xgi.readwrite.bigg_data

Load a metabolic network from the BiGG models database.

Functions

xgi.readwrite.bigg_data.load_bigg_data(dataset=None, cache=True)[source]

Load a metabolic network from the BiGG models database.

The Biochemical, Genetic and Genomic (BiGG) knowledge base is hosted at http://bigg.ucsd.edu/. It contains metabolic reaction networks at the genome scale.

We represent metabolites as nodes and metabolic reactions as directed edges where reactants are the tail of the directed edge and the products are the head of the directed edge.

Parameters:

dataset (str, default: None) – Dataset name. Valid options are the “bigg_id” tags in http://bigg.ucsd.edu/api/v2/models. If None, prints the list of available datasets.
cache (bool, optional) – Whether to cache the input data

Returns:

The loaded dihypergraph.

Return type:

DiHypergraph

Raises:

XGIError – The specified dataset does not exist.

References

Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D515–D522, https://doi.org/10.1093/nar/gkv1049