Knowledge Brain

Knowledge Brain

An Obsidian plugin that turns your markdown notes into a connected knowledge graph — a directed acyclic graph (DAG) of thoughts — with a built-in streaming AI chat (DeepSeek / OpenAI / Gemini / Claude) that can suggest tags, statuses, links, follow-up questions, and even turn chat answers into new notes.

Any markdown note in your vault is already a thought. The plugin reads standard YAML frontmatter, so your knowledge base stays plain, portable markdown.

Author: Kerekes Stefan · Version: 0.4.1 · Desktop only

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Features

🧠 Thoughts as plain markdown

• Every markdown note is a thought, indexed live from your vault (create, edit, rename, delete — the index follows automatically).
• Thoughts link to each other through a parents list in frontmatter, forming a directed acyclic graph — the plugin validates links and refuses cycles, self-links, and duplicates.
• Optional frontmatter metadata: tags, status (idea / in progress / done), questiontype (scientific, practical, comparative, historical, causal, critical), source, edge parentlabels.
• Renaming a note automatically rewrites every parent reference that points at it.

🕸️ Interactive graph view

• Cytoscape.js-powered graph with Breadth-first, Concentric, or CoSE layouts, node size mapped to link degree, and arrows on edges.
• Color-coded by status (idea / in progress / done) with an auto-generated legend.
• Filter by status or tag, adjust node spacing with a slider (persisted in settings).
• Neighborhood view: show only the notes within 1–3 hops of a thought, centered on the active note (or a thought you pick).
• Path highlighting: pick two thoughts and the shortest connecting path is highlighted, with the rest dimmed.
• Hover a node for a preview tooltip (title, status, type, tags, content); click to open the note.
• Right-click a node for AI tag suggestions, AI status suggestions, or delete.
• Statistics modal: totals, links, breakdown by thought type and follow-up groups.
• Check similarity: finds near-duplicate thoughts locally (token-cosine over title + content — no API calls).

💬 Streaming AI chat

• Bring your own key for DeepSeek, OpenAI (ChatGPT), Google Gemini, or Anthropic Claude — pick a model from the list or type any custom model id.
• Streaming responses with visible reasoning/thinking output for models that support it (DeepSeek thinking, OpenAI reasoning effort, Gemini thinking, Claude extended thinking).
• Context thought: pin the active note (or a graph node) as chat context.
• After each answer, get follow-up suggestions and save the answer as a new thought — the AI suggests the best existing parent(s) to file it under, or lets you create a new root.
• Everything is copyable: individual messages, suggestions, the whole conversation.

❓ Automatic follow-up questions

• Opening a note in the sidebar generates follow-up questions grouped by type (scientific, practical, comparative, historical, causal, critical) to deepen your thinking.
• Choose which groups to generate and how many questions per group; pause/resume automatic generation; regenerate on demand.
• Questions already answered elsewhere in the graph are marked as answered in ….
• Click a follow-up to load it straight into the chat with the right context set.

🗂️ Sidebar panes

• Backlinks — thoughts that link to the active note (with edge labels).
• Siblings — thoughts that share a parent with the active note.
• Follow-ups — generated questions for the active note.
• Optionally combine all three into a single sidebar tab (setting), or keep them as separate panes.

🔍 Local search & retrieval

• BM25 full-text search over all thoughts (memoized index, rebuilt on change) with English and Romanian stopword handling.
• Used both for the search modal and to retrieve relevant thoughts as context for AI operations — cheap and private, no embeddings API needed.

🤖 AI-assisted organization

• Suggest tags and suggest status for a thought (toggleable in settings).
• Suggest parents when saving a new thought — ranked best-first with reasons.
• Suggest titles — 3–5 short, specific noun-phrase titles extracted from the content.

Commands

There's also a ribbon icon and status bar items (KB Graph, KB Chat) for quick access.

Frontmatter format

A thought is just a markdown file. The plugin manages these frontmatter keys (anything else is preserved untouched):

---
parents:
  - Some Parent Thought
parent_labels:
  Some Parent Thought: contradicts
tags:
  - knowledge-management
  - ai
status: idea
question_type: causal
source: https://example.com/article
created_at: 2026-08-01T12:00:00.000Z
updated_at: 2026-08-09T18:30:00.000Z
---

The body of the note is the thought's content — free-form markdown.

Installation

Manual

1. Download main.js, manifest.json, and styles.css from the latest release.
2. Create a folder <your-vault>/.obsidian/plugins/knowledge-brain/ and copy the three files into it.
3. Restart Obsidian, then enable Knowledge Brain in Settings → Community plugins.

BRAT (beta testing)

1. Install the BRAT plugin.
2. Add this repository: Stef4678/knowledge-brain.

Setup

1. Open Settings → Knowledge Brain.
2. Pick a provider (DeepSeek, OpenAI, Gemini, or Claude) and paste your API key.
3. Choose a model (sensible defaults per provider, custom ids allowed) and tune temperature / thinking mode.
4. Click Test connection to verify the key.
5. (Optional) Set a default folder for new thoughts — the graph, similarity check, and sidebar panes focus on this folder.

The graph, search, similarity, and all note management work without an API key. Only chat and AI-assisted suggestions need one.

Settings reference

Development

npm install
npm run dev      # esbuild watch mode
npm run build    # production bundle

Written in TypeScript, bundled with esbuild, graph rendering via Cytoscape.js. The plugin talks to AI providers directly (OpenAI-compatible chat completions, Gemini generateContent, Claude Messages API) with SSE streaming and non-streaming fallbacks.

Roadmap ideas

Potential future improvements include:

• OpenAI-compatible endpoint support — custom base URL + key, unlocking local models (LM Studio, Ollama) and alternative providers (Mistral, Groq, OpenRouter) with one code path
• Canvas / Excalidraw export — render the thought graph as an Obsidian Canvas file for presentations and sharing
• Chat with multiple thoughts as context — pin several notes, not just one; auto-retrieve top-k relevant thoughts via BM25 as chat context (RAG-lite)
• Graph import/export — JSON dump/restore of nodes, edges, and metadata for backups and migration (the logic already exists internally)

Privacy

• Notes never leave your vault except as explicit context in requests to your chosen AI provider, using your own API key.
• Search, similarity, statistics, and the graph are computed entirely locally.

License

MIT © 2026 Kerekes Stefan