build-domain-ontology

Purpose

Construct a tool-independent domain ontology: scope the domain, atomize concepts, type relations, build hierarchy, audit consistency, detect gaps, and refine confidence.

Input contract

required: [domain_scope, concept_records, relation_evidence]
optional: [assumptions, prior_findings, evidence_updates]
constraints: [consume named scientific objects; preserve provenance; keep unresolved uncertainty visible]

Execution protocol

Do not perform called SOP operations inline; each loaded SOP owns its contract and thresholds.

1. You MUST load skill scope-domain to freeze the domain question, inclusion boundary, granularity, and reopening trigger before extracting entities.
2. You MUST load skill extract-concepts to capture source-defined concepts and relation candidates while retaining aliases, qualifiers, and unresolved meanings.
3. You MUST load skill atomize-concept to split broad concepts into mechanism-, function-, level-, or context-specific facets.
4. You MUST load skill type-relation to type each in-scope relation while preserving direction, rejected alternatives, and evidence.
5. You MUST load skill construct-hierarchy to insert supported edges into an acyclic hierarchy and quarantine cycles, orphans, and missing levels.
6. You MUST load skill audit-structure-consistency to check node and relation schemas with hierarchy, dependency, cardinality, and cycle constraints.
7. You MUST load skill detect-coverage-gap to prioritize absent, thin, disconnected, or weak regions.
8. You MUST load skill canonicalize-entity to merge only semantically identical aliases and near-duplicates while retaining rejected merges.
9. You MUST load skill update-confidence-from-evidence to update confidence after identities and structure are stable. If the ontology is ready to express directed mechanisms, consider construct-causal-model as the next tactic.

Deviation: reorder only when a dependency is already satisfied or unavailable; record the reason and confidence effect.

Output contract

produces: [scoped_ontology, typed_relations, consistency_findings, coverage_gaps]
delta_fields: [findings, decisions]

Thresholds and quality gates

• Each output is traceable to an input object, operation, and evidence reference.
• Scope, assumptions, and unresolved alternatives remain explicit.
• Retain $\alpha$ 0.05 and power 0.8 wherever the predeclared statistical design requires them.

Failure and counterexamples

Stop synthesis when a required object is absent, a precondition is violated, or a counterexample invalidates the proposed conclusion; return the partial delta with the failure recorded.

Provenance map

• intermediate: knowledge-structuring/ontology-building [campaign]
• resolved: domain-scoping
• resolved: concept-extraction
• resolved: relation-typing
• resolved: taxonomy-validation
• resolved: ontology-refinement
• resolved: hierarchy-construction
• intermediate: consistency-checking [tactic]

Preserved source criteria ledger

source	criterion	treatment
resolved v3 entries above	node-specific criteria	retained and specialized to the v4 object contract
experiment-execution/statistical-testing	$\alpha$ = 0.05	fixed value retained where applicable
experiment-execution/sample-size-estimation	power = 0.8	fixed value retained where applicable

Context checkpoint / Delta notes

Return the node-specific research-state delta and preserve findings, evidence updates, uncertainties, decisions, open questions, and recommended jumps as applicable.