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

Chris Fields cjfields at illinois.edu
Mon Jul 20 16:31:03 UTC 2009

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.


> 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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