Knowledge artifact contracts

Knowledge artifacts are the durable memory between analytical execution and a decision. They must preserve enough context to reproduce a claim's support, challenge it, and detect when its evidence has become stale.

Canonical artifacts

Artifact	Durable content
evidence record	source, context, quantitative support, flags, confidence, lineage
evidence bundle	target-scoped records plus schema and provenance envelope
governed bundle	evidence plus digested runtime, summary, and review references
evidence graph	explicit relationships among evidence, claims, targets, and decisions
claim dossier	support, contradictions, assumptions, falsifiers, and resolution route
decision brief	evidence posture translated for a bounded review decision
resolution report	matched, ambiguous, missing, and unresolved biological mappings

Every artifact has a different trust claim. A source digest establishes content identity, a graph establishes recorded connectivity, and a decision brief establishes a review view. None alone establishes biological truth.

Provenance and reconciliation

Conflict resolution produces a new resolution record; it does not edit the losing evidence into agreement. Provenance lines retain the claim, source, artifact, and decision route. Escalation queues capture unresolved conflicts that need human or experimental adjudication.

flowchart TD
    records["immutable evidence records"] --> graph["evidence graph"]
    graph --> conflict["conflict detection"]
    conflict -->|policy can resolve| resolution["new resolution record"]
    conflict -->|insufficient basis| queue["escalation queue"]
    resolution --> brief["decision brief"]
    queue --> brief

Literature freshness audits, unsupported-claim ledgers, contradiction dossiers, knowledge-deficit reports, and replay-proof ledgers expose weaknesses instead of removing them from publication artifacts.

Biological reference artifacts

Resolution reports carry structured entries and summaries. Their TSV renderers provide stable reviewer columns for protein IDs, features, pathways, complexes, kinases, drugs, disease terms, orthologs, and coverage. Publish the typed report beside a TSV when ambiguity, policy, or nested provenance cannot be represented faithfully in a flat row.

Reference packs should be versioned and attributable. A result without the reference-pack identity cannot be distinguished from drift caused by updated aliases, memberships, or annotations.

Publication checklist

Before publishing a knowledge artifact, confirm:

1. schema, artifact, target, and evidence identifiers are stable;
2. source URI or locator, source type, origin, extraction method, and curator are recoverable;
3. biological and experimental context is present where it constrains meaning;
4. supporting, contradicting, stale, ambiguous, and unresolved states remain visible;
5. reference-pack and policy identity accompany biological resolution;
6. canonical JSON is retained when a TSV or narrative is emitted;
7. derived decisions reference rather than replace their upstream artifacts.

This set is the minimum needed to audit what was known at the time of a decision.