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Why every academic needs to use a note-taking app

Imagine if the internet operated like traditional card catalogues and printed encyclopedias. You’d miss out on the dynamic, interconnected, and ever-evolving world of information access that Wikipedia or Google Search has brought to your fingertips. Now consider your academic research and note-taking. Are you still reliant on traditional linear tools like Microsoft Word and Google Docs or even emails and Post-Its to record and discover new ideas? Just as Google and Wikipedia revolutionised information access, the next-generation note-taking platforms like Logseq, Capacities, Heptabase, Scrintal, Obsidian, Notion, and Roam Research can do the same for your knowledge management.

Think of your brain as a vast web of interconnected thoughts and ideas. All these platforms are designed like a GPS or Google Maps for your thoughts allowing you to navigate your own mental terrain. Let’s look into the actual benefits of a note-taking app:

  1. Global Search – save time: find your exact content and not document titles
  2. Note tagging – group unrelated notes together and identify patterns
  3. Note linking – connect your documents and build your knowledge habitually
  4. Backlinks – an underutilized hack to help in content discovery
  5. Unlinked Mentions – discover new and unlikely connections in your notes
  6. PDF Integration – annotate seamlessly between your PDF and notes
  7. Graph View – discover reading and research gaps instantly with a visual overview of your notes
  8. Obsidian Canvas – organise your ideas on an infinite canvas, a sort of “digital Post-Its”
  9. Note Templates – Make better notes and don’t waste time on tedium
  10. Boost Memory – cultivate your domain expertise with a research wiki that grows with you
  11. Tables – get a quick, automated overview of PDFs, notes, and tasks
  12. Work Offline – work offline safely, securely, and privately
  13. Curious? Try out Obsidian with the Effortless Academic 7-day email course or jump right in and learn note-taking effortlessly.

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Global Search – Save time and find your exact content

How many times have you spent hours looking for that one draft or note for this one brilliant idea but, sadly, you could never find it again? We’ve all been there. This is the limitation of the folder-only functionality of Microsoft Word or Google Docs. The simple search bar of Explorer or email search box was designed to search for titles nested within folders. Not content. Using a dedicated note-taking software will save you frustration as it combs through ALL your notes (not just titles within a particular folder)

Obsidian Global Search function means that you will never lose any note or idea.

Quickly find data patterns with note tagging

Tags are a way to organise your notes by adding keywords or phrases to them to make it easier to find and group related notes together. To add a tag to a note, you simply type a hashtag symbol (#) followed by the keyword you want to use as a tag like #method or #method/functionalism. Tags are powerful doorways into the content of your notes. Once tagged, every note that you make can now live in multiple folders. You don’t have to just rely solely on clever folder titles or document titles to search and display the notes and ideas when you need to find them. Next-generation note-taking apps have the capability to display your tagged search results and find the exact content.

In this Obsidian example, I will show you how tag results show without leaving the document pane that you are currently working on. you can see the tags #ml in green (1). If you press that, the window on the left shows all the documents that have the #ml tag (2). You can see right away that you have 24 results across all your files. Obsidian also has a nifty feature of displaying a third pane. On the right pane, you can click on the tag icon and display tags in an outline format just like a folder structure. You can quickly get an overview of where these related notes are stored and what type of notes they are.

If you want to know every detail of Obsidian for academics and learn a strategy to organize 100s of notes, check out the Effortless Academic Note-Taking course.

Obsidian tags also create another layer of folder structure that you can search via the left pane and building an outline of other tagged notes which you could see on the right pane

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Connect ideas and build your knowledge habitually

Building knowledge is the foundation of science. The more you can stack and connect your learning, the faster research advances. Your note-taking software should be able to help you connect data points quickly and arrive at insights. In a note-taking app like Obsidian, you can easily create a direct link between two separate documents by using double brackets [[ ]]. With that, you have connected two data notes without any fear of losing that insight.

Let’s say you are working on a note (1). While writing, for example, you realise that another author actually agrees with the findings except using a different method. You can add [[ ]] (double brackets) and the title of the note like in (2). Effectively, the two notes are now linked (3). The more links you make, the more your notes will slowly build into your personal research wiki. What you will have is a map of contents or a collection of linked notes crucial for review and discovery.

