task tracking, you name it. It’s endlessly customizable, which means you can shape the tool to match your workflow, not the other way around.

Obsidian’s template system is another important feature that helps facilitate note-taking. If you’re doing recurring types of notes, like meeting summaries or article critiques, you can set up a reusable template so you’re not reinventing the wheel every time. For instance, we have a template for research notes that includes fields like author, publication date, summary, key arguments, and personal reflections. With just a few keystrokes, it’s there and we can jump right into the content.

2.2. Notion

Notion is another powerful note-taking tool that offers a customizable and highly flexible workspace which is more or less similar to Obsidian. Notion goes beyond text-based notes by allowing you to build interconnected pages, databases, and structured wikis to manage research projects effectively.

Notion is highly visual. You can drag and drop blocks of content, embed images, videos, PDFs, and even spreadsheets. Notion is also great for collaborative projects. If you’re collaborating with others, say you’re part of a research team or co-writing a paper, Notion will help a lot with streamlining your workflow. You can share pages, tag your collaborators, and comment directly on specific sections of text. Everyone sees updates in real time, and you can even publish your notes or research outlines to the web if you want to share them more broadly. It’s a lot like Google Docs, but way more customizable.

For repeatable tasks, like summarizing journal articles or outlining chapters, Notion’s template feature is a lifesaver. You can use it to create ready-made templates for literature reviews, weekly planning, conference prep, etc. And yes, Notion has integrated generative AI into its ecosystem. You can ask it to summarize dense text, draft sections of writing, rephrase ideas, or brainstorm content based on your existing notes.

Besides Obsidian and Notion which we see as the best platforms for building a solid slip-box, there are plenty of other great note-taking tools out there that can support your research in different ways. Some are more visual, others more structured or lightweight, but each brings something unique to the table. Let us walk you through a few worth exploring.

2.3. Evernote

We used to be fans of Evernote back in its early days, back when it felt like the go-to solution for organizing ideas, research, and random bits of inspiration. But with the rapid evolution of web-based tools and more research-focused platforms like Obsidian and Notion entering the scene, we find ourselves reaching for Evernote less often. Still, that doesn’t mean it’s not worth your attention, especially if you’re looking for an all-in-one tool that’s familiar, reliable, and packed with thoughtful features.

Evernote’s notebook system is intuitive, you can create a separate notebook for each project, paper, or research theme, and within those notebooks, break things down further with individual notes. You can tag notes across notebooks which makes it easier to search and find specific notes. Evernote also supports mixed media. You’re not just stuck with text, you can clip full web pages, add PDFs, insert voice memos, or even snap a photo of that whiteboard brainstorm session and make it searchable thanks to OCR. That’s particularly handy when you’re dealing with printed articles or handwritten notes you want to bring into your digital workflow without retyping everything.

While it’s not a slip-box system like what you’d build in Obsidian, Evernote can still be a solid place for organizing project-specific notes, keeping research materials accessible, and collaborating with others.

2. 4. OneNote

OneNote is another good alternative note taking platform to consider especially if you’re already in the Microsoft ecosystem. OneNote is flexible, cross-platform, and good at helping you keep a sprawling research project from turning into a chaotic mess.

OneNote offers a strong notebook-based structure. You can create separate notebooks for different projects, then break those down into sections and pages. It mimics the feel of an actual research binder, which can be really helpful if you like to compartmentalize your work. Add to that the ability to tag notes by topic or priority, and you’ve got a system that’s both intuitive and powerful when it comes to keeping things organized and easy to retrieve.

When it comes to capturing content from different sources, OneNote does an awesome job. Thanks to its built-in OCR, you can snap a photo of a book page or upload a scanned article, and OneNote will extract the text so you can edit or annotate it. And using the formatting tools, you can highlight key ideas, mark up drafts, or color-code your thoughts however you like. If you’re working with collaborators or part of a research team, OneNote makes it easy to share notebooks and co-edit in real time. And like the previous tools, OneNote offers templates with ready-made layouts for project planning, meeting notes, to-do lists, and more.

OneNote also supports multimedia including audio and video recording. That means you can record an interview, a seminar, or even your own reflections directly inside your note, no need to switch apps. With Microsoft’s Copilot starting to roll out, you’ll also get AI support for summarizing, drafting, and organizing content which could be a huge productivity boost when synthesizing dense research materials.

2.5. Google Keep

If you’re already working within the Google ecosystem, Google Keep is a lightweight note-taking alternative worth exploring. We wouldn’t call it a full-blown research management tool like Obsidian or Notion, but it definitely stands out when it comes to speed, simplicity, and accessibility. Google Keep is especially useful for capturing ideas quickly (i.e., fleeting notes) and in a variety of formats. You can jot down text notes, record audio (which it transcribes automatically), snap a photo of a book page or slide, and even create to-do lists. It’s especially handy when you’re reading something on the go or need to capture a fleeting thought without overthinking structure.

You can color-code your notes, label them by project or theme, pin the important ones, and search through everything with ease. Its OCR (optical character recognition) feature is great when you’re trying to extract quotes or passages from images, just snap a picture and Keep will pull the text out for you. Since it integrates seamlessly with Google Docs, you can move from rough ideas in Keep to polished outlines in Docs without skipping a beat. And if you’re working with collaborators, you can share and co-edit notes in real time.

2. 6. Traverse

Traverse.link is one of the more recent tools we’ve come across and while we haven’t used it as extensively as Obsidian or Notion we can definitely see its appeal especially for researchers who want a more visual and memory-focused approach to managing information. Traverse brings together mind mapping, spaced repetition flashcards, and bi-directional linking into a single workspace which is pretty unique in the note-taking world.

One of the main strengths of Traverse is the ability to help you visualize your thinking. You can map out complex topics on what is called “traverses” which are essentially visual whiteboards where you group related ideas, papers, or arguments. This kind of structure is great if you’re someone who needs to organize research visually especially when you’re juggling overlapping themes in a literature review or trying to untangle theoretical frameworks.

Flashcards creation is another interesting feature provided by Traverse. With a single click you can convert notes into flashcards using spaced repetition and active recall to reinforce what you’ve learned. That means you’re not just passively reading your highlights, you’re actively working with them, testing your understanding, and improving long-term retention.

The addition of bi-directional links and mind maps also helps you track how ideas connect across different projects. If you’re exploring multiple concepts that intersect you can trace those links visually which makes it easier to spot patterns and build original arguments. The interface is clean, the learning curve is gentle, and there’s even a mobile app for quick note capture or reviewing flashcards on the go.