Denote-Org Skills for Claude
Bringing Anthropic's Life Sciences paradigm to Life Everything
Comprehensive Denote PKM system support for Claude AI, validated with 3,000+ org files in production knowledge bases.
Denote-first. Org-mode powered. Life-scale proven.
🌟 Vision: Life Sciences → Life Everything
Anthropic proved that domain context + AI = expert-level collaboration with Life Sciences (PubMed, Benchling, 10x Genomics).
This project extends that paradigm from Biology to Living:
Life Sciences (Biology) → Life Everything (Living)
Just as Claude becomes a scientist with PubMed context, Claude becomes your personal knowledge partner with Denote context.
The Pattern
| Domain | Context | Result |
|---|---|---|
| Anthropic | PubMed (millions of papers) + Claude | Scientific AI |
| This Project | Denote (3,000+ org files) + Claude | Personal Knowledge AI |
Same methodology. Different domain. Universal paradigm.
Why This is a Skill, Not Just a Prompt
Anthropic's Skills Philosophy:
"Skills transform Claude from a general-purpose agent into a specialized agent equipped with procedural knowledge that no model can fully possess."
Just like:
- PDF Skill solves complex forms (8 Python scripts for bounding boxes, validation...)
- XLSX Skill maintains formulas (recalc.py with LibreOffice integration)
- Denote-Org Skill handles 3,000-file knowledge graphs (finder, graph builder, silo manager)
Skills are NOT prompts. They are operational systems.
The Problem This Solves
Without This Skill
❌ Claude doesn't know Denote file naming: 20251021T105353--title__tags.org
❌ Finding files in 3,000+ requires repeated token-heavy searches
❌ Knowledge graph navigation is slow and error-prone
❌ Literate programming (:tangle, :results) often breaks org structure
❌ Multiple silos (~/org/, ~/claude-memory/) cause confusion
With This Skill
✅ Denote domain knowledge bundled (file naming, frontmatter, links) ✅ Python scripts for efficient operations (finder, graph, executor) ✅ Knowledge graph cached and reusable ✅ Safe code execution (org-babel compatible) ✅ Silo management (multiple knowledge domains)
Not a file converter. An operational knowledge system.
🎯 What is Denote?
Denote is a simple yet powerful note-taking system for Emacs:
- File naming convention:
YYYYMMDDTHHMMSS--title__tag1_tag2.org - Knowledge graph:
[[denote:TIMESTAMP]]links - Silo concept: Separate directories for different knowledge domains
- Org-mode foundation: Headings, properties, timestamps, code blocks
Created by: Protesilaos Stavrou
📊 Scale: Production-Validated
This skill is built for real-world PKM systems, not toy examples:
- ✅ 3,000+ org files (validated at scale)
- ✅ Multiple silos (
~/org/,~/claude-memory/, projectdocs/) - ✅ Denote knowledge graph (thousands of
[[denote:ID]]links) - ✅ Daily usage with Claude Code
- ✅ Part of 9-layer "Tools for Life" system
🏗️ Part of the 9-Layer System
This skill is Layer 3 (Knowledge Understanding) in a complete AI-human collaboration architecture:
Layer 7: Knowledge Publishing (notes.junghanacs.com)
Layer 6: Agent Orchestration (meta-config)
Layer 5a: Migration (memex-kb)
Layer 5b: Life Timeline (memacs-config)
Layer 4: AI Memory (claude-config)
Layer 3.5: RAG/Vector DB (embedding-config)
Layer 3: Knowledge Mgmt (Zotero, denote-org 🆕)
Layer 2: Dev Environment (Doom Emacs)
Layer 1: Infrastructure (NixOS)
Related projects:
- claude-config - AI Memory System with PARA methodology
- memex-kb - Universal KB Migration (Google Docs, Dooray...)
- embedding-config - Vector RAG (9,477 blocks, 85% success rate)
Philosophy: Same as Anthropic Life Sciences - AI as Partner, not Tool
🚀 Real Use Cases
Case 1: Knowledge Graph Navigation
User: "Find all files linked to 20251021T105353"
Claude: Uses denote_graph.py
Result: Connected files in <1 second (not repeated token searches)
Case 2: Tag-based Search Across 3,000 Files
User: "All llmlog files from October 2025"
Claude: Uses denote_finder.py --tags llmlog --date 202510*
Result: Instant results with metadata
Case 3: Silo Management
User: "Is this in ~/org/ or ~/claude-memory/?"
Claude: Uses denote_silo.py find_in_silos()
Result: Resolves ambiguity automatically
Case 4: Literate Programming
User: "Execute code blocks in this org file"
Claude: Uses org_execute.py (org-babel compatible)
Result: Safe execution, structure preserved, :results updated
Case 5: Denote Link Resolution
File contains: [[denote:20251021T105353]]
Claude: Uses denote_links.py resolve_link()
Result: ~/org/llmlog/20251021T105353--full-filename.org
💡 Features
Denote Core
- ✅ File naming:
20251021T105353--title__tag1_tag2.org - ✅ Frontmatter parsing (title, date, filetags, identifier)
- ✅ Link resolution (
[[denote:ID]]) - ✅ Tag-based search
- ✅ Silo management (multiple knowledge domains)
- ✅ Knowledge graph (3,000+ files validated)
Org-mode Base
- ✅ Heading/property parsing
- ✅ Code block execution (literate programming)
- ✅ Timestamp handling
- ✅ Export (markdown, PDF, HTML)
- ✅ Table operations
Performance
- ✅ Python scripts (not token generation)
- ✅ Caching for repeated operations
- ✅ Efficient graph traversal
- ✅ Batch processing support
📦 Installation
Prerequisites
# Python 3.8+
pip install orgparse pypandoc pyyaml
# Pandoc (for export)
# Install via your package manager
Claude Code
git clone https://github.com/junghan0611/orgmode-skills.git
cd orgmode-skills
/plugin add .
Claude API
# See API documentation for skills integration
import anthropic
client = anthropic.Client(api_key="your-api-key")
# Skills API usage
🔧 Quick Start
Example 1: Find Denote File
from scripts.denote_finder import find_denote_file
# By identifier
filepath = find_denote_file("20251021T105353", silos=["~/org/"])
# Returns: ~/org/llmlog/20251021T105353--full-filename.org
# By tags
files = find_by_tags(["llmlog", "denote"], silo="~/org/")
Example 2: Extract Knowledge Graph
from scripts.denote_graph import build_knowledge_graph, get_connected_nodes
# Build graph (cached)
graph = build_knowledge_graph("~/org/")
# Get connected files
connected = get_connected_nodes("20251021T105353", hops=2)
Example 3: Execute Org Code Blocks
from scripts.org_execute import execute_org_blocks
# Execute all code blocks (respects :tangle, :results)
results = execute_org_blocks("file.org")
📂 Project Structure
orgmode-skills/
├── README.md # This file
├── README-KO.md # Korean version
├── LICENSE # Apache 2.0
├── SKILL.md # Claude's main guide
├── docs/ # Development logs (Denote format)
│ └── 20251021T113500--*.org
├── denote-core.md # Denote specification
├── denote-silo.md # Silo management
├── denote-knowledge-graph.md # Graph operations
├── orgmode-base.md # Org-mode features
├── literate.md # Literate programming
├── export.md # Export capabilities
└── scripts/
├── denote_finder.py # File search
├── denote_links.py # Link resolution
├── denote_silo.py # Silo management
├── denote_graph.py # Knowledge graph
├── org_parser.py # Org parsing
├── org_execute.py # Code execution
├── org_export.py # Export
└── requirements.txt
🗺️ Roadmap to 0.1
Phase 1: Core (Current)
- Project setup
- README.md, README-KO.md
- Development log (docs/)
- SKILL.md (Denote-focused)
Phase 2: Denote Core
- denote_finder.py (file search)
- denote_links.py (link resolution)
- denote_silo.py (silo management)
- denote-core.md documentation
Phase 3: Org-mode Base
- org_parser.py (orgparse)
- org_execute.py (code blocks)
- orgmode-base.md documentation
Phase 4: 0.1 Release
- Testing with 3,000+ files
- Examples
- Public release
🤝 Contributing
This project is validated with real-world 3,000+ file Denote PKM systems. Denote users welcome!
📖 Philosophy: Tools for Life
From the creator:
"저에게 필요한 것은 경쟁력 있는 지식 노동자로 살 수 있는 방법이었습니다."
"도구는 존재에 녹아든다"
This skill embodies the "Tools for Life" philosophy - extending Anthropic's Life Sciences approach from biology research to personal knowledge work.
Life Sciences (Biology) → Life Everything (Living)
📚 Resources
- Denote Package by Protesilaos Stavrou
- Anthropic Skills Documentation
- Agent Skills Engineering Blog
- Org-mode
🔗 Related Projects
Part of the "시간과정신의방" (Hyperbolic Time Chamber) ecosystem:
- nixos-config - Declarative infrastructure
- doomemacs-config - Terminal-optimized Emacs
- zotero-config - AI-queryable bibliography (156k+ lines)
Digital Garden: notes.junghanacs.com
📄 License
Apache 2.0 (compatible with Anthropic Skills ecosystem)
🙏 Acknowledgments
- Anthropic for the Agent Skills paradigm and Life Sciences blueprint
- Protesilaos Stavrou for creating Denote
- Org-mode community for the foundation
- AIONS Clubs International for the vision of collective intelligence
Status: 🟡 Development (targeting 0.1 public release) Maintainer: @junghan0611 Created: 2025-10-21