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validation-report.json
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{
  "timestamp": "2026-01-05T22:34:08.223880",
  "biolink_version": "4.3.6",
  "data_directory": "single_file_validation",
  "sources": {
    "single_validation": {
      "timestamp": "2026-01-05T22:34:07.603451",
      "biolink_version": "4.3.6",
      "files": {
        "nodes_file": "/home/ubuntu/translator-ingests/src/translator_ingest/../../data/ctkp/3.1.26/1.0/normalization_2025sep1/merged_nodes.jsonl",
        "edges_file": "/home/ubuntu/translator-ingests/src/translator_ingest/../../data/ctkp/3.1.26/1.0/normalization_2025sep1/merged_edges.jsonl"
      },
      "statistics": {
        "total_nodes": 40947,
        "total_edges": 433373,
        "unique_nodes_in_edges": 0,
        "missing_nodes_count": 0,
        "orphaned_nodes_count": 0,
        "validation_errors": 0,
        "validation_warnings": 67999,
        "edge_sample_size": 43337,
        "node_sample_size": 19092,
        "note": "Large file - validation performed on random edge sample with matching nodes"
      },
      "validation_status": "PASSED",
      "issues": {
        "errors": [],
        "warnings": [
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/0 has potentially invalid category 'biolink:PhysicalEssence'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/0 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/0 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/0 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/0 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
          },
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            "type": "biolink-model validation",
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            "message": "Node at /nodes/0 has potentially invalid category 'biolink:OntologyClass'",
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          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1 has potentially invalid category 'biolink:PhysicalEssence'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
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          },
          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/2 has potentially invalid category 'biolink:PhysicalEssence'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/2 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/2 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2 has potentially invalid category 'biolink:OntologyClass'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/4 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5 has potentially invalid category 'biolink:ThingWithTaxon'",
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            "type": "biolink-model validation",
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            "message": "Node at /nodes/6 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
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          {
            "type": "biolink-model validation",
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            "type": "biolink-model validation",
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            "message": "Node at /nodes/6 has potentially invalid category 'biolink:PhysicalEssence'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/6 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/6 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
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            "type": "biolink-model validation",
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            "message": "Node at /nodes/7 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/8 has potentially invalid category 'biolink:ThingWithTaxon'",
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            "type": "biolink-model validation",
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            "message": "Node at /nodes/9 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/10 has potentially invalid category 'biolink:GeneProductMixin'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/10 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/10 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/10 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/10 has potentially invalid category 'biolink:GeneOrGeneProduct'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/10 has potentially invalid category 'biolink:MacromolecularMachineMixin'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/11 has potentially invalid category 'biolink:PhysicalEssence'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/11 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/11 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/11 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/11 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/11 has potentially invalid category 'biolink:OntologyClass'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/12 has potentially invalid category 'biolink:ThingWithTaxon'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/13 has potentially invalid category 'biolink:GeneOrGeneProduct'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/13 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/13 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/13 has potentially invalid category 'biolink:PhysicalEssence'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/13 has potentially invalid category 'biolink:OntologyClass'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/13 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/13 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/13 has potentially invalid category 'biolink:MacromolecularMachineMixin'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/13 has potentially invalid category 'biolink:GeneProductMixin'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/13 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/14 has potentially invalid category 'biolink:PhysicalEssence'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/14 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/14 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/14 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/14 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/15 has potentially invalid category 'biolink:GeneProductMixin'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/15 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/15 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/15 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/15 has potentially invalid category 'biolink:GeneOrGeneProduct'",
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/15 has potentially invalid category 'biolink:MacromolecularMachineMixin'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/16 has potentially invalid category 'biolink:ThingWithTaxon'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
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            "message": "Node at /nodes/17 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/18 has potentially invalid category 'biolink:ThingWithTaxon'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/19 has potentially invalid category 'biolink:ThingWithTaxon'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/20 has potentially invalid category 'biolink:PhysicalEssence'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/20 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/20 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/20 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/20 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/20 has potentially invalid category 'biolink:OntologyClass'",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/21 has potentially invalid category 'biolink:ThingWithTaxon'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/22 has potentially invalid category 'biolink:PhysicalEssence'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/22 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/22 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/22 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/22 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/23 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/23 has potentially invalid category 'biolink:OntologyClass'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/23 has potentially invalid category 'biolink:PhysicalEssence'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/23 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/23 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/23 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/24 has potentially invalid category 'biolink:PhysicalEssence'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/24 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
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            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/24 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/25 has potentially invalid category 'biolink:ThingWithTaxon'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/26 has potentially invalid category 'biolink:PhysicalEssence'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/26 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/26 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/26 has potentially invalid category 'biolink:ChemicalEntityOrProteinOrPolypeptide'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/26 has potentially invalid category 'biolink:PhysicalEssenceOrOccurrent'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/27 has potentially invalid category 'biolink:ThingWithTaxon'",
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          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
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          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/28 has potentially invalid category 'biolink:ChemicalOrDrugOrTreatment'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/28 has potentially invalid category 'biolink:ChemicalEntityOrGeneOrGeneProduct'",
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        ],
        "missing_nodes": [],
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        "truncated": true
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  "summary": {
    "total_sources": 1,
    "passed": 1,
    "failed": 0,
    "overall_status": "PASSED"
  }
}