Claude Obsidian Wiki

---
name: claude-obsidian-wiki
description: Claude Code skill for building and maintaining a persistent, compounding Obsidian wiki vault using AI-powered ingestion, querying, linting, and autonomous research.
triggers:
  - "set up claude obsidian wiki"
  - "build a second brain with obsidian"
  - "ingest sources into my wiki vault"
  - "query my obsidian knowledge base"
  - "lint my obsidian wiki"
  - "run autoresearch on a topic"
  - "save this conversation to my wiki"
  - "set up persistent knowledge base with claude"
---

# claude-obsidian-wiki

> Skill by [ara.so](https://ara.so) — Daily 2026 Skills collection.

claude-obsidian is a Claude Code skill that turns Obsidian into a self-organizing AI knowledge engine. Drop sources, ask questions, run autonomous research — Claude handles ingestion, cross-referencing, contradiction flagging, session memory, and vault health. Knowledge compounds with every ingest.

Based on [Andrej Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f). 10 skills. Zero manual filing. Multi-agent support.

---

## Installation

### Option 1: Clone as vault (recommended)

```bash
git clone https://github.com/AgriciDaniel/claude-obsidian
cd claude-obsidian
bash bin/setup-vault.sh

Open the folder in Obsidian: Manage Vaults → Open folder as vault → select claude-obsidian/

Open Claude Code in the same folder. Type /wiki to begin.

setup-vault.sh configures graph.json, app.json, and appearance.json. Run it once before first Obsidian open.

Option 2: Claude Code plugin install

# Add the marketplace catalog
claude plugin marketplace add AgriciDaniel/claude-obsidian

# Install the plugin
claude plugin install claude-obsidian@claude-obsidian-marketplace

# Verify
claude plugin list

Then in any Claude Code session: /wiki

Option 3: Add to an existing vault

# Copy WIKI.md into your vault root, then paste into Claude:

Read WIKI.md in this project. Then:
1. Check if Obsidian is installed. If not, install it.
2. Check if the Local REST API plugin is running on port 27124.
3. Configure the MCP server.
4. Ask me ONE question: "What is this vault for?"
Then scaffold the full wiki structure.

MCP Setup (Optional but Recommended)

MCP lets Claude read and write vault notes directly without copy-paste.

Option A: REST API (requires Obsidian Local REST API plugin)

1. Install Local REST API plugin in Obsidian
2. Copy your API key from plugin settings
3. Run:

claude mcp add-json obsidian-vault '{
  "type": "stdio",
  "command": "uvx",
  "args": ["mcp-obsidian"],
  "env": {
    "OBSIDIAN_API_KEY": "$OBSIDIAN_API_KEY",
    "OBSIDIAN_HOST": "127.0.0.1",
    "OBSIDIAN_PORT": "27124",
    "NODE_TLS_REJECT_UNAUTHORIZED": "0"
  }
}' --scope user

Set the env var before running:

export OBSIDIAN_API_KEY=your-key-from-plugin-settings

Option B: Filesystem (no plugin needed)

claude mcp add-json obsidian-vault '{
  "type": "stdio",
  "command": "npx",
  "args": ["-y", "@bitbonsai/mcpvault@latest", "/path/to/your/vault"]
}' --scope user

Core Commands

Vault Structure

After /wiki scaffolds your vault:

your-vault/
├── wiki/
│   ├── index.md          # Master catalog of all wiki pages
│   ├── log.md            # Append-only operation log
│   ├── hot.md            # Recent context cache (session memory)
│   ├── overview.md       # Executive summary
│   └── meta/
│       ├── dashboard.base    # Native Obsidian Bases dashboard
│       └── dashboard.md      # Legacy Dataview dashboard (fallback)
├── _templates/           # Templater templates for each note type
├── .obsidian/
│   └── snippets/
│       └── vault-colors.css  # Color-coded file explorer
└── CLAUDE.md             # Auto-loaded project instructions

Wiki Modes

Select one or combine during /wiki setup:

Ingestion Workflow

Single source

ingest research-paper.pdf

Claude will:

1. Read the source
2. Extract entities, concepts, and key claims
3. Create 8–15 wiki pages with proper frontmatter
4. Update wiki/index.md with new entries
5. Append to wiki/log.md
6. Cross-reference related existing pages
7. Flag contradictions with [!contradiction] callouts

Batch ingestion

ingest all of these:
- paper1.pdf
- paper2.pdf
- https://example.com/article
- notes.md

Claude spawns parallel agents per source, then runs a cross-reference pass.

Web Clipper workflow

Install the Obsidian Web Clipper browser extension. Pages saved via clipper land in .raw/. Then:

ingest everything in .raw/

Query Workflow

what do you know about transformer attention mechanisms?

Claude's resolution order:

1. Reads wiki/hot.md (recent context cache)
2. Scans wiki/index.md for relevant pages
3. Drills into matching wiki pages
4. Synthesizes answer with citations to specific wiki pages — not training data

Autonomous Research

/autoresearch "retrieval augmented generation"

Claude runs 3 rounds:

