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GitHub Issues for ProtegeDesk Development

Team Structure

  • Lead Developer: Alex Chen (Frontend Architect, React/TypeScript specialist)
  • Backend Engineer: Sarah Johnson (WASM/Reasoning specialist)
  • UI/UX Developer: Miguel Rodriguez (React Flow/Visualization expert)
  • AI/ML Engineer: Dr. Priya Patel (LLM integration specialist)
  • DevOps Engineer: James Wilson (Build/Testing/Deployment)
  • QA Engineer: Lisa Zhang (Testing/Accessibility)
  • Technical Writer: Emma Davis (Documentation)

High Priority Issues

#1: Set up project structure with TypeScript/React/Next.js

Assignee: Alex Chen (Lead Developer)
Labels: infrastructure, setup, high-priority
Estimated Effort: 2 days
Dependencies: None

## Description

Initialize the project with proper TypeScript/React/Next.js structure following enterprise best practices.

## Tasks

- [ ] Create Next.js 14+ project with TypeScript
- [ ] Set up ESLint, Prettier, and Husky pre-commit hooks
- [ ] Configure folder structure (components, services, types, utils)
- [ ] Set up environment variables configuration
- [ ] Create basic README and contributing guidelines

## Acceptance Criteria

- Project builds successfully with `npm run build`
- TypeScript strict mode enabled
- Code formatting enforced on commit
- Folder structure follows scalable patterns

## Technical Requirements

- Next.js 14+ with App Router
- TypeScript 5+ with strict mode
- ESLint + Prettier configuration
- Husky for pre-commit hooks

#2: Install and configure core dependencies

Assignee: Alex Chen (Lead Developer)
Labels: infrastructure, dependencies, high-priority
Estimated Effort: 1 day
Dependencies: #1

## Description

Install and configure all core dependencies required for the ontology editor.

## Tasks

- [ ] Install Monaco Editor for code editing
- [ ] Install React Flow (XyFlow) for graph visualization
- [ ] Install ELK.js for graph layout algorithms
- [ ] Install N3.js for RDF parsing/serialization
- [ ] Install Zustand + Immer for state management
- [ ] Install and configure Tailwind CSS
- [ ] Install Lucide React for icons
- [ ] Install Shadcn/ui components
- [ ] Configure all dependencies with proper TypeScript types

## Acceptance Criteria

- All dependencies installed with correct versions
- TypeScript types resolved for all packages
- Basic integration tests pass for each major dependency
- Configuration files properly set up

## Technical Requirements

- Monaco Editor 0.45+
- @xyflow/react 12+
- ELK.js 0.9+
- N3.js 1.17+
- Zustand 4+
- Tailwind CSS 3+

#3: Implement ontology data model and state management

Assignee: Alex Chen (Lead Developer)
Labels: backend, state-management, high-priority
Estimated Effort: 3 days
Dependencies: #2

## Description

Create the core ontology data model and implement state management with Zustand.

## Tasks

- [ ] Define TypeScript interfaces for OWL entities (Class, Property, Individual, Axiom)
- [ ] Create ontology store structure with Zustand
- [ ] Implement CRUD operations for ontology entities
- [ ] Add Immer integration for immutable updates
- [ ] Create selectors for derived state
- [ ] Implement undo/redo functionality
- [ ] Add validation for ontology operations

## Acceptance Criteria

- Complete type-safe ontology model
- State persists across component re-renders
- CRUD operations work correctly
- Undo/redo maintains state consistency
- Performance tests pass with 1000+ entities

## Technical Requirements

- Zustand store with middleware
- Immer for immutable updates
- TypeScript interfaces for all OWL constructs
- Performance optimization for large ontologies

#4: Create main application layout with resizable panels

Assignee: Miguel Rodriguez (UI/UX Developer)
Labels: frontend, ui, high-priority
Estimated Effort: 3 days
Dependencies: #2, #3

## Description

Implement the main application layout with resizable panels following the SRS specifications.

