Simple pipeline for quest of information from the Human Metabolome Database (HMDB, https://hmdb.ca/).

1. download the latest database from https://hmdb.ca/system/downloads/current/hmdb_metabolites.zip
2. unzip downloaded file
3. mv downloaded file to ./data/ and name it as hmdb_metabolites.xml

1. 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.
2. change corresponding param file names in running.sh and run with bash running.sh
3. 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