[Bioperl-l] EUtilities term handling

Sendu Bala bix at sendu.me.uk
Thu Oct 5 10:08:01 EDT 2006


Hilmar Lapp 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.


> Aside from that, one of the advantages of having the service wrapped in 
> Bioperl is in fact that you can have it accept a wider variety of 
> parameters that the actual service would allow you to have, e.g., 
> arrays, hashes, or whatever seems appropriate.

I was going to suggest that terms be supplied as an array, leaving 
Bioperl code to decide how to 'AND' all the terms (elements in the 
array) together. It would also further force the user not to think of 
how eutils normally works, but to only consider the Bioperl instructions 
on how to form a query. But I'm not sure of the value of all that.



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