{
 "name": "Sniff cross-species substrate \u2014 KGX federation export",
 "generated_by": "scripts/build-kgx-export.py",
 "date": "2026-07-11",
 "generated": "2026-07-21T07:00:14Z",
 "export_git": "9a2ed2b",
 "export_sha256": "1eadd8e866f6dce8394b5de39f8985043699211dd0764e69718c835da03592a7",
 "format": "KGX TSV (nodes + edges)",
 "biolink_conformant": true,
 "conformance_issues": 0,
 "status": "INGESTABLE BUNDLE \u2014 not live federation. Live flow into Translator/Monarch requires registering infores:sniff (Matt, deferred). Build now; register on your timeline.",
 "included_facts_only": true,
 "excluded": "ALL prediction/candidate atoms (Dog10K natural-model candidates, discovery candidates) \u2014 lock_state:proposed / knowledge_level:prediction. Per INV-54 a prediction never enters a steward's graph as a fact. The gate bars any edge with knowledge_level=prediction.",
 "counts": {
  "nodes": 36915,
  "edges": 19823,
  "nodes_by_category": {
   "biolink:Gene": 36315,
   "biolink:Disease": 600
  },
  "edges_by_predicate": {
   "biolink:orthologous_to": 19073,
   "biolink:causes": 492,
   "biolink:associated_with_increased_likelihood_of": 66,
   "biolink:gene_associated_with_condition": 192
  },
  "orthology_edges_by_tier": {
   "high-corroborated": 15344,
   "high": 1870,
   "moderate": 1859
  },
  "orthology_dropped_no_human_ensg": 15,
  "clinvar_gene_disease_edges": 558,
  "gnomad_constrained_gene_nodes": 16116,
  "canine_disease_edges": 192,
  "canine_diseases": 190
 },
 "node_label_coverage": {
  "gene_nodes": 36315,
  "gene_nodes_with_symbol": 33263,
  "human_gene_nodes": 17236,
  "human_gene_nodes_with_symbol": 17229,
  "dog_gene_nodes": 19079,
  "dog_gene_nodes_with_symbol": 16034,
  "disease_nodes": 600,
  "disease_nodes_with_name": 596,
  "mondo_label_cache_size": 663,
  "note": "Real labels exclude Ensembl/MONDO/OMIA id-shaped strings. Gene symbols fixed 2026-07-21; Mondo disease names from Monarch API cache."
 },
 "orthology_reconciliation": {
  "input_dog_genes_evaluated": 29053,
  "edged_by_tier": {
   "high-corroborated": 15344,
   "high": 1870,
   "moderate": 1859
  },
  "edged_total": 19073,
  "abstained_by_reason": {
   "unmapped_no_ortholog_found": 8191,
   "only_co-ortholog_support": 1261,
   "methods_disagree_on_clean_target": 224,
   "edge-eligible_dropped_no_human_ensembl_id": 15,
   "compara_ambiguous_no_clean_recovery": 289
  },
  "abstained_total": 9980,
  "reconciles": true,
  "note": "edged_total + abstained_total == input_dog_genes_evaluated. Abstentions are recorded per-gene in output/gene-orthology.json (confidence tier + ladder.abstain_reason + complex_targets); this manifest block is the bundle-level audit that the exclusion is honest, not lossy."
 },
 "sources": {
  "infores:ensembl": "Ensembl Compara orthology (one2one) \u2014 CC-BY-style open, DOI 10.1093/nar/gkae1071",
  "infores:orthodb": "OrthoDB v11 orthology (concordance rung) \u2014 CC-BY-4.0, DOI 10.1093/nar/gkac998",
  "infores:oma": "OMA orthology (concordance rung) \u2014 CC-BY-4.0, DOI 10.1093/nar/gkad1020",
  "infores:panther": "PANTHER v19.0 orthology (concordance rung, LDO) \u2014 CC-BY-4.0, DOI 10.1002/pro.4218; the axis Monarch itself ingests (infores:panther)",
  "infores:ncbi": "NCBI Gene orthologs (concordance rung, synteny) \u2014 public domain, DOI 10.1007/s00239-025-10268-2",
  "infores:clinvar": "ClinVar 3-star gene->disease \u2014 public domain, DOI 10.1093/nar/gkx1153",
  "infores:gnomad": "gnomAD v4.1 gene constraint (node properties) \u2014 open, DOI 10.1038/s41586-020-2308-7",
  "infores:omia": "OMIA Online Mendelian Inheritance in Animals \u2014 CC-BY-4.0, DOI 10.25910/2AMR-PV70; canine disease gene associations consumed, never authored by Sniff (INV-47)",
  "infores:sniff": "aggregator (this substrate) \u2014 infores id NOT YET REGISTERED (Matt)"
 },
 "provenance_note": "Every edge carries the full provenance quad (primary + aggregator knowledge source, knowledge_level, agent_type). primary is the external authority (INV-47 consumed-never-authored); aggregator is infores:sniff.",
 "canine_bridge_note": "canine_disease_edges are OMIA-established dog gene\u2194disease associations (biolink:gene_associated_with_condition). primary_knowledge_source=infores:omia. skipped={'no_dog_ensembl': 3}"
}