Parsing Database (pdb)

The parsing_database module (pdb) provides functions to parse various biological databases (e.g., Reactome, HMDB, KEGG) in XML formats and extract structured data into pandas DataFrames. It also includes utilities to infer relationships between genes and compounds based on the parsed data.

Key Functions

• pdb.apply_mapping_and_cleanup(): Applies mapping to standardize identifiers and cleans up the DataFrame by removing duplicates and handling missing values.
• pdb.create_adata(): Creates an AnnData object from the parsed data for downstream analysis.
• pdb.construct_kegg_relations(): Constructs relationships between genes and compounds from KEGG pathway XML files.
• pdb.download_all_kegg_pathway_xml(): Downloads all KEGG pathway XML files for a specified species.
• pdb.parse_hmdb_xml()&pdb.extract_hmdb_relations(): Parses HMDB data files to extract metabolite information.
• pdb.parse_kegg_relations()&pdb.parse_all_kegg_pathways(): Parses KEGG pathway XML files to extract gene and compound relationships.
• pdb.parse_reactome_sbml()&pdb.extract_reactome_relations()&pdb.process_all_reactome_pathways(): Parses Reactome SBML files to extract pathway information.