Simple pipeline for quest of information from the Human Metabolome Database (HMDB, https://hmdb.ca/).
- download the latest database from https://hmdb.ca/system/downloads/current/hmdb_metabolites.zip
- unzip downloaded file
- mv downloaded file to ./data/ and name it as hmdb_metabolites.xml
- go to running/ and build two configuration files to specify the queried elements (`input_info.param') and the desired columns (`desired_info.param') as the form shown in corresponding example files.
- change corresponding param file names in running.sh and run with bash running.sh
- find desired table file in results/
version
creation_date
update_date
accession
status
secondary_accessions/accession
name
description
synonyms/synonym
chemical_formula
average_molecular_weight
monisotopic_molecular_weight
iupac_name
traditional_iupac
cas_registry_number
smiles
inchi
inchikey
taxonomy/description
taxonomy/direct_parent
taxonomy/kingdom
taxonomy/super_class
taxonomy/class
taxonomy/sub_class
taxonomy/molecular_framework
taxonomy/alternative_parents
taxonomy/substituents
taxonomy/external_descriptors
ontology/root
state
experimental_properties/property
predicted_properties/property
spectra/spectrum
biological_properties/cellular_locations
biological_properties/biospecimen_locations
biological_properties/tissue_locations
biological_properties/pathways
normal_concentrations/concentration
abnormal_concentrations/concentration
diseases/disease
kegg_id
foodb_id
chemspider_id
drugbank_id
pdb_id
chebi_id
pubchem_compound_id
biocyc_id
wikipedia_id
knapsack_id
phenol_explorer_compound_id
bigg_id
metlin_id
vmh_id
fbonto_id
synthesis_reference
general_references/reference
protein_associations/protein