Download a HMDB XML file and process it into a table
Arguments
- dataset
Character: name of an HMDB XML dataset, such as "metabolites", "proteins", "urine", "serum", "csf", "saliva", "feces", "sweat".
- fields
Character: fields to extract from the XML. This is a very minimal parser that is able to extract the text content of simple fields and multiple value fields which contain a list of leaves within one container tag under the record tag. A full list of fields available in HMDB is available by the
hmdb_protein_fieldsandhmdb_metabolite_fieldsfunctions. By default, all fields available in the dataset are extracted.
Examples
hmdb_table()
#> # A tibble: 217,920 × 33
#> accession name version status description chemical_formula
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 HMDB0000001 1-Methylhistidine 5.0 quant… "1-Methylh… C7H11N3O2
#> 2 HMDB0000002 1,3-Diaminopropane 5.0 quant… "1,3-Diami… C3H10N2
#> 3 HMDB0000005 2-Ketobutyric acid 5.0 quant… "2-Ketobut… C4H6O3
#> 4 HMDB0000008 2-Hydroxybutyric acid 5.0 quant… "2-Hydroxy… C4H8O3
#> 5 HMDB0000010 2-Methoxyestrone 5.0 quant… "2-Methoxy… C19H24O3
#> 6 HMDB0000011 3-Hydroxybutyric acid 5.0 quant… "3-Hydroxy… C4H8O3
#> 7 HMDB0000012 Deoxyuridine 5.0 quant… "Deoxyurid… C9H12N2O5
#> 8 HMDB0000014 Deoxycytidine 5.0 quant… "Deoxycyti… C9H13N3O4
#> 9 HMDB0000015 Cortexolone 5.0 quant… "Cortexolo… C21H30O4
#> 10 HMDB0000016 Deoxycorticosterone 5.0 quant… "11-Deoxyc… C21H30O3
#> # ℹ 217,910 more rows
#> # ℹ 27 more variables: average_molecular_weight <chr>,
#> # monisotopic_molecular_weight <chr>, iupac_name <chr>,
#> # traditional_iupac <chr>, cas_registry_number <chr>, smiles <chr>,
#> # inchi <chr>, inchikey <chr>, state <chr>, synthesis_reference <chr>,
#> # chemspider_id <chr>, drugbank_id <chr>, foodb_id <chr>,
#> # pubchem_compound_id <chr>, pdb_id <chr>, chebi_id <chr>, …