Foundation¶

The foundation section explains the durable role of bijux-proteomics-knowledge before it explains implementation detail. Use it to resolve why evidence truth belongs here before decision or lab layers consume it.

flowchart TB
    observations["observations"]
    claims["claims"]
    confidence["confidence"]
    contradictions["contradictions"]
    knowledge["knowledge foundation"]
    consumers["intelligence, lab, runtime"]

    observations --> claims
    observations --> confidence
    observations --> contradictions
    claims --> knowledge
    confidence --> knowledge
    contradictions --> knowledge
    knowledge --> consumers

What This Section Protects¶

a stable place for truth claims before they become decisions
contradiction as structured information instead of something to hide
confidence semantics that downstream packages can consume without redefining

Start With¶

Open Package Overview for the shortest statement of the package role.
Open Ownership Boundary when the question is whether a change belongs here or in a neighbor.
Open Scope and Non-Goals when a proposed change risks broadening the package.
Open Capability Map when you need the concrete work the package is allowed to do.

Section Pages¶

What This Section Settles¶

when a change is really about evidence state rather than about downstream use
how confidence and contradiction should remain explicit
when a proposed change belongs in intelligence, lab, or runtime instead of here

First Proof Check¶

packages/bijux-proteomics-knowledge/src/bijux_proteomics_knowledge
packages/bijux-proteomics-knowledge/tests
neighboring handbooks once the change crosses the local boundary

Neighbors¶

Open bijux-proteomics-intelligence when the question leaves claims, confidence, contradictions, and evidence state.
Open bijux-proteomics-lab when the issue is clearly outside this package's local role.