[Bioperl-l] EUtilities term handling
bix at sendu.me.uk
Thu Oct 5 12:22:36 EDT 2006
Chris Fields wrote:
> On Oct 5, 2006, at 10:30 AM, Sendu Bala wrote:
>> Exactly. You're assuming an entrez user and expecting an entrez query.
>> I don't think its silly given the name of the modules for the user to
>> assume the code needs an eutils query, which is a different thing with
>> different behaviour /independent/ of URI encoding.
> It's a silly distinction. The POD for Bio::DB::EUtilities states:
> Bio::DB::EUtilities - interface for handling web queries and data
> retrieval from NCBI's Entrez Utilities.
> My question is this : why would anyone (particularly the everyday
> bioperl user) want to use URL-encoded parameters for a query?
Well I'll tell you why I was trying to use URL-encoded parameters, if
that helps you any.
I read the pod for EUtilities but all the examples have very simple
-term s defined with just a single word. So I wonder how I'm supposed to
make an 'AND' term. I also have no idea what utilities I'm supposed to
use, or what databases etc. I need to get the answer I want.
The POD points me here:
Combined with the EUtilities synopsis I know I'm supposed to start with
esearch so I look at:
And figure out what my terms are supposed to be.
Then I test some example terms in my web browser using the esearch base
url (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?) to see
if they work, and copy/paste the terms into my EUtilities-using perl
script, replacing variable terms with perl variables.
Then I find that my terms don't work, ask you about it, and you fail to
tell me I should be testing my terms at
If you think I'm stupid, fine, but I'm probably not the only stupid
person on the planet. Which is why I suggested a POD addition. You don't
have to make any POD change if you don't want to. I simply thought it
might help avoid anyone 'badgering' you in the future with a similar
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