Second Brain Method

A Detailed Comparison Between Heptabase vs Obsidian

Trying to decide between Heptabase vs Obsidian? This detailed comparison will highlight the key features and benefits of each tool.

May 12, 2024

Second Brain Method

A Detailed Comparison Between Heptabase vs Obsidian

Trying to decide between Heptabase vs Obsidian? This detailed comparison will highlight the key features and benefits of each tool.

May 12, 2024

Second Brain Method

A Detailed Comparison Between Heptabase vs Obsidian

Trying to decide between Heptabase vs Obsidian? This detailed comparison will highlight the key features and benefits of each tool.

May 12, 2024

woman choosing from Heptabase vs Obsidian
woman choosing from Heptabase vs Obsidian
woman choosing from Heptabase vs Obsidian

Looking to optimize your note-taking game and find the best Second Brain method for you? In this blog, we’ll break down the differences between Heptabase and Obsidian to help you understand the benefits of each platform. By the end, you’ll have a better idea of which tool might be the best fit for your Second Brain Method. Let’s dive in!

Table of Contents

What Are Knowledge Management Tools?

a bulb with blue waves - Heptabase vs Obsidian

Personal knowledge management tools are essential for individuals to collect, organize, and access personal knowledge effectively. These tools help individuals gather, classify, store, search, retrieve, and share information that is relevant to their daily activities, work, and personal interests. Personal knowledge management systems, often referred to as PKM tools, enable users to create a structured repository of knowledge that can be easily accessed and utilized when needed.

Database Management with Heptabase

Heptabase and Obsidian are two personal knowledge management tools that can help individuals manage their information and knowledge effectively. Heptabase is a database tool that allows users to create their own custom databases to store and organize information. It enables users to create and manage their databases with ease, making it an excellent tool for managing personal knowledge effectively. 

Obsidian, on the other hand, is a note-taking app that allows users to create a digital knowledge base of notes, ideas, and information. It is a powerful tool for collecting and organizing personal knowledge and can help users streamline their workflows and enhance their learning processes.

Note-taking with Obsidian

Both Heptabase and Obsidian offer unique features that make them suitable for different types of users. Heptabase is more suitable for individuals who need to create and manage structured databases of information, while Obsidian is ideal for those who prefer a note-taking app to collect and organize their knowledge. Depending on your preferences and needs, you can choose one of these tools to help you manage your personal knowledge effectively. 

By implementing a personal knowledge management system, you can streamline your workflows, improve your learning processes, and enhance your overall productivity and effectiveness in managing information and knowledge.

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What Is Obsidian?

person making notes - Heptabase vs Obsidian

Obsidian is a free note-taking and knowledge management software that operates on Markdown files. Users can create a personal knowledge base by making connections between notes through internal links and visualizing those connections. Its standout feature is bidirectional linking, enabling users to create a network of interconnected ideas to facilitate nonlinear thinking and exploration of complex topics. 

Tags, backlinks, and search functionality help with productivity and organization. Obsidian also supports plugins and themes for customization and extension of its functionality, making it a versatile tool for various workflows and use cases. Popular among knowledge workers, researchers, writers, and anyone looking to manage digital information effectively.

Features & Functionalities Of Obsidian

professor using Heptabase vs Obsidian

Bidirectional Linking

Obsidian allows users to create bidirectional links between notes, enabling seamless navigation and exploration of interconnected ideas. Users can easily establish connections between related concepts and topics, fostering nonlinear thinking and idea generation. This feature promotes a web-like structure of notes, allowing users to dive deeper into specific topics and discover unexpected connections between different ideas

Markdown Support

Obsidian utilizes Markdown, a lightweight markup language, for formatting text. This allows users to create structured and well-formatted notes using simple syntax, including headings, lists, bold and italic text, and more. Markdown makes it easy to write and edit notes without distracting formatting options. This feature streamlines the note-taking process and enables users to focus on capturing their thoughts without getting bogged down by complex formatting tools.

Tagging and Organization

Users can tag their notes with keywords to categorize and organize them effectively. Tags provide a flexible way to group related content and enable quick access to specific topics or themes. Obsidian also supports hierarchical organization through nested folders and file structures. This feature helps users manage large collections of notes and facilitates efficient retrieval of information based on specific criteria.


Obsidian automatically generates backlinks to show connections between different notes. This feature allows users to see all the notes that reference a particular topic, providing context and facilitating cross-referencing. Backlinks enhance discoverability and help users navigate their notes more efficiently. Users can explore different perspectives on a topic and gain a comprehensive understanding of interconnected concepts through backlinks.

