Architecture¶

bijux-proteomics-knowledge architecture is about keeping evidence usable even when sources disagree. This section should help a reader see how claims, graphs, confidence, contradiction handling, and review outputs fit together without collapsing into recommendation policy or generic storage plumbing.

flowchart LR
    evidence["evidence records"]
    claims["claims"]
    knowledge_graph["knowledge graph"]
    confidence["confidence segments"]
    resolution["contradiction resolution"]
    review["review and repository outputs"]

    evidence --> claims --> knowledge_graph
    knowledge_graph --> confidence
    knowledge_graph --> resolution
    confidence --> review
    resolution --> review

Architectural Promise¶

contradictory evidence should become inspectable structure, not silent data loss
trust scoring and contradiction handling should remain close to the claims they justify
repository boundaries should preserve the reasoning trail, not just the final answer

Start With¶

open Execution Model when the question is how raw evidence becomes reviewable knowledge
open Integration Seams when a change starts to blur knowledge work with recommendation policy or generic persistence concerns
open Module Map when you need the owner for claims, graphs, confidence, or resolution code

Read By Tension¶

when evidence volume grows: State and Persistence and Dependency Direction
when contradictions grow: Error Model and Architecture Risks
when new source or resolution logic is proposed: Extensibility Model and Code Navigation

First Proof Check¶

src/bijux_proteomics_knowledge/claims.py, evidence.py, and graph.py for canonical knowledge structures
src/bijux_proteomics_knowledge/confidence/segments.py, resolution.py, and review.py for trust and contradiction handling
src/bijux_proteomics_knowledge/repositories.py, schema.py, and serialization.py for durable boundaries

Boundary Test¶

If the architecture can show a final conclusion but not the path through conflict and confidence, it is hiding the most important part of the package.