{
  "base_commit": "f3df177789af41976971b15edbb91d65f0c67cc1",
  "module_sha256": "da021fda1cef4d9c91793f932f06eeb28c8d6b292ef7b38d9fc1a6ed4e0a4b52",
  "schema_sha256": "d8b157b1130598eb7410ec1f20a6ef683eb5f8c03982981f7fab0b5725310241",
  "checks": [
    {
      "command": "uv run linkml-validate -s src/dismech/schema/dismech.yaml -C Disease kb/modules/cellular_senescence.yaml",
      "exit_code": 0,
      "output": "No issues found"
    },
    {
      "command": "just validate-terms kb/modules/cellular_senescence.yaml",
      "exit_code": 0,
      "output": "scripts/run_term_validator.sh validate-data kb/modules/cellular_senescence.yaml -s src/dismech/schema/dismech.yaml -t Disease --labels -c conf/oak_config.yaml\n\u2705 Validation passed"
    },
    {
      "command": "scripts/run_reference_validator.sh validate data kb/modules/cellular_senescence.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 kb/modules/cellular_senescence.yaml against schema src/dismech/schema/dismech.yaml\n\nValidation Summary:\n  Files validated: 1\n  Total checks: 0\n  All validations passed!\n  Snippets checked: 46/46 verified against cached references"
    },
    {
      "command": "just check-qualifier-terms kb/modules/cellular_senescence.yaml",
      "exit_code": 0,
      "output": "uv run python scripts/check_qualifier_terms.py \"$@\"\nOK: 0 qualifier term label(s) match the ontology cache."
    },
    {
      "command": "just check-coarse-phenotypes kb/modules/cellular_senescence.yaml",
      "exit_code": 0,
      "output": "uv run python scripts/check_coarse_phenotypes.py \"$@\"\nOK: no new unexplained coarse phenotype bindings (396 grandfathered)."
    },
    {
      "command": "just check-duplicate-keys kb/modules/cellular_senescence.yaml",
      "exit_code": 0,
      "output": "uv run python scripts/check_duplicate_yaml_keys.py \"$@\"\nOK: no duplicate mapping keys in 1 YAML file(s)."
    },
    {
      "command": "just check-entity-refs kb/modules/cellular_senescence.yaml",
      "exit_code": 0,
      "output": "uv run python scripts/check_entity_refs.py \"$@\"\nOK: entity references resolve in 1 KB file(s)."
    }
  ],
  "module_content_qc": {
    "folded_hyphens": {
      "current_findings": [],
      "baseline_findings": []
    },
    "short_snippets": {
      "current_findings": [],
      "baseline_findings": []
    },
    "snippet_grading": {
      "current_findings": [],
      "baseline_findings": []
    },
    "environmental_evidence": {
      "current_findings": [],
      "baseline_findings": []
    },
    "title_only_snippets": {
      "current_findings": [],
      "baseline_findings": []
    },
    "reference_title_mismatches": {
      "current_findings": [],
      "baseline_findings": []
    },
    "graph": {
      "edges": 28,
      "orphan_targets": []
    }
  },
  "design_fixtures": [
    {
      "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"
    }
  ],
  "precommit_ontology_searches": [
    {
      "ontology": "cl",
      "query": "senescent",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=senescent&ontology=cl&rows=40&queryFields=label%2Csynonym&local=true",
      "numFound": 0,
      "results": [],
      "previous_numFound": 0
    },
    {
      "ontology": "cl",
      "query": "senescence",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=senescence&ontology=cl&rows=40&queryFields=label%2Csynonym&local=true",
      "numFound": 0,
      "results": [],
      "previous_numFound": 0
    },
    {
      "ontology": "cl",
      "query": "skin fibroblast",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=skin+fibroblast&ontology=cl&rows=40&queryFields=label%2Csynonym&local=true",
      "numFound": 7,
      "results": [
        {
          "obo_id": "CL:0002620",
          "label": "skin fibroblast"
        },
        {
          "obo_id": "CL:2000013",
          "label": "fibroblast of skin of abdomen"
        },
        {
          "obo_id": "CL:4006001",
          "label": "fibroblast of skin of scalp"