Search and Filter

Obsidian includes robust search functionality that allows users to quickly find specific information within their notes. Users can search for keywords, phrases, or tags, and the software provides relevant results in real-time. Obsidian offers filtering options to refine search results based on various criteria. This feature enables users to locate information efficiently and retrieve relevant content based on specific parameters.

Plugins and Customization

Obsidian supports a plugin ecosystem that enables users to extend its functionality and add new features. Users can install plugins to enhance productivity, integrate with other tools and services, or customize the user interface according to their preferences. Obsidian allows users to create custom themes and styles to personalize the app's appearance. This feature empowers users to tailor their note-taking experience and optimize the software for their workflow.

Graph View

Obsidian offers a graph view that visualizes the connections between different notes in a network diagram. This feature provides users with a visual representation of their knowledge base, making it easier to understand the relationships between ideas and explore complex topics. The graph view enhances the cognitive mapping of information and supports users in identifying patterns and associations across their notes.

Version History and Sync

Obsidian automatically saves version history for each note, allowing users to review and revert to previous versions if needed. The software also supports syncing notes across multiple devices, ensuring that users can access their information from anywhere and collaborate with others seamlessly. This feature promotes data security and accessibility, enabling users to maintain a consistent and updated repository of notes across various platforms.

What Is Heptabase?

Heptabase is a visual note-taking tool designed to help users learn complex topics by allowing them to put rich-text notes on whiteboards to record their thinking process. It is a platform that enables users to create a visual representation of their notes and thinking processes, making it easier to understand and remember complex information. The tool is available as a mobile app on the App Store and Google Play, providing full access to all cards and journals, and allowing users to read all their whiteboards. 

Heptabase is described as a unique research tool that centralizes information into a workspace for documenting and compiling thought processes, notes, and ideas, making research and learning processes seamless and efficient. It is praised for its ability to solve challenges in research workflows and provide a workspace for capturing and organizing information effectively.

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Features & Functionalities Of Heptabase

man working on his laptop - Heptabase vs Obsidian

Visual Note-Taking: Dive Into Creativity and Clarity

Heptabase is a platform that has been meticulously designed to allow users to take visual notes. By creating whiteboards and mind maps, users have the ability to organize their thoughts and ideas. The visual aspect of this platform is crucial as it helps users connect their thoughts and ideas, making complex information more manageable. 

Whiteboards: Unleash Creativity and Connect Ideas

The whiteboard functionality of Heptabase is a unique space for users to track their thinking process. By linking these whiteboards to other notes and ideas, users have the opportunity to visualize their knowledge and connections. This feature is especially useful for those who need a visual representation of their thought process.

PDF Features: Harness the Power of PDFs

Heptabase provides advanced features for PDFs, including the ability to highlight and annotate PDFs within the app. This allows users to easily capture and organize information from various sources, enhancing the overall user experience.

Journal: Capture Thoughts and Ideas on the Fly

The journal feature of Heptabase serves as a catch-all for fleeting thoughts, ideas, and to-do lists. This feature is beneficial for capturing random bits of information that may be useful later on. By having a dedicated space for these fleeting thoughts, users can ensure that no idea goes unrecorded.

Tag Database: Organize and Categorize Notes Efficiently

The tag database in Heptabase is a powerful tool for researchers and learners. This feature allows users to categorize and connect their notes and ideas using tags, making it easier to find and organize related information. With the tag database, users can ensure that their notes are easily accessible and well-organized.

AI Integration: The Future of Research and Learning

Heptabase includes AI integration, which can assist users with research and learning tasks. While the AI features are still in development, they have the potential to enhance the capabilities of the app significantly in the future. With AI integration, users can expect a more streamlined and efficient note-taking experience.

Cross-Platform Compatibility: Seamlessly Access Your Ideas

Heptabase is available on multiple platforms, including desktop and mobile devices, ensuring that users can access their notes and ideas seamlessly across different devices. This cross-platform compatibility makes it easy for users to access their notes whenever they need them, regardless of the device they are using.

Customization: Tailor the App to Your Needs

Heptabase offers customization options, such as the ability to create nested whiteboards and mind maps. This allows users to tailor the app to their specific needs and workflows, ensuring that they can make the most of its features. With customization options, users can adapt Heptabase to suit their unique preferences and requirements.

A Detailed Comparison Of Heptabase vs Obsidian

woman working from home - Heptabase vs Obsidian

When it comes to organizing notes and cards, Obsidian takes a different approach compared to Heptabase. In Obsidian, each note is stored as a file on your hard drive, giving you control over where it's saved and how it's managed. 

On the other hand, Heptabase is more cloud-focused, syncing cards similarly to Notion. Cards are displayed in a Card Library by default, with options to view them in a table or filter by tags. While Obsidian's notes are stored in folders as files, Heptabase's notes are called cards and are organized using blocks, offering a user-friendly approach similar to Notion.

