Annotations

The Annotations section contains various metadata annotations for HPO terms.

GeneSingleton class

class pyhpo.annotations.GeneSingleton(**kwargs)

An instance of GeneSingleton represents a single gene.

Note

GeneSingleton should never be initiated directly, but only via GeneDict to ensure that every gene is only created once.

id

HGNC gene ID

Type:

int

name

HGNC gene synbol

Type:

str

symbol

HGNC gene symbol (alias of GeneSingleton.name)

Type:

str

hpo

all HPOTerms associated to the gene

Type:

set of pyhpo.term.HPOTerm

Parameters:

• id (int) – HGNC gene ID

• name (str) – HGNC gene synbol

toJSON

GeneSingleton.toJSON(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 HGNC ID

• name - The gene symbol

• hpo - (If verbose == True): set of pyhpo.term.HPOTerm

Return type:

dict

GeneDict class

class pyhpo.annotations.GeneDict

An associative dict of all genes

Ensures that every gene is a single GeneSingleton instance and no duplicate instances are generated during parsing of the Gen-Pheno-HPO associations.

This class is initilized once and genes are created by calling the instance of GeneDict to ensure that the same gene exists only once.

For example

Gene = GeneDict()
gba = Gene(symbol='GBA')
ezh2 = Gene(symbol='EZH2')
gba_2 = Gene(symbol='GBA')

gba is ezh2
>> False
gba is gba_2
>> True

Parameters:

• cols (list, default: None) –

  Only used for backwards compatibility reasons. Should have the following entries

  • None

  • None

  • HGNC-ID

  • Gene symbol

• hgncid (int) – The HGNC ID

• symbol (str) – The gene symbol (alternative to name)

Return type:

GeneSingleton

DiseaseSingleton class

class pyhpo.annotations.DiseaseSingleton(**kwargs)

This class represents a single disease.

Note

DiseaseSingleton should never be initiated directly, but only via the appropriate disease dictionary, e.g. OmimDict (DiseaseDict) to ensure that every disease is only created once.

id

Disease ID

Type:

int

name

disease name

Type:

str

hpo

all HPOTerms associated to the disease

Type:

set of pyhpo.term.HPOTerm

negative_hpo

HPOTerms not associated to the disease

Type:

set of pyhpo.term.HPOTerm

Parameters:

• id (int) – Disease ID

• name (str) – Disease name

toJSON

DiseaseSingleton.toJSON(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 HGNC ID

• name - The gene symbol

• hpo - (If verbose == True): set of pyhpo.term.HPOTerm

Return type:

dict

DiseaseDict class

class pyhpo.annotations.DiseaseDict

An associative dict of all Omim Diseases

Ensures that every Omim Disease is a single OmimDisease instance and no duplicate instances are generated during parsing of the Gen-Pheno-HPO associations.

This class is initilized once and diseases are created by calling the instance of DiseaseDict to ensure that the same disease exists only once.

For example

Disease = OmimDict()
gaucher = Disease(diseaseid=1)
fabry = Disease(diseaseid=2)
gaucher_2 = Disease(diseaseid=1)

gaucher is fabry
>> False
gaucher is gaucher_2
>> True

Parameters:

• cols (list, default: None) –

  Only used for backwards compatibility reasons. Should have the following entries

  • None

  • Disease ID

  • Disease Name

• diseaseid (int) – The Disease ID

• name (str) – The disease name

Return type:

DiseaseSingleton

Omim

Instance of pyhpo.annotations.DiseaseDict to handle Omim diseases. Ensures that diseases are not duplicated through use of Singletons.

Orpha

Instance of pyhpo.annotations.DiseaseDict to handle Orphanet diseases. Ensures that diseases are not duplicated through use of Singletons.

Decipher

Instance of pyhpo.annotations.DiseaseDict to handle Decipher diseases. Ensures that diseases are not duplicated through use of Singletons.