Manager

Manager for Bio2BEL HMDD.

class bio2bel_hmdd.manager.Manager(*args, **kwargs)[source]

Bio2BEL Manager for HMDD.

count_associations() → int[source]

Count the number of miRNA-disease associations in the database.

count_diseases() → int[source]

Count the number of diseases in the database.

count_mirnas() → int[source]

Count the number of miRNAs in the database.

get_disease_by_name(name: str) → Optional[bio2bel_hmdd.models.Disease][source]

Gets a Disease from the database if it exists

Parameters:name – A MeSH disease name
get_mirna_by_name(name: str) → Optional[bio2bel_hmdd.models.MiRNA][source]

Gets an miRNA from the database if it exists

Parameters:name – A mirBase name
get_or_create_disease(name: str) → bio2bel_hmdd.models.Disease[source]

Get a Disease from the database or creates it if it does not exist

Parameters:name – A MeSH disease name
get_or_create_mirna(name: str) → bio2bel_hmdd.models.MiRNA[source]

Gets an miRNA from the database or creates it if it does not exist

Parameters:name – A mirBase name
is_populated() → bool[source]

Check if the database is already populated.

list_associations() → List[bio2bel_hmdd.models.Association][source]

List all associations.

populate(url: Optional[str] = None)[source]

Populate the database.

summarize() → Mapping[str, int][source]

Summarize the database.

to_bel() → pybel.struct.graph.BELGraph[source]

Build a BEL graph containing all of the miRNA-disease associations in the database.