How linking notes on Obsidian connects two different notes

When you create an active link between note 1 and note 2, a backlink from note 2 to 1 is created automatically. This is called bi-directional linking which is unavailable in Microsoft Word and Google Docs. This means that for every note you make, there is also an automated rear-view mirror built-in that can show you which notes have cited your current note. This doubles the number of links you make without lifting a finger and delivers twice the capacity for content and idea discovery.

For instance, you are writing down insights for a particular paper (1). You want more fresh ideas. You can click on the backlinks icon on the third pane (2). It will display a list of all the backlinks of your note, that is, all the notes that have used Connell 1964. As you can see there are 16 other notes that mention Connell 1964. Not only that, you can quickly glance at its folder location or what type of notes referenced it. You are now in a better position to write an incisive analysis. More details of how much information is produced by your backlinks can be found below (4).

Try it out and sign up for a 7-day email course to see what connected note-taking looks like.

Obsidian backlinks is another feature that doubles the amount of your links and content discovery

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Discover unlikely connections from separate notes

This is the automated feature that you have been looking for! Let’s say you were freewriting or just quickly needed to jot a note and did not know how to label, link, or tag them. Obsidian continues to track references to key terms, concepts, or topics mentioned within your notes but are not explicitly tagged or actively linked. This feature is called ‘unlinked mentions.’

Unlinked mentions can help you discover implicit relationships or associations between different ideas that you may not have realised existed. Use this list to review your notes to create active links, enhance your idea exploration process, and see new patterns that may not be apparent when you first wrote your notes. If you are looking to improve your notes, this is one example of what a successful note-taking system looks like.

If you are working on your note (1) in Obsidian, this is how it happens. You wanted to know if there are other notes that mention ‘species diversity’ or ‘ecological regulation.’ Click the outgoing links icon on the third pane to display the active links you made from this note to others. However, you will also notice that there is a section that says ‘unlinked mentions.’ It’s hidden at first but when you click it, it displays a list of notes with the keyword ‘diversity.’ Now you have discovered potential papers unconnected! These can potentially lead to new unexpected connections with Connell 1964.

Obsidian Unlinked Mentions is an added feature that allows you to search and discover unlabelled notes

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Seamless PDF annotation and note-taking

It is frustrating when you have your annotations in one software like Zotero or Mendeley and your notes in another note-taking app like Obsidian. You can either search in one or the other, but never both at the same time. With Obsidian, you can do so in a single click. Never get lost again trying to track a phrase or a notation, scrolling endlessly in the PDF, or even finding (and yes, misplacing) your PDFs. No more lags because they now live together with your notes. Here are five other tips for becoming a Zotero and Obsidian note-taking hero.

Annotate your PDF all in one platform that will make search much easier. Store your PDF files locally and never misplace it again.

With the recent Obsidian 1.4.5 update, you can now right-click on your PDF annotations to copy them with the option to link.

You can now copy your PDF annotations directly to your Obsidian Note

Once you copy and paste the highlight into your note, you can use the CMD+CTRL key on Mac or the CTRL key on Windows to hover over the link and display the full context of that quote. Quickly refresh your memory without endless PDF searching!

Copy and link PDF annotations into your note. Next time you need context, you can hover over them and view the PDF with your highlights! Stop endless searching!

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See research gaps instantly with a graph view

Sometimes you need a different perspective. Visual cues help activate different parts of our brain. Obsidian has a graph view that can quickly display the network and connections within your notes and other materials like attachments. You can easily view which are important and which ones you may have missed. The web of links allows you to quickly go to your notes and analyse your own reading gaps and critical papers.

Here’s an example of one. Click the Graph icon (1) on the left toolbar and the Settings Gear icon to display the filters (2). You can see how all your notes are connected or unconnected. Each dot is clickable and you can go directly to each note.

Obsidian Graph View visually displays gaps and patterns of all your notes

While the global graph view looks impressive it happens to become less useful as your note collection grows. Luckily Obsidian has a local graph, that shows only the vicinity of a single note. You can find a tutorial on the local graph here, the video below shows you how this might look:

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Organise your thinking, converse with yourself, and save it

I understand why you have Post-It’s on your wall — it’s a way for you to visualise an overview of your projects. What if you could do it digitally with no need to learn another art tool? Obsidian Canvas allows you to drag and drop cards, notes, PDFs, or pictures on an infinite canvas. Label and connect them to create sense in a big collection of notes. Use it to organise your thinking, provoke yourself with critical questions, review, and be your own daily supervisor.

