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Field infrastructure / federation

Federate Sniff into your graph.

Sniff is a governed, cited, cross-species knowledge substrate. Its dog to human bridge, the human clinical and population evidence hung off it, and (when present) the canine disease layer are exported as a Biolink-conformant KGX bundle a steward can ingest. Trust at the seam: every edge carries provenance and evidence level, and nothing that is a prediction is allowed to enter your graph as a fact.

Status: ingestable bundle, not live Translator/Monarch routing. Registering infores:sniff is human-gated and not done yet.

What this bundle carries

  • Dog↔human ortholog spine in this export

    19,073 edges · 15,344 high-corroborated (5 methods)

  • Human clinical (3★ ClinVar) in this export

    558 gene→disease edges through the ortholog

  • Human constraint (gnomAD) in this export

    16,116 gene nodes carry LOEUF / pLI / missense-Z

  • Canine disease bridge (OMIA) in this export

    192 OMIA-established disease-gene edges on the ortholog spine

Counts (from the manifest)

36,915
nodes
19,823
edges
36,315
gene nodes
600
disease nodes
  • 19,073 biolink:orthologous_to - dog to human ortholog spine, confidence-tiered (15,344 high-corroborated across five methods).
  • 492 biolink:causes + 66 associated_with_increased_likelihood_of - 3-star ClinVar gene to disease, attached through the resolved ortholog.
  • 16,116 gene nodes carry gnomAD constraint (LOEUF / pLI / missense-Z) as node properties.

The canine disease bridge

This is the half a cross-species steward cannot get anywhere else. 192 OMIA-established canine disease genes are hung on the corroborated ortholog spine, so the dog stops being only a recipient of human annotations and becomes a model organism that contributes evidence. The path is traversable end to end: dog disease to dog gene to corroborated ortholog to human gene to human disease, every hop cited. Primary source is infores:omia, aggregator infores:sniff; Sniff consumes OMIA, never authors it. Facts only: these are OMIA's established disease genes, not our hypotheses. The Dog10K natural-model candidates stay barred (INV-54).

Why you can trust it at the seam

  • Facts only. Every prediction and candidate atom is excluded by construction. Sniff's Dog10K natural-disease-model candidates are knowledge_level prediction and the exporter bars them, so a hypothesis can never enter your graph as an assertion. Biolink-conformant, 0 conformance issues.
  • A provenance quad on every edge. Each edge names its primary_knowledge_source and aggregator_knowledge_source (infores:sniff), its knowledge_level, and its agent_type. An orthology edge also carries the tier and the supporting methods; a ClinVar edge carries its review stars.
  • Abstention is recorded, not hidden. Of 29,053 dog genes evaluated, 19,073 were edged and 9,980 abstained with a per-gene reason (8,191 with no ortholog found, the rest one-way / ambiguous / no clean human id). Edged plus abstained equals the input: the exclusion is honest, not lossy.

Sources, each cited

  • infores:ensembl - Ensembl Compara orthology (one2one) - CC-BY-style open, DOI 10.1093/nar/gkae1071
  • infores:orthodb - OrthoDB v11 orthology (concordance rung) - CC-BY-4.0, DOI 10.1093/nar/gkac998
  • infores:oma - OMA orthology (concordance rung) - CC-BY-4.0, DOI 10.1093/nar/gkad1020
  • infores:panther - PANTHER v19.0 orthology (concordance rung, LDO) - CC-BY-4.0, DOI 10.1002/pro.4218; the axis Monarch itself ingests (infores:panther)
  • infores:ncbi - NCBI Gene orthologs (concordance rung, synteny) - public domain, DOI 10.1007/s00239-025-10268-2
  • infores:clinvar - ClinVar 3-star gene->disease - public domain, DOI 10.1093/nar/gkx1153
  • infores:gnomad - gnomAD v4.1 gene constraint (node properties) - open, DOI 10.1038/s41586-020-2308-7
  • infores:omia - OMIA Online Mendelian Inheritance in Animals - 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) - infores id NOT YET REGISTERED (Matt)

For stewards: how to pull and evaluate

  1. Treat this page as the contract. Counts, facts-only guarantee, reconciliation math, and layer status (live vs pending) are bound to the committed manifest. If a claim is not here, do not assume it is in the bundle.
  2. Format. KGX TSV (nodes + edges). Biolink-shaped nodes + edges TSVs (KGX). Built by scripts/build-kgx-export.py. Manifest stamp: 2026-07-20T03:06:37Z . Bundle sha256 97f7048fb411f5a7… (recompute over the nodes + edges TSVs you received to confirm match).
  3. How you get the TSV files. The Forge research-compute box is powered down. The bundle is built on the research git lane and published for stewards at s3://sniffdog-data/federation/kgx/ (sniff_nodes.tsv, sniff_edges.tsv, manifest.json) in the Sniff AWS account, and on the Steward host under ~/sniff-research/output/kgx/. This page does not expose a public anonymous HTTPS dump; request access if you do not already have the account. We will not invent a download URL that 404s.
  4. What to check first. (a) edged + abstained = input orthology genes; (b) no prediction/candidate edges; (c) primary sources keep credit; (d) canine disease layer status matches this page (live count or pending). Then sample orthology tiers and a few ClinVar attachments.
  5. What this is not. Not live Translator routing. Not a score of pathogenicity. Not a claim that dog allele = human allele. Companion instruments for model finding live at Spectra and oncology.

Status: an ingestable bundle, honestly

The KGX TSV bundle (nodes plus edges) is ready to ingest as a facts-only package. It is not yet a live federation flow: routing Sniff into Translator or Monarch as an aggregator requires registering infores:sniff, which is a deliberate, human-gated step, not an automatic one. So this is a bundle you can pull and evaluate, with live routing to follow once that registration is done, on our timeline, never before it is honest to do so.