paper-flow

# Paper Flow

Generate citation tree visualizations and Obsidian vault structure from academic paper research.

## When to Use This Skill

Use when user wants to:
- "Research paper flow for [field/topic]"
- "Create citation tree for [paper]"
- "Visualize development flow of [research area]"
- "Generate paper flow diagram"
- "Build citation network visualization"

## When NOT to Use This Skill

- General paper management tasks (use Zotero, Mendeley, etc.)
- Simple citation tracking without visualization
- Non-academic graph visualization tasks
- Quick single-paper lookups without analysis

## Workflow

### Phase 1: Paper Discovery

**Trigger**: User provides research field name or seed paper title/DOI/ID

**Actions**:
1. Query Semantic Scholar API for papers matching search criteria
2. Query arXiv API for additional metadata (if needed)
3. Extract paper metadata: title, authors, year, venue, citation count
4. Return list of candidate papers

**MCP Tools Used**:
- `search_papers(query, limit=20, filters)` - Semantic Scholar + arXiv
- `get_paper_details(paper_id)` - Full metadata extraction

### Phase 2: Citation Network Extraction

**Trigger**: Papers identified from Phase 1

**Actions**:
1. For each paper, get forward citations (who cited this paper)
2. For each paper, get backward references (what this paper cites)
3. Build bidirectional citation graph
4. Analyze citation relationships to identify influence flow

**MCP Tools Used**:
- `get_citations(paper_id, limit)` - Forward citations
- `get_references(paper_id, limit)` - Backward references

### Phase 3: Tree Structure Analysis

**Trigger**: Citation network built from Phase 2

**Actions**:
1. Identify root paper (highest citation count or most recent influential paper)
2. Determine parent-child relationships based on citation direction
3. Apply tree layout algorithm (Reingold-Tilford for clean trees)
4. Calculate node positions (x, y coordinates)
5. Assign hierarchy levels (depth, influence metrics)

**Decision