Managing a personal knowledge base can be a challenge, especially when you’re not in the mood to properly format and structure your notes. AI can help streamline this process by organizing, processing and manipulating data for you.
1
Processing Large Blocks of Information With ChatGPT
Let’s say I need to write firmware to run a display using a specific microchip. Now I don’t really know how this microchip works, but the manufacturer has provided a PDF of all the technical details needed to program one. What I would do in this situation is to use ChatGPT to read through the PDF, get all the relevant information I need, and let it format the info for my note-taking app. To do this effectively, I follow a simple three-step approach.
Step 1: Upload File/s and Configure ChatGPT
When using ChatGPT to extract notes from a file, I always turn off the Search functionality to ensure all my notes come from my source material. I then enable Reason for technical topics such as manuals, and disable it for more creative subjects such as literature.
Here’s what the process usually looks like for me:
- Upload source material/s
- Turn off Search functionality
- Enable Reason for technical source materials and disable creative topics
- Choose the best AI model for the job. Use o3-mini model for a reason, and GPT-4o for creative
Step 2: Prompt
The quality of notes you get out of ChatGPT will heavily rely on your prompt. While various topics require different prompts, I always follow a structure where the prompt is divided into three key sections: Goal, Filter, and Format.
- Goal: Give ChatGPT a clear and defined goal of your motive and what you want to achieve.
- Filter: Be specific about the info you want to get out of the source material.
- Format: Provide formatting rules, best practices, and examples specific to your note-taking app.
Since the section on proper formatting is often long and reusable, I typically place it on another text file separate from the main prompt. This file typically contains a condensed version of the official formatting rules and guidelines of Logseq (my preferred note-taking app) along with my personal examples.

Curious about Logseq?
I Use This Tool to Take and Organize Notes From Books and PDFs
Logseq turns my scattered book notes into a well-organized, searchable knowledge base.
Step 3: Save Notes to Note-Taking App
If you’ve prompted well, you should be able to directly copy the notes from ChatGPT to your note-taking app. However, there are instances where you’ll have to put a little more effort into ensuring everything is displayed correctly on your note-taking app.
In this case, the images and diagrams I requested are not displayed properly. While ChatGPT has properly nested and provided image links for the diagrams and images I requested, I still needed to manually download them and place them in my assets folder.
After downloading the images from ChatGPT, the image now works!
My notes are now properly formatted, populated with useful tags and backlinks to make note navigation easier, images are nested within notes, and I have the necessary info to program my firmware.
2
Expanding My Knowledge Base With Perplexity
AI Chatbots today can be accessed in a multitude of ways. This makes taking notes with AI much more convenient, allowing me to expand my knowledge base throughout the day.
I personally like using Perplexity services as my daily note-taking assistant as they integrate well with how I take notes throughout the day.
I use the Perplexity Chrome extension to query web pages. Let’s say I’m interested in learning about hydroponics. What I do is open a niche hydroponic website (you can tell because of the name of the site), go to their landing page, click on the Perplexity extension, and select This Domain as the focus.
I can then start querying anything about hydroponics, and I’m going to get answers filtered from the entire website.
When I’m not on my laptop, I like to use Perplexity’s mobile app as my daily AI assistant. I love using Perplexity as my daily AI assistant because it’s convenient. For note-taking, all I do is long-press the power button at any time and use voice functionality to ask my questions.
I like this approach because I often have quick questions throughout the day, and having an AI assistant allows me to take notes even without me actively doing research.
At the end of the day, I then go to the Perplexity web or desktop app to process all my notes.
Since Perplexity keeps all your queries in its Library section, I can simply Ctrl + a then Ctrl + c to copy all the notes, paste them as a prompt, then upload my Logseq formatting rules text file (the one from earlier) and process the data just like how I would with ChatGPT.
And voilà! I got all my Perplexity queries throughout the day as Logseq notes.
3
Organizing, Querying, and Generating Flashcards With Logseq and Gemini
After using ChatGPT and Perplexity to funnel data to Logseq, I then use Gemini as a way to query and further manipulate data within the note-taking app. While Logseq doesn’t natively support AI integration, I use a plugin that allows me to connect to various AI models within the app and use it to manipulate data.
To try it out for yourself, install AssistSeq as a Logseq plugin. Open AssistSeq’s settings and place your API key, and you’re done!
I personally use a Gemini API key (1.5 Flash) since they provide them for free. To get your own free Gemini API key, simply visit Google AI Studio, sign up with your Google account, and then hit Create API to generate one that you can use with AssistSeq.
There are a few ways I like to use Gemini in my Logseq knowledge base. The first one would be for querying information.
Another way I use Gemini would be for organizing or manipulating my notes. In the picture below, I noticed that the “tags” and “Related” sections shared similar keywords. To fix this, I asked the AI assistant to remove any redundant keywords from the “Related” section. I then clicked on the Add to Page to append the newly formatted version on the page.
Lastly, I also used Gemini to make flashcards when memorizing information. In the example below, Gemini was able to generate 14 flashcards based on my knowledge base on hydroponics.
However, since you cannot upload files on AssistSeq, I had to manually prompt the Logseq flashcards format, which took a few extra steps. Overall, it was still a faster way to create flashcards than doing them manually.

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While there are a lot of other ways to integrate AI into your note-taking system, consistency is key to building an effective knowledge base. That said, I recommend starting with a solid core system (like I did here) and then experimenting with new AI tools over time. The most important thing is finding a consistent and reliable system.