Skip to main content
Topic: Python script to process HMDB xml file (Read 166 times) previous topic - next topic

Python script to process HMDB xml file

HMDB is a well annotated database and I use this database a lot for my study. However, I noticed that people with HMDB as reference database don't update them. Here I would share my code to extract HMDB compounds information by python. You could use this code to update the corresponding database.

Step 1: download HMDB's huge xml file for all compounds here and unzip the file: https://hmdb.ca/system/downloads/current/hmdb_metabolites.zip

Step 2: use the following python code to define a function to extract information for HMDB compounds

Code: [Select]
from io import StringIO
from lxml import etree
import csv
def hmdbextract(name, file):
  ns = {'hmdb': 'http://www.hmdb.ca'}
  context = etree.iterparse(name, tag='{http://www.hmdb.ca}metabolite')
  csvfile = open(file, 'w')
  fieldnames = ['accession', 'monisotopic_molecular_weight', 'iupac_name', 'name', 'chemical_formula', 'InChIKey', 'cas_registry_number', 'smiles', 'drugbank','chebi_id', 'pubchem', 'phenol_explorer_compound_id','food','knapsack', 'chemspider', 'kegg', 'meta_cyc','bigg','metlin_id','pdb_id', 'logpexp','kingdom',  'direct_parent', 'super_class', 'class', 'sub_class', 'molecular_framework']
  writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
  writer.writeheader()
  for event, elem in context:

    accession = elem.xpath('hmdb:accession/text()', namespaces=ns)[0]
    try:
        monisotopic_molecular_weight = elem.xpath('hmdb:monisotopic_molecular_weight/text()', namespaces=ns)[0]
    except:
        monisotopic_molecular_weight = 'NA'
    try:
        iupac_name = elem.xpath('hmdb:iupac_name/text()', namespaces=ns)[0].encode('utf-8')
    except:
        iupac_name = 'NA'
    name = elem.xpath('hmdb:name/text()', namespaces=ns)[0].encode('utf-8')
    try:
        chemical_formula = elem.xpath('hmdb:chemical_formula/text()', namespaces=ns)[0]
    except:
        chemical_formula = 'NA'
    try:
        inchikey = elem.xpath('hmdb:inchikey/text()', namespaces=ns)[0]
    except:
        inchikey = 'NA'
    try:
        cas_registry_number = elem.xpath('hmdb:cas_registry_number/text()', namespaces=ns)[0]
    except:
        cas_registry_number = 'NA'
    try:
        smiles = elem.xpath('hmdb:smiles/text()', namespaces=ns)[0]
    except:
        smiles = 'NA'
    try:
        drugbank = elem.xpath('hmdb:drugbank_id/text()', namespaces=ns)[0]
    except:
        drugbank = 'NA'
    try:
        chebi_id = elem.xpath('hmdb:chebi_id/text()', namespaces=ns)[0]
    except:
        chebi_id = 'NA'
    try:
        pubchem = elem.xpath('hmdb:pubchem_compound_id/text()', namespaces=ns)[0]
    except:
        pubchem = 'NA'
    try:
        phenol_explorer_compound_idt = elem.xpath('hmdb:phenol_explorer_compound_id/text()', namespaces=ns)[0]
    except:
        phenol_explorer_compound_id = 'NA'
    try:
        food = elem.xpath('hmdb:foodb_id/text()', namespaces=ns)[0]
    except:
        food = 'NA'
    try:
        knapsack = elem.xpath('hmdb:knapsack_id/text()', namespaces=ns)[0]
    except:
        knapsack = 'NA'
    try:
        chemspider = elem.xpath('hmdb:chemspider_id/text()', namespaces=ns)[0]
    except:
        chemspider = 'NA'
    try:
        kegg = elem.xpath('hmdb:kegg_id/text()', namespaces=ns)[0]
    except:
        kegg = 'NA'
    try:
        meta_cyc = elem.xpath('hmdb:meta_cyc_id/text()', namespaces=ns)[0]
    except:
        meta_cyc = 'NA'
    try:
        bigg = elem.xpath('hmdb:bigg_id/text()', namespaces=ns)[0]
    except:
        bigg = 'NA'
    try:
        metlin_id = elem.xpath('hmdb:metlin_id/text()', namespaces=ns)[0]
    except:
        metlin_id = 'NA'
    try:
        pdb_id = elem.xpath('hmdb:pdb_id/text()', namespaces=ns)[0]
    except:
        pdb_id = 'NA'
    try:
        logpexp = elem.xpath('hmdb:experimental_properties/hmdb:property[hmdb:kind = "logp"]/hmdb:value/text()', namespaces=ns)[0]
    except:
        logpexp = 'NA'
    try:
        kingdom = elem.xpath('hmdb:taxonomy/hmdb:kingdom/text()', namespaces=ns)[0]
    except:
        kingdom = 'NA'
    try:
        direct_parent = elem.xpath('hmdb:taxonomy/hmdb:direct_parent/text()', namespaces=ns)[0]
    except:
        direct_parent = 'NA'
    try:
        super_class = elem.xpath('hmdb:taxonomy/hmdb:super_class/text()', namespaces=ns)[0]
    except:
        super_class = 'NA'
    try:
        classorg = elem.xpath('hmdb:taxonomy/hmdb:class/text()', namespaces=ns)[0]
    except:
        classorg = 'NA'
    try:
        sub_class = elem.xpath('hmdb:taxonomy/hmdb:sub_class/text()', namespaces=ns)[0]
    except:
        sub_class = 'NA'
    try:
        molecular_framework = elem.xpath('hmdb:taxonomy/hmdb:molecular_framework/text()', namespaces=ns)[0]
    except:
        molecular_framework = 'NA'

    writer.writerow({'accession': accession, 'monisotopic_molecular_weight': monisotopic_molecular_weight, 'iupac_name': iupac_name, 'name': name, 'chemical_formula': chemical_formula, 'InChIKey': inchikey, 'cas_registry_number': cas_registry_number, 'smiles': smiles,'drugbank': drugbank,'chebi_id': chebi_id,'pubchem': pubchem,'phenol_explorer_compound_id':phenol_explorer_compound_id, 'food': food,'knapsack': knapsack, 'chemspider': chemspider,'kegg': kegg, 'meta_cyc': meta_cyc, 'bigg':bigg, 'metlin_id': metlin_id, 'pdb_id':pdb_id,'logpexp':logpexp, 'kingdom': kingdom, 'direct_parent': direct_parent, 'super_class': super_class, 'class': classorg, 'sub_class': sub_class, 'molecular_framework': molecular_framework})
    # It's safe to call clear() here because no descendants will be
    # accessed
    elem.clear()
# Also eliminate now-empty references from the root node to elem
    for ancestor in elem.xpath('ancestor-or-self::*'):
        while ancestor.getprevious() is not None:
            del ancestor.getparent()[0]
  del context
  return;

Step 3: Run the function on the unzipped xml files to get a fresh csv files

Code: [Select]
hmdbextract('hmdb_metabolites.xml','hmdb.csv')

Now you could have a csv file with information. This code is for my publication on PMD based reactomics: https://www.nature.com/articles/s42004-020-00403-z

I forgot to include them in the supporting information and I released here just in case someone need this.

PS:I also write a blog (https://yufree.cn/en/2020/12/01/metabolites-diseases-database-based-on-hmdb/) to use HMDB to check metabolites-disease association. That analysis is based on python and R.

Re: Python script to process HMDB xml file

Reply #1
Thanks for sharing, yufree.

I'm sure that will be helpful for people. Plus, it was good to find your paper. I look forward to having a good read later today.