{
  "ontology": {
    "name": "ConceptKernel BFO Ontology",
    "version": "v3.5-alpha3",
    "draft": "ALPHA",
    "date": "2026-03-25",
    "description": "Formal ontology mapping ConceptKernel architecture to Basic Formal Ontology (BFO)",
    "baseUri": "https://conceptkernel.org/ontology/v3.5/",
    "bfoVersion": "2020",
    "bfoUri": "http://purl.obolibrary.org/obo/bfo.owl"
  },
  "files": {
    "core": {
      "filename": "core.ttl",
      "path": "ontology/v3.5/core.ttl",
      "format": "text/turtle",
      "description": "Core BFO mappings for ConceptKernel continuants (Kernel, Edge, Instance, Ontology)",
      "coverage": {
        "entities": [
          "ckp:Kernel",
          "ckp:HotKernel",
          "ckp:ColdKernel",
          "ckp:Edge",
          "ckp:Instance",
          "ckp:KernelOntology",
          "ckp:EdgeKernel",
          "ckp:ConsensusKernel",
          "ckp:WssHubKernel"
        ],
        "bfoClasses": [
          "bfo:IndependentContinuant",
          "bfo:MaterialEntity",
          "bfo:GenericallyDependentContinuant",
          "bfo:SpecificallyDependentContinuant",
          "bfo:Quality",
          "bfo:Disposition"
        ]
      }
    },
    "kernel-metadata": {
      "filename": "kernel-metadata.ttl",
      "path": "ontology/v3.5/kernel-metadata.ttl",
      "format": "text/turtle",
      "description": "RDF schema for kernel metadata (runtime, ports, capabilities, dependencies, status)"
    },
    "kernel-entity-template": {
      "filename": "kernel-entity-template.ttl",
      "path": "ontology/v3.5/kernel-entity-template.ttl",
      "format": "text/turtle",
      "description": "BFO-aligned template for defining individual kernel entities"
    },
    "processes": {
      "filename": "processes.ttl",
      "path": "ontology/v3.5/processes.ttl",
      "format": "text/turtle",
      "description": "Occurrent (Process) definitions for ConceptKernel temporal events",
      "coverage": {
        "entities": [
          "ckpp:InvocationProcess",
          "ckpp:EdgeCommunicationProcess",
          "ckpp:EdgeSubscriptionProcess",
          "ckpp:ConsensusProcess",
          "ckpp:BroadcastProcess",
          "ckpp:TemporalPart",
          "ckpp:ProcessBoundary",
          "ckpp:StatusChangeEvent"
        ],
        "bfoClasses": [
          "bfo:Process",
          "bfo:ProcessBoundary",
          "bfo:TemporalRegion"
        ]
      }
    },
    "relations": {
      "filename": "relations.ttl",
      "path": "ontology/v3.5/relations.ttl",
      "format": "text/turtle",
      "description": "Relationships and inference rules for automatic reasoning",
      "coverage": {
        "properties": [
          "ckpr:connected_by",
          "ckpr:depends_on",
          "ckpr:participates_in",
          "ckpr:mediates",
          "ckpr:created_by_process",
          "ckpr:can_reach",
          "ckpr:upstream_of",
          "ckpr:downstream_of",
          "ckpr:sibling_of",
          "ckpr:authorizes_edge",
          "ckpr:requires_consensus"
        ],
        "swrlRules": [
          "InstanceProvenanceRule",
          "EdgeCommunicationInferenceRule",
          "SiblingKernelRule",
          "WorkflowChainRule",
          "AuthorizationRequirementRule",
          "InstanceDependencyRule",
          "ConsensusRequirementRule"
        ],
        "propertyChains": [
          "connected_by (hasOutgoingEdge o hasTarget)",
          "creates (hasOutputInstance)",
          "can_reach (transitive closure)"
        ]
      }
    },
    "shapes": {
      "filename": "shapes.ttl",
      "path": "ontology/v3.5/shapes.ttl",
      "format": "text/turtle",
      "description": "SHACL shapes for triple validation constraints"
    },
    "rbac": {
      "filename": "rbac.ttl",
      "path": "ontology/v3.5/rbac.ttl",
      "format": "text/turtle",
      "description": "Role-Based Access Control ontology for agents, roles, and permissions"
    },
    "workflow": {
      "filename": "workflow.ttl",
      "path": "ontology/v3.5/workflow.ttl",
      "format": "text/turtle",
      "description": "CKDL formalization for declarative workflow orchestration"
    },
    "self-improvement": {
      "filename": "self-improvement.ttl",
      "path": "ontology/v3.5/self-improvement.ttl",
      "format": "text/turtle",
      "description": "Autonomous self-improvement and ontology-driven validation processes"
    },
    "base-instances": {
      "filename": "base-instances.ttl",
      "path": "ontology/v3.5/base-instances.ttl",
      "format": "text/turtle",
      "description": "Base instance shapes: InstanceManifest, SealedInstance, LedgerEntry (from SPEC.CKP.v3.5.alpha-3 Section 4.1)",
      "new_in": "v3.5-alpha3",
      "coverage": {
        "entities": [
          "ckp:InstanceManifest",
          "ckp:SealedInstance",
          "ckp:LedgerEntry"
        ],
        "bfoClasses": [
          "bfo:GenericallyDependentContinuant"
        ],
        "provOClasses": [
          "prov:wasGeneratedBy",
          "prov:wasAttributedTo",
          "prov:generatedAtTime"
        ]
      }
    },
    "proof": {
      "filename": "proof.ttl",
      "path": "ontology/v3.5/proof.ttl",
      "format": "text/turtle",
      "description": "Proof verification: ProofRecord, ProofCheck, ProofOutcome, CheckType",
