Bioperl: follow up to BOSC

[Ewan Birney]

On Sun, 23 Apr 2000, Elia Stupka wrote:

> A question about our SeqIO and AnnSeqIO...
> 
> Why is it that in the 06 release we find:
> 
> /Bio/Index/EMBL.pm
> /Bio/SeqIO/swiss.pm
> /Bio/DB/GenBank.pm
> 
> when before they were all nicely put together in AnnSeqIO?

They were not. Previously there were 

Bio/Index/EMBL, Bio/AnnSeqIO/EMBL, Bio/DB/GenBank. The only change has
been that AnnSeqIO has merged with SeqIO.


The problem comes from the inherent naming confusion. The word 