1. Web search for the topic
2. Fetch and read top sources
3. Synthesize findings, identify gaps, repeat
4. File all results as wiki pages with cross-references

Configure research objectives in:

skills/autoresearch/references/program.md

Session Memory (Hot Cache)

wiki/hot.md persists recent context between sessions. At session end:

update hot cache

At session start, Claude automatically reads hot.md — no recap needed.

Lint the Wiki

lint the wiki

Claude checks 8 categories:

• Orphans: pages with no incoming links
• Dead links: internal links pointing to missing pages
• Stale claims: content that may be outdated
• Missing cross-references: related pages not yet linked
• Duplicate concepts: similar pages that could be merged
• Missing frontmatter: pages lacking required properties
• Empty sections: placeholder headings with no content
• Index gaps: pages not cataloged in wiki/index.md

Cross-Project Knowledge Base

Point any Claude Code project at this vault. Add to that project's CLAUDE.md:

## Wiki Knowledge Base
Path: ~/path/to/claude-obsidian

When you need context not already in this project:
1. Read wiki/hot.md first (recent context cache)
2. If not enough, read wiki/index.md
3. If you need domain details, read the relevant domain sub-index
4. Only then drill into specific wiki pages

Do NOT read the wiki for general coding questions unrelated to [your domain].

Canvas Commands

/canvas                          # Open or create the visual canvas
/canvas add image [path-or-url]  # Add image with auto-layout
/canvas add text [content]       # Add markdown text card
/canvas add pdf [path]           # Add PDF as rendered preview node
/canvas add note [wiki-page]     # Pin a wiki page as linked card
/canvas zone [name]              # Add labeled zone for organization
/canvas from banana              # Capture recently generated images

Pairs with claude-canvas for 12 templates, 6 layout algorithms, and AI image generation.

Wiki Note Frontmatter

All ingested pages use this frontmatter schema:

---
title: "Attention Is All You Need"
type: source          # source | concept | entity | hub | log
tags: [transformers, attention, nlp]
created: 2026-04-11
updated: 2026-04-11
status: current       # current | stale | stub
source: "https://arxiv.org/abs/1706.03762"
related:
  - "[[Transformer Architecture]]"
  - "[[Self-Attention Mechanism]]"
banner: "_attachments/images/transformer.png"
banner_icon: "🤖"
---

Contradiction Callout Pattern

When Claude detects conflicting information across sources:

> [!contradiction]
> **Source A** (2024) claims X. **Source B** (2025) claims Y.
> Last verified: 2026-04-11. Needs resolution.

Obsidian Plugins

Pre-installed (ship with vault)

Install from Community Plugins

Core Plugins (built-in, no install)

• Bases — powers dashboard.base (requires Obsidian v1.9.10+)
• Properties — visual frontmatter editor
• Backlinks, Graph view, Outline

CSS Snippets (auto-enabled)

Troubleshooting

/wiki doesn't respond

# Confirm plugin is installed
claude plugin list

# Reinstall if missing
claude plugin install claude-obsidian@claude-obsidian-marketplace

MCP connection refused

# Check Local REST API plugin is running in Obsidian
# Verify port
curl http://127.0.0.1:27124/vault/ -H "Authorization: Bearer $OBSIDIAN_API_KEY"

# Check env var is set
echo $OBSIDIAN_API_KEY

setup-vault.sh fails on Excalidraw download

# Run manually
bash bin/setup-vault.sh

# Or skip Excalidraw — enable it later from Community Plugins

Graph view looks empty

# Re-run setup to apply graph.json filter + colors
bash bin/setup-vault.sh

# Then restart Obsidian

Hot cache is stale

update hot cache

Run this at the end of every significant session.

Dataview dashboard shows errors The primary dashboard now uses Bases (Obsidian v1.9.10+). The legacy dashboard.md requires the Dataview community plugin. Install it if you need the fallback view.

File Structure Reference

claude-obsidian/
├── .claude-plugin/
│   ├── plugin.json          # Plugin manifest
│   └── marketplace.json     # Distribution metadata
├── skills/
│   ├── wiki/                # Orchestrator + 7 reference files
│   ├── wiki-ingest/         # INGEST operation skill
│   ├── wiki-query/          # QUERY operation skill
│   ├── wiki-lint/           # LINT operation skill
│   ├── save/                # /save skill
│   ├── autoresearch/        # /autoresearch skill
│   │   └── references/
│   │       └── program.md   # Configurable research objectives
│   └── canvas/              # /canvas visual layer skill
│       └── references/
├── bin/
│   └── setup-vault.sh       # One-time vault configuration
├── wiki/                    # Your actual knowledge base
│   ├── index.md
│   ├── log.md
│   ├── hot.md
│   └── meta/
└── WIKI.md                  # Standalone install instructions