---
name: schema
description: Generate knowledge schemas and ontologies from any input format. Extract semantic structures, relationships, and hierarchies. Output as Obsidian markdown with YAML frontmatter, wikilinks, tags, and mermaid diagrams, or export to semantic formats (JSON-LD, RDF, Neo4j Cypher, GraphQL). Supports fractal mode (strict hierarchical constraints) and free mode (flexible generation). Auto-activates for queries containing "schema", "ontology", "knowledge graph", "extract structure", or "generate outline".
---

# Schema: Knowledge Ontology Generator

Transform any input into structured knowledge schemas with rich semantic metadata.

## Overview

Generate ontologies from:
- Plain text and natural language
- Structured data (JSON, YAML, CSV, XML)
- Markdown files with metadata
- Code repositories

Output formats:
- **Primary**: Obsidian markdown (YAML frontmatter, wikilinks, tags, callouts, mermaid)
- **Secondary**: JSON-LD, RDF/OWL, Neo4j Cypher, GraphQL schemas

## Modes

### Fractal Mode
Strict hierarchical constraints for self-similar structures:
- 2-3 children per non-leaf node
- Homonymic inheritance (child labels contain parent stem)
- Uniform relation types per parent
- Topology score ≥4.0

### Free Mode
Flexible generation optimized for semantic coherence:
- Variable branching factor
- Relaxed naming constraints
- Focus on meaningful relationships

## Installation

**Quick Install** (recommended):
```bash
cd ~/.claude/skills/hm-skills/schema
./install.sh
```

This will:
- Install Python dependencies (jinja2, pyyaml)
- Download spaCy language model (en_core_web_sm)
- Create global `schema-gen` wrapper in ~/bin
- Configure PATH in your shell rc file

**Manual Setup**:
```bash
pip3 install --user jinja2 pyyaml
python3 -m spacy download en_core_web_sm
```

## Architecture

Four-layer pipeline with graceful degradation:

1. **Layer 1: Structural Extraction** - AST parsing (markdown-oxide, tree-sitter, pandas)
2. **Layer 2: Semantic Analysis** - NLP (spaCy, networkx)
3. **Layer 3: LLM Enrichment** - Optional deep analysis (Claude API, MCP tools)
4. **Layer 4: Output Generation** - Template-based formatting (Jinja2)

## Usage

**Recommended**: Use the global wrapper `schema-gen` (automatically installed to `~/bin/schema-gen`)

```bash
# Basic usage - text to Obsidian markdown
schema-gen --input "text content" --output schema.md

# Fractal mode with deep analysis
schema-gen --input data.json --mode fractal --deep

# Export to multiple formats
schema-gen --input code/ --format obsidian,jsonld,cypher
```

**Alternative**: Direct invocation from skill directory

```bash
cd /Users/mikhail/.claude/skills/hm-skills/schema
python3 -m scripts.schema_cli --input "text content" --output schema.md
```

## Usage Examples

### Input Formats

#### Text to Schema
```bash
# Simple text input
schema-gen --input "AI analyzes data" --output ai-schema.md

# From text file
schema-gen --input document.txt --output schema.md --mode fractal
```

#### JSON to Schema
```bash
# Structured data
schema-gen --input data.json --output schema.md
```

#### Markdown to Schema
```bash
# Extract hierarchy from markdown headings
schema-gen --input notes.md --output schema.md --verbose
```

#### Code to Schema
```bash
# Parse Python code structure (classes, functions, methods)
schema-gen --input mymodule.py --output code-schema.md --verbose
```

### Output Formats

#### Single Format
```bash
# Obsidian markdown (default)
schema-gen --input data.json --output schema.md
```

#### Multiple Formats
```bash
# Export to all formats
schema-gen \
  --input document.txt \
  --format obsidian,jsonld,cypher,graphql \
  --output output/schema.md \
  --verbose

# Generates:
# - output/schema.md (Obsidian markdown)
# - output/schema.jsonld (JSON-LD linked data)
# - output/schema.cypher (Neo4j graph database)
# - output/schema.graphql (GraphQL schema)
```

### Advanced Usage

#### Fractal Mode with Deep Analysis
```bash
schema-gen \
  --input complex.txt \
  --mode fractal \
  --deep \
  --verbose
```

#### Custom Output Directory
```bash
schema-gen \
  --input data.json \
  --output custom/path/schema.md \
  --format obsidian,cypher
```

## Output Example

Generated Obsidian markdown includes:

```markdown
---
created: 2025-01-05T12:00:00
tags: [knowledge, schema]
ontology_type: free
node_count: 10
edge_count: 15
topology_score: 2.50
---

# Schema Title

> [!info] Schema Overview
> Description of the schema

## Structure

```mermaid
graph TD
    root["Root"] --> child1["Child 1"]
    root --> child2["Child 2"]
    class root,child1,child2 internal-link
```

## Entities

### Root

**Properties:**
- `category`: example
- `weight`: 0.8

**Relationships:**
- parent of → [[Child 1]]
- parent of → [[Child 2]]
```

## Configuration

Edit mode configuration files:
- [[config/fractal-mode.yaml]] - Strict hierarchical constraints
- [[config/free-mode.yaml]] - Flexible generation settings

Customize output templates:
- [[config/templates/obsidian.md.j2]] - Obsidian markdown
- [[config/templates/jsonld.json.j2]] - JSON-LD
- [[config/templates/cypher.cypher.j2]] - Neo4j Cypher

## Features

### Property Inheritance
Child nodes automatically inherit properties from ancestors, following breadcrumb-plugin patterns.

### Multi-Dimensional Navigation
Generate alternate navigation paths:
- Temporal (creation order, lifecycle)
- Conceptual (domain hierarchies, abstraction)
- Spatial (containment, proximity)
- Functional (purpose-based, process flows)

### Implicit Relationship Inference
Automatically detect relationships based on:
- Co-occurrence in context
- Tag overlap (>50% shared)
- Structural proximity
- Semantic similarity

## Error Handling

Graceful degradation ensures output even on failures:
- Layer 1 fails → Plain text fallback
- Layer 2 fails → Heuristic relationships
- Layer 3 fails → Skip enrichment
- Template fails → Raw JSON output

## References

- [[references/ast-parsing-guide|AST Parsing Guide]]
- [[references/semantic-patterns|Semantic Pattern Reference]]
- [[references/template-syntax|Template Variable Reference]]
- [[references/mcp-integration|MCP Tool Integration]]

## Examples

- [[examples/text-to-schema|Text to Schema]]
- [[examples/json-to-schema|JSON to Schema]]
- [[examples/markdown-to-schema|Markdown to Schema]]
- [[examples/code-to-schema|Code to Schema]]