External evidence audit

Use this skill only after the host or researcher has supplied a JSON envelope for a completed external capability call.

Boundary

• Do not choose, call, retry, or schedule another plugin.
• Do not infer producer authenticity from a declared plugin name.
• Do not treat a content hash as a signature.
• Do not convert a database record, paper, viewer observation, or successful analysis run into independent validation.
• Do not assign scientific maturity; intake always starts UNASSESSED.
• Do not infer whether an envelope supports or contradicts a claim. The host must supply one review-bound adjudication per envelope.
• Do not treat PASS as final scientific acceptance. The named decision_owner remains accountable for the final decision.

Input

Create bionexus.external-evidence-envelope.v1 with the producer identity, capability family, exact returned payload, originating request, and the family-specific source context documented in docs/ecosystem-collaboration.md.

Audit it with:

python skills/external-evidence-audit/scripts/audit_external_evidence.py envelope.json

Write a reusable JSON audit artifact with:

python skills/external-evidence-audit/scripts/audit_external_evidence.py envelope.json --out audit.json

VALID means only that the payload hash and required declared context are internally consistent. Producer identity remains DECLARED_NOT_AUTHENTICATED. INCOMPLETE or INVALID must not enter the Claim–Evidence Ledger as support.

Multi-source claim assessment

After each envelope is VALID, create bionexus.ecosystem-claim-packet.v1 with:

• the exact envelopes;
• a declared claim and explicit claim_context constraints;
• exactly one supports, contradicts, context, or depends_on adjudication per envelope;
• rationale, named adjudicator, and SHA-256 adjudication receipt for every claim-bearing edge;
• a named human decision_owner.

Then run:

python skills/external-evidence-audit/scripts/assess_ecosystem_claim.py claim-packet.json --out assessment.json

The result contains Warrant, Audit, EvidenceCard, and Claim–Evidence Ledger artifacts. Duplicate payloads count once, declared context conflicts block all claim-bearing edges, explicit contradictory evidence yields CONFLICTED, and final_decision always remains PENDING_HUMAN_DECISION.

Epistemic Lineage & Independence Graph

When multiple connectors (e.g. PubMed, Consensus, bioRxiv, Open Targets, ChEMBL) return distinct payloads, the Evidence Independence Graph resolves their epistemic lineage (origin_id, derived_from, same_study_as, dataset_identity, assay_identity) to eliminate epistemic double counting. Derived syntheses, preprints, and secondary database mirrors are grouped into primary study clusters:

Raw Evidence Count = 8
Independent Origins = 2
Primary Studies = 2
Derived Syntheses = 4
Database Mirrors = 2

The resulting EvidenceCard reports the exact resolution: "8 evidence objects were retrieved through 5 connectors, but they resolve to only 2 independent primary studies."

Connector Profile Registry

Scientific contracts for external capabilities are governed declaratively in standards/connector-profiles/profiles/ (e.g. enrichr.yaml, pubmed.yaml, chembl.yaml). Each profile defines required_context, default_evidence_role, maximum_default_claim, forbidden_claims, and BNS-019 semantic_profile. BioNexus Core knows only the protocol and does not act as an MCP router or marketplace.