GraphNotes and the apps you already use
GraphNotes and Obsidian
Yes, keep Obsidian as your archive: plain Markdown files that you own, linked every way. And add GraphNotes as the place you read and write by hand, with highlights that link back to their passage.
What this page says about Obsidian was read in its maker’s own pages on November 11, 2026, and its Claude row in its maker’s pages and Anthropic’s on November 14, 2026; they are listed at the end. Prices are US prices on that day. Apps change, so check there for what it does today.
Side by side
| Obsidian | GraphNotes | |
|---|---|---|
| Made for | Typed notes kept as Markdown files in a folder you own, linked to each other | Reading PDFs and writing by hand, with every note linked to where it came from |
| Runs on | Windows, Mac, Linux, iPhone, iPad and Android | iPad, iPhone and Mac. The Mac shows handwriting but does not take new handwriting |
| Price | Free. Sync, from $4 a month, and Publish, from $8 a month, are optional | Free, with no subscription. In public beta on TestFlight |
| Handwriting | None built in. Community plugins add drawing | Apple Pencil. Handwriting stays handwriting, search finds it, and it becomes typed text only on request |
| PDFs | Opens and embeds PDFs, without highlights or annotations of its own. On desktop a link can point to a selection | Highlights, with your notes beside each passage in Margin view. The file is never changed; Export with Highlights makes a copy with them in it |
| Links between notes | Links to notes, headings and blocks, with backlinks and a graph | Every doc, highlight, block and board has a link. Each shows what it links to and what links to it, and a link can say why |
| Boards | Canvas: notes, text and media as cards with connections, saved in the open JSON Canvas format | Boards with no edge. Cards are the docs themselves, and connectors join cards, sticky notes and the notes in PDFs’ margins |
| Where notes live | In a folder on your device, with no account. Obsidian Sync or iCloud carries it to other devices | On your devices and in your own iCloud. No account |
| Getting notes out | They are already Markdown files | Export Everything: docs as Markdown with their links, PDFs with highlights written in, handwriting as images, boards as JSON Canvas. Also a one-file backup |
| Claude | No connection to Claude from Obsidian, and no assistant features built in. Community plugins connect a vault to Claude, unofficially | From GraphNotes for Mac, once you turn it on: Claude reads your library, PDFs’ pages included, and what it proposes waits for you to keep it. How it works |
Where Obsidian is the better tool
- Owning your notes as plain Markdown files that any app can open.
- Typed, linked notes at scale: links to headings and blocks, backlinks and a graph.
- Thousands of community plugins and themes.
- Windows, Linux and Android, as well as Apple devices.
- Publishing notes to the web, with Obsidian Publish.
What GraphNotes adds
- Handwriting with Apple Pencil as a note in its own right, which search can find.
- Notes that stay tied to their passage. Each highlight is a note of its own, with a link to its page and words, and your notes on it sit beside the passage in Margin view.
- A link to an exact PDF passage, made on iPad or iPhone.
- Links that say why. A connection can carry a reason, such as Supports, Contradicts or Cites, and a label of your own.
- Boards where a card is the doc itself, handwriting included.
Using both
Copy Link in GraphNotes gives a graphnotes.app link to a doc, a highlight or a board. It is a web link like any other, and it opens that note in GraphNotes on an iPad or iPhone that has it. Put it in an Obsidian note as a Markdown link, and the note in your vault points to the handwriting or the passage.
Export Everything writes your library in formats Obsidian reads: docs and highlights as Markdown with their links, and boards as JSON Canvas.
PDFs come with your highlights written in, and handwriting as images, with its recognized words as their alt text.
GraphNotes is free and in public beta on TestFlight. Join the Beta.
Sources
- Obsidian: pricing
- Obsidian Help: how Obsidian stores data
- Obsidian Help: PDF
- Obsidian Help: internal links
- Obsidian Help: Canvas
- Obsidian Help: core plugins
- Claude: connectors
- Obsidian: community plugins