/build-domain-ontology

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

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.