## Tasks

- [ ] Create main layout component with 4-panel structure
- [ ] Implement resizable panel functionality
- [ ] Add collapsible sidebar functionality
- [ ] Create responsive design for different screen sizes
- [ ] Implement layout persistence to localStorage
- [ ] Add status bar component
- [ ] Create menu bar and toolbar

## Acceptance Criteria

- Layout matches SRS specifications (left sidebar, center editor, right properties, bottom status)
- Panels resize smoothly with mouse drag
- Layout preferences persist across sessions
- Responsive design works 1280x720 to 3840x2160
- Accessibility compliant with keyboard navigation

## Technical Requirements

- React with TypeScript
- CSS Grid or Flexbox for layout
- Mouse event handling for resize
- localStorage for persistence
- WCAG 2.1 Level AA compliance

#5: Build hierarchical class tree sidebar component

Assignee: Miguel Rodriguez (UI/UX Developer)
Labels: frontend, ui, high-priority
Estimated Effort: 4 days
Dependencies: #3, #4

## Description

Create a hierarchical class tree sidebar for navigating ontology classes.

## Tasks

- [ ] Build tree component with expand/collapse functionality
- [ ] Implement lazy loading for large hierarchies
- [ ] Add search and filter capabilities
- [ ] Create context menu for class operations
- [ ] Implement drag and drop for reorganization
- [ ] Add keyboard navigation
- [ ] Create custom tree node rendering

## Acceptance Criteria

- Tree displays class hierarchy correctly
- Expand/collapse works smoothly
- Search filters tree and highlights matches
- Context menu provides relevant actions
- Drag and drop updates ontology structure
- Keyboard navigation works without mouse

## Technical Requirements

- React Tree component (custom or library)
- Virtual scrolling for large trees
- Search with debouncing
- Drag and drop API
- Keyboard event handling

#6: Implement axiom editor with Monaco Editor and Manchester Syntax

Assignee: Alex Chen (Lead Developer)
Labels: frontend, editor, high-priority
Estimated Effort: 5 days
Dependencies: #2, #3

## Description

Create an advanced axiom editor using Monaco Editor with Manchester Syntax support.

## Tasks

- [ ] Integrate Monaco Editor into React component
- [ ] Define Manchester Syntax language specification
- [ ] Implement syntax highlighting with Tree-sitter
- [ ] Create intelligent autocomplete provider
- [ ] Add real-time syntax validation
- [ ] Implement quick fixes and suggestions
- [ ] Add entity navigation (Ctrl+Click, F12)
- [ ] Create error diagnostics display

## Acceptance Criteria

- Monaco Editor renders correctly in React
- Manchester Syntax keywords highlighted properly
- Autocomplete suggests ontology entities
- Syntax errors detected and displayed inline
- Navigation jumps to entity definitions
- Performance < 50ms latency for typing

## Technical Requirements

- Monaco Editor 0.45+
- Tree-sitter grammar for Manchester Syntax
- Custom language provider
- Completion provider API
- Diagnostics provider API
- Performance optimization

#7: Build ontology graph visualization with React Flow and ELK.js

Assignee: Miguel Rodriguez (UI/UX Developer)
Labels: frontend, visualization, high-priority
Estimated Effort: 6 days
Dependencies: #3, #4

## Description

Create interactive ontology graph visualization using React Flow and ELK.js layout.

## Tasks

- [ ] Integrate React Flow for graph rendering
- [ ] Implement ELK.js automatic layout
- [ ] Create custom node types (Class, Property, Individual)
- [ ] Create custom edge types (subClassOf, ObjectProperty, etc.)
- [ ] Implement incremental loading for large ontologies
- [ ] Add zoom, pan, and fit-to-screen controls
- [ ] Implement node interaction (select, expand, edit)
- [ ] Add search and highlight functionality
- [ ] Optimize performance for 1000+ nodes

## Acceptance Criteria

- Graph renders ontology structure correctly
- Automatic layout arranges nodes clearly
- Interactive nodes respond to mouse/keyboard
- Performance ≥30 FPS with 1000 nodes
- Incremental loading works smoothly
- Search highlights matching nodes

## Technical Requirements

- @xyflow/react 12+
- ELK.js 0.9+ for layout
- Custom node/edge components
- Viewport-based loading
- Canvas optimization
- Event handling

#8: Implement ontology import/export using N3.js

Assignee: Alex Chen (Lead Developer)
Labels: backend, io, high-priority
Estimated Effort: 4 days
Dependencies: #3

## Description

Implement ontology import/export functionality supporting multiple RDF formats.

