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Note-taking tools Obsidian vs. Heptabase compared

Obsidian is a popular academic knowledge management app, known for its ability to be personalized with plugins and, as of December 2022, a visual canvas for organizing notes. Heptabase is a recently released app developed by a notion user who wanted to make an app geared more towards visual learning and mind mapping. Both cater to a similar niche from a different angle: helping the user organize large databases of information using connections, synthesize information, and learn. Which one better suits you depends on your use case. Read on.

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Organization of Notes/Cards

Each note in Obsidian is a file stored locally on your hard drive. It never leaves your computer if you do not want it to. Hepatabase on the other hand works just like Notion and syncs your Cards with the cloud.

Cards in Heptabase will by default show up in the “Card Library” and are displayed as a card with a preview. There is also an option to display them in a table and filter them by various tags. Obsidian’s notes are stored just like files on your computer in folders. Personally, none of this matters so much, because once your collection of notes/cards grows to 100s and 1000s you will not be able to find it using either method.

Note: What Obsidian calls a note or file, Heptabase calls a card. However, cards in Obsidian are elements of the canvas that are not notes/do not have a dedicated file 🤔.

Formatting: Obsidian’s Markdown vs Heptabase’s Block

A defining feature of Obsidian is that the notes are formatted using markdown. This means that there is an initial learning curve. For example, to make a heading you type in a #, to make something bold you surround the text in asterisks: **bold**. The result, however, is a plain-text file that you can read with many different apps (markdown is very common) and that you can take with you if you decide to move apps.

With Heptabase, notes are organized with blocks. This is a very user-friendly approach that is the same format used in Notion. It feels more like a simplified version of Microsoft Word. Formatting can be done entirely by using the mouse. You can however type in Markdown commands like # for titles and Heptabase will understand it. Experienced users will feel “right at home”.

So, overall Obsidian’s approach will feel more natural for users with some technical experience (e.g. knowledge of markdown, file system, etc). Heptabase removes the learning curve at the expense of a somewhat slower experience.

A middle-ground can be used by installing a plugin that makes Obsidian feel more like Notion/Heptabase.

Obsidian’s Calendar vs Heptabase’s Journal

No research workflow is complete without a calendar for meeting notes, todos, and progress notes. By default, Obsidian only supports daily notes. These are notes that have the date as a title and reside in a separate folder. Installing the Calendar plugin allows you to display these notes in a calendar located in the right sidebar.

Heptabase comes with a built-in Journal. Except for the name, the result is almost identical.

A neat feature in Heptabase is how it deals with checkboxes or todos in your daily notes. You can reschedule them with one click which simply moves the checkbox to the journal entry of another date. In Obsidian this is not possible. However, installing the Tasks plugin gives you an even more powerful way of bundling and moving around tasks, adding priorities, and so on.

Searching Notes in Obsidian vs Heptabase

Searching your notes is something you do frequently. Heptabase’s global search is a mixture of Obsidian’s Quick switcher and global search. Frankly, Obsidian’s UI around search is not great and Heptabase’s approach makes more sense. There is however a plugin called Floating Search that replicates Heptabase’s behavior in Obsidian.

However, Obsidian allows you to customize your search in very detailed ways. For example, you can limit the search to a specific folder, tag, or even property. This can come in handy when you run advanced search queries like finding all notes on papers published in a certain journal. You can even embed search queries into your notes which creates dynamic notes.

A hugely requested feature in Obsidian is to be able to search within the canvas. At the time of writing this is not possible. Heptabase however easily takes care of it and zooms into the selection.

Heptabase’s global search is a mixture of Obsidian’s Quick switcher and global search. Frankly, Obsidian’s UI around search is not great and Heptabase’s approach makes more sense. There is however a plugin called Floating Search that replicates behavior in Obsidian.

The third alternative is to use which is an even more powerful tool for mind mapping. It is, however, disconnected from your notes and can not fully replace this feature.

LaTeX support and formulae in Obsidian vs Heptabase

Both apps support mathematical formulae using LaTeX. In Obsidian you have to type in $$…$$ and fill in your formula, while in Heptabase there is a block for this and a small window pops up. However Obsidian allows you to also use inline-formula by typing $…$ (single $ instead of $$).

Inline formulae sometimes can increase readability.

Obsidian’s Canvas vs Heptabase’s Whiteboard

As stated on their website: “Heptabase empowers you to visually make sense of your learning, research, and projects.” Naturally, the whiteboard or canvas is very well polished. Much more so than Obsidian’s canvas, if you are heavily relying on visual layouts.

This main board feature is where all of the connections take place. In Heptabase this feature is called Whiteboard, while in Obsidian it’s called Canvas. On the whiteboard/canvas, you have cards/notes. The card/note represents the idea, while the whiteboard/canvas is the broader topic. In Heptabase each element of the whiteboard is called a card and it can be accessed separately from the whiteboard.

The workflow is quite often to open your whiteboard in split view with a card (as depicted above), write a journal entry or open a PDF, and start dragging parts of it onto the canvas. It feels very natural, but requires you to manage your cards with tags as you will have many of them, and finding them eventually gets difficult.

In Obsidian you can place notes onto your canvas, which behave exactly like Heptabase cards. However, you can also add elements that only live inside the canvas for small boxes of text not deserving a note. These elements are confusingly called cards in Obsidian. Lastly, when you add a long note into an Obsidian canvas you can right click it and narrow down to a section/heading within the note. This somewhat replicates the behavior of Heptabase.

The Obsidian canvas while having fewer features is more of a multi-purpose tool and can be used to manage projects not only to break down information:

You can find a very detailed version of the Obsidian project management workflow in this article.

