Sources

Protein Interactions Database (PID)

PID Importer.

bio2bel.sources.pid.iterate_graphs()[source]

List network uuids.

Return type

Iterable[Tuple[str, BELGraph]]

bio2bel.sources.pid.get_graph_from_cx(network_uuid, cx)[source]

Get a PID network from NDEx.

Return type

BELGraph

class bio2bel.sources.pid.Protein(**kwargs)[source]

Protein from PID.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

entrez_id

entrez id of the protein

hgnc_id

HGNC id of the protein

hgnc_symbol

HGN symbol of the protein

to_pybel()[source]

Return a protein.

Return type

Protein

class bio2bel.sources.pid.Pathway(**kwargs)[source]

Pathway from PID.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

identifier

HGNC gene family id of the protein

name

HGNC gene family name of the protein

class bio2bel.sources.pid.Manager(*args, **kwargs)[source]

Manager for PID.

Doesn’t let this class get instantiated if the pathway_model.

namespace_model

alias of Pathway

pathway_model

alias of Pathway

protein_model

alias of Protein

populate(*args, **kwargs)[source]

Populate the PID database.

Return type

None

TFRegulons

Exporter for TFregulons.

bio2bel.sources.tfregulons.get_df()[source]

Get the TFregulons dataframe.

Return type

DataFrame

bio2bel.sources.tfregulons.get_hgnc_ids(graph)[source]

Get HGNC identifiers for nodes in the graph.

Return type

Set[str]

bio2bel.sources.tfregulons.get_bel()[source]

Get the entirety of TFregulons as BEL.

Return type

BELGraph

bio2bel.sources.tfregulons.enrich_graph(graph)[source]

Enrich a graph with transcription factors effecting the genes/rnas/proteins in the graph.

Return type

None