Question: How to map ChEMBL ID to Entrez Gene?
0
gravatar for Elmira
5 weeks ago by
Elmira0
London
Elmira0 wrote:

I am looking for a database/API to map ''Target ChEMBL ID" to "Entrez Gene". For example, given CHEMBL6196 I would like to get 7363 (UGT2B4).

How about "Molecule ChEMBL ID" to "DrugBank Id", e.g. 'CHEMBL1256957': 'DB00264'?

Currently, I have to do this manually by searching for each ID in https://www.ebi.ac.uk/chembl.

drugbank entrez chembl • 108 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Elmira0

It works, thanks, Jean. Do you also know how can I change "Molecule ChEMBL ID" to "DrugBank Id"?

ADD REPLYlink written 5 weeks ago by Elmira0

Please use ADD COMMENT/ADD REPLY when responding to existing answers/comments to keep threads logically organized.

SUBMIT ANSWER is for new answers to the original question.

ADD REPLYlink written 5 weeks ago by genomax85k

I found biomaRt helpful in toggling between different database ids, I guess this would also work to jump from ChEMBL to Entrez. I have not tried that combination however in the past I have managed to jump from ensembl to uniprot, as an example.

A sample code which does this for me is :

  uniprot_id = getBM(mart = thaliana_mart, attributes = "uniprotswissprot" , values = item, filter = "ensembl_gene_id")

More information on the parameters can be found in this manual which I find extremely helpful - https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html

ADD REPLYlink written 5 weeks ago by manaswwm110
1
gravatar for Jean-Karim Heriche
5 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

ChEMBL targets are primarily associated with Uniprot accessions so you'll probably need to do it in two steps. The first is to retrieve the Uniprot accession number, the second to convert Uniprot accession to Entrez gene ID. For the first step, you have a few options:

ADD COMMENTlink written 5 weeks ago by Jean-Karim Heriche22k
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