Let’s dive into a few features that make the Heptabase whiteboard stand out.

Adding PDF annotations to the Heptabase Whiteboard

Heptabase allows for highlighting within a PDF file (e.g. a paper or book you are reading). This is a feature that is on the Obsidian roadmap but so far has not been implemented( A workaround at the moment is the annotator plugin). The nifty feature is that you can drag each highlight onto the whiteboard to create a card. This highlight is now linked to the card and PDF, allowing for easy information searching. Annotations can be either text or images.

This feature is extremely useful as you can break down your paper as you read it and link it with many other papers on the same whiteboard as well as reuse annotations in a different context.

Styling Heptabase’s Whiteboard elements

Once your board grows, making connections between far away elements becomes somewhat messy. In Obsidian the path of the connection is determined automatically and quite often runs right across other notes. Heptabase allows you to add anchor points to guide your connections. A small but important feature supporting the design of large boards.

Connections and cards on the whiteboard can additionally be styled in a few additional ways not available in Obsidian.

Adding a Whiteboard into a Whiteboard

In Heptabase whiteboards can be integrated, or nested, within each other. This means that you can create a whiteboard within a whiteboard. Cards can be repeated in any of these layers. This organizational system helps to manage large numbers of cards. While Heptabase will display a simple collection of cards in your sub-whiteboard Obsidian will display a schematic preview of your linked dashboard.

Integrations: A main feature of Obsidian, nonexistent in Heptabase

Obsidian is known for numerous third-party plugins extending what you can do with it and adding integrations with other tools, most notably Zotero for reference management or PanDoc for exporting into Word and LaTeX formats. For many, this will be a deal breaker when it comes to choosing an app.

For researchers especially, the Zotero integration is a huge timesaver. This integration automatically creates a note with metadata (journal, author, year, etc.) and allows you to quickly capture papers using the browser. If you are less focused on academic knowledge management the Readwise integration might be something you find missing in Heptabase.

Generally, the ecosystem of plugins in Obsidian is huge and it has a large community building new features on top of it. While most of these plugins end up being understaffed (as they are often hobby projects) some of them grow into highly supported communities and eventually end up in the Obsidian core (like the canvas for example).

It is often quite fun to explore the 1000+ plugins Obsidian has to tweak your workflow a bit. If you want a simple one-size-fits-all solution, Heptabase will be a good choice.

Mobile apps for iOS and Android

Heptabase and Obsidian tools offer mobile apps for iOS and Android. The mobile version will likely be more of a look-up database rather than something you use primarily. This means that you will synchronize it with your main vault. In Heptabase this comes with your (paid) account. Since Obsidian is free you can use the mobile app separately and synchronize it using the paid Obsidian sync or “hack” it using Google Drive/Dropbox.

Pricing (in US$): Is Heptabase free?

Obsidian and plugins are free. You can pay 8-10$ / month if you want your notes to be synchronized in an encrypted cloud (If encryption is not necessary use this tutorial to get it done for free via Google Drive).

Heptabase costs 9-12$ / month with a 7-day free trial. This includes synchronization to the cloud.

Decide for yourself if the additional usability is worth a lock-in to a company. If you decide to quit Heptabase there is an option to export your notes to Markdown or PDF.

How does Obsidian compare to Heptabase?

Heptabase is a great newcomer to note-taking apps and shines with its user friendly and beautiful interface. It heavily focuses on visual mind mapping and works perfectly with PDFs and annotations. Heptabase can only be used for 9-12$ month.

Obsidian is a free and very mature app with 1000s of plugins making it the most versatile note-taking app, with almost nothing that you could not somehow connect to it. More advanced features will require a bit of a learning curve and some things will not work out of the box. It focuses heavily on organizing information and making it future-proof by using open standards for data like markdown.

Decide: Obsidian or Heptabase?


Note managementNote is a file on hard driveNotes synced in the cloud
UsabilityLearning CurveEasier
PDF AnnotationsAnnotator Plugin or PDF deep linking, can be improvedSuperb and built-in
Integrations/PluginsYes, 1,200+No
Mobile AppYesYes
Reference Manager IntegrationPaperpile or ZoteroNone
Design100s of themes but design can be improvedBeautiful single design
LaTeX/Math supportYes, type in $$…$$Yes via block
SearchCan search by text, path, tag, property or any combinationText search
SharingPublish via Obsidian publish (8$/mo) otherwise not easily possible.Whiteboards can be shared (view only) with a single click
8$/mo for sync across devices (free alternative via google drive)
8$/mo for publishing to website
7-day free trial
ImportImport from Notion, Evernote, Bear, Google Kepp (Importer plugin)None
Exportnatively to PDF
via PanDoc Plugin: Word, LaTeX etc
Only to Makdown
(or HTML via sharing)

If your primary goal is learning something new, Heptabase will provide you with visualization tools and the simplicity that you need to succeed at almost no learning curve. Heptabase is focused on learning and breaking down complex topics into smaller elements to grasp them easier. This caters towards someone working towards a project or knowledge goal, rather than building a large information vault for synthesis (e.g. a semester course for a student, not a PhD project). However, this comes at the price of 12$ a month.

If you are a little deeper in academia and your goal is primarily synthesis of large knowledge databases, Obsidian will give you numerous personalization options with plugins to tailor it to your niche needs. These plugins become more and more essential as your vault grows to organize and build a custom structure for your knowledge (think Masters, PhD projects, or beyond). While it requires you to learn markdown and a few other techniques, the learning curve is well worth it to create a life-long personal database that lasts.

If you want to get started learning Obsidian please download the Effortless Academic’s manual that will teach you everything an academic needs to know about this app.