        },
        {
          "obo_id": "CL:0011022",
          "label": "fibroblast of skin of back"
        },
        {
          "obo_id": "CL:2000012",
          "label": "fibroblast of pedal digit skin"
        },
        {
          "obo_id": "CL:2000014",
          "label": "fibroblast of upper leg skin"
        },
        {
          "obo_id": "CL:0011021",
          "label": "fibroblast of upper back skin"
        }
      ],
      "previous_numFound": 7
    },
    {
      "ontology": "cl",
      "query": "dermal fibroblast",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=dermal+fibroblast&ontology=cl&rows=40&queryFields=label%2Csynonym&local=true",
      "numFound": 1,
      "results": [
        {
          "obo_id": "CL:0020013",
          "label": "dermal sheath fibroblast"
        }
      ],
      "previous_numFound": 1
    },
    {
      "ontology": "go",
      "query": "senescence",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=senescence&ontology=go&rows=40&queryFields=label%2Csynonym&local=true",
      "numFound": 25,
      "results": [
        {
          "obo_id": "GO:1904249",
          "label": "negative regulation of age-related resistance"
        },
        {
          "obo_id": "GO:1904250",
          "label": "positive regulation of age-related resistance"
        },
        {
          "obo_id": "GO:0035985",
          "label": "senescence-associated heterochromatin focus"
        },
        {
          "obo_id": "GO:1900056",
          "label": "negative regulation of leaf senescence"
        },
        {
          "obo_id": "GO:1900057",
          "label": "positive regulation of leaf senescence"
        },
        {
          "obo_id": "GO:1904727",
          "label": "negative regulation of replicative senescence"
        },
        {
          "obo_id": "GO:1904728",
          "label": "positive regulation of replicative senescence"
        },
        {
          "obo_id": "GO:0010282",
          "label": "senescence-associated vacuole"
        },
        {
          "obo_id": "GO:0080187",
          "label": "floral organ senescence"
        },
        {
          "obo_id": "GO:1990636",
          "label": "reproductive senescence"
        },
        {
          "obo_id": "GO:0090400",
          "label": "stress-induced premature senescence"
        },
        {
          "obo_id": "GO:0090402",
          "label": "oncogene-induced cell senescence"
        },
        {
          "obo_id": "GO:0090403",
          "label": "oxidative stress-induced premature senescence"
        },
        {
          "obo_id": "GO:1900055",
          "label": "regulation of leaf senescence"
        },
        {
          "obo_id": "GO:1904726",
          "label": "regulation of replicative senescence"
        },
        {
          "obo_id": "GO:2000772",
          "label": "regulation of cellular senescence"
        },
        {
          "obo_id": "GO:2000773",
          "label": "negative regulation of cellular senescence"
        },
        {
          "obo_id": "GO:2000774",
          "label": "positive regulation of cellular senescence"
        },
        {
          "obo_id": "GO:0010150",
          "label": "leaf senescence"
        },
        {
          "obo_id": "GO:0090398",
          "label": "cellular senescence"
        },
        {
          "obo_id": "GO:0090399",
          "label": "replicative senescence"
        },
        {
          "obo_id": "GO:0090693",
          "label": "plant organ senescence"
        },
        {
          "obo_id": "GO:0090644",
          "label": "age-related resistance"
        },
        {
          "obo_id": "GO:1904248",
          "label": "regulation of age-related resistance"
        },
        {
          "obo_id": "GO:0009835",
          "label": "fruit ripening"
        }
      ],
      "previous_numFound": 25
    },
    {
      "ontology": "go",
