Manager

Manager for Bio2BEL miRTarBase.

class bio2bel_mirtarbase.manager.Manager(*args, **kwargs)[source]

miRNA-target interactions.

edge_model

alias of bio2bel_mirtarbase.models.Interaction

is_populated() → bool[source]

Check if the database is already populated.

populate(source: Optional[str] = None, update: bool = False) → None[source]

Populate database with the data from miRTarBase.

Parameters

  • source – path or link to data source needed for get_data()

  • update – Should HGNC an miRBase be updated?

count_targets() → int[source]

Count the number of targets in the database.

count_mirnas() → int[source]

Count the number of miRNAs in the database.

count_interactions() → int[source]

Count the number of interactions in the database.

count_evidences() → int[source]

Count the number of evidences in the database.

list_evidences() → List[bio2bel_mirtarbase.models.Evidence][source]

List the evidences in the database.

count_species() → int[source]

Count the number of species in the database.

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

Return a summary dictionary over the content of the database.

query_mirna_by_mirtarbase_identifier(mirtarbase_id: str) → Optional[bio2bel_mirtarbase.models.Mirna][source]

Get an miRNA by the miRTarBase interaction identifier.

Parameters

mirtarbase_id – An miRTarBase interaction identifier

query_mirna_by_mirtarbase_name(name: str) → Optional[bio2bel_mirtarbase.models.Mirna][source]

Get an miRNA by its miRTarBase name.

Parameters

name – An miRTarBase name

query_mirna_by_hgnc_identifier(hgnc_id: str) → Optional[bio2bel_mirtarbase.models.Mirna][source]

Query for a miRNA by its HGNC identifier.

Parameters

hgnc_id – HGNC gene identifier

query_mirna_by_hgnc_symbol(hgnc_symbol: str) → Optional[bio2bel_mirtarbase.models.Mirna][source]

Query for a miRNA by its HGNC gene symbol.

Parameters

hgnc_symbol – HGNC gene symbol

query_target_by_entrez_id(entrez_id: str) → Optional[bio2bel_mirtarbase.models.Target][source]

Query for one target.

Parameters

entrez_id – Entrez gene identifier

query_target_by_hgnc_symbol(hgnc_symbol: str) → Optional[bio2bel_mirtarbase.models.Target][source]

Query for one target.

Parameters

hgnc_symbol – HGNC gene symbol

query_target_by_hgnc_identifier(hgnc_id: str) → Optional[bio2bel_mirtarbase.models.Target][source]

Query for one target.

Parameters

hgnc_id – HGNC gene identifier

enrich_rnas(graph: pybel.struct.graph.BELGraph)[source]

Add all of the miRNA inhibitors of the RNA nodes in the graph.

enrich_mirnas(graph: pybel.struct.graph.BELGraph)[source]

Add all target RNAs to the miRNA nodes in the graph.

get_mirna_interaction_evidences()[source]

Get interaction evidences.

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

Serialize miRNA-target interactions to BEL.