[Bioperl-l] Finding all bioactive substances through EUtils or PUG_SOAP

bar tomas bartomas at gmail.com
Tue Jul 21 14:43:12 UTC 2009

Thanks a lot for your help and your ideas.
I had the impression that 'pcassay_taxonomy'  refers to the taxonomy of the
screening substance not the screened substance which is what I'm interested
in. But I'll have a better look.
Thanks again
Tomas Bar

On Mon, Jul 20, 2009 at 5:31 PM, Chris Fields <cjfields at illinois.edu> wrote:

> On Jul 18, 2009, at 1:38 PM, bar tomas wrote:
> Dear Chris,
>> Thank you again for you helpful reply and your code.
>> I've been trying to find a way to extend your BioPerl code to be able to
>> retrieve the NCBI Taxonomy db IDs of the species in which the bioactive
>> compounds are found.
>> (The query that I'm interested in, is to find bioactive compounds found in
>> natural organisms. I'd like to identify the species where the nautral
>> compounds are found).
>> I've looked in the web page you mention in your mail (
>> http://pubchem.ncbi.nlm.nih.gov/help.html#PubChem_index)
>> and have found a linking filter pcassay_taxonomy for the bioassay
>> database, but I think(?) that this does not refer to the taxonomy of the
>> species in which the active screened compound is found.
> I think this represents a legit link to taxonomy, either the species the
> assay is performed on the species of the protein target.
> Do you know if it is possible to retrieve the link between a natural
>> compound and the species in which the compound can be found?
> I would think this is achievable through 'pcassay_taxonomy' or
> 'pccompound_taxonomy'.  This appears to be
> assay/compound/substance-dependent, though, and a lot of them don't have
> links (it doesn't look like they are reported, or maybe the assay is
> generic).  You may have to do some digging, unfortunately.
> chris
> Thanks very much for any help or hints.
>> (sorrys if the email is a bit misplaced in this discussion list as it is
>> not really specific to bioperl, although I'm trying to implement it using
>> Bioperl tools. I have not been able to find a general discussion list about
>> querying Entrez databases, unspecific to any particular proramming
>> language).
>> Thanks again
>> Tomas Bar

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