Processing sensitive data

[svedziok]

add section for working with sensitive data in the ELIXIR-on-Cloud framework

Summary by Sourcery

Add a new ELIXIR-on-Cloud documentation guide on processing sensitive human data, covering legal frameworks, secure environment definitions, and use cases, and expose it in the site navigation.

Build:

• Update mkdocs.yml navigation to include the new guides index and Sensitive Data page

Documentation:

• Add docs/guides/index.md as the main entry point for ELIXIR-on-Cloud documentation
• Add docs/guides/guide-info/sensitive_data.md with guidance on legal requirements, environments (TEE, SPE, TRE), similarities, differences, and use cases for sensitive data processing

[sourcery-ai]

Reviewer's Guide

This PR adds a new section on processing sensitive data to the ELIXIR-on-Cloud documentation by updating the site navigation, creating a guides index page, and introducing a detailed guide covering legal frameworks, secure environments, and use cases.

Class diagram for secure environments in sensitive data processing

classDiagram
    class Environment {
      +Isolation
      +Security
      +Integrity
      +Confidentiality
      +Controlled Access and Authentication
      +Collaboration and Analysis
    }
    class TEE {
      +Secures startup, code, and data during execution
      +Used in secure mobile/cloud environments
    }
    class SPE {
      +Ensures secure data processing and computation
      +Applied in secure analytics/cryptographic computation
    }
    class TRE {
      +Comprehensive secure research environment
      +Emphasizes privacy, governance, compliance
    }
    Environment <|-- TEE
    Environment <|-- SPE
    Environment <|-- TRE

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Flow diagram for sensitive data processing use cases

flowchart TD
    A[Researcher needs to process sensitive data]
    B{Where is the data stored?}
    C[Central data]
    D[Federated data]
    E{Where is the data processed?}
    F[Local processing]
    G[Cloud processing]
    H[Data repository]
    I[Cloud platform]
    J[Federated database]
    K[Federated processing]

    A --> B
    B --> C
    B --> D
    C --> E
    D --> E
    E --> F
    E --> G
    C --> E
    D --> E
    C --> F --> H
    C --> G --> I
    D --> F --> J
    D --> G --> K

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File-Level Changes

Change	Details	Files
Updated documentation navigation	Added guides index entry under Guides Inserted 'Sensitive Data' sub-section under Information Updated mkdocs.yml nav structure	mkdocs.yml
Introduced Guides landing page	Created ELIXIR-on-Cloud overview content Described project goals and GA4GH Cloud Work Stream compliance Outlined documentation scope and best practices	docs/guides/index.md
Added processing sensitive data documentation	Outlined GDPR and EHDS legal frameworks Defined and compared TEE, SPE, and TRE environments Detailed use cases with a storage vs. processing matrix	docs/guides/guide-info/sensitive_data.md

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[sourcery-ai]

Hey @svedziok - I've reviewed your changes and they look great!

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[Copilot]

Pull Request Overview

This PR introduces a new documentation guide for handling sensitive human data within the ELIXIR-on-Cloud framework and exposes it in the site navigation.

• Update mkdocs.yml to add a Guides index and link to the Sensitive Data page
• Create docs/guides/index.md as the main entry point for ELIXIR-on-Cloud documentation
• Add docs/guides/guide-info/sensitive_data.md covering legal frameworks, secure environments, and use cases

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
mkdocs.yml	Inserted new nav entries for the guides index and Sensitive Data page
docs/guides/index.md	Added top-level documentation landing page
docs/guides/guide-info/sensitive_data.md	Added detailed guide on processing sensitive human data

Comments suppressed due to low confidence (1)

mkdocs.yml:85

• [nitpick] The navigation entry for the guides index uses only the file path. Consider adding a user-friendly title (e.g., Guides Overview: guides/index.md) so the link displays clearly in the site menu.

      - "guides/index.md"

[uniqueg]

Thanks, @svedziok - looks good.

Perhaps three minor suggestions:

• Perhaps better to name the new section "General" rather than "Information", given that all the other guides also contain "information"?
• Throughout the organization, we are using semantic commit messages of 50 chars or less as PR titles. The precise guidelines are here: https://elixir-cloud-aai.github.io/guides/guide-contributor/general-guidelines/#commit-messages Together with squash merging commits from a feature branch, this keeps our commit histories clean, consistent and amenable to release automation when we squash merge commits. See example titles here (admittedly, it's a little boring for a docs page): https://github.com/elixir-cloud-aai/elixir-cloud-aai.github.io/pulls?q=is%3Apr+is%3Aclosed
• Note that throughout the repo, only named references are used, and that all of the named references are listed in file includes/references.md. This makes it easier to read the raw files and makes the reuse and maintenance of references easier. Btw, there is also includes/abbreviations.md, where one can define abbreviations centrally. Every time an abbreviation listed in the file is used, there will be a tool tip created in the docs that resolves the abbreviation. Very useful!