[Bioperl-l] EUtilities term handling

Sendu Bala bix at sendu.me.uk
Thu Oct 5 14:32:49 UTC 2006

Hilmar Lapp wrote:
> On Oct 5, 2006, at 10:08 AM, Sendu Bala wrote:
>> 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.

Right... I don't see that that changes the answer to my question though 
does it?

"The question is, should a Bioperl module always work with
queries that the web-service it is a front-end to works with?"

For me, the answer is still yes.

> 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.

That's a reasonable attitude to take. Which comes back to the question I 
asked of Chris - naively, if you send + as + you can please everyone, 
can't you? Both people who have read the docs on the web-service and 
those who haven't? Or are there real queries in which a user may want to 
search for a phrase with a literal + in it (and where such a search 
works via eutils)?

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