Knowledge policy configuration

Knowledge has no global settings file or implicit annotation database. Each operation receives its evidence, reference pack, expected biological context, and policy explicitly. This prevents deployment state from silently changing the trust or interpretation of a durable evidence bundle.

Trust policy

TrustPolicy names the source and strength weights used to score records. It also controls penalties for stale records, detected conflicts, duplicate groups, and preferred maximum age by source type. Defaults distinguish lab assays, literature, external databases, structure models, and curated notes, but a project-specific policy should have its own stable policy_id.

Trust is not record count. Preserve both the quantity and quality components, decisive-record count, modality diversity, and integrated score. A large bundle of duplicated or stale records must not appear stronger merely because it is large.

Conflict and resolution policies

ConflictPolicy controls which disagreements are detected: shared decision tags, same-source assay disagreement, opposite quantitative direction, and effect-size divergence. Detection records a conflict; it does not select a winner.

ResolutionPolicy separately defines:

• the minimum confidence gap for automatic acceptance;
• source-type precedence;
• whether high-severity conflicts force a hold;
• whether biological-context or modality disagreement should be split rather than collapsed.

These policies answer different questions and must remain separately versioned. Weakening detection because resolution is inconvenient hides evidence; strengthening source precedence does not make two biological contexts comparable.

Decision and biological-resolution policies

DecisionGateProfile sets minimum trust and triangulation for a direct advance recommendation in a knowledge brief. Coverage policies for pathways, complexes, and knowledge entities set their own resolution thresholds. Context scoring profiles define how species, biological system, and sample type affect compatibility.

Configuration invariants

• Pass the reference or annotation pack explicitly and preserve its identity.
• Store policy identifiers with reports; a numeric trust score without its policy cannot be reproduced.
• Keep confidence, evidence strength, and source precedence distinct.
• Treat expiry and age policy as review signals, not deletion instructions.
• Never auto-accept high-severity conflicts when the selected resolution policy requires a hold.
• A schema-compatible payload may still be scientifically stale, contextually incompatible, duplicated, or contradictory.