cognitive/docs/tools/obsidian_usage.md

# Obsidian Usage Guide

## Overview
Obsidian serves as our knowledge management system, providing powerful linking and visualization capabilities for cognitive modeling networks.

## Vault Structure

### Core Directories
```
📁 knowledge_base/          # Main knowledge repository
├── agents/                # Agent definitions
├── beliefs/              # Belief networks
├── goals/               # Goal hierarchies
├── actions/             # Action repertoires
├── observations/        # Observation patterns
└── relationships/       # Node relationships

📁 templates/              # Template definitions
└── node_templates/      # Node type templates

📁 docs/                  # Documentation
```

## Node Types and Templates

### Core Node Types
- [[agent_template]] - Agent definitions
- [[belief_template]] - Belief structures
- [[goal_template]] - Goal definitions
- [[action_template]] - Action patterns
- [[observation_template]] - Observation models
- [[relationship_template]] - Node relationships

See [[node_types]] for detailed specifications.

## Linking Patterns

### Internal Links
- Use `[[filename]]` for direct links
- Use `[[filename|alias]]` for custom link text
- Reference [[linking_patterns]] for conventions

### Backlinks
- Automatically tracked by Obsidian
- View in right sidebar
- Essential for [[network_analysis]]

## Knowledge Organization

### Tags
Common tags:
- #agent
- #belief
- #goal
- #action
- #observation
- #relationship

See [[tagging_guide]] for conventions.

### YAML Frontmatter
```yaml
---
type: agent
id: "agent_001"
created: 2024-02-05
modified: 2024-02-05
tags: [agent, cognitive-model]
aliases: []
---
```

## Visualization

### Graph View
- Access via Graph View button
- Shows knowledge network structure
- Color-coded by [[node_types]]
- Configurable layouts

### Filters
- Filter by node type
- Filter by tags
- Filter by relationships
- See [[visualization_guide]]

## Integration Features

### With Cursor
- Markdown preview
- Code block syntax highlighting
- Integration with [[cursor_integration]]

### With Git
- Version control integration
- Collaboration features
- See [[git_workflow]]

## Workflows

### Creating New Nodes
1. Use template hotkeys
2. Fill in frontmatter
3. Add content
4. Establish links
See [[workflow_guides]] for details.

### Maintaining Networks
- Regular updates
- Link verification
- Network analysis
- See [[maintenance_guide]]

## Plugins and Extensions

### Core Plugins
- Graph View
- Backlinks
- Tags
- Templates

### Community Plugins
- Dataview (for queries)
- Calendar (for temporal tracking)
- Mind Map (for hierarchies)

## Best Practices

### Organization
- Use consistent naming
- Maintain clean hierarchy
- Follow [[template_guide]]
- Regular [[maintenance_guide]]

### Linking
- Be specific with links
- Use bidirectional linking
- Maintain link context
- Follow [[linking_patterns]]

### Documentation
- Keep notes updated
- Use templates consistently
- Follow [[documentation_guide]]

## Tips and Tricks

### Keyboard Shortcuts
- `Ctrl/Cmd + O` - Quick switcher
- `Ctrl/Cmd + E` - Toggle edit/preview
- `[[` - Create link
- See [[shortcuts_guide]]

### Search
- Use tags for categorization
- Use frontmatter for metadata
- Full-text search available
- See [[search_guide]]

## Troubleshooting

### Common Issues
- Broken links
- Template issues
- Plugin conflicts
See [[troubleshooting]] for solutions.

## Related Guides
- [[getting_started]]
- [[template_guide]]
- [[network_analysis]]
- [[maintenance_guide]]

## References
- [Obsidian Documentation](https://help.obsidian.md)
- [[code_organization]]
- [[contribution_guide]]

## Advanced Features

### Graph Analysis Tools
- [[network_metrics]] - Analyzing knowledge structure
  - Centrality measures
  - Clustering coefficients
  - Path analysis
- [[graph_layouts]] - Visualization options
  - Force-directed
  - Hierarchical
  - Circular
- [[graph_filtering]] - Custom views
  - Tag-based filters
  - Node type filters
  - Relationship filters

### Knowledge Management Patterns

#### Information Architecture
- [[information_architecture]] - Structural design
  - Hierarchical organization
  - Networked relationships
  - Semantic grouping
- [[metadata_management]] - Content enrichment
  - YAML frontmatter
  - Custom properties
  - Automatic tracking
- [[content_lifecycle]] - Document management
  - Creation workflows
  - Review processes
  - Archival procedures

#### Advanced Linking
- [[advanced_linking]] - Complex connections
  - Embedded links
  - Aliased references
  - Block references
- [[transclusion_patterns]] - Content reuse
  - Block embedding
  - File embedding
  - Dynamic content
- [[semantic_relationships]] - Meaning connections
  - Typed links
  - Relationship metadata
  - Semantic networks

### Automation and Scripting

#### Custom Scripts
- [[automation_scripts]] - Task automation
  - File creation
  - Content processing
  - Batch operations
- [[templater_scripts]] - Dynamic templates
  - Context-aware templates
  - Dynamic content
  - Conditional logic
- [[dataview_queries]] - Data extraction
  - Custom queries
  - Data visualization
  - Report generation

#### Integration Points
- [[api_integration]] - External connections
  - REST APIs
  - GraphQL endpoints
  - Webhook triggers
- [[plugin_development]] - Custom extensions
  - Plugin architecture
  - API documentation
  - Development guides
- [[automation_workflows]] - Process automation
  - GitHub Actions
  - Local scripts
  - Scheduled tasks

### Collaborative Features

#### Multi-User Workflows
- [[collaboration_patterns]] - Team practices
  - Shared repositories
  - Change management
  - Conflict resolution
- [[review_workflows]] - Content review
  - Peer review process
  - Quality assurance
  - Version control
- [[knowledge_sharing]] - Team learning
  - Best practices
  - Learning resources
  - Knowledge transfer

#### Version Control
- [[git_workflows]] - Source control
  - Branch management
  - Merge strategies
  - Conflict resolution
- [[backup_strategies]] - Data protection
  - Automated backups
  - Recovery procedures
  - Redundancy planning
- [[change_tracking]] - History management
  - Version history
  - Change logs
  - Audit trails

### Advanced Visualization

#### Custom Views
- [[custom_views]] - Specialized displays
  - Timeline views
  - Kanban boards
  - Mind maps
- [[data_visualization]] - Information display
  - Charts and graphs
  - Data tables
  - Interactive diagrams
- [[presentation_mode]] - Content sharing
  - Slide shows
  - Live presentations
  - Export formats

#### Network Analysis
- [[network_analysis]] - Graph analytics
  - Centrality metrics
  - Cluster analysis
  - Path optimization
- [[visualization_techniques]] - Display methods
  - Layout algorithms
  - Color schemes
  - Interactive features
- [[pattern_recognition]] - Structure analysis
  - Common patterns
  - Anti-patterns
  - Best practices

### System Integration

#### Development Tools
- [[ide_integration]] - Code editing
  - Cursor integration
  - VSCode workflow
  - Git support
- [[build_tools]] - Project management
  - Task runners
  - Build scripts
  - Deploy processes
- [[testing_framework]] - Quality assurance
  - Unit tests
  - Integration tests
  - Documentation tests

#### External Tools
- [[external_tools]] - Tool connections
  - Reference managers
  - Note-taking apps
  - Task managers
- [[data_exchange]] - Information flow
  - Import/export
  - Sync protocols
  - Data migration
- [[api_documentation]] - Interface specs
  - REST APIs
  - GraphQL schemas
  - WebSocket endpoints

## Performance Optimization

### Content Organization
- [[content_structure]] - File organization
  - Directory layouts
  - Naming conventions
  - File grouping
- [[indexing_strategies]] - Quick access
  - Search indexing
  - Tag systems
  - Metadata indexing
- [[cache_management]] - Performance
  - File caching
  - Search caching
  - Graph caching

### Resource Management
- [[resource_optimization]] - System efficiency
  - Memory usage
  - CPU utilization
  - Storage management
- [[scaling_strategies]] - Growth handling
  - Large vaults
  - Many files
  - Complex graphs
- [[backup_management]] - Data protection
  - Backup strategies
  - Recovery plans
  - Archive policies

## Security and Privacy

### Access Control
- [[access_management]] - Permission systems
  - User roles
  - File permissions
  - Share settings
- [[encryption_options]] - Data protection
  - File encryption
  - Key management
  - Secure sharing
- [[audit_logging]] - Activity tracking
  - User actions
  - System events
  - Change history

### Data Protection
- [[data_security]] - Information safety
  - Encryption methods
  - Secure storage
  - Safe sharing
- [[privacy_controls]] - Information control
  - Data visibility
  - Access logging
  - Usage tracking
- [[compliance_management]] - Regulation adherence
  - Data regulations
  - Privacy laws
  - Industry standards

## Maintenance and Support

### System Maintenance
- [[maintenance_procedures]] - Upkeep tasks
  - Regular checks
  - Updates
  - Optimization
- [[troubleshooting_guide]] - Problem solving
  - Common issues
  - Solutions
  - Prevention
- [[support_resources]] - Help access
  - Documentation
  - Community
  - Professional support

### Documentation
- [[documentation_standards]] - Writing guides
  - Style guides
  - Templates
  - Best practices
- [[api_documentation]] - Interface docs
  - Endpoints
  - Parameters
  - Examples
- [[user_guides]] - Usage docs
  - Tutorials
  - How-tos
  - Reference guides

## References and Resources

### Official Resources
- [Obsidian Documentation](https://help.obsidian.md)
- [Obsidian Forum](https://forum.obsidian.md)
- [Obsidian Discord](https://discord.gg/obsidian)

### Community Resources
- [[community_plugins]] - Plugin list
- [[theme_gallery]] - Visual themes
- [[snippet_library]] - Code snippets
- [[template_collection]] - Template examples

### Learning Resources
- [[tutorial_series]] - Learning guides
- [[best_practices]] - Usage tips
- [[example_vaults]] - Sample setups
- [[video_tutorials]] - Visual guides

## Appendices

### Configuration Reference
- [[config_options]] - Settings guide
- [[hotkey_reference]] - Keyboard shortcuts
- [[plugin_settings]] - Plugin configuration

### Template Library
- [[note_templates]] - Content templates
- [[frontmatter_templates]] - Metadata templates
- [[script_templates]] - Code templates

### Glossary
- [[terminology]] - Key terms
- [[abbreviations]] - Common shortcuts
- [[file_formats]] - Supported formats