Bioperl: Bio::NCBI

Gunther Birznieks
Wed, 06 May 1998 19:21:19 -0400

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:
>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.

   Gunther Birznieks (

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