napistu.ingestion.bigg

Functions

`bigg_sbml_download`(bg_pathway_root[, overwrite])	BiGG SBML Download
`construct_bigg_consensus`(pw_index_inp[, ...])	Construct a BiGG SBML DFs pathway representation.

napistu.ingestion.bigg.bigg_sbml_download(bg_pathway_root: str, overwrite: bool = False) → None

BiGG SBML Download

Download SBML models from BiGG. Currently just the human Recon3D model

Parameters:

bg_pathway_root (str) – Paths to a directory where a “sbml” directory should be created.
overwrite (bool) – Overwrite an existing output directory.

Return type:

None

napistu.ingestion.bigg.construct_bigg_consensus(pw_index_inp: str | PWIndex, organismal_species: str | None = None) → SBML_dfs

Construct a BiGG SBML DFs pathway representation.

Parameters:

pw_index_inp (str or indices.PWIndex) – PWIndex object or URI pointing to PWIndex
organismal_species (str or None, optional) – One or more species to filter by, by default None (no filtering)
outdir (str or None, optional) – Output directory used to cache results, by default None

Returns:

A consensus SBML representation

Return type:

sbml_dfs_core.SBML_dfs

Notes

Currently this only works for a single model. Integration of multiple models is not yet supported in BiGG.

The function: 1. Loads/validates the pathway index 2. Constructs SBML DFs dictionary 3. Processes the single model:

Infers compartmentalization for species without location

Names compartmentalized species

Validates the final model

Raises: