My Obsidian inbox had 40 fleeting notes (fragments from books, podcasts, conversations, and half-formed ideas). In the past I would set aside time to make them into proper Zettelkasten notes for my vault with 1000+ notes. I know that this is an important part of the Zettelkasten, but in the spirit of experimentation I wanted to see how AI could help with it. I tried delegating the process to AI, and it worked better than I expected.

Here’s the process I used.

  1. I started with a steering file. Before touching a single note, I wrote a steering file that defined exactly what a good note looks like: one idea per note, written as a direct timeless claim (not “this article says”), a headline that states the idea rather than the topic, five tags maximum, up to three cross-links to related notes, and a source field. The steering file also defined when to create a Map of Content (only when five or more notes cluster around a coherent theme).
  2. I let the AI read the inbox, then write to a separate folder. I’m not yet ready to test something new on my full Obsidian vault, so I limited the AI to a single folder with a test batch of 40 notes. I kept the folder read-only (so I could check work) and asked the AI to write notes to a separate folder. Claude read all 40 notes in one pass, identified which ones contained multiple ideas, and wrote each cleaned note from scratch in the Zettelkasten format. Three long research documents became seven separate notes. Four Maps of Content emerged naturally from the clusters that formed.

The result was 40 notes processed in one session, properly formatted, tagged, and linked. What I’m looking for ultimately is not the note rewriting, it’s the cross-linking and the ability to see patterns within notes. So I expect to continue testing beyond this first batch to explore that idea.

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4 responses to “How I used AI to clean my Obsidian Inbox”

  1. PDFAnnotations Avatar

    One thing that makes an inbox worth cleaning is knowing where each fragment came from. When a fragment is a sentence or passage from a book or paper, I keep the source line with it: author, page, and the exact quoted text, so the note stays honest when it grows into a permanent vault note. Exporting the highlights and margin notes out of the PDF at the end of a reading session makes that step feel like filing rather than archaeology.

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    1. Basement Wha Avatar

      I agree. My steering file keeps the source information included. I am super interested in how you make decisions on what to keep and what to delete. I often find myself with tons of notes, and getting rid of them is tricky. How do you manage it?

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      1. PDFAnnotations Avatar

        Great question. Getting rid of notes feels painful because of the sunk cost of reading and highlighting them.

        My rule of thumb is: “Will this spark a conversation with a future note, or is it just a fact?” Facts can be re-googled; unique perspectives cannot. If a fragment doesn’t give me an immediate angle to argue with or expand on, I archive or delete it without guilt.

        To make this decision painless, I separate the “capture” phase from the “curate” phase. When reading, I highlight freely. But before sending anything into Obsidian, I run the document through PDFAnnotations.com (a tool I built). It exports all the annotations cleanly with page anchors, which lets me quickly review everything at a glance and decide what actually deserves a permanent spot in the inbox.

        Once the low-signal stuff is weeded out at the source, the inbox doesn’t feel nearly as overwhelming to process!

        Curiously, did you give Claude any rules in your steering file for discarding notes entirely, or does it try to turn every single fragment into a keeper?

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      2. Basement Wha Avatar

        That’s a helpful heuristic to look at it. What do you mean spark a conversation with a future note?

        BTW, your tool solves a very real problem. I just encountered it yesterday. For people who like to read PDFs in an app (like Apple Books) there are very few options – very, very few – to look at all the highlights in one place and determine how to work with them. Kindle does this but Kindle is for a different format and use case. Thanks for sharing your tool!

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