[Bioperl-l] [bioperl newbie] Retrieving link to protein from PubChem

Chris Fields cjfields at illinois.edu
Tue Nov 10 09:05:51 EST 2009

On Nov 10, 2009, at 5:41 AM, saikari keitele wrote:

> Thanks again very much for your help and the script.
> i've been trying it, however I fail to find any protein record  
> linked to a
> record in the pcsubstance database.
> Do you think that its is because  no links have been defined between  
> the 2
> databases, or that I am just unlucky and that no link exists for the
> particular records I'm testing?
> Thanks again
> saikari

It's probably that no links have been defined.  I have found similar  
problems in the past with pubchem, in that not all substances have  
proteins associated with them.  Most proteins linked to are those with  
a deposited structure.

There are a few other databases to check out; KEGG, the BioCyc dbs  
(like EcoCyc), come to mind.  I don't think we have a generic remote  
query engine set up for any of those unfortunately (unless there is  
one I'm unaware of), but I know BioCyc comes with it's own set of  
tools (including perl- and java-based query tools) and can be set up  
locally, which is likely much faster and more in lines with what you  



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