uPheno
The cross-species phenotype layer. A dog's cough, a human's cough, and a mouse's cough are different observations of the same kind of thing, and uPheno is the ontology that lets them be compared.
Every species has its own catalogue of clinical signs. Humans have the Human Phenotype Ontology (HPO), mice have the Mammalian Phenotype ontology (MP), zebrafish have ZP, and so on. For decades those lived in separate worlds. uPheno, built by the Monarch Initiative, unifies them: it maps each species-specific term up to a species-neutral phenotype class, so a sign observed in one species can be compared to a sign in another. The cross-species mappings are published openly as SSSOM in the Monarch Mapping Commons, and the Monarch knowledge graph runs on uPheno.
It matches a belief Sniff was built on: a dog's genome is its own, but a phenotype, a sign you can see, is a thing that travels across species. That is why the honest way to connect canine medicine to the far larger human literature runs through phenotypes.
OMIA records the clinical signs of a canine disease using borrowed human (HP) and mouse (MP) terms, a field called omia_uphenolink. On its own that is a list of codes. Sniff resolves those codes through uPheno into a governed phenotype dimension, so a disease's signs become first-class, cited, cross-species entities rather than prose. That does two things: it tells an owner, in plain terms, what signs they might actually see, and it deepens the dog-to-human bridge from the disease level (this dog condition models this human disease) down to the phenotype level (these specific signs are shared).
A human phenotype term applied to a dog is a borrowed term, not a canine-native one. So Sniff renders every such sign as a model of the human phenotype, provenance-tagged to the species it came from, never as a claim that the dog has the human sign itself. This is the same model-of discipline we hold for the disease bridge, extended to phenotypes. A mapping that is a strong logical equivalence is shown as such; a looser lexical match is shown as looser. And where a disease has no recorded signs, we say so, rather than inventing one. Coverage is a number we report, not a gap we hide.
uPheno and the Monarch Mapping Commons are products of the Monarch Initiative, released under CC-BY 4.0. Sniff consumes their mappings; we do not curate the ontology.
Matentzoglu N, et al. (2025). uPheno: a unified cross-species phenotype ontology. Genetics, doi:10.1093/genetics/iyaf027. Ontology: obophenotype/upheno. Mappings: Monarch Mapping Commons (SSSOM).