Scope and Non-Goals

bijux-proteomics-knowledge owns durable evidence state: what source was observed, which biological subject and context it concerns, which claim it supports or contradicts, how disagreement was reviewed, and what remains unknown. It preserves evidence for later judgment without making the judgment itself.

In Scope

• source, retrieval, release, license, and derivation provenance;
• protein, gene, isoform, ortholog, pathway, complex, disease, drug, feature, and assay identity resolution;
• evidence records, bundles, claims, typed relationships, and decision lineage;
• biological context, quantitative uncertainty, artifact flags, and source independence;
• evidence graphs, integrity checks, coverage, freshness, and knowledge gaps;
• contradiction detection, clustering, reconciliation, escalation, and holds;
• decision-scoped briefs that preserve support, adverse evidence, and unresolved questions; and
• append-only belief updates linked to named evidence and policy revisions.

Explicit Non-Goals

Not owned here	Responsible boundary
parsing raw proteomics formats, statistical analysis, and scientific acceptance	Core
executing, resuming, or replaying work	Runtime
ranking candidates, choosing an action, and promoting advisory policy	Intelligence
assay feasibility, custody, observations, and evidence-promotion execution	Lab
shared identifiers, document envelopes, canonical bytes, and schema primitives	Foundation
source access credentials, database transactions, and service transport	deploying application

Knowledge does not claim exhaustive coverage merely because a graph is valid. It does not treat a citation as contextual support, a resolved identifier as biological equivalence, record count as independent replication, or confidence as calibrated decision probability.

flowchart LR
    source["versioned source"] --> record["contextual evidence record"]
    record --> claim["support or contradiction"]
    claim --> graph["validated evidence graph"]
    graph --> review{"reconciliation and sufficiency"}
    review --> brief["decision-scoped evidence brief"]
    review --> hold["gap, dispute, or hold"]
    brief -. "consumed by" .-> judgment["Intelligence judgment"]

Ownership test

A behavior belongs here when it changes what evidence is retained, connected, qualified, or considered sufficient while leaving the underlying scientific calculation and downstream decision policy unchanged. It belongs elsewhere when it creates the scientific observation, executes work, ranks actions, or authorizes a laboratory handoff.

A trustworthy handoff includes the source and retrieval identity, subject and context, relationship direction, quantitative uncertainty, derivation and independence, freshness, competing evidence, resolution history, coverage, gaps, and review disposition.