Is there any way to map ChEMBL compound IDs to KEGG Drug IDs?

Question

[Misha]

Dear All,

I am looking for a way in which I can map or get the ChEMBL compound IDs to KEGG Drug IDs compounds.

For eg. Say the ChEMBl compound id is CHEMBL113, the corresponding KEGG Drug ID for this ChEMBL compound is D00528. Similarly, I have a list of many ChEMBl compound ids for which I have to find their corresponding KEGG Drug IDs. Any Suggestions?

Thanks.

Answer 1

[Wolf Ihlenfeldt]

Cactvs toolkit www.xemistry.com/academic free software for academic users only):

a) Python

pycactvs>Ens('CHEMBL113').E_KEGG_DRUG_ID
'D00528'

b) Tcl

cactvs>ens get CHEMBL113 E_KEGG_DRUG_ID
D00528

Answer 2

[tamerg]

Alternatively you can use biobtree for this mapping locally. It has both R and Python clients. For example with R in following way

# retrieve chembl related database 
bbBuiltInDB(type = '4')
# start biobtreeR
bbStart()
# perform mapping
bbMapping('CHEMBL113','map(chebi).map(kegg)')

Answer 3

[fotis.aisopos]

This Java project can be helpful for cross-mapping drug ids from different databases ( Drugbank, ChEMBL PubChem, UMLS, TTD, KEGG, ZINC ): https://github.com/iit-Demokritos/drug_id_mapping

You can directly use the resulting TSV file: https://github.com/iit-Demokritos/drug_id_mapping/blob/main/drug-mappings.tsv as long as you use this only for academic/research use and provide a citation to the paper referred in the github repository.