[Bioperl-l] EUtilities term handling

Hilmar Lapp hlapp at gmx.net
Thu Oct 5 10:21:49 EDT 2006


On Oct 5, 2006, at 10:08 AM, Sendu Bala wrote:

>>
>> On Oct 5, 2006, at 3:19 AM, Sendu Bala wrote:
>>
>>> This is actually a general question and not limited to  
>>> EUtilities. As I
>>> see it EUtiltiies lets you do queries in Bioperl that you can do  
>>> on a
>>> website. The question is, should a Bioperl module always work with
>>> queries that the website it is a front-end to works with?
>>
>> I think yes, but stick to this definition.
>>
>> Using your example, if you input 'BRCA2+9606[taxid]' on the Entrez
>> website it will actually not work. Hence, it should be no surprise  
>> that
>> it doesn't work either using Bio::DB::EUtilities.
>
> On the contrary, I find it a surprise because EUtilities is an  
> interface
> to NCBI's eutils, not the entrez website.
>
> If I had previously read instructions on using eutils:
> http://www.ncbi.nlm.nih.gov/books/bv.fcgi? 
> rid=coursework.section.constructing-urls
> I might (do) expect that I /should/ use + in my term.

This is my point - stick to your definitions. Are you wrapping a  
query form on a website or are you wrapping a web service (i.e., a URL)?

The examples you give are about wrapping a web-service. Your original  
question was about wrapping a website. Yet another question is what  
the author of Bio::DB::EUtilities intended to wrap.

The other thing to consider is user-friendliness. If you are wrapping  
a web-service, do you still make not URL-encoding the user input the  
default? What will 90% of the users probably want or expect to be  
able to do? URL-encode all input themselves or expect the module to  
do this for them unless they turn it off?

As far as I'm concerned, I'll happily count myself among those who  
are lazy and ignorant, don't read NCBI's documentation, don't want to  
know how to URL encode and why this needs to be done, but just want  
it to work.

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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