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