Module Map¶

bijux-proteomics-knowledge is the evidence-memory and biological-grounding layer. It represents claims and their support, protects graph integrity, resolves external biological identifiers, and reports what the available knowledge does—and does not—cover.

flowchart LR
    R[references] --> N[normalization]
    N --> M[evidence memory]
    M --> G[graph integrity]
    M --> X[reconciliation]
    B[biological resolvers] --> M
    G --> V[reviews]
    X --> V
    C[coverage] --> V

Evidence memory¶

memory.models defines EvidenceRecord, EvidenceClaim, and EvidenceBundle. Normalization turns incoming material into those contracts. Integrity code validates relationships among claims, evidence, and provenance. Reconciliation represents disagreement and resolution without deleting the conflicting source record.

Biological grounding¶

Family	Resolution surface
`identity`	Protein identifier resolution and status reporting
`pathways`, `complexes`	Membership resolution and confidence or coverage policy
`kinases`	Kinase–substrate relationships and match type
`drugs`	Drug–target relationships and relationship type
`disease`	Disease-term resolution
`orthologs`	Cross-species mapping, ambiguity, and evidence status
`features`	Protein feature intervals and overlap queries
`coverage`	Entity-set coverage reports under an explicit policy

Each resolver returns typed entries, summaries, and reports, with stable TSV renderers for external review. The package root exposes these scientific contracts directly alongside the three memory models.

Contracts and reviews¶

contracts.schema assesses schema compatibility at the knowledge boundary. references declares public reference material. reviews turns evidence state into decision briefs, explanations, provenance views, trends, and flagship-evidence records. These projections do not replace the underlying evidence bundle: they point back to it.

Knowledge records what sources assert and how those assertions connect. It does not rank program candidates, choose a laboratory action, or operate a service.