Ontology

The Ontology is provided as a singleton. It must be instantiated once to load all terms and annotations. Afterwards, the complete Ontology is available from the global scope across all submodules.

Instantiation

The Ontology must be instantiated once in every running program. This loads all HPO terms, their connections and annotation into memory.

Arguments

data_folder: str: Path to the source files (default: None) Leave blank to load the builtin Ontology (recommended)
from_obo_file: bool: Whether the input format is the standard from Jax HPO (default True)

Examples

from pyhpo import Ontology

Ontology()

term = Ontology.hpo(11968)
term.name()  # ==> 'Feeding difficulties'
term.id()    # ==> 'HP:0011968'
int(tern)    # ==> 11968

# Altenatively, you can use direct access to HPOTerms:

term = Ontology[11968]
# ...

The following code with multiple modules works, because the Ontology must only be loaded once:

File main.py

from pyhpo import Ontology

import submodule
from submodule import foo

Ontology()

foo()
submodule.bar()

File submodule.py

from pyhpo import Ontology

def foo():
    print(len(Ontology))

def bar():
    print(len(Ontology))

Attributes

__class__.genes

A list of all genes included in the ontology

Returns: All genes that are associated to the pyhpo.HPOTerm in the ontology
Return type: list[pyhpo.Gene]

Important

The return type of this method will very likely change into an Iterator of Gene. (Info about likely API changes)

Raises: NameError – Ontology not yet constructed:

__class__.omim_diseases

A list of all Omim Diseases included in the ontology

Returns: All Omim diseases that are associated to the pyhpo.HPOTerm in the ontology
Return type: list[pyhpo.Omim]

Important

The return type of this method will very likely change into an Iterator of Omim. (Info about likely API changes)

Raises: NameError – Ontology not yet constructed:

Methods

get_hpo_object(self, /, query)

Returns a single HPOTerm based on its name, synonym or id

Parameters

query (str or int) –

str HPO term (e.g.: Scoliosis)
str HPO-ID (e.g.: HP:0002650)
int HPO term id (e.g.: 2650)

Returns

A single matching HPO term instance

Return type

pyhpo.HPOTerm

Raises

NameError – Ontology not yet constructed
RuntimeError – No HPO term is found for the provided query
TypeError – The provided query is an unsupported type and can’t be properly converted
ValueError – The provided HPO ID cannot be converted to the correct integer representation

Examples

from pyhpo import Ontology
Ontology()

# Search by ID (int)
Ontology.get_hpo_object(3)
# >> HP:0000003 | Multicystic kidney dysplasia

# Search by HPO-ID (string)
Ontology.get_hpo_object('HP:0000003')
# >> HP:0000003 | Multicystic kidney dysplasia

# Search by term (string)
Ontology.get_hpo_object('Multicystic kidney dysplasia')
# >> HP:0000003 | Multicystic kidney dysplasia

match(self, /, query)

Returns a single HPOTerm based on its name

Parameters

query (str) – Name of the HPO term, e.g. Scoliosis

Returns

A single matching HPO term instance

Return type

pyhpo.HPOTerm

Raises

NameError – Ontology not yet constructed
RuntimeError – No HPO term is found for the provided query

Examples

from pyhpo import Ontology
Ontology()

Ontology.match('Multicystic kidney dysplasia')
# >>> HP:0000003 | Multicystic kidney dysplasia

path(self, /, query1, query2)

Returns the shortest path from one to another HPO Term

Parameters

query1 (str or int) – Name, HPO-ID (HP:0040064) or integer ID of source term e.g: Abnormality of the nervous system
query2 (str or int) – Name, HPO-ID (HP:0040064) or integer ID of target term e.g: Abnormality of the nervous system

Returns

int – Length of path
list – List of HPOTerms in the path
int – Number of steps from term1 to the common parent (Not implemented. Returns 0)
int – Number of steps from term2 to the common parent (Not implemented. Returns 0)

Raises

NameError – Ontology not yet constructed
RuntimeError – No HPO term is found for the provided query
TypeError – The provided query is an unsupported type and can’t be properly converted
ValueError – The provided HPO ID cannot be converted to the correct integer representation

Examples

from pyhpo import Ontology
Ontology()

Ontology.path(40064, 'Multicystic kidney dysplasia')
# >> (
# >>     8,
# >>     [
# >>         <HpoTerm (HP:0040064)>, <HpoTerm (HP:0000118)>,
# >>         <HpoTerm (HP:0000119)>, <HpoTerm (HP:0000079)>,
# >>         <HpoTerm (HP:0010935)>, <HpoTerm (HP:0000077)>,
# >>         <HpoTerm (HP:0012210)>, <HpoTerm (HP:0000107)>,
# >>         <HpoTerm (HP:0000003)>
# >>     ],
# >>     0,
# >>     0
# >> )

search(self, /, query)

Returns a list of HPOTerms that match the query

Parameters: query (str) – Query for substring search of HPOTerms
Returns: All terms matching the query string
Return type: list[HPOTerm]

Important

The return type of this method will very likely change into an Iterator of HPOTerm. (Info about likely API changes)

Raises: NameError – Ontology not yet constructed

Examples

from pyhpo import Ontology
Ontology()

for term in Ontology.search("kidney dis"):
    print(term)

# >> HP:0003774 | Stage 5 chronic kidney disease
# >> HP:0012622 | Chronic kidney disease
# >> HP:0012623 | Stage 1 chronic kidney disease
# >> HP:0012624 | Stage 2 chronic kidney disease
# >> HP:0012625 | Stage 3 chronic kidney disease
# >> HP:0012626 | Stage 4 chronic kidney disease

hpo(self, /, id)

Returns the HpoTerm with the provided id

Parameters

id (int) – ID of the term as int (HP:0000123 –> 123)

Returns

The HPO-Term

Return type

pyhpo.HPOTerm

Raises

NameError – Ontology not yet constructed
KeyError – No HPO term is found for the provided query

Examples

from pyhpo import Ontology

Ontology()

term = Ontology.hpo(11968)
term.name()  # >> 'Feeding difficulties'
term.id()    # >> 'HP:0011968'
int(tern)    # >> 11968

version(self, /)

Returns the HPO version

Returns: The HPO version, e.g. 2023-04-05
Return type: str
Raises: NameError – Ontology not yet constructed

Examples

from pyhpo import Ontology

Ontology()

Ontology.version()
# >> "2023-04-05"