TL;DR
I built my own AI-assisted knowledge management system — I call it AKM — using Obsidian, Claude, and a custom 3x3 grid. It’s not a Second Brain; I’m still doing the thinking.
This article walks through why I built it, how it’s structured, what Claude actually does versus what I do myself, and what’s still missing from it. You can build it yourself using this guide.
Premium members get the full system: four copy-paste Claude prompts that build your own 3x3 grid, your own starting themes, your own vault structure, and a scheduled check that keeps it all honest over time — plus an installable Claude Skill that files your writing into it automatically from then on.
None of it requires copying my exact grid, my themes, or my setup. Every prompt walks you through defining your own, based on what you actually write about.
You’ll need Claude Cowork (Pro plan or higher) for the vault-building, filing, and scheduled-check steps, since those write real files and folders on your computer.
Three decades ago, as I started working at a law firm in the IT department, there was a lot of talk about Knowledge Management. From Lotus Notes to Microsoft Exchange, and many other options.
I’ve seen how a global organization, Siemens, shared best practices and other info globally. It was amazing! Can you imagine hundreds of offices from all over the world united by a common repository of information? Thousands of knowledge workers looking for what made some marketing campaigns succeed, others looking for engineers with extremely specific skills around the organization.
But after some years of experience, I noticed that finding the right information was always painful. It was a constant issue to motivate the teams to keep updating the Knowledge Base.
Jumping 30 years to the present, we finally have a unique opportunity to solve most of the issues of Knowledge Management using AI.
I don’t want to call it a Second Brain
There is a lot written about Second Brains. The term is most closely tied to Tiago Forte, whose book Building a Second Brain frames it as a system for capturing, organizing, distilling, and expressing knowledge outside your own head, so nothing gets lost and your thinking compounds over time. Nick Milo pushed the idea further into note-linking with his “Linking Your Thinking” approach. Both trace back to Niklas Luhmann’s Zettelkasten, the slip-box method he used to produce a lifetime of scholarly work by letting notes connect to each other instead of sitting isolated in folders.
When I read “second brain,” I imagine a machine thinking for me, using my ideas, writings, and instructions. But I’m sincerely trying to do the thinking myself.
There are two Substackers I enjoy reading, Jenny and Nate, and they have different ideas about Second Brains. As I understand it, Jenny treats it as infrastructure, a shared vault that multiple AI tools read and write to automatically, complete with dashboards, scheduled jobs, and skills that update themselves. Nate does something different: he argues the classic second brain fails because it asks too much of you in the moment, so his fix is a single frictionless capture point where AI does the interpreting, classifying, and routing for you, with almost no filtering on your end. Both are impressive systems. Both also ask me to trust a lot of AI judgment I have no easy way to check.
I call it Assisted Knowledge Management, or AKM. And in this article, I’ll show you how I did it for myself and what is missing in my system.
If you are not ready to join as a premium member, this article is enough for you to build your own system using Claude Cowork. If you are a premium member, you’ll see at the end of this article all the resources and step-by-step instructions to save yourself some hours of work.
What did I want to achieve?
Initially, the idea was to use this Assisted Knowledge Management (AKM) system for my Substack articles and notes. I wanted to include all the notes and posts I ever made.
I also wanted to solve a problem I had with Notion. Claude can use the Notion MCP to directly interact with it. I had a few Claude Skills running to update Notion databases and sometimes make queries, like for example: What were the 5 latest Substack notes I made about Digital Sovereignty? The results were a disaster: slow, unreliable, and the process would easily consume my Claude credits very fast.
Something else I wanted to do was to find modern standards that could be used to manage my knowledge in the age of AI. I found Google Open Knowledge Format (OKF) and also Karpathy’s Wiki gist.
Both of them complement each other and would help me make it easy to share information with others if desired.
Karpathy’s gist describes a workflow: use an LLM to build and maintain a growing personal wiki, one markdown file per idea, letting the model do the drafting and cross-referencing as your knowledge grows.
