[Bioperl-l] EUtilities term handling

[Chris Fields]

On Oct 5, 2006, at 9:44 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> The bug is in the query and not in the code, i.e. is is a  user- 
>> generated bug, not an EUtilities bug.  And it shouldn't be  
>> unexpected, as NCBI has very specific rules for building queries  
>> for Entrez (just like any other database).
>
> So I guess this comes down to something Hilmar mentioned and I  
> never even considered before. You consider your EUtilities stuff as  
> a frontend to entrez, and therefore consider valid queries as  
> queries that are valid for entrez and not eutils?

The eutils tools access the same databases as the web page, in the  
same way, using the same search terms.  From the EUtilities docs:

"The eUtils access the core search and retrieval engine of the Entrez  
system and, therefore, are only capable of retrieving data that are  
already in Entrez."

> If that's the case, fine. I understand why you don't think this is  
> a bug. Again, something that might warrant a mention in the POD.
> Currently the naming of the modules and the explicit references to  
> eutils (and me knowing the implementation uses eutils) got me  
> confused.

I'll note that in there is URI encoding in POD, but that should be a  
no-brainer.  I don't think every Bio::DB* class specifies this,  
mainly because it is taken for granted.  Pretty much anything that  
builds URL strings needs to encode based on the URI standard, and any  
server that accepts URLs is expected to decode using the same standard.

So, again, why does that have to be specifically outlined in POD?

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign