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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.

That role is materially richer now than a general evidence ledger. Stronger workflow packets, public trust surfaces, and downstream recommendation pressure mean this section has to own exact grounding, contradiction discipline, literature audit routes, and biological context with enough clarity that the rest of the repository cannot improvise why a sentence should be believed.

Why Readers Should Start Here More Deliberately

  • this is where the repository proves it has memory, contradiction, and grounding discipline instead of only benchmark packets and careful prose
  • the package now carries more real biological context than older docs admitted, including pathway, complex, kinase, disease, drug, and ortholog lookup owners
  • if this section is weak, every stronger recommendation or trust sentence above it becomes less honest immediately
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

What This Section Now Carries

  • claim grounding that ties public language back to named evidence owners
  • contradiction and confidence routes that keep hesitation visible
  • literature and biological review surfaces that prevent downstream packages from inventing scientific memory

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.
  • Open This Package Does Not Own when a proposal is trying to turn evidence state into recommendation policy, workflow law, or runtime behavior.
  • Open Workflow Claim Grounding when the question is whether public trust language is actually tied to exact evidence owners.
  • Open Workflow Literature Audits when the question is whether the shipped citations, bibliography, or gap stories are still current enough.

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

Reader Questions This Section Can Answer Well

  • why a public trust sentence is grounded rather than only rhetorically careful
  • where contradiction pressure still keeps a family sentence narrow
  • which biological context the repository really owns instead of borrowing loosely from external memory
  • how literature and evidence state differ from recommendation posture or lab consequence

Strongest Knowledge Proof

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