[Bioperl-l] EUtilities term handling

Chris Fields cjfields at uiuc.edu
Thu Oct 5 15:24:39 UTC 2006

>> 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.

I can specify in POD that URI encoding is in effect if that placates  
you, and maybe add a bit about how terms are to be built (based on  
the website).  I also noticed that the esearch POD doesn't have a  
demo in the SYNOPSIS yet (my fault).

However, I think this is all a bit silly.  This is something most  
people already realize and take for granted (it's standard for any  
CGI interface to use URI encoding).

Also, most Entrez users do not use a term like 'BRCA2+Human 
[ORGANISM]'.  They use 'BRCA2 AND Human[ORGANISM]' or 'BRCA2 Human 
[ORGANISM]', the latter which is implicit.  All of this is on the  
Entrez website.

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

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