Annotations

The Annotations module contains the gene and disease associations of HPOTerms.

from pyhpo import Ontology
from pyhpo.annotations import Omim, Orpha

Ontology()

# All genes and diseases can be accessed through the Ontology

for gene in Ontology.genes:
    print(gene.name)
    # >> "EZH2"
    # ...

for orpha in Ontology.orpha_diseases:
    print(orpha.id)
    # >> 231401
    # ...


# or accessed directly from the `Orpha`, `Omim`, `Gene` class

orpha_disease = Orpha.get(77260)
omim_disease = Omim.get(230900)


# Annotations can be converted to `HPOSet`

orpha_set = orpha_disease.hpo_set()
omim_set = omim_disease.hpo_set()

similarity = orpha_set.similarity(omim_set)
print(similarity)
# >> 0.6620065792484546

class GeneSingleton

An instance of a gene, associated to several pyhpo.term.HPOTern.

Note

Since version 4.0 genes do not contain references to HPOTerms transitively, i.e. only directly associated HPOTerms are linked to the gene.

id

Return Type:: int
Returns:: The HGNC ID of the gene

name

Return Type:: str
Returns:: The HUGO gene synbol of the gene

symbol

Return Type:: str
Returns:: The HUGO gene synbol of the gene (alias of GeneSingleton.name)

hpo

Return Type:: set(int)
Returns:: The HPO-IDs of all associated pyhpo.term.HPOTerm s

toJSON(self, verbose=False)

Backwards compatibility method BaseModel include .json method

Parameters:

verbose (bool, default: False) – Return all associated HPOTerms

Returns:

A dict with the following keys (additional keys might be present, depending on the class)

id - The gene or disease ID
name - The gene or disease name
hpo - (If verbose=True): set of pyhpo.term.HPOTerm

Return type:

dict

hpo_set(self)

Returns an HPOSet of all associated HPOTerm

Returns:: An HPOSet containing all associated HPOTerm
Return type:: pyhpo.set.HPOSet

Examples

from pyhpo import Ontology
Ontology()

gene = list(Ontology.genes)[0]
gene.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

omim_disease = list(Ontology.omim_diseases)[0]
omim_disease.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

orpha_disease = list(Ontology.orpha_diseases)[0]
orpha_disease.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

class Gene

Gene holds all GeneSingleton instances and ensures they are not duplicated. It does not need to be instantiated, as it is already created as a singleton during the setup of the Ontology.

get(query, default=None)

Get the Gene based on query parameters. This method is the fastest and safest way to retrieve a single Gene instance.

Parameters:: query (str or int) – The gene symbol or HGNC-ID
Returns:: If a gene is found, it is returned. Otherwise an Error is raised
Return type:: GeneSingleton
Raises:: KeyError – The queried gene does not exist

Examples

from pyhpo import Ontology
from pyhpo.annotations import Gene

Ontology()

ezh2 = Gene.get("EZH2")

print(ezh2.id)
# >> 2146

print(len(ezh2.hpo))
# >> 99

__call__(hgncid, symbol)

Instantiates a new GeneSingleton or returns an already existing one.

The method will first check if the gene already exists. It does so by first searching via the gene symbol and then via hgncid. If both don’t exist, a new instance will be created.

Warning

There is rarely ever any need to instantiate genes manually. All genes that are present in JAX’s HPO masterdata are automatically added and can be retrieved using Gene.get(). pyhpo contains logic to ensure that the same gene is not instantiated multiple times and will return an already existing gene instance, whenever possible.