Google’s OKF takes that same pattern and formalizes it into an actual specification, defining the exact file structure, YAML (a data format built for storing structured information, not for styling) frontmatter, and conventions needed so a wiki built this way can be read, shared, and reused across different AI tools without custom translation. Karpathy gave me the why and the rough shape; OKF gave me the how, a concrete standard to build against instead of inventing my own conventions from scratch, which also means anything in my vault is already in a shape others could read or adopt if I ever wanted to share it.
But something that bothered me is giving AI too much power to decide how to categorize and store my information. I remembered a system I built in the past that could help me manage large amounts of information in a cohesive manner. I call it the 3x3, and it is a matrix for organizing themes:
The intersections, I call them cells, hold the pieces of knowledge relevant to them. And that gives me the power to organize info and access it easily.
And the last and probably most important thing I wanted to achieve is to store all my information locally. That is a very important part of my process towards Digital Sovereignty.
At this point, my Substack articles were scattered in Substack, chats with AI, and even different word processors. Finding the knowledge I produced was as hard for me as it is for anyone else, and that suggested I had poor control over it.
Obsidian is the app that can help me solve this need. It stores MD files, a format that AI is very familiar with, and it is accessible by Claude.
Today, and for some weeks now, I produce knowledge with the assistance of Claude and let the AI write, store, and categorize every single piece into what Obsidian calls a vault.
But wait, it is so much more than having a local storage of files with perfect categorization. It is searchable and accessible by Claude as if it is its context for your conversations.
At this point, Claude consults my local files instead of having to search online; that’s much faster, more efficient, and cheap.
Let’s talk about Obsidian
First of all, it is free to use and download (obsidian.md).
It can be configured to work like your personal Wikipedia, and that means that your files can interlink to each other. For example, if many files share the theme “Personal Development,” when you click that theme, you will be able to see a list of all the articles under the same theme. This is not an automatic feature, but it is part of the AKM system I built; otherwise, the search function would easily list all the documents in your vault corresponding to your keywords, tags, themes, and any other attribute on your documents.
Your vault is a folder in your local file system. Something that I did was to include that folder to synchronize with my iCloud; in that way, I have backed up all my files. You can do the same with any other online storage service.
As I mentioned earlier, Claude is in charge of creating files and maintaining the categorization, interlinking, and keeping score of all changes. So, I have to make it clear to you because I found it amazing: I have never written one letter in Obsidian; it is fully managed by Claude.
Here are some screen recordings of how my Obsidian looks and how it works:
And what about Notion?
Previously, my workflow was roughly like this:
Jose drafts texts with AI > AI helps adjust the text using formulas > AI pushes the content to Notion > Jose publishes on Substack > Jose requests status and URL updates to Notion DB to AI
Today my workflow is like this:
Jose drafts text > AI Skill coaches Jose based on specific criteria (as I’ll explain more later) > Jose rewrites text > AI updates the AKM vault (Assisted Knowledge Management) in Obsidian > AI updates Notion using scheduled tasks.
So, that means that Notion today is more of a backup space, and no longer a database I use to query or research.
Additionally, you can probably see that my current workflow is more focused on me writing by myself. I made some new skills to coach me to write better, instead of writing better for me.
The solution architecture
First, I defined the content types I wanted to work with: Substack Articles and Substack Notes. Because both document types are in Substack, their metadata is very similar. Now that is important, because each MD file in my Obsidian will have the following structure: Metadata (properties), Content, and themes.
Second, I needed a list of Tags I will call Themes from here on that I would use to categorize the content I create. For example: fearlessness, AI, personal development, etc. These themes will be the glue that unites the entire body of content. With that, I will be able to see which themes are most prevalent in my writing and thinking, and it will also help Claude to reach the information I need it to use as context in chat, research, and even app development.
Third, I needed an additional layer of filtering, and for that I will use the 3x3 I showed you before.
The intersection between columns and rows is called a cell. The column categories are: Seeing (S), Living(L), and Wisdom (W).
The row categories are: Individual (I), Community (C), and Global (G). A cell, for example, is CL or Community + Living, and that would categorize documents that are relevant to practical action in the context of groups or collectives. As you can see, the 3x3 matrix actually adds a layer of intelligence to the system.
