Dear Harry, Although ChEBI has an API this uses SOAP and I am not familiar with it https://www.ebi.ac.uk/chebi/webServices.do But PubChem has a great API system and pubchempy https://github.com/mcs07/PubChemPy provides an easy way to interact with it. Pubchem entries appear to have the CHEBI identifier as one of there synonyms. The attached python script access this information. For instance: $ ./lookup_smiles_in_pubchem.py "c1ccccc1O" PubChem_CID:996 ChEBI_ID:15882 (phenol) $./lookup_smiles_in_pubchem.py "Cn1cnc2n(C)c(=O)n(C)c(=O)c12" PubChem_CID:2519 ChEBI_ID:27732 (caffeine) $./lookup_smiles_in_pubchem.py "CCCC1=NN(C2=C1N=C(NC2=O)C3=C(C=CC(=C3)S(=O)(=O)N4CCN(CC4)C)OCC)C" PubChem_CID:135398744 ChEBI_ID:9139 (sildenafil) Hope this is useful Oliver To unsubscribe from the CCP4BB list, click the following link: |
#!/usr/bin/env python """ little script to lookup a SMILES string at PubChem and print out the CHEBI and ChEMBL identifiers """ import pubchempy as pcp import argparse
# get smiles from command line
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('smiles', metavar='SMILES',
help='SMILES string to lookup')
args = parser.parse_args()
smiles = args.smiles
compound = pcp.get_compounds(smiles, 'smiles')[0]
if compound:
cid = compound.cid
synonyms = compound.synonyms
chebi_ids = [s for s in synonyms if s.startswith('CHEBI:')]
if chebi_ids:
chebi_id = chebi_ids[0].replace('CHEBI:', '')
else:
chebi_id = None
print(f'PubChem_CID:{cid} ChEBI_ID:{chebi_id} ({synonyms[0]})')
else:
print('smiles string not found')
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