bionty.base.Phenotype

class bionty.base.Phenotype(organism=None, source=None, version=None, **kwargs)

Bases: PublicOntology

Phenotype.

1. Human Phenotype Ontology https://hpo.jax.org/app/

2. Mammalian Phenotype Ontology mgijax/mammalian-phenotype-ontology

3. Zebrafish Phenotype Ontology obophenotype/zebrafish-phenotype-ontology

4.Phecodes ICD10 map https://phewascatalog.org/phecodes_icd10

Parameters:

  • organism (Literal['human', 'mammalian', 'zebrafish', 'all'] | None, default: None) – name of Organism entity.

  • source (Literal['hp', 'phe', 'mp', 'zp', 'pato'] | None, default: None) – The key of the source in the local.yml versions file. Get all available databases with .display_available_sources().

  • version (str | None, default: None) – The version of the ontology. Typically a date or an actual version. Get available versions with .display_available_sources().

Attributes

property fields: set

All PublicOntology entity fields.

property organism

The name of Organism.

property source

Name of the source.

property version

Version of the source.

Methods