Obsidian Canvas allows you to drag any of your notes in your screen to organise your thinking

The best thing is you can export the entire result or a portion of it as an image for your PowerPoint presentations. Integrate your diagrams and charts under one content discovery platform and enhance your connected thinking without leaving your workspace. The strategic and tactical uses of Obsidian Canvas may be interesting for you as well.

Outline your ideas on Obsidian Canvas and export it as an image for Microsoft Powerpoint

Other note-taking apps like Scrintal and Heptabase are visual-first products with a predominantly whiteboard experience for those who prefer the Miro-like experience.

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Minimise writer’s block by automating your writing structure

There are two major blocks when you start writing — facing an intimidating blank page and finding missing details from a source that you can no longer track down. You can minimise these distractions by designing pre-structured questions and call-out boxes in your notes and store them as templates. This way you can start with short sentences and phrases to get you ‘warmed up’. Besides it saves time and makes your notes more coherent.

Avoid writer's block with automated prompts in your writing template

Never miss a literature meta-data because you have already automated that process once with a template. You guarantee yourself that you won’t waste more time cutting and pasting sources or formatting your document every single time. This applies to your daily work journal entries, personal diary entries, supervisor meeting notes, reviewer feedback, and presentation feedback – as much as you need. Set one template each and write without anxiety. Bonus: You get to search, tag, find, and display them just like your other notes!

Never forget any details from your literature

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Boost your memory – cultivate your domain expertise

You are not expected to remember everything you’ve read or written. There’s no need to. Obsidian and other similar apps can be your networked brain on a computer. Thanks to its built-in system of cross-referencing using bi-directional linking, you can create your own personal research wiki page. This is called a gateway note, inspired by the Zettlekasten method of knowledge management. It looks like a high-level, topical, or thematic hierarchical structure linked to your notes. Its primary purpose is to quickly locate relevant information. These pages continually grow with you as your knowledge increases.

Improve memory and recall through gateway and linked notes

You will easily identify those notes in your graph view because they have so many connections to the rest of your notes.

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Get a quick overview of your PDF references and notes

The big problem in academic knowledge management is that your PDFs, annotations, and notes are separate. E.g. the PDF and annotations are in Zotero while the notes are somewhere else. You can’t easily search both and thus miss out on the synergy that comes with a big knowledge database.

This is why embedding PDFs into your notes is a good idea, if you additionally add more information on the publication, e.g. a summary or your personal “relevance rating” you end up with a reference manager inside your notes – a very powerful combination. Here is an example:

List your Notes and PDFs all in one table using Dataview

One use case is to keep a list of unread papers that is updated automatically as you add new papers or add ratings to existing ones.

You can customise your table view on Obsidian according to your needs

If you want to go one step further combine the canvas, mentioned above, with notes on PDFs and you get a visual reference manager.

A Visual reference manager showing PDFs layed out on Obsidian vcanvas.

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Work anywhere with full control over your notes

Unlike cloud-based note-taking apps (e.g. Notion), Obsidian and its alternative Logseq are installed by default on your local hard drive. This has several advantages:

  • Work offline – No disruption even on a plane or remote field sites with poor internet connectivity
  • Design your own level of security, connectivity, and privacy according to the IRB (Institutional Research Board) Ethics guidelines and GDPR regulations
  • No online data leak especially when working with sensitive material or third-party client data
  • Enjoy blazing fast performance for searches and navigation even if dealing with big images/videos/PDFs in your vault

While Obsidian also allows you to sync your files via the cloud, other companies like Capacities, Heptabase, Scrintal, Notion, and Roam Research are cloud-based platforms that make collaboration much easier and benefit from AI and Machine Learning services. These advantages come with monthly, annual, or lifetime subscriptions.

Whichever product you decide on, embracing the next-generation note-taking apps can revolutionise your academic research journey. These tools allow you to continuously stack your knowledge, evolve your understanding as a domain expert, track your progress, and become a more productive academic.

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Which software to choose?

Honestly, I don’t think it matters all that much. An old saying goes: “A good craftsman never blames their tools”, or in other words: “Your skill with one tool will outweigh the advantage you get with another”. Each tool in my opinion has only a small advantage over the others. Notion for example excels when it comes to sharing and collaborating, while it may feel sluggish, especially with images and PDFs.

My tool of choice is Obsidian, as you noticed in the examples above.

I know that switching to a new software or disrupting your current workflow is daunting. Start small. You can sign up for a free 7-day email course on this website to learn the Obsidian basics. If you want to transform your research join the course on academic note-taking.