liana.rs.get_metalinks

liana.rs.get_metalinks(db_path=None, types=None, cell_location=None, tissue_location=None, biospecimen_location=None, disease=None, pathway=None, hmdb_ids=None, uniprot_ids=None, source=None)

Fetches edges of metabolite-proteins with specified annotations, applying filters if they are not None.

Allows filtering by lists of hmdb and uniprot IDs and avoids duplicate column names, and returns the results as a pandas DataFrame. Filters are applied using INNER JOINs and WHERE clauses - i.e. the results are the intersection of the filters.

Parameters:

db_path str | Path | None (default: None)

Path to the SQLite database file. If None, the database will be downloaded to the current working directory.

types str | list[str] | None (default: None)

Desired edge types. Options are: [‘lr’, ‘pd’], where ‘lr’ stands for ‘ligand-receptor’ and ‘pd’ stands for ‘production-degradation’.

cell_location str | list[str] | None (default: None)

Desired metabolite cell locations.

tissue_location str | list[str] | None (default: None)

Desired metabolite tissue locations.

biospecimen_location str | list[str] | None (default: None)

Desired metabolite biospecimen locations.

disease str | list[str] | None (default: None)

Desired metabolite diseases.

pathway str | list[str] | None (default: None)

Desired metabolite pathways.

hmdb_ids str | list[str] | None (default: None)

Desired HMDB IDs.

uniprot_ids str | list[str] | None (default: None)

Desired UniProt IDs.

source str | list[str] | None (default: None)

Desired source databases.

Return type:

DataFrame

Returns:

A pandas DataFrame containing the query results without the source column.

Examples

This function downloads MetalinksDB on first use, so it is not run here. Metabolite-receptor edges restricted to secreted metabolites are obtained with:

resource = get_metalinks(
    types=["lr"],
    biospecimen_location="Blood",
)