Bio-DID-Sequencer

Bio-DID-Seq is a GDPR compliant Decentralized Identifier (DID) system designed for research data, integrating with Dataverse and powered by AI agents.

System Overview

Bio-DID-Seq provides a robust, decentralized approach to managing identifiers for research data. By implementing the W3C DID specification and integrating with existing persistent identifier infrastructures (like DOI and Handle), it offers a sustainable and user centric solution for the research community.

Core Components

1. Layered Architecture

Bio-DID-Seq implements a 5 layer architecture:

Storage Layer

• IPFS Cluster: Provides redundant, decentralized storage for research data
• Content Addressing: All data is referenced by its cryptographic hash
• Private IPFS Network: Ensures data security while maintaining decentralization

Identity Layer

• did:bio DID Method: A W3C DID 1.0 conformant method with a published specification, anchored on Solana
• Generative Resolution: Every valid identifier resolves - with no on-chain state, it resolves to a deterministic document at zero cost
• ML-DSA-87 Verification Methods: Post-quantum (FIPS 204) assertion keys as a first-class verification method type
• DID Resolution: Full resolution algorithm with resolution metadata, deactivation, and version tracking

Authorization Layer

• UCAN Integration: User Controlled Authorization Network for capability based security
• Post-Quantum Signatures: Capability tokens signed with ML-DSA-87; capabilities live inside the signed payload
• Delegated Permissions: Attenuated delegation with proof chains and cascading revocation
• GDPR Compliance: Built in privacy controls and user data ownership

Application Layer

• Actix Web API: High performance web service endpoints
• Async Processing: Efficient handling of compute intensive operations
• Rate Limiting: Protection against abuse and DoS attacks

Integration Layer

• BioAgents Connector: Integration with AI powered data processing
• Dataverse Adapter: Seamless connection with Harvard Dataverse
• DOI & Handle Bridge: Interoperability with existing identifier systems

2. Key System Entities

DID Document

The core data structure representing a decentralized identifier for research data:

{
  "@context": [
    "https://www.w3.org/ns/did/v1",
    "https://www.w3.org/ns/cid/v1"
  ],
  "id": "did:bio:devnet:2T6zLFvMx7NJac5qQtiKTaPhMwHLkwKETWjUK1yKv4tc",
  "verificationMethod": [
    {
      "id": "did:bio:devnet:2T6zLFvMx7NJac5qQtiKTaPhMwHLkwKETWjUK1yKv4tc#default",
      "type": "Multikey",
      "controller": "did:bio:devnet:2T6zLFvMx7NJac5qQtiKTaPhMwHLkwKETWjUK1yKv4tc",
      "publicKeyMultibase": "z6MkfuN2vWAoHermh6vY6TgAJfwhBWZCApZb9XeQ9HwLqHfz"
    }
  ],
  "authentication": ["did:bio:devnet:2T6zLFvMx7NJac5qQtiKTaPhMwHLkwKETWjUK1yKv4tc#default"],
  "assertionMethod": ["did:bio:devnet:2T6zLFvMx7NJac5qQtiKTaPhMwHLkwKETWjUK1yKv4tc#default"],
  "service": [
    {
      "id": "did:bio:devnet:2T6zLFvMx7NJac5qQtiKTaPhMwHLkwKETWjUK1yKv4tc#storage",
      "type": "IPFSStorage",
      "serviceEndpoint": "https://ipfs.bio-did-seq.example/api"
    }
  ],
  "metadata": {
    "title": "CRISPR-Cas9 Gene Editing Dataset",
    "researchers": [
      {
        "name": "Jane Smith",
        "orcid": "0000-0001-2345-6789",
        "role": "Principal Investigator"
      }
    ],
    "keywords": ["CRISPR", "gene editing", "genomics"],
    "dataverse_link": "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/EXAMPLE"
  }
}

System Workflows

1. DID Creation and Registration

2. BioAgents Processing

3. UCAN Authorization Flow

Technical Specifications

API Endpoints

Create a DID

curl -X POST http://localhost:8080/api/did \
-H "Authorization: Bearer <YOUR_TOKEN>" \
-H "Content-Type: application/json" \
-d '{
  "controller": "did:bio:controller123",
  "public_key": "z6MkhaXgBZDvotDkL5257faiztiGiC2QtKLGpbnnEGta2doK",
  "metadata": {
    "title": "Research Dataset",
    "researchers": [{"name": "John Doe", "role": "Lead Researcher"}],
    "keywords": ["biology", "genomics"],
    "license": "CC-BY-4.0"
  }
}'

Security Considerations

GDPR Compliance

The system is designed with privacy as a core principle:

• Data Minimization: Only essential data is collected
• User Control: Researchers maintain control over their data
• Right to be Forgotten: DIDs can be deactivated/deleted
• Transparency: Clear audit trails for data access
• Consent Management: Explicit permission required for data sharing

Decentralized Security

• No Single Point of Failure: Distributed architecture
• Capability Based Security: Fine grained access control with UCAN
• Tamper Evident Storage: Content addressing ensures data integrity
• Decentralized Identity: No central authority for identity management