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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.

Inspect the seam

These rows are taken from the published TSV bundle (sha256 1eadd8e866f6dce8… ). Every sample is a knowledge_assertion with primary credit outside Sniff and aggregator infores:sniff. This is not a demo script. It is how you check the claim before you ingest.

biolink:orthologous_to

ENSCAFG00805000006 (ENSEMBL:ENSCAFG00805000006) → PARD6G (ENSEMBL:ENSG00000178184)

  • primary: infores:ensembl
  • aggregator: infores:sniff
  • knowledge_level: knowledge_assertion · agent: automated_agent
  • orthology: high-corroborated · methods: ensembl|ncbi|oma|orthodb|panther
biolink:orthologous_to

ADNP2 (ENSEMBL:ENSCAFG00805000008) → ADNP2 (ENSEMBL:ENSG00000101544)

  • primary: infores:ensembl
  • aggregator: infores:sniff
  • knowledge_level: knowledge_assertion · agent: automated_agent
  • orthology: high-corroborated · methods: ensembl|ncbi|orthodb|panther
biolink:causes

ABCA4 (ENSEMBL:ENSG00000198691) → cone dystrophy (MONDO:0000455)

  • primary: infores:clinvar
  • aggregator: infores:sniff
  • knowledge_level: knowledge_assertion · agent: manual_agent
  • ClinVar review_stars: 3
biolink:causes

ABCA4 (ENSEMBL:ENSG00000198691) → blindness (disorder) (MONDO:0001941)

  • primary: infores:clinvar
  • aggregator: infores:sniff
  • knowledge_level: knowledge_assertion · agent: manual_agent
  • ClinVar review_stars: 3
biolink:associated_with_increased_likelihood_of

ACTA1 (ENSEMBL:ENSG00000143632) → progressive scapulohumeroperoneal distal myopathy (MONDO:0014800)

  • primary: infores:clinvar
  • aggregator: infores:sniff
  • knowledge_level: knowledge_assertion · agent: manual_agent
  • ClinVar review_stars: 3
biolink:gene_associated_with_condition

ABCA4 (ENSEMBL:ENSCAFG00805024722) → Stargardt disease 1 (MONDO:0019353)

  • primary: infores:omia
  • aggregator: infores:sniff
  • knowledge_level: knowledge_assertion · agent: manual_agent
biolink:gene_associated_with_condition

AGL (ENSEMBL:ENSCAFG00805017945) → Glycogen storage disease IIIa (MONDO:0009291)

  • primary: infores:omia
  • aggregator: infores:sniff
  • knowledge_level: knowledge_assertion · agent: manual_agent
biolink:gene_associated_with_condition

ABCB1 (ENSEMBL:ENSCAFG00805024080) → Multidrug resistance 1, ABCB1-related (OMIA:001402)

  • primary: infores:omia
  • aggregator: infores:sniff
  • knowledge_level: knowledge_assertion · agent: manual_agent

Node label coverage (honest)

A steward graph needs human-readable labels, not only CURIEs. Gene symbols and MONDO disease names are filled from owned orthology joins and the Monarch entity API (cached). Any remaining gap is reported here, not papered over.

  • human gene symbols: 17,229 / 17,236
  • dog gene symbols: 16,034 / 19,079
  • disease names (non-id): 596 / 600

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 (held for steward guidance)

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: 2026-07-21T07:00:14Z . Bundle sha256 1eadd8e866f6dce8… (recompute over the nodes + edges TSVs you received to confirm match).
  3. How you get the TSV files. Built on the research git lane (no box required): python sniff-research/scripts/build-kgx-export.py. Published under s3://sniffdog-data/federation/kgx/ and available over public HTTPS (verified pull path): Recompute sha256 over the two TSVs and match export_sha256 in the manifest. We will not invent a download URL that 404s. If you prefer an archival Zenodo DOI over S3 HTTPS, we will deposit one on request.
  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

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.