## Tasks

- [ ] Integrate N3.js for RDF parsing and serialization
- [ ] Support Turtle (.ttl) format import/export
- [ ] Support RDF/XML format import/export
- [ ] Support OWL/XML format import/export
- [ ] Support N-Triples format import/export
- [ ] Implement format auto-detection
- [ ] Add validation for imported ontologies
- [ ] Create progress indicators for large files
- [ ] Handle import errors gracefully

## Acceptance Criteria

- All specified formats import without data loss
- Export produces valid RDF files
- Round-trip testing passes
- Large files (>10MB) handled efficiently
- Error messages are clear and actionable
- Progress indicators work for long operations

## Technical Requirements

- N3.js 1.17+
- File System Access API
- Stream processing for large files
- Error handling and validation
- Progress tracking

Medium Priority Issues

#9: Integrate client-side reasoning with EYE-JS WASM

Assignee: Sarah Johnson (Backend Engineer)
Labels: reasoning, wasm, medium-priority
Estimated Effort: 5 days
Dependencies: #3, #8

## Description

Integrate EYE-JS WebAssembly reasoner for client-side ontology reasoning.

## Tasks

- [ ] Integrate EYE-JS WASM module
- [ ] Implement ontology serialization to Turtle
- [ ] Create reasoner service facade
- [ ] Implement consistency checking
- [ ] Add classification functionality
- [ ] Create instance realization
- [ ] Generate inference explanations
- [ ] Handle reasoning errors gracefully
- [ ] Optimize performance for 500+ classes

## Acceptance Criteria

- Consistency checking completes < 5s for 500 classes
- Classification produces correct hierarchy
- Inferences displayed in visualization
- Explanations are human-readable
- Errors handled without crashing
- Memory usage stays within limits

## Technical Requirements

- EYE-JS WASM integration
- WebAssembly loading and initialization
- RDF serialization for reasoner input
- Result parsing and validation
- Performance optimization

#10: Implement AI co-pilot with command palette and LLM integration

Assignee: Dr. Priya Patel (AI/ML Engineer)
Labels: ai, llm, medium-priority
Estimated Effort: 6 days
Dependencies: #3, #6

## Description

Create AI co-pilot functionality with command palette and LLM integration.

## Tasks

- [ ] Implement command palette UI (⌘+K)
- [ ] Integrate Vercel AI SDK
- [ ] Create prompt templates for ontology generation
- [ ] Implement natural language to ontology conversion
- [ ] Add class hierarchy suggestion
- [ ] Create property recommendation system
- [ ] Implement axiom generation from natural language
- [ ] Add suggestion review and approval UI
- [ ] Secure API key management
- [ ] Handle rate limiting and errors

## Acceptance Criteria

- Command palette opens with ⌘+K
- AI generates valid ontology structures
- Suggestions are relevant and useful
- API keys stored securely
- Rate limiting handled gracefully
- Response time < 10 seconds

## Technical Requirements

- Vercel AI SDK 3+
- OpenAI/Anthropic API integration
- Prompt engineering
- Response parsing and validation
- Secure storage (Crypto API)
- Error handling

#11: Add properties panel for entity details editing

Assignee: Miguel Rodriguez (UI/UX Developer)
Labels: frontend, ui, medium-priority
Estimated Effort: 3 days
Dependencies: #3, #4

## Description

Create a properties panel for viewing and editing entity details.

## Tasks

- [ ] Create properties panel component
- [ ] Implement class properties editor
- [ ] Add property characteristics editor
- [ ] Create individual facts editor
- [ ] Add annotation property support
- [ ] Implement validation for property values
- [ ] Add bulk editing capabilities
- [ ] Create property change history

## Acceptance Criteria

- Panel displays all entity properties
- Editing updates ontology in real-time
- Validation prevents invalid values
- Changes reflected in other views
- Bulk editing works efficiently
- History tracks all changes

## Technical Requirements

- React forms with validation
- Real-time state synchronization
- Input validation and sanitization
- Undo/redo integration
- Performance optimization

#12: Implement auto-save and crash recovery with IndexedDB

Assignee: James Wilson (DevOps Engineer)
Labels: persistence, storage, medium-priority
Estimated Effort: 4 days
Dependencies: #3

## Description

Implement auto-save functionality and crash recovery using IndexedDB.

