System Architecture

The Bio-DID-Seq ecosystem integrates multiple components including decentralized identifiers, AI powered processing, knowledge graphs, and secure data management to create a comprehensive platform for research data.

Overview

The system integrates several key components:

• Bio-DID-Seq Core: The foundation providing decentralized identifiers and GDPR compliant data management
• BioAgents: AI powered agents for research data processing and knowledge extraction
• Knowledge Graph: Semantic representation of biological entities and relationships
• IPFS Storage Layer: Decentralized and content addressed storage
• UCAN Authorization: Capability based security model

Core Component Interactions

Integration Architecture

Component Responsibilities

System Integration Workflows

1. Research Paper Processing Workflow

2. Knowledge Query Workflow

3. UCAN Delegation Workflow

Technical Integration Details

1. API Integration

// Example API routes showing system integration
const apiRoutes = {
  // Bio-DID-Seq Core Routes
  "/api/did": "DID document management",
  "/api/auth": "Authentication & UCAN issuance",
  
  // BioAgents Integration Routes
  "/api/bioagents/process": "Process research papers",
  "/api/bioagents/query": "Natural language queries",
  
  // Knowledge Graph Routes
  "/api/kg/sparql": "SPARQL query endpoint",
  "/api/kg/search": "Semantic search interface",
  
  // Data Integration Routes
  "/api/dataverse": "Dataverse integration",
  "/api/ipfs": "IPFS storage operations"
};

2. Service Communication

Services communicate using a combination of:

• REST APIs: For synchronous operations
• Event Bus: For asynchronous workflows
• WebSockets: For real time updates
• gRPC: For high performance internal service communication

Security Integration

1. Authentication Flow

2. UCAN Authorization

async function validateCapability(ucanToken, requiredCapability, resourceId) {
  const valid = await ucanService.verify(ucanToken);
  if (!valid) return false;
  
  const hasCapability = await ucanService.hasCapability(
    ucanToken, 
    requiredCapability,
    resourceId
  );
  
  return hasCapability;
}

Deployment Architecture

All components are containerized using Docker with microservices architecture supporting horizontal scaling.

Integration Benefits

• Data Sovereignty: Researchers maintain control of their data
• Enhanced Discoverability: Knowledge graphs make data more findable
• Simplified Collaboration: UCAN delegation enables secure sharing
• Reduced Integration Burden: Standardized APIs and formats
• Future Proof Architecture: Extensible and modular design