bionty_base.Phenotype#

class bionty_base.Phenotype(organism=None, source=None, version=None, **kwargs)#

Bases: PublicOntology

Phenotype.

1. Human Phenotype Ontology Edits of terms are coordinated and reviewed on: https://hpo.jax.org/app/

2. Mammalian Phenotype Ontology Edits of terms are coordinated and reviewed on: mgijax/mammalian-phenotype-ontology

3. Zebrafish Phenotype Ontology Edits of terms are coordinated and reviewed on: obophenotype/zebrafish-phenotype-ontology

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

Parameters:

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

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

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

Attributes

fields set#

All PublicOntology entity fields.

organism property#

The name of Organism.

source property#

Name of the source.

version property#

Version of the source.