[Bioperl-l] EUtilities term handling

Sendu Bala bix at sendu.me.uk
Thu Oct 5 11:02:01 EDT 2006


Chris Fields wrote:
> 
> On Oct 5, 2006, at 9:08 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.
> 
> It uses NCBI's CGI interface for eutils, not the SOAP interface.  Very 
> different.  I have considered using the NCBI SOAP-based interface, but 
> the web services are still somewhat incomplete, unlike the CGI interface.

I don't know anything about the SOAP interface. I'm talking about the 
CGI interface that you use.


>> 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.
> 
> You are looking at part of the naked URL on that page.  Here's what that 
> page says:

I know what it says...

>     * Correct: &term=biomol+mrna[properties]+AND+mouse[organism]

The correct query is the one that has +s in it.


> I use URI for building the URL with the parameters.  URI specifically 
> encodes all of this for you, so spaces convert to '+' and '+' converts 
> to %2B.

Well, yes. This causes what I thought of as a bug. It prevents me from 
submitting a /correct/ eutils term. However it isn't a bug if you 
explain to users they shouldn't be submitting valid eutils terms, but 
only valid /entrez/ terms.


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