Export your notes as an Obsidian-compatible Markdown vault
ScholarThread notes round-trip cleanly with Obsidian: every note becomes a Markdown file with YAML frontmatter, and note links become [[wikilinks]]. Here are the three ways to export.
One of ScholarThread's core promises is that your notes are yours — portable, in a plain format, and never trapped. The clearest expression of that is Obsidian export: any note you write can leave as standard Markdown that Obsidian reads natively.
What the export produces
Every note becomes one .md file with a YAML frontmatter block, and note-to-note links are rendered as [[wikilinks]] — the exact syntax Obsidian resolves automatically. Drop the files into an Obsidian vault and you have a working knowledge base with clickable links between notes, no conversion step required.
Everything is UTF-8 Markdown. There's no proprietary wrapper: what you get is what Obsidian (or any text editor, or Git, or grep) sees.
Three ways to export
1. A single note. Open the note and click the Download icon in its header. Your browser saves <slug>-<short-uuid>.md to your downloads folder. Good for grabbing one note to drop somewhere.
2. The whole vault. From the notes tree in the left pane, click Export vault. You get a ZIP containing one folder per ScholarThread folder, an Unfiled/ folder for notes that aren't filed, and a README.md at the root explaining the layout. Unzip it into your Obsidian vault directory and you're done.
3. One folder subtree. Hover a folder row in the tree, open the "⋯" menu, and choose Export as ZIP. Same layout as the whole-vault export, but scoped to just that folder and its children.
What travels, and what doesn't
Note bodies, frontmatter, and note-to-note links all round-trip. Paper and passage links do not — those aren't Markdown files in your vault, so there's nothing for Obsidian to point at. ScholarThread's own graph keeps those connections intact; they simply don't have an Obsidian equivalent to export into.
That's the one thing to keep in mind: an exported vault is a faithful copy of your notes and how they link to each other, not of the full ScholarThread graph that also ties notes to sources.
When to use export vs. Git sync
A one-off export is perfect for a backup, a hand-off, or moving notes into an existing Obsidian setup. If you want your notes and Obsidian to stay continuously in step — edit in either place, see it in the other — that's a job for Git sync, which we cover in Connect a private Git repo — and get two-way Obsidian sync.
Either way, the underlying guarantee is the same: your notes are plain Markdown you can take anywhere.