Ontology

The Ontology contains all HPO terms, their connections to each other and associations to genes and diseases. It provides some helper functions for HPOTerm search functionality

Examples

from pyhpo import Ontology, HPOSet

# initilize the Ontology (this must be done only once)
_ = Ontology()

# Get a term based on its name
term = Ontology.get_hpo_object('Scoliosis')
print(term)
#> HP:0002650 | Scoliosis

# ...or based on HPO-ID
term = Ontology.get_hpo_object('HP:0002650')
print(term)
#> HP:0002650 | Scoliosis

# ...or based on its index
term = Ontology.get_hpo_object(2650)
print(term)
#> HP:0002650 | Scoliosis

# shortcut to retrieve a term based on its index
term = Ontology[2650]
print(term)
#> HP:0002650 | Scoliosis

# Search for term
for term in Ontology.search('olios'):
    print(term)

"""
HP:0002211 | White forelock
HP:0002290 | Poliosis
HP:0002650 | Scoliosis
HP:0002751 | Kyphoscoliosis
HP:0002943 | Thoracic scoliosis
HP:0002944 | Thoracolumbar scoliosis
HP:0003423 | Thoracolumbar kyphoscoliosis
HP:0004619 | Lumbar kyphoscoliosis
HP:0004626 | Lumbar scoliosis
HP:0005659 | Thoracic kyphoscoliosis
HP:0008453 | Congenital kyphoscoliosis
HP:0008458 | Progressive congenital scoliosis
HP:0100884 | Compensatory scoliosis
"""

(This script is complete, it should run β€œas is”)

The Ontology is a Singleton and should only be initiated once. It can be reused across several modules, e.g:

main.py

from pyhpo import Ontology, HPOSet

import module2

# initilize the Ontology
_ = Ontology()

if __name__ == '__main__':
    module2.find_term('Compensatory scoliosis')

module2.py

from pyhpo import Ontology

def find_term(term):
    return Ontology.get_hpo_object(term)