Summarizing, now you can store two types of documents; they have properties or metadata that will help you search and categorize. You also have a way to add a set of cells to define the scope of each piece as an additional layer of intelligence.
But what happens if you need a new Theme? Or what if you would like to send your content for backup to Notion, for example?
So here is where you will need some scheduled tasks. Let’s focus on the new theme situation:
Imagine you have 200 Notes, 45 articles, all of them perfectly included in your Obsidian vault, with tags or themes, metadata, etc. And just today you wrote a new piece that obviously calls for a new theme, for example: Business Management.
Adding the theme would be easy for Claude, but remember that you have 245 other files already in your vault that will need to be reassessed and matched. That task will take some more time for Claude, so I chose to make it a scheduled task that can run once a week.
In the case of my backups to Notion, the scheduled task will take any new note or article I publish and copy it to a Notion database every day.
At the end of the article, you will find how to access the prompts you can use to recreate the system for you using Claude.
So, now you understand how the knowledge is stored and categorized, and you also know how Claude can help you efficiently maintain the structure in your Obsidian vault.
But there’s one piece I haven’t explained yet: who takes care of the vault structure?
As I said earlier, I never ever write anything in Obsidian itself; I write my drafts using a word processor or Claude desktop directly.
And that means that Claude is in charge of creating the MD files, filling up all the document properties, updating the status of the documents from unpublished to published, assigning the appropriate themes, and updating anything else in my Obsidian vault to keep everything I write interlinked and current.
To do that, I built two Claude Skills, which I call coaches. One helps me with Substack Notes, and the other with Substack articles. Those skills are instructed to interact with my Obsidian vault, and they complement the scheduled tasks I mentioned earlier.
Each coach skill also keeps the vault’s structure current, not just the individual file. Every time a piece is created, updated, or published, the skill updates the index pages tied to it: the main Index, the page for each theme it belongs to, and the page for each 3x3 cell it’s classified under. That way the vault’s navigation pages are never stale; they reflect exactly what’s in the vault at that moment, without me having to rebuild them by hand.
If you are curious about why I call these skills coaches, it is because I got tired of the previous Skills that helped me write. Why? Because they used formulas and tactics I got from experts to write effectively, and the result was that my texts didn’t feel like mine anymore. They expressed the ideas correctly, but what about my Spanish-to-English mistakes? What about the order I usually use to present my ideas? The old skills sacrificed me for a better text. So the coaches today just challenge my writing in terms of what I say explicitly, what I communicate implicitly, and also evaluate whether my text includes the reader’s imagination and participation.
Summarizing, we have an Obsidian vault that stores files on my Mac, and those files get automatically backed up with iCloud. Claude writes the files and assigns properties or metadata. Claude manages the vault day to day, using the 3x3 to place each piece within its scope. In order to do that, I integrated two skills to coach my writing and update the vault when required. I also have regular scheduled Claude tasks ready to keep the vault structure intact, back up my content in a database in Notion, and update a visualization of my vault.
But I found something I’m missing
The entire system works so well that I started asking myself, why not include other document types? For example, offers, meeting summaries, ideas, etc. And that is my next big project with AI; lots of changes will be needed and I will have to evaluate if the 3x3 should be redefined, if the current themes are relevant, or if I should keep those new document types in separate Obsidian vaults with parallel systems. What do you think?
So how is Claude doing?
After already a couple of years working with AI LLMs, a level of expertise is materializing. I have a feeling of the kind of work LLMs can do easily, quickly, and with low risk.
Many people use LLMs for mathematical operations and other deterministic tasks, but in my opinion, those are better addressed by different technologies. I lean toward using Large Language Models specifically for what they’re built for: language.
So, in my experience, I see that LLMs like Claude are very good at interpreting, categorizing, and executing pre-scripted tasks. The results are not perfect, but it is better than if I do it myself. Of course, my criteria and expertise are something Claude can’t replace, but if I find an error or suggestion, updating the system to respect the additional criteria is usually easy.