Formatting: Obsidian’s Markdown vs Heptabase’s Block

Obsidian's notes are formatted using markdown, which requires a bit of a learning curve. This means you use symbols like '#' for headings and asterisks for bold text. It results in a plain-text file that's readable by many apps and easily portable. 

On the other hand, Heptabase uses blocks for formatting notes, which is more user-friendly and familiar to those who use Notion. Formatting can be done entirely using the mouse, although you can also use Markdown in Heptabase.

Obsidian’s Calendar vs Heptabase’s Journal

Obsidian primarily supports daily notes by default, which are notes titled with the date and stored in a separate folder. You can use the Calendar plugin to view these notes in a calendar in the right sidebar. 

In comparison, Heptabase features a built-in Journal that offers similar functionality to Obsidian's daily notes. Heptabase allows for easy rescheduling of checkboxes or todos in your daily notes with a single click, moving them to the journal entry of another date, which is not possible in Obsidian.

Searching Notes in Obsidian vs Heptabase

Heptabase’s global search is a combination of Obsidian’s Quick Switcher and global search. While Obsidian's UI around search isn't the most intuitive, Heptabase offers a more straightforward approach. Obsidian allows for detailed search customization, letting you limit searches to specific folders, tags, or properties. This is handy for advanced search queries like finding notes on papers from a specific journal. Obsidian lets you embed search queries into notes, creating dynamic notes.

Obsidian’s Canvas vs Heptabase’s Whiteboard

Heptabase's whiteboard feature offers a well-polished visual layout for managing learning, research, and projects. This is where all connections take place, with each element being called a card. Opening the whiteboard in split view with a card allows you to easily drag parts of your work onto the canvas, making organization natural. While Obsidian's canvas is less feature-rich, it's a versatile tool for managing projects and breaking down information.

Integrations: A main feature of Obsidian, nonexistent in Heptabase

Obsidian stands out for its wide range of third-party plugins and integrations, extending its functionality and allowing for connections with various tools. Notable integrations include Zotero for reference management and PanDoc for exporting into other formats like Word and LaTeX. 

These integrations are especially helpful for researchers, saving time and enhancing productivity. While Obsidian offers a large ecosystem of plugins and a supportive community, Heptabase lacks these integrations, making it less versatile for some users.


Obsidian and its plugins are free to use, with optional paid plans for encrypted cloud synchronization. Heptabase, on the other hand, costs a monthly fee with a 7-day free trial, offering synchronization to the cloud as part of the package.

Which Tool Is Best For You?

woman on her study desk - Heptabase vs Obsidian

My Take on Heptabase

Heptabase provides visualization tools and simple functions that cater to learning and breaking down complex topics for easy understanding, making it ideal for beginners or those looking to learn something new. Heptabase is designed to help with projects or knowledge goals, rather than building a large information vault for synthesis. The simplicity of Heptabase comes at the cost of $12 per month.

My Take on Obsidian

Obsidian offers numerous personalization options with plugins to tailor it to your unique needs, making it an excellent choice for those looking to synthesize large knowledge databases. As your vault grows, the plugins become more essential to organize and build a custom structure for your knowledge. While it might require you to learn markdown and a few other techniques, the payoff is creating a lifelong personal database that stands the test of time.

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Why Otio Beats Both Heptabase And Obsidian — Try Otio for Free Today

Otio is a comprehensive solution to the content overload problem faced by knowledge workers, researchers, and students nowadays. It streamlines the workflow with its AI-native workspace, which stands out from the fragmented and complex tools that are often used to manage content overload. The platform empowers users to collect a wide range of data sources, from bookmarks to YouTube videos, and even extensive books. 

Otio's Innovative Approach

One of the innovative features of Otio is its ability to extract key takeaways from the collected data, generating detailed AI-generated notes and source-grounded Q&A chats. This feature is a game-changer in the research process, helping users move efficiently from a reading list to a first draft. Otio streamlines the entire process, making it easier and faster to create draft outputs using the sources collected. 

AI Assistance in Writing

Otio also offers AI-generated notes on all bookmarks, including YouTube videos, PDFs, articles, and more. With Otio, users can engage in chats with individual links or entire knowledge bases, similar to conversing with ChatGPT. The AI assistance in writing significantly accelerates the research and writing processes. 

Research Made Easier with Otio

Otio serves as your personal AI research and writing partner, enhancing productivity and efficiency in the research process. Researchers can benefit from the platform's cutting-edge features and functionalities, making it easier and faster to write research papers and essays. 

Try Otio for free today and experience the difference it can make in your research endeavors.

Join thousands of other scholars and researchers

Join thousands of other scholars and researchers

Join thousands of other scholars and researchers