Parameters:

hgncid (int) – The gene’s HGNC-ID
symbol (str) – The gene’s HUGO gene synbol

Returns:

Either creates a new instance or returns an existing one, if already present

Return type:

GeneSingleton

class OmimDisease

An instance of an Omim disease, associated to several pyhpo.term.HPOTerm.

id

Return Type:: int
Returns:: The Omim ID

name

Return Type:: str
Returns:: The Omim disease name

hpo

Return Type:: set(int)
Returns:: The HPO-ID of all associated HPOTerm s

toJSON(self, verbose=False)

Backwards compatibility method BaseModel include .json method

Parameters:

verbose (bool, default: False) – Return all associated HPOTerms

Returns:

A dict with the following keys (additional keys might be present, depending on the class)

id - The gene or disease ID
name - The gene or disease name
hpo - (If verbose=True): set of pyhpo.term.HPOTerm

Return type:

dict

hpo_set(self)

Returns an HPOSet of all associated HPOTerm

Returns:: An HPOSet containing all associated HPOTerm
Return type:: pyhpo.set.HPOSet

Examples

from pyhpo import Ontology
Ontology()

gene = list(Ontology.genes)[0]
gene.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

omim_disease = list(Ontology.omim_diseases)[0]
omim_disease.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

orpha_disease = list(Ontology.orpha_diseases)[0]
orpha_disease.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

class Omim

Omim holds all OmimDisease instances and ensures they are not duplicated. It does not need to be instantiated, as it is already created as a singleton during the setup of the Ontology.

get(self, query, default=None)

Get the disease based on query parameters. This method is the fastest and safest way to retrieve a single disease instance.

Parameters:: query (int) – The (most likely user supplied) query for Disease ID.
Returns:: If a disease is found, it is returned. Otherwise a KeyError is raised
Return type:: DiseaseSingleton (based on disease type)

Examples

from pyhpo import Ontology
from pyhpo.annotations import Omim, Orpha

Ontology()

orpha_disease = Orpha.get(77260)
omim_disease = Omim.get(230900)

print(orpha_disease.name)
# >> "Gaucher disease type 2"

print(omim_disease.name)
# >> "Gaucher disease, type II"

Return type:: OmimDisease

__call__(self, diseaseid, name)

Instantiates a new DiseaseSingleton or returns an already existing one.

The method will first check if the disease already exists. If it doesn’t exist, a new instance will be created.

Warning

There is rarely ever any need to instantiate diseases manually. All diseases that are present in JAX’s HPO masterdata are automatically added and can be retrieved using the diseases get method. pyhpo contains logic to ensure that the same disease is not instantiated multiple times and will return an already existing disease instance, whenever possible.

Parameters:

diseaseid (int) – The ID of the disease
name (str) – The diseases’s name

Returns:

Either creates a new instance or returns an existing one, if already present

Return type:

DiseaseSingleton

class OrphaDisease

An instance of an Orpha disease, associated to several pyhpo.term.HPOTerm.

id

Return Type:: int
Returns:: The Orpha ID

name

Return Type:: str
Returns:: The Orpha disease name

hpo

Return Type:: set(int)
Returns:: The HPO-ID of all associated HPOTerm s

toJSON(self, verbose=False)

Backwards compatibility method BaseModel include .json method

Parameters:

verbose (bool, default: False) – Return all associated HPOTerms

Returns:

A dict with the following keys (additional keys might be present, depending on the class)

id - The gene or disease ID
name - The gene or disease name
hpo - (If verbose=True): set of pyhpo.term.HPOTerm

Return type:

dict

hpo_set(self)

Returns an HPOSet of all associated HPOTerm

Returns:: An HPOSet containing all associated HPOTerm
Return type:: pyhpo.set.HPOSet

Examples

from pyhpo import Ontology
Ontology()

gene = list(Ontology.genes)[0]
gene.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

omim_disease = list(Ontology.omim_diseases)[0]
omim_disease.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

orpha_disease = list(Ontology.orpha_diseases)[0]
orpha_disease.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

class Orpha

Orpha holds all OrphaDisease instances and ensures they are not duplicated. It does not need to be instantiated, as it is already created as a singleton during the setup of the Ontology.
get(self, query, default=None)
Get the disease based on query parameters. This method is the fastest and safest way to retrieve a single disease instance.