So I take Claude similarly to working with a human assistant, imperfect, well-intentioned, and always improving. Therefore, I delegate tasks to Claude that are low risk for me. I do not care too much if one article I write misses one theme or keyword; the effect of that isn’t dramatic. In contrast, I’m not willing to trust AI with tax reports or cash flows without the proper combination of deterministic tools and layers of revision.
I take from Jenny and Nate’s way the awesome idea of keeping AI tools participating in the process of documenting and generating valuable information.
Jenny Ouyang’s work inspires me especially because she shows us the best potential of using AI, but I still think implementing a system like hers would require too much attention from me.
Actually, we engaged in a conversation about this opinion, and she came up with a great article I’d like to share with you: AI Scheduled Tasks: The Complete Map.
This is the system I made for you
Let me tell you that writing this article has been a long process for the right reasons. I found some errors in my own system that are now fixed, and reviewing all that helped me find a way to build a sequence of prompts and a skill that will create a custom AKM for you. I removed parts of my system that are not relevant to you, and the prompts are ready to guide you step by step.
I have used and tested Claude Cowork for this AKM. You will need to have a paid tier of Claude to make it work. Why? Because you need Claude Cowork to access your local file system.
I haven’t tried or used ChatGPT for this solution, and I do not know if their new Cowork-like features can support such an implementation, but feel free to use the prompts and skill and ask ChatGPT if there is a way to adapt them to it.
One more thing: all the prompts and the skill itself are plain text; read them before you use them. You might get some new ideas or future edits. You will understand so much more when you see how Claude Cowork functions, so take this as a way to strengthen your AI skills.
You’ll find each prompt below as its own copy-paste block — copy the whole thing and paste it as a message in Claude. The skill works a little differently, since it has to be installed rather than pasted: I’ll walk you through that when we get there.
This is a description of the prompts in sequence, so you understand what their function is:
1. Prompt - Define Your 3×3 Grid
Run this first, in any regular Claude chat — Cowork isn’t needed yet. It walks you through my grid, then asks whether you want to use it as-is or define your own three scopes and three depths based on what you actually write about. Before it’s done, it tests itself: Claude classifies a paragraph you write, you tell it whether it got it right, and you repeat that until you trust it. Saves as Grid.md.
2. Prompt - Define Your Themes
Run this right after, in the same chat. This is where you define your tags — what I call themes — starting with 5 to 10, each with a definition in your own words. It checks every new one against the list so far so you don’t end up with three themes that mean the same thing. Saves as Themes.md.
Once these first two are done, download or save Grid.md and Themes.md somewhere you’ll remember — Desktop or Downloads is fine. You’ll want them on hand for the next prompt.
3. Prompt - Build Your Vault Structure
This is where Cowork becomes required, since this prompt writes real folders and files on your computer. Point it at a new, empty folder, hand it Grid.md and Themes.md, and it builds the actual vault: a folder for your content, an index page for every cell and every theme, a page documenting the whole system in plain language, and a log. It also walks you through opening that folder as a vault in Obsidian once it’s done — so have Obsidian installed before you start this one (it’s free, at obsidian.md). You can run this in the same chat as the first two prompts, or open a fresh one — if Claude can’t find Grid.mdand Themes.md on its own, it’ll just ask you to paste them in.
4. Skill - The “File to My Vault” Skill
Not a prompt — a Claude Skill you install once, and it’s on automatically after that. Give it something new you’ve written, or point it at an existing markdown file, and it classifies it into a cell and a set of themes, writes it into your vault correctly, and keeps every index page in sync. It never touches the words you actually wrote.
5. Task description - Set Up Your Scheduled Vault Check
Run this last, once you’ve filed at least one thing with the skill. It sets up a recurring Cowork scheduled task that catches drift — links or counts that fell out of sync — and flags any recently filed piece whose themes look like a forced fit, suggesting a new one instead of leaving it mismatched. It never adds a theme on its own; suggestions wait for you to confirm them.
If you would like to upgrade your membership now, this is a good opportunity; the prompts and skill after the button are only visible for premium members: