Question: Convert drug target data from DrugBank "EB" format to Entrez format?
0
gravatar for EverInEarnest
18 months ago by
EverInEarnest30 wrote:

I have extracted data from the DrugBank database (in XML format); this includes the Target ID info available via the path <targets> --> <target> --> <id> value. These data are in the format "BE0000XXX" where X are numerals.

I need to convert these target IDs into Entrez ID format, but first need to determine in which format these "BE" identifiers are. I have reviewed the DrugBank documentation (https://www.drugbank.ca/documentation), which lists Target ID info as GenBank, UniProt, and PDB formats. However, when I searched for some example "BE" identifiers on those three sites, there were no results, indicating that the "BE" format does not correspond to any of these platforms. These identifiers are listed on the DrugBank site. However, the ID conversion tools that I have encountered, such as DAVID, require gene IDs to be supplied, whereas I am not finding tools to convert from a DrugBank target "BE" ID to Entrez ID format.

Ideally, I am seeking to do this in R, but will be happy if I can locate any method to accomplish this.

I will appreciate any clarification about how I might convert my "BE"-type target identifiers from the DrugBank database into Entrez ID format. Thanks in advance for your advice.

drugbank conversion entrez • 720 views
ADD COMMENTlink written 18 months ago by EverInEarnest30
1

Hi, BE is means 'bio entities', is the id of target, you can map the BE id to uniprot id , then to entrez id . for example: BE0000048 maped to uniprot id P00734

ADD REPLYlink modified 18 months ago • written 18 months ago by Sparrow_kop190

Thanks for your clarification and suggestion, Sparrow_kop; that is very helpful.

ADD REPLYlink written 18 months ago by EverInEarnest30
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