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bijux-proteomics-knowledge

bijux-proteomics-knowledge owns evidence state in bijux-proteomics. It is where claims, confidence, contradiction handling, grounding, and knowledge-level review rules stay explicit instead of being spread across runtime or scoring code. Serious systems do not only need facts; they need structured disagreement, confidence, and traceable reasons to hesitate.

This package is much richer now than a passive evidence ledger. It owns selective scientific memory, contradiction-aware review, workflow claim grounding, literature audit routes, and biological context surfaces that stop the rest of the product from improvising why a workflow result should be believed.

flowchart LR
    inputs["observations, records,<br/>derived findings"]
    claims["claims"]
    confidence["confidence"]
    contradictions["contradictions"]
    knowledge["knowledge<br/>evidence state"]
    intelligence["intelligence"]
    lab["lab"]
    runtime["runtime"]

    inputs --> claims
    inputs --> confidence
    inputs --> contradictions
    claims --> knowledge
    confidence --> knowledge
    contradictions --> knowledge
    knowledge --> intelligence
    knowledge --> lab
    knowledge --> runtime

What This Package Protects

  • recommendation code cannot quietly rewrite evidence state
  • runtime code cannot smuggle operational convenience in as scientific truth
  • contradiction is preserved as information instead of being treated as failure
  • stronger workflow stories can be slowed by real grounding pressure instead of by vague caution language

What It Owns

  • evidence records and claim state
  • confidence semantics and contradiction handling
  • knowledge-level review boundaries used by downstream packages
  • grounding, literature-pressure, and biological-context surfaces that stop the repository from sounding more certain than its evidence state earns

Concrete Knowledge Families

owner band visible package substance why it matters
memory and reviews evidence bundles, claims, confidence, contradiction, review state public belief can be challenged against structured memory
references workflow grounding, literature audits, curated scientific support release language can be read against explicit citation pressure
biological context owners pathways, complexes, kinases, drugs, disease, features, coverage, orthologs scientific meaning stays concrete instead of generic
contracts and identity compatibility and entity reconciliation downstream packages inherit one knowledge-state contract

Why This Package Matters More Now

  • public trust language is now challenged by explicit grounding routes instead of general scientific tone
  • stronger workflow packets need stronger contradiction and citation discipline
  • downstream recommendation and lab consequence can now be traced back to visible evidence state instead of inferred background knowledge
  • biological reasoning is now explicit enough that readers can inspect where confidence came from, where contradiction remains open, and why hesitation is scientifically responsible instead of operationally inconvenient

Shared Reader Routes

  • Use Decision Support when the question is still about evidence, contradiction, or public belief posture rather than one knowledge-owner module.
  • Use Workflow Consequence Maps when the question is how contradiction pressure should narrow the current recommendation before assay spend is approved.
  • Use What Changed The Recommendation when the question is whether literature pressure, comparator pressure, or lab burden actually moved the call.
  • Use Workflow Families when the family route is clearer than the package route.

Start Inside This Package

  • Open Foundation for the package role and boundary.
  • Open Workflow Claim Grounding when the question is which exact public sentence the repository can still justify.
  • Open Workflow Literature Audits when the question is where curated reading pressure already outruns the shipped benchmark or comparator packet.
  • Open Architecture when the concern is how claims, confidence, and contradiction handling stay separated.
  • Open Interfaces when the question is a claim, evidence, or confidence-facing contract.

Reader Questions This Package Can Answer

  • which parts of a workflow story are directly grounded and which still depend on bounded inference
  • where contradiction remains unresolved instead of being smoothed into a single recommendation sentence
  • how literature pressure, comparator pressure, and biological-context pressure reshape confidence before a lab or decision surface is allowed to promote the claim
  • whether a public workflow sentence has earned trust through explicit evidence state rather than tone

What Changed Since v0.3.7

  • biological context is now visible enough to count as real product substance, not implied support material
  • contradiction and grounding routes are now concrete enough to slow an over-optimistic workflow story
  • the package now shows where scientific hesitation comes from instead of only insisting that hesitation exists

Evidence Proof Surfaces

  • decision-support pages when the question is still cross-package and public facing
  • workflow grounding and literature audit pages when the real issue is whether the repository can justify what it says
  • architecture pages for claim, contradiction, and confidence separation
  • interfaces pages for evidence and claim-facing contracts that downstream packages must not rewrite

What It Refuses

  • scoring and recommendation policy
  • execution orchestration and operator surfaces
  • assay planning and outcome promotion

Strongest Proof Route

First Proof Check

  • packages/bijux-proteomics-knowledge/src/bijux_proteomics_knowledge
  • packages/bijux-proteomics-knowledge/tests
  • confidence and contradiction modules once the claim narrows to one seam
  • grounding, citation, and contradiction-review artifacts when the public claim itself is under scrutiny