      "query": "senescence-associated secretory phenotype",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=senescence-associated+secretory+phenotype&ontology=go&rows=40&queryFields=label%2Csynonym&local=true",
      "numFound": 0,
      "results": [],
      "previous_numFound": 0
    },
    {
      "ontology": "hsapdv",
      "query": "Carnegie stage 12",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=Carnegie+stage+12&ontology=hsapdv&rows=8&queryFields=label%2Csynonym&local=true",
      "numFound": 1,
      "results": [
        {
          "obo_id": "HsapDv:0000019",
          "label": "Carnegie stage 12"
        }
      ],
      "previous_numFound": 1
    },
    {
      "ontology": "uberon",
      "query": "developmental stage",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=developmental+stage&ontology=uberon&rows=8&queryFields=label%2Csynonym&local=true",
      "numFound": 1,
      "results": [
        {
          "obo_id": "UBERON:0000105",
          "label": "life cycle stage"
        }
      ],
      "previous_numFound": 1
    },
    {
      "ontology": "go",
      "query": "S phase",
      "url": "https://www.ebi.ac.uk/ols4/api/search?q=S+phase&ontology=go&rows=8&queryFields=label%2Csynonym&local=true",
      "numFound": 109,
      "results": [
        {
          "obo_id": "GO:0051320",
          "label": "S phase"
        },
        {
          "obo_id": "GO:1902576",
          "label": "negative regulation of nuclear cell cycle DNA replication"
        },
        {
          "obo_id": "GO:1903464",
          "label": "negative regulation of mitotic cell cycle DNA replication"
        },
        {
          "obo_id": "GO:1903465",
          "label": "positive regulation of mitotic cell cycle DNA replication"
        },
        {
          "obo_id": "GO:1904860",
          "label": "DNA synthesis involved in mitotic DNA replication"
        },
        {
          "obo_id": "GO:0047454",
          "label": "phaseollidin hydratase activity"
        },
        {
          "obo_id": "GO:0051332",
          "label": "meiotic S phase"
        },
        {
          "obo_id": "GO:0000087",
          "label": "mitotic M phase"
        }
      ],
      "previous_numFound": 109
    }
  ],
  "reference_cache_scope": "Chris explicitly authorized inclusion of the four tool-generated public reference caches, including full article content where available. The uploaded PDF and its local text extraction remain excluded.",
  "reference_caches": [
    {
      "path": "references_cache/PMID_31160572.md",
      "sha256": "901c5ee5e3c3f83b40d9c0768e5723872088489e8c9293ddf92acc487cff5972",
      "frontmatter_and_consumer_compatibility": "passed"
    },
    {
      "path": "references_cache/PMID_37001502.md",
      "sha256": "9c1e24e2884326c1e3af548ccb74b2238111e5689090f7c6a251eda839d92851",
      "frontmatter_and_consumer_compatibility": "passed"
    },
    {
      "path": "references_cache/PMID_39121846.md",
      "sha256": "eba857a08ea2d5e098e8f855429d82240214306db607be66e1236a058b5719c1",
      "frontmatter_and_consumer_compatibility": "passed"
    },
    {
      "path": "references_cache/PMID_42518598.md",
      "sha256": "68144599bca695d3c265e6d50c234106ae059f3bcacf68055a3f3acbee97b7a7",
      "frontmatter_and_consumer_compatibility": "passed"
    }
  ],
  "cache_inclusion_validation": {
    "command": "scripts/run_reference_validator.sh validate data kb/modules/cellular_senescence.yaml 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 kb/modules/cellular_senescence.yaml against schema src/dismech/schema/dismech.yaml\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: 3\n  Total checks: 0\n  All validations passed!\n  Snippets checked: 50/50 verified against cached references",
    "module_snippets": 46,
    "design_fixture_snippets": 4
  },
  "repository_hook_normalization": "The required pre-commit hooks added final newlines to the four generated caches and removed three trailing spaces from the Pereira article LaTeX preamble. No cache was hand-edited, and source content is otherwise unchanged."
}