{
  "date": "2026-09-20",
  "base_commit": "1cc412fddde5aacb0cc66311a96e25d67465fdb9",
  "source_pdf_sha256_before_and_after": "4eec4659227597d37717344de0e6fe527861f78f33cb9834e4f279dd38a53701",
  "versions": {
    "linkml": "1.10.0",
    "linkml-runtime": "1.10.0",
    "oaklib": "0.7.4",
    "PyYAML": "6.0.3"
  },
  "structural_validation_command": [
    "uv",
    "run",
    "python",
    "docs/reports/senescent-cell-representation/validate_design.py"
  ],
  "structural_validation": [
    {
      "data": "existing-schema.yaml",
      "schema": "production",
      "expected_valid": true,
      "exit_code": 0,
      "output": "No issues found"
    },
    {
      "data": "existing-schema.yaml",
      "schema": "proposal",
      "expected_valid": true,
      "exit_code": 0,
      "output": "No issues found"
    },
    {
      "data": "existing-schema.yaml",
      "orphan_targets": [],
      "graph_edges": 2
    },
    {
      "data": "wound-context.yaml",
      "schema": "production",
      "expected_valid": true,
      "exit_code": 0,
      "output": "No issues found"
    },
    {
      "data": "wound-context.yaml",
      "schema": "proposal",
      "expected_valid": true,
      "exit_code": 0,
      "output": "No issues found"
    },
    {
      "data": "wound-context.yaml",
      "orphan_targets": [],
      "graph_edges": 1
    },
    {
      "data": "candidate-state.yaml",
      "schema": "proposal",
      "expected_valid": true,
      "exit_code": 0,
      "output": "No issues found"
    },
    {
      "data": "candidate-state.yaml",
      "schema": "production",
      "expected_valid": false,
      "exit_code": 1,
      "output": "[ERROR] [candidate-state.yaml/0] Additional properties are not allowed ('cell_states' was unexpected) in /pathophysiology/0/cell_types/0"
    },
    {
      "data": "unsupported-state.yaml",
      "schema": "proposal",
      "expected_valid": false,
      "exit_code": 1,
      "output": "[ERROR] [unsupported-state.yaml/0] 'EXHAUSTED' is not one of ['SENESCENT'] in /pathophysiology/0/cell_types/0/cell_states/0/state"
    },
    {
      "data": "missing-state-evidence.yaml",
      "schema": "proposal",
      "expected_valid": false,
      "exit_code": 1,
      "output": "[ERROR] [missing-state-evidence.yaml/0] [] should be non-empty in /pathophysiology/0/cell_types/0/cell_states/0/evidence"
    }
  ],
  "inventory_reproduction": {
    "command": [
      "uv",
      "run",
      "python",
      "docs/reports/senescent-cell-representation/scan_kb.py"
    ],
    "equal_to_recorded_json": true
  },
  "checks": [
    {
      "command": [
        "just",
        "validate-terms",
        "docs/reports/senescent-cell-representation/existing-schema.yaml"
      ],
      "exit_code": 0,
      "output": "scripts/run_term_validator.sh validate-data docs/reports/senescent-cell-representation/existing-schema.yaml -s src/dismech/schema/dismech.yaml -t Disease --labels -c conf/oak_config.yaml\n✅ Validation passed"
    },
    {
      "command": [
        "just",
        "validate-terms",
        "docs/reports/senescent-cell-representation/wound-context.yaml"
      ],
      "exit_code": 0,
      "output": "scripts/run_term_validator.sh validate-data docs/reports/senescent-cell-representation/wound-context.yaml -s src/dismech/schema/dismech.yaml -t Disease --labels -c conf/oak_config.yaml\n✅ Validation passed"
    },
    {
      "command": [
        "scripts/run_reference_validator.sh",
        "validate",
        "data",
        "docs/reports/senescent-cell-representation/existing-schema.yaml",
        "docs/reports/senescent-cell-representation/wound-context.yaml",
        "--schema",
        "src/dismech/schema/dismech.yaml",
        "--target-class",
        "Disease",
        "--config",
        "conf/reference_validator_config.yaml",
        "--no-full-text"
      ],
      "exit_code": 0,
      "output": "Cache directory: references_cache\n\nValidating docs/reports/senescent-cell-representation/existing-schema.yaml against schema src/dismech/schema/dismech.yaml\n\nValidating docs/reports/senescent-cell-representation/wound-context.yaml against schema src/dismech/schema/dismech.yaml\n\nValidation Summary:\n  Files validated: 2\n  Total checks: 0\n  All validations passed!\n  Snippets checked: 4/4 verified against cached references"
    },
    {
      "command": [
        "just",
        "check-duplicate-keys",
        "docs/reports/senescent-cell-representation/existing-schema.yaml",
        "docs/reports/senescent-cell-representation/wound-context.yaml",
        "docs/reports/senescent-cell-representation/extension-delta.yaml"
      ],
      "exit_code": 0,
      "output": "uv run python scripts/check_duplicate_yaml_keys.py \"$@\"\nOK: no duplicate mapping keys in 3 YAML file(s)."
    },
    {
      "command": [
        "just",
        "check-entity-refs",
        "docs/reports/senescent-cell-representation/existing-schema.yaml",
        "docs/reports/senescent-cell-representation/wound-context.yaml"
      ],
      "exit_code": 0,
      "output": "uv run python scripts/check_entity_refs.py \"$@\"\nOK: entity references resolve in 2 KB file(s)."
    },
    {
      "command": [
        "just",
        "check-causal-targets",
        "docs/reports/senescent-cell-representation/existing-schema.yaml",
        "docs/reports/senescent-cell-representation/wound-context.yaml"
      ],
      "exit_code": 0,
      "output": "uv run python scripts/check_causal_targets.py \"$@\"\nOK: no new broken pathograph targets (121 dangling target(s) grandfathered)."
    },
    {
      "command": [
        "uv",
        "run",
        "linkml-validate",
        "-s",
        "src/dismech/schema/dismech.yaml",
        "-C",
        "Disease",
        "docs/reports/senescent-cell-representation/wound-context.yaml"
      ],
      "exit_code": 0,
      "output": "No issues found",
      "reason": "After adding the primary study Expression of Concern caveat in notes; evidence quotation unchanged."
    }
  ],
  "scope": "Local design fixtures only. Production schema and KB unchanged. Proposed state assertion validation is structural; renderer, export and nested-reference support remain future work.",
  "artifact_checks": {
    "existing_local_links": 27,
    "report_in_mkdocs_nav": true,
    "ontology_table_matches_lookup_records": 21,
    "source_pdf_unchanged": true
  },
  "follow_up": "Recommendation updated to BP reuse after user feedback. Developmental-stage discussion and five-term live lookup added. Proposed happens_during YAML is explicitly hypothetical and was not schema-validated; original fixture validation results remain unchanged.",
  "shared_report_review": {
    "url": "https://share.onorca.dev/a/DNdT1gKaYZP4",
    "read_in_full": true,
    "linked_artifacts_returning_404": [
      "validation/export-probe.json",
      "02-ipf-compatible.yaml",
      "VALIDATION.md"
    ],
    "wound_study_expression_of_concern": {
      "reference": "PMID:42412492",
      "concerns": "PMID:25499914",
      "doi": "10.1016/j.devcel.2026.04.004",
      "first_publication_date": "2026-05-29",
      "verified_against": [
        "https://pubmed.ncbi.nlm.nih.gov/42412492/",
        "Europe PMC MED record 42412492"
      ]
    }
  }
}