Parameters:

query (int) – The (most likely user supplied) query for Disease ID.

Returns:

If a disease is found, it is returned. Otherwise a KeyError is raised

Return type:

DiseaseSingleton (based on disease type)

Examples
from pyhpo import Ontology
from pyhpo.annotations import Omim, Orpha

Ontology()

orpha_disease = Orpha.get(77260)
omim_disease = Omim.get(230900)

print(orpha_disease.name)
# >> "Gaucher disease type 2"

print(omim_disease.name)
# >> "Gaucher disease, type II"
Return type:

OrphaDisease

__call__(self, diseaseid, name)

Instantiates a new DiseaseSingleton or returns an already existing one.

The method will first check if the disease already exists. If it doesn’t exist, a new instance will be created.

Warning

There is rarely ever any need to instantiate diseases manually. All diseases that are present in JAX’s HPO masterdata are automatically added and can be retrieved using the diseases get method. pyhpo contains logic to ensure that the same disease is not instantiated multiple times and will return an already existing disease instance, whenever possible.

Parameters:

diseaseid (int) – The ID of the disease
name (str) – The diseases’s name

Returns:

Either creates a new instance or returns an existing one, if already present

Return type:

DiseaseSingleton

class DecipherDisease

An instance of an Decipher disease, associated to several pyhpo.term.HPOTerm.

id

Return Type:

int

Returns:

The Decipher ID

name

Return Type:: str
Returns:: The Decipher disease name

hpo

Return Type:: set(int)
Returns:: The HPO-ID of all associated HPOTerm s

toJSON(self, verbose=False)

Backwards compatibility method BaseModel include .json method

Parameters:

verbose (bool, default: False) – Return all associated HPOTerms

Returns:

A dict with the following keys (additional keys might be present, depending on the class)

id - The gene or disease ID
name - The gene or disease name
hpo - (If verbose=True): set of pyhpo.term.HPOTerm

Return type:

dict

hpo_set(self)

Returns an HPOSet of all associated HPOTerm

Returns:: An HPOSet containing all associated HPOTerm
Return type:: pyhpo.set.HPOSet

Examples

from pyhpo import Ontology
Ontology()

gene = list(Ontology.genes)[0]
gene.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

omim_disease = list(Ontology.omim_diseases)[0]
omim_disease.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

orpha_disease = list(Ontology.orpha_diseases)[0]
orpha_disease.hpo_set()
# >> HPOSet.from_serialized(7+118+152+234+271+315, ....)

class Decipher

Decipher holds all DecipherDisease instances and ensures they are not duplicated.
get(self, query, default=None)
Get the disease based on query parameters. This method is the fastest and safest way to retrieve a single disease instance.

Parameters:

query (int) – The (most likely user supplied) query for Disease ID.

Returns:

If a disease is found, it is returned. Otherwise a KeyError is raised

Return type:

DiseaseSingleton (based on disease type)

Examples
from pyhpo import Ontology
from pyhpo.annotations import Omim, Orpha

Ontology()

orpha_disease = Orpha.get(77260)
omim_disease = Omim.get(230900)

print(orpha_disease.name)
# >> "Gaucher disease type 2"

print(omim_disease.name)
# >> "Gaucher disease, type II"
Return type:

DecipherDisease

__call__(self, diseaseid, name)

Instantiates a new DiseaseSingleton or returns an already existing one.

The method will first check if the disease already exists. If it doesn’t exist, a new instance will be created.

Warning

There is rarely ever any need to instantiate diseases manually. All diseases that are present in JAX’s HPO masterdata are automatically added and can be retrieved using the diseases get method. pyhpo contains logic to ensure that the same disease is not instantiated multiple times and will return an already existing disease instance, whenever possible.

Parameters:

diseaseid (int) – The ID of the disease
name (str) – The diseases’s name

Returns:

Either creates a new instance or returns an existing one, if already present

Return type:

DiseaseSingleton