      "new_in": "v3.5-alpha3",
      "coverage": {
        "entities": [
          "ckp:ProofRecord",
          "ckp:ProofCheck",
          "ckp:ProofOutcome",
          "ckp:CheckType"
        ],
        "individuals": [
          "ckp:ProofOutcome-PASS",
          "ckp:ProofOutcome-FAIL",
          "ckp:ProofOutcome-PARTIAL",
          "ckp:CheckType-SCHEMA",
          "ckp:CheckType-SHACL",
          "ckp:CheckType-PROVENANCE",
          "ckp:CheckType-STRUCTURE",
          "ckp:CheckType-INTEGRITY",
          "ckp:CheckType-OPERATIONAL"
        ]
      }
    },
    "schema": {
      "filename": "schema.yaml",
      "path": "ontology/v3.5/schema.yaml",
      "format": "application/x-yaml",
      "description": "LinkML schema governing Concept Kernel shape (drives scaffolding tool)"
    }
  },
  "coverage": {
    "overall": {
      "score": 0.65,
      "description": "Overall BFO alignment coverage: 65%"
    },
    "continuants": {
      "score": 0.85,
      "status": "WELL_IMPLEMENTED",
      "entities": {
        "Kernel": {
          "score": 0.85,
          "status": "WELL_IMPLEMENTED",
          "gaps": [
            "Process URN tracking missing",
            "Temporal lifecycle events not tracked"
          ]
        },
        "Edge": {
          "score": 0.85,
          "status": "WELL_IMPLEMENTED",
          "gaps": [
            "Edge creation doesn't trigger consensus",
            "SHACL validation stub only"
          ]
        },
        "Instance": {
          "score": 0.80,
          "status": "WELL_IMPLEMENTED",
          "gaps": [
            "No Process URN linkage",
            "ckp:// URI not fully implemented"
          ]
        },
        "InstanceManifest": {
          "score": 1.0,
          "status": "NEW_IN_V3.5",
          "description": "Base instance shape with PROV-O provenance properties"
        },
        "SealedInstance": {
          "score": 1.0,
          "status": "NEW_IN_V3.5",
          "description": "Finalized instance with data, tool_ref, ck_ref"
        },
        "LedgerEntry": {
          "score": 1.0,
          "status": "NEW_IN_V3.5",
          "description": "Append-only action log entry"
        },
        "ProofRecord": {
          "score": 1.0,
          "status": "NEW_IN_V3.5",
          "description": "Verification record with checks, hashes, and outcome"
        },
        "ProofCheck": {
          "score": 1.0,
          "status": "NEW_IN_V3.5",
          "description": "Individual verification check (schema, shacl, provenance, etc.)"
        }
      }
    },
    "occurrents": {
      "score": 0.45,
      "status": "PARTIAL",
      "processes": {
        "Invocation": {
          "score": 0.60,
          "status": "PARTIAL",
          "gaps": [
            "No Process URN generation",
            "Temporal parts not tracked"
          ]
        },
        "EdgeCommunication": {
          "score": 0.65,
          "status": "PARTIAL",
          "gaps": [
            "No Process URN generation",
            "Temporal parts implicit only"
          ]
        },
        "EdgeSubscription": {
          "score": 0.00,
          "status": "NOT_IMPLEMENTED",
          "gaps": [
            "Edge creation is manual (ck create-edge)",
            "No consensus integration",
            "No WssHub announcements"
          ]
        },
        "Consensus": {
          "score": 0.50,
          "status": "PARTIAL",
          "gaps": [
            "No Process URN",
            "Approved proposals don't auto-execute",
            "No WssHub integration"
          ]
        },
        "Broadcast": {
          "score": 0.70,
          "status": "PARTIAL",
          "gaps": [
            "No Process URN",
            "No consensus event handling",
            "No client filtering"
          ]
        }
      }
    },
    "mediators": {
      "EdgeKernel": {
        "score": 0.85,
        "status": "WELL_IMPLEMENTED",
        "role": "Communication Mediator"
      },
      "ConsensusKernel": {
        "score": 0.50,
        "status": "PARTIAL",
        "role": "Governance Mediator",
        "criticalGap": "Not integrated with EdgeKernel"
      },
      "WssHubKernel": {
        "score": 0.70,
        "status": "WELL_IMPLEMENTED",
        "role": "Broadcast Mediator",
        "criticalGap": "No consensus announcements"
      }
    }
  },
  "changelog": {
    "v3.5": {
      "date": "2026-03-25",
      "changes": [
        "Unified all namespaces under https://conceptkernel.org/ontology/v3.5/ (was mixed http/https unversioned)",
        "NEW: base-instances.ttl — InstanceManifest, SealedInstance, LedgerEntry (SPEC.CKP.v3.5.alpha-3 Section 4.1)",
        "NEW: proof.ttl — ProofRecord, ProofCheck, ProofOutcome, CheckType for verifiable instance integrity",
        "Updated schema.yaml with LinkML classes for InstanceManifest, SealedInstance, LedgerEntry, ProofRecord, ProofCheck",
        "Added ProofOutcome and CheckType enums to schema.yaml",
        "All sub-namespaces versioned: process/, relation/, workflow/, rbac/, improvement/"
      ]
    }
  },
  "references": {
    "bfo": "http://purl.obolibrary.org/obo/bfo.owl",
    "bfoSpecification": "https://basic-formal-ontology.org/",
    "provO": "http://www.w3.org/ns/prov#",
    "spec": "SPEC.CKP.v3.5.alpha-3.md"
  }
}