[Bioperl-l] Finding all bioactive substances through EUtils or PUG_SOAP
cjfields at illinois.edu
Mon Jul 20 12:31:03 EDT 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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