Local development

Knowledge owns scientific memory: contextual evidence, claims, contradiction resolution, provenance, biological mappings, coverage, and review briefs. A local change must preserve the route from every derived statement back to its source and context. Convenience fallbacks that erase ambiguity or provenance are contract regressions.

Run package-scoped gates

From the repository root, use:

make lint PACKAGE=bijux-proteomics-knowledge
make test PACKAGE=bijux-proteomics-knowledge
make quality PACKAGE=bijux-proteomics-knowledge
make api PACKAGE=bijux-proteomics-knowledge

Run make build PACKAGE=bijux-proteomics-knowledge when public exports, packaged reference fixtures, metadata, or compatibility forwarding changes. Keep generated evidence and reports under artifacts/.

Follow evidence lineage

flowchart LR
    source["source and context"]
    evidence["EvidenceRecord"]
    claim["claim and polarity"]
    conflict["contradiction or resolution"]
    brief["reviewable decision brief"]
    source --> evidence --> claim --> conflict --> brief

Begin with the owned model or resolver. Evidence and claim changes route through memory/models/; graph invariants through memory/integrity/; conflict policy through memory/reconciliation/; entity resolution through its named domain package; and reviewer output through reviews/. Keep source retrieval, curation, and persisted memory distinct so network behavior cannot silently change evidence meaning.

Select proof by failure mode

Change	Required evidence
evidence or claim schema	valid round trip, missing context, invalid reference, and old artifact load
graph logic	orphan, duplicate, invalid edge, and cycle cases
conflict resolution	supporting, contradicting, unresolved, and escalated cases retain all inputs
entity mapping	resolved, ambiguous, unresolved, and source-version cases
freshness policy	current, stale, expired, and superseded records remain distinguishable
review artifact	every citation and resolution identifier reaches its source record

Reference fixtures must record source identity, retrieval or curation date, license posture, and version where available. A test dataset is not evidence of current external truth unless it is explicitly governed as such.

Preserve boundaries

Knowledge records and reconciles evidence; it does not perform Core scientific calculations, choose Intelligence actions, or authorize Lab execution. A mapping reports database membership or ambiguity, not pathway activity, causality, therapeutic effect, or experimental confirmation.

The change is ready when source context survives, ambiguous and conflicting states remain visible, graph integrity passes, persisted inputs have an explicit compatibility result, and review outputs can be audited without access to hidden retrieval state.