Examples

This section provides examples for various functions of PyHPO.

Some high-level examples are already provided in the README file:

Some examples for basic functionality of PyHPO

How similar are the phenotypes of two patients

from pyhpo import Ontology
from pyhpo.set import HPOSet

# initilize the Ontology ()
_ = Ontology()

# Declare the clinical information of the patients
patient_1 = HPOSet.from_queries([
    'HP:0002943',
    'HP:0008458',
    'HP:0100884',
    'HP:0002944',
    'HP:0002751'
])

patient_2 = HPOSet.from_queries([
    'HP:0002650',
    'HP:0010674',
    'HP:0000925',
    'HP:0009121'
])

# and compare their similarity
patient_1.similarity(patient_2)
#> 0.7594183905785477

How close are two HPO terms

from pyhpo import Ontology

# initilize the Ontology ()
_ = Ontology()

term_1 = Ontology.get_hpo_object('Scoliosis')
term_2 = Ontology.get_hpo_object('Abnormal axial skeleton morphology')

path = term_1.path_to_other(term_2)
for t in path[1]:
    print(t)

"""
HP:0002650 | Scoliosis
HP:0010674 | Abnormality of the curvature of the vertebral column
HP:0000925 | Abnormality of the vertebral column
HP:0009121 | Abnormal axial skeleton morphology
"""