Validation of KG2.10.3c against latest KGX format

[bazarkua]

We need to assess whether the RTX-KG2 2.10.3c build outputs are valid KGX and Biolink-compliant under the current translator-ingests validation tooling.

[bazarkua]

Running kgx validation tooling on the kg2-normalized-2.10.3-edges_patched.jsonl and kg2-normalized-2.10.3-nodes_patched.jsonl from the rtx-kg2 S3 bucket.

Found 5,986,547 nodes with 5,986,547 unique IDs
Found 37,065,346 edges, sampled 3,706,534 for validation (10.0%)
Created node sample of 582,361 nodes for validation
Sample validation found 0 errors, 3773941 warnings
Found 3773941 validation warnings (sample)
Streaming validation PASSED

Full report:

{
  "timestamp": "2025-12-16T16:10:15.119742",
  "biolink_version": "4.3.6",
  "data_directory": "single_file_validation",
  "sources": {
    "single_validation": {
      "timestamp": "2025-12-16T16:09:20.099128",
      "biolink_version": "4.3.6",
      "files": {
        "nodes_file": "/Users/bazarkua/Work/translator-ingests/data/rtxkg2c_patched/source_data/kg2-normalized-2.10.3-nodes_patched.jsonl",
        "edges_file": "/Users/bazarkua/Work/translator-ingests/data/rtxkg2c_patched/source_data/kg2-normalized-2.10.3-edges_patched.jsonl"
      },
      "statistics": {
        "total_nodes": 5986547,
        "total_edges": 37065346,
        "unique_nodes_in_edges": 0,
        "missing_nodes_count": 0,
        "orphaned_nodes_count": 0,
        "validation_errors": 0,
        "validation_warnings": 3773941,
        "edge_sample_size": 3706534,
        "node_sample_size": 582361,
        "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/247 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/290 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/315 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/346 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/409 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/603 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/607 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/612 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/635 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/955 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/972 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1095 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1129 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1204 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1291 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1455 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/1892 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2100 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2151 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2424 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2577 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2736 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2754 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2827 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/2854 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3042 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3161 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3187 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3357 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3520 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3590 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3656 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3731 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3859 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/3969 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/4044 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/4160 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/4176 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/4307 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/4321 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/4867 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/4920 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5015 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5034 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5056 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5357 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5506 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5561 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5790 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5798 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5900 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5901 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5904 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/5996 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6217 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6408 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6416 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6566 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6830 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6844 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6925 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6957 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/6978 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7166 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7231 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7311 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7456 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7459 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7464 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7479 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7519 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7526 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7581 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7593 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7598 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7881 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7942 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/7991 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8045 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8082 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8266 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8308 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8406 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8468 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8504 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8683 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8686 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8806 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8895 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8927 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/8947 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9037 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9090 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9106 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9160 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9336 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9401 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9471 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9473 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/9717 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          }
        ],
        "missing_nodes": [],
        "orphaned_nodes": [],
        "truncated": true
      }
    }
  },
  "summary": {
    "total_sources": 1,
    "passed": 1,
    "failed": 0,
    "overall_status": "PASSED"
  }
}

[bazarkua]

Also, upon @dkoslicki request, I have asked Everaldo (DOGSURF) and Willow (DOGSURF) about what version of the kg2 they've used in the Retriever and I did get confirmation that they used
kg2c-2.10.2-v1.0-nodes.jsonl
kg2c-2.10.2-v1.0-edges.jsonl

So, I ran validation pipeline in Translator pipeline to validate against latest KGX format.
Found 6,782,084 nodes with 6,782,084 unique IDs
Found 27,257,461 edges, sampled 2,725,746 for validation (10.0%)
Created node sample of 727,697 nodes for validation
Sample validation found 796 errors, 2852028 warnings
Streaming validation FAILED

Complete validation report:

{
  "timestamp": "2025-12-17T10:20:48.188167",
  "biolink_version": "4.3.6",
  "data_directory": "single_file_validation",
  "sources": {
    "single_validation": {
      "timestamp": "2025-12-17T10:20:32.778958",
      "biolink_version": "4.3.6",
      "files": {
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            "message": "Node at /nodes/259957 has invalid CURIE format for id 'OBO:EnsemblBacteria#_BAB2_0054'",
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          {
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          {
            "type": "biolink-model validation",
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          {
            "type": "biolink-model validation",
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          {
            "type": "biolink-model validation",
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          {
            "type": "biolink-model validation",
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          {
            "type": "biolink-model validation",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/223 is missing recommended 'name' field",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
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          {
            "type": "biolink-model validation",
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          {
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          {
            "type": "biolink-model validation",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/417 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/425 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/439 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/443 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/446 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/457 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/461 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/468 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/491 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/492 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/493 is missing recommended 'name' field",
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          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/502 is missing recommended 'name' field",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/529 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/532 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/547 is missing recommended 'name' field",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/548 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/552 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/562 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/572 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/573 is missing recommended 'name' field",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/586 is missing recommended 'name' field",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/587 is missing recommended 'name' field",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/593 is missing recommended 'name' field",
            "instance_path": "unknown"
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/598 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/600 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/607 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "WARN",
            "message": "Node at /nodes/616 has potentially invalid category 'biolink:GenomicEntity'",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/618 is missing recommended 'name' field",
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          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/621 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/622 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/634 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/635 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/636 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/642 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/653 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/668 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/696 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/698 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/699 is missing recommended 'name' field",
            "instance_path": "unknown"
          },
          {
            "type": "biolink-model validation",
            "severity": "INFO",
            "message": "Node at /nodes/702 is missing recommended 'name' field",
            "instance_path": "unknown"
          }
        ],
        "missing_nodes": [],
        "orphaned_nodes": [],
        "truncated": true
      }
    }
  },
  "summary": {
    "total_sources": 1,
    "passed": 0,
    "failed": 1,
    "overall_status": "FAILED"
  }
}

[saramsey]

OK, so GenomicEntity is an allowed category name. I think the validator is incorrectly issuing a warning here. It is a "mixin", and maybe that's the reason?

[saramsey]

See this document for information about how the validation was run:
https://github.com/RTXteam/RTX-KG2/blob/master/docs/KGX-validation-guide.md

[saramsey]

Also, see this issue regarding GenomicEntity:
biolink/biolink-model#1405

[saramsey]

I've opened an issue in the NCATSTranslator/translator-ingests project area, to ask why we are getting this warning.
NCATSTranslator/translator-ingests#214

[saramsey]

OK, Sierra confirms that we shouldn't be getting a warning about GenomicEntity. It's some issue with the validate_translator_kgx.py or tooling underneath it. We can thus ignore that warning, pending resolution of NCATSTranslator/translator-ingests#214