Vahtian · Obsidian vault · free, pay what you want

PhD Thesis Vault

A reviewer will ask what you actually know. Your notes should already answer.

Two things go wrong in a PhD's notes. You lose track of the state of your knowledge: what you can defend, what you are still assuming, what is open, what you ruled out and why. And you lose the evidence itself: the claim survives in the draft, but the source behind it cannot be found when a reviewer asks. Most vaults go quiet on both. They store material; they do not record judgement.

This vault does one thing differently: colour is the epistemic state of a note, not its topic.

The vault's sidebar after setup: four folders, colour-blind-safe (shape and colour, so it reads in greyscale and dark mode too).

A new note starts grey: not judged yet. It earns its colour when you appraise it, by dragging it into a folder. The graph colours by state, so your whole thesis becomes a map of what you know. And a thesis is not the sum of your green notes: it is an argument that also carries its limitations (Working, Open) and the contrasting evidence you ruled out.

Every note keeps its source as a Zotero citekey, so the chain from claim to paper is one click, not an afternoon of searching. If a source is later retracted, the same chain finds every note that leaned on it.

Thesis already written?

Run the vault backwards. Map your written claims into the four folders and it becomes defence preparation: every claim standing on a Working note is a question you will be asked, and every Ruled out note is your answer to "why not X?". The late-stage audit note walks you through it.

What is inside

• Four colour-coded state folders: the one opinionated layer, everything else native Obsidian
• Templates: Paper, Literature note, Research question, Reviewer comment
• A Build your PhD canvas: topic, question, evidence, limitations, contrasting evidence, thesis, discussion, gaps, conclusion
• A Building your argument guide, The four states, by task, and The late-stage audit
• Other disciplines: a rename table so the same system fits history, law, or theory
• A Zotero flow linking every finding to its source by citekey, and Dataview dashboards for what to work on next and how much you can already defend
• How to use this vault: five moves for anyone new to Obsidian

What it is not

It shows you where your evidence is thin. It does not decide whether your thesis is good, and it does not check whether a source supports the sentence you cite it for. You stay the judge.

The method behind the vault, free to read: vahtian.com/learn/epistemic-notes