## Tasks

- [ ] Set up IndexedDB database schema
- [ ] Implement auto-save every 30 seconds
- [ ] Create crash recovery mechanism
- [ ] Add manual save functionality
- [ ] Implement save conflict resolution
- [ ] Create save history and versions
- [ ] Add storage quota management
- [ ] Implement data cleanup and maintenance

## Acceptance Criteria

- Auto-save works without user intervention
- Crash recovery restores unsaved work
- Manual save saves immediately
- Conflicts resolved intelligently
- Storage usage stays within limits
- Performance impact is minimal

## Technical Requirements

- IndexedDB API
- Background processing
- Error handling and recovery
- Storage quota management
- Performance optimization

#13: Build comprehensive test suite

Assignee: Lisa Zhang (QA Engineer)
Labels: testing, quality, medium-priority
Estimated Effort: 8 days
Dependencies: All high-priority issues

## Description

Create comprehensive test suite covering unit, integration, and E2E testing.

## Tasks

- [ ] Set up testing framework (Jest, React Testing Library)
- [ ] Write unit tests for all utility functions
- [ ] Create component tests for UI components
- [ ] Implement integration tests for workflows
- [ ] Set up E2E testing with Playwright
- [ ] Add performance testing for large ontologies
- [ ] Create accessibility testing suite
- [ ] Implement visual regression testing
- [ ] Set up CI/CD pipeline with testing

## Acceptance Criteria

- Code coverage ≥ 80%
- All tests pass consistently
- E2E tests cover critical user journeys
- Performance tests meet requirements
- Accessibility tests pass WCAG checks
- CI/CD runs tests automatically

## Technical Requirements

- Jest + React Testing Library
- Playwright for E2E
- Axe for accessibility
- Storybook for visual testing
- GitHub Actions for CI/CD

Low Priority Issues

#14: Implement light/dark theme support

Assignee: Miguel Rodriguez (UI/UX Developer)
Labels: ui, theme, low-priority
Estimated Effort: 2 days
Dependencies: #4

## Description

Implement light and dark theme support with system preference detection.

## Tasks

- [ ] Create theme configuration with CSS variables
- [ ] Implement theme toggle in settings
- [ ] Add system preference detection
- [ ] Theme all UI components consistently
- [ ] Persist theme preference
- [ ] Create custom theme support

## Acceptance Criteria

- Light/dark themes toggle smoothly
- System preference respected
- All components themed consistently
- Preference persists across sessions
- Custom themes can be added

## Technical Requirements

- CSS custom properties
- Theme context provider
- System preference API
- localStorage persistence

#15: Add keyboard shortcuts and command palette

Assignee: Miguel Rodriguez (UI/UX Developer)
Labels: ui, accessibility, low-priority
Estimated Effort: 3 days
Dependencies: #10

## Description

Implement comprehensive keyboard shortcuts and enhance command palette.

## Tasks

- [ ] Define keyboard shortcut system
- [ ] Implement shortcuts for all common actions
- [ ] Add shortcut help overlay
- [ ] Enhance command palette with fuzzy search
- [ ] Add recent commands history
- [ ] Create customizable shortcuts

## Acceptance Criteria

- 80%+ actions accessible via keyboard
- Shortcuts work consistently
- Help overlay shows all shortcuts
- Command palette searches efficiently
- Shortcuts can be customized

## Technical Requirements

- Keyboard event handling
- Command pattern implementation
- Fuzzy search algorithm
- localStorage for preferences

#16: Ensure WCAG 2.1 Level AA accessibility compliance

Assignee: Lisa Zhang (QA Engineer)
Labels: accessibility, quality, low-priority
Estimated Effort: 4 days
Dependencies: All UI components

## Description

Ensure the application meets WCAG 2.1 Level AA accessibility standards.

## Tasks

- [ ] Conduct accessibility audit with axe
- [ ] Fix color contrast issues
- [ ] Ensure keyboard navigation works
- [ ] Add screen reader support
- [ ] Implement focus management
- [ ] Add ARIA labels and descriptions
- [ ] Test with screen readers
- [ ] Create accessibility documentation

## Acceptance Criteria

- axe audit passes with zero violations
- Color contrast meets WCAG AA standards
- All functionality accessible via keyboard
- Screen readers announce content correctly
- Focus moves logically through interface

## Technical Requirements

- axe-core for testing
- ARIA attributes
- Focus management
- Screen reader testing

#17: Write comprehensive documentation and user guides

Assignee: Emma Davis (Technical Writer)
Labels: documentation, low-priority
Estimated Effort: 5 days
Dependencies: All features implemented

## Description

Create comprehensive documentation for users and developers.

## Tasks

- [ ] Write user manual and tutorials
- [ ] Create developer documentation
- [ ] Document API reference
- [ ] Create troubleshooting guide
- [ ] Add inline help tooltips
- [ ] Create video tutorials
- [ ] Document contribution guidelines
- [ ] Set up documentation website

## Acceptance Criteria

- User manual covers all features
- Developer docs enable contributions
- API reference is complete
- Help system assists users
- Tutorials guide new users

## Technical Requirements

- Documentation framework (Docusaurus)
- API documentation generation
- Video recording tools
- Help tooltip system

Issue Dependencies Graph

High Priority (Foundation):
#1 → #2 → #3 → #4, #6, #8
#3, #4 → #5, #7
#3, #8 → #9
#3, #6 → #10
#3, #4 → #11
#3 → #12

Medium Priority (Enhancement):
All High Priority → #13

Low Priority (Polish):
#4 → #14, #15
All UI → #16
All Features → #17

Sprint Planning

Sprint 1 (Week 1-2): Foundation

  • #1: Project setup (Alex)
  • #2: Dependencies (Alex)
  • #3: Data model (Alex)

Sprint 2 (Week 3-4): Core UI

  • #4: Main layout (Miguel)
  • #5: Class tree (Miguel)
  • #6: Axiom editor (Alex)

Sprint 3 (Week 5-6): Visualization & I/O

  • #7: Graph visualization (Miguel)
  • #8: Import/export (Alex)

Sprint 4 (Week 7-8): Advanced Features

  • #9: Reasoning (Sarah)
  • #10: AI co-pilot (Priya)
  • #11: Properties panel (Miguel)

Sprint 5 (Week 9-10): Quality & Polish

  • #12: Persistence (James)
  • #13: Testing (Lisa)
  • #14: Themes (Miguel)
  • #15: Shortcuts (Miguel)

Sprint 6 (Week 11-12): Final Polish

  • #16: Accessibility (Lisa)
  • #17: Documentation (Emma)
  • Bug fixes and optimization

Team Responsibilities

Alex Chen (Lead Developer)

  • Project architecture and technical decisions
  • Core ontology model and state management
  • Axiom editor implementation
  • Code review and quality assurance

Sarah Johnson (Backend Engineer)

  • WASM integration and reasoning engine
  • Performance optimization
  • API design and implementation

Miguel Rodriguez (UI/UX Developer)

  • Graph visualization and layout
  • User interface components
  • Responsive design and interactions
  • Theme and accessibility implementation

Dr. Priya Patel (AI/ML Engineer)

  • LLM integration and prompt engineering
  • AI co-pilot functionality
  • Natural language processing

James Wilson (DevOps Engineer)

  • Build systems and CI/CD
  • Testing infrastructure
  • Deployment and monitoring
  • Persistence and storage

Lisa Zhang (QA Engineer)

  • Test strategy and implementation
  • Accessibility compliance
  • Performance testing
  • Quality assurance processes

Emma Davis (Technical Writer)

  • User documentation
  • Developer guides
  • API documentation
  • Training materials

Risk Mitigation

  1. Technical Complexity: Pair programming for complex features
  2. Performance Issues: Early performance testing and optimization
  3. Dependencies: Regular dependency updates and security scanning
  4. Browser Compatibility: Cross-browser testing throughout development
  5. Accessibility: Continuous accessibility testing and review