[Bioperl-l] EUtilities term handling

Sendu Bala 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:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
Combined with the EUtilities synopsis I know I'm supposed to start with 
esearch so I look at:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
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 
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene.

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 
problem.


More information about the Bioperl-l mailing list