map-literature

When to Use This Skill

Use this skill to evaluate the completeness of your existing research collection and discover gaps in your literature review.

Trigger phrases:

• "Map my literature"
• "Analyze my research vault"
• "What gaps do I have in my literature?"
• "Evaluate my paper collection"

Workflow

Step 1: Read Existing Vault Contents

1. Scan all folders in ~/Research/cortical-columns/:
   • 00 - Inbox/ — papers awaiting review
   • 01 - Foundational Papers/ — confirmed relevant papers
   • 02 - Recent Discoveries/ — papers from periodic scans
   • 03 - Concepts/ — concept notes
2. For each paper note, extract:
   • Title, authors, arXiv ID, tags
   • Relevance score
   • Topic/subtopic from tags and content
3. Build a topic map: count papers per subtopic

Step 2: Categorize by Subtopic

Organize papers into these subtopics:

1. Cortical column anatomy (Mountcastle, minicolumns)
2. Hierarchical Temporal Memory (HTM)
3. Predictive coding
4. Sparse Distributed Representations (SDRs)
5. Thousand Brains Theory
6. Canonical microcircuit
7. Neuroscience-inspired AI
8. State space models (Mamba, RWKV)
9. Continual learning

Step 3: Perform Gap Analysis

Claude performs the gap analysis directly using its AI capabilities:

• Analyze the organized paper collection across all subtopics
• Identify underrepresented or missing subtopics
• Assess the depth and breadth of current coverage
• Suggest specific papers or search queries to fill identified gaps
• Return:
  • Current coverage assessment
  • Identified gaps
  • Suggested papers to add
  • Recommended search queries

Step 4: Generate Gap Report

Create or update ~/Research/cortical-columns/04 - Literature Map/gaps.md:

1. Include the full gap analysis
2. Sections: Current Coverage, Identified Gaps, Suggested Papers, Recommended Search Queries, Synthesis Notes
3. Add timestamp: **Last updated**: {current date}

Step 5: Handle Empty Vault

If the vault has no paper notes (first run):

1. Inform the user: "Votre vault est vide. Je vais créer une analyse initiale des domaines clés à couvrir."
2. Generate a "starter gap analysis" listing all key subtopics with foundational papers that should be collected
3. Save to gaps.md as a baseline

Step 6: Output Summary to User

Present the gap analysis with:

• Overview: "Votre collection couvre X sous-domaines avec Y articles."
• Top 3 gaps identified
• Top 3 suggested papers to add
• Recommended next action (e.g., "Lancez /find-papers avec la query '[suggested query]'")

Error Handling

• Vault not found: "Vault Obsidian introuvable. Lancez d'abord /find-papers pour le créer."
• Empty vault: Generate starter analysis (see Step 5)
• No gaps found: "Votre collection semble bien couverte. Excellent travail !"

Output Format

The skill outputs:

1. Gap report in 04 - Literature Map/gaps.md
2. A summary message to the user with key findings and recommended actions