Preparing documentation structure

[minrk]

We're getting underway sketching out what documentation needs to exist here and how it should be organized (#25).

This is being drafted here, and will break out here into more specific tasks.

[minrk]

Docs structure outline:

Documentation Structure

Tutorial

Step-by-step guides for new users to install, configure, and run JupyterHealth in different environments.

• Installation and First Setup
• Acquiring Data from Wearables (Dexcom, Oura, CareX)
• Ingesting FHIR Data into JHE
• Running Your First Analysis in a Notebook
• Uploading an existing dataset intoJHE
• “Zero to JupyterHealth” - deploying JupyterHealth in the cloud on AWS (or whatever)
• Deploying a standalone JupyterHealth Exchange
• Deploying a standalone JupyterHealth Hub
• Fetching and viewing data from the Exchange with JupyterHealth Client
• Launch a JupyterHealth-powered dashboard via SMART-on-FHIR (medplum example)

How-to Guides

Practical guides for more specific needs.

• Deploying JupyterHealth on Kubernetes more of a tutorial
• Configuring JupyterHealth for HIPAA-compliant storage
• Connecting JupyterHealth to a new wearable API
• Using the JupyterHealth REST API
• Upgrading JupyterHealth
• Troubleshooting common ingestion errors
• create a study
• add a patient
• fetch data from the exchange
• Add a data source, data type

Explanation

Conceptual overviews and design choices behind JupyterHealth.

• JupyterHealth: A conceptual overview
• Data flow: Acquisition → Exchange → Analysis
• Consent and Identity Management
• Security Overview (HIPAA, GDPR considerations)
• Interoperability with FHIR, OMOP, Open mHealth
• JupyterHealth RBAC and Governance
• Architecture of JupyterHealth components, and how they work together
• Access control design of the Exchange

Reference (mostly link to separate docs built from package repos)

• JHE Implementation Guide Draft

• (link out) JupyterHealth client API (Python)

• (link out) JupyterHealth Exchange API (REST, maybe Python)

• Technical Overview of JupyterHealth

• API Reference (Exchange API, Sync API)

• Configuration Reference (config.yaml)

• Data Models and Schemas (FHIR, OMOP, IEEE 1752.1)

• Event Logging and Audit Trails

• Monitoring and Telemetry

• Deployment Reference Architectures

Contributing

• Setting up a development environment
• Contributor guide
• Links to other references

[minrk]

Note that the diataxis organization is more about how to think about writing each document. We can put them in folders matching the name for simple organization, but it does not mean that these concepts dictate navigation of the content. That's a separate question, independent of the content.

[KirstieJane]

Wooooo! Exciting!

Is there a way to have the docs site built with MyST? As a JupterBook 2? Because then we can re-use content across other team compasses etc!

[minrk]

This is already a myst site, but not built with Jupyter book (yet?)