liana.resource.get_metalinks

liana.resource.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 | None (default: None)) – Path to the SQLite database file. If None, the database will be downloaded to the current working directory.

• types (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 (list[str] | None (default: None)) – Desired metabolite cell locations.

• tissue_location (list[str] | None (default: None)) – Desired metabolite tissue locations.

• biospecimen_location (list[str] | None (default: None)) – Desired metabolite biospecimen locations.

• disease (list[str] | None (default: None)) – Desired metabolite diseases.

• pathway (list[str] | None (default: None)) – Desired metabolite pathways.

• hmdb_ids (list[str] | None (default: None)) – Desired HMDB IDs.

• uniprot_ids (list[str] | None (default: None)) – Desired UniProt IDs.

• source (list[str] | None (default: None)) – Desired source databases.

Return type:

DataFrame

Returns:

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