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Best way to deal with numerous synonyms when converting between drug identifiers?
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13 months ago
sam237337 • 50

I have a file with over 1 million ChEMBL drug identifiers, for which I need to acquire the common name of each drug. I have used the PubChem Identifier Exchange to map the ChEMBL IDs to synonyms, but the challenge I'm finding is that each ChEMBL ID can have numerous synonyms, and the drug names that I need don't appear to be listed in any particular order within each drug's synonyms (e.g. the drug name is sometimes listed as the first synonym, but often buried later in the list).

I'm wondering whether anyone has experience in mapping ChEMBL/drug IDs to drug names in an efficient way, as it will not be feasible for me to manually select the correct choice for each drug. Thanks for any suggestions you can provide.

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I am not sure it is the best way, but some people use it:

https://www.nlm.nih.gov/research/umls/pdf/Missed_Synonymy.pdf

There is some discussion in these 3 posts below as well:

A: Database Of Drugs Targeting Genes

Converting between drug identifier formats

mapping gene synonyms to uniprot recommended gene name

And see the panel at the right side, there are some similar questions.

If you go to Chembl:

https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL654

1) Additional synonyms for CHEMBL654 found using NCI Chemical Identifier Resolver

https://www.ebi.ac.uk/chembl/ws

2) search for ‘synonym’:

Molecule Molecule information, including properties, structural representations and synonyms

https://www.ebi.ac.uk/chembl/api/data/molecule

2a)Search molecule by synonym from chembl_webresource_client.new_client import new_client

molecule = new_client.molecule

res = molecule.search('viagra')

3)... or directly in the target synonym field from chembl_webresource_client.new_client import new_client

target = new_client.target

gene_name = 'GABRB2'

res = target.filter(target_synonym__icontains=gene_name)

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Many thanks for the info you provided, Natasha! I will review it in detail, as it seems like it will be very helpful.

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I (and others I'm sure) would be very interested to hear how you get on with this. AWAK one of the problems is there is no usable definition of common name (although synonym PubMed counts could do as a rough proxy)

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