Bioperl: Bio::NCBI

Lincoln Stein
Thu, 7 May 1998 09:21:38 -0400

I'm hoping that the NCBI modules will be integrated into the BioPerl
framework, rather than a 1:1 mapping of the NCBI toolkit (although
there will probably be an 1:1 NCBI layer down below).  Lewis tells me
that this might not be too hard to accomplish.


Gunther Birznieks writes:
 > I would like to add my own personal voice to the enthusiastic noise.  
 > I am also extremely interested and excited to hear about a perl interface
 > to the NCBI Libraries.  Some additional comments appear below:
 > At 09:13 PM 5/6/98 +0100, Ewan Birney wrote:
 > >Namespace:
 > >
 > >So - my take on this is that it would be better to make NCBI the root
 > >namespace. Reasons -
 > >
 > >	a) NCBI is unique (?) and its inclusion in the Bio:: heirarchy 
 > >is just for 'documentation' purposes.
 > >	
 > >	b) There are things in NCBI (eg ASN stuff) that is not directly
 > >anything to do with biology
 > >
 > >	c) (and most importantly) the functionality inside Bio:: 
 > >heirarchy can be assummed to sensibly work together - and the
 > >functionality coming out of the NCBI may well work seemlessly with
 > >everything else, - but - not for certain. By drawing a valid distinction
 > >at the top level between NCBI:: and Bio:: people can understand what
 > >they are using and who to expect what from (rather like some collaborative
 > >C programming projects where function names start with your initials ;)).
 > >
 > >	I think you'll be confusing more people by trying to present once
 > >seemless Bio:: view to people than the necessary 'pick up the following 2
 > >module trees - Bio::, NCBI::...
 > >
 > I think it depends on the intent of this Perl integration and how far this
 > will be taken. 
 > If a strong effort is made to make the NCBI hierarchy meld with other
 > modules in the Bio:: hierarchy, I think it should be under Bio:: if possible.
 > However, if this is primarily an effort to simply provide a plain vanilla
 > 1-to-1 mapping perl interface to the NCBI Toolkit libraries, then I agree
 > with the above statement about being less confusing if it is part of its
 > own package.
 > Anyway, regardless of the hierarchy, I am really excited to hear about this.
 > Later,
 >    Gunther Birznieks (
Lincoln D. Stein                           Cold Spring Harbor Laboratory			                  Cold Spring Harbor, NY
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