Sensitive data management

Legal framework

Sensitive data is managed within a well-established technical and regulatory framework:

• Technical specifications reviewed by the Confederation for the automatic exchange of data from SPSP to the Federal Office of Public Health.
• Data Protection Impact Assessment reviewed annually with the Data Protection Officer of SIB.
• Data Transfer and Use Agreement established with each data provider.
• Sensitive data hosted on BioMedIT, managed by SIB.

Secure IT infrastructure

The diagram above outlines the SPSP IT infrastructure, structured across several zones with a focus on secure genomic data processing and sharing. We explain below each zone and its components:

1. SIB ACCESS ZONE (Public but filtered / whitelisting)

• Purpose: Acts as the entry point for external institutions (e.g., reference laboratories) to upload genomic data. Also used to securely exchange data with federal authorities.

• Components:

  • sFTP: Used by data providers to transfer files securely.

  • Protocols: Uses sftp for file transfers, HTTPS for secure communications.

  • Data Flow: Data is sent into the secure zone.

2. SIB SECURE ZONE (SENSA)

• Purpose: Handles all sensitive data, ensures data is cleaned (removal of any human contamination) and stored securely.

• Key Components:

  • Loader: Parses and loads data into the system.

  • Cleaner: Cleans raw data and de-identifies metadata.

  • Reporter: Prepares summaries or reports for federal authorities.

  • SPHN Connector: Connects to other BioMedIT nodes.

  • Database: spspsensitivedb stores all sensitive data.

3. SIB INTERNAL SPSP ZONE

• Purpose: Processes and stores non-sensitive data using modular, pathogen-specific microservices.

• Pathogen Instances (each accessed via HTTPS):

  • SCV2, VIRAL, INFLUENZA, BACTERIA, WASTEWATER, etc.

• Databases:

  • Store cleaned, non-sensitive data for each instance.

• Jobs Execution:

  • Handled on two HPC clusters, spsp-bio01 and spsp-bio02, both running SLURM.

  • Bioinformatics pipelines and tools centrally stored on /tools.

4. DMZ (Demilitarized Zone)

• Purpose: Exposes controlled interfaces to users and external systems.

• Components:

  • SPSP Portal (HTTPS): Web frontend for accessing data and dashboards.

    • /api provides access to non-sensitive data.

  • Reverse Proxy: Controls traffic between external users and internal services.

  • Keycloak: Manages authentication (SSO).

Data Flows & Security

• Protocols (in purple):

  • sFTP, HTTPS, TCP/IP, SSH:22, SLURM REST

• Color Coding:

  • Blue boxes: Virtual machines (VMs)

  • Orange borders: Frontend components

  • Zones: Separated by security level and function

Security Highlights

• Strict segregation of sensitive and non-sensitive data.

• Differentiated access control (e.g., Keycloak SSO).

• Data passes through cleaning and de-identification before any public/internal access.

• Integration with BioMedIT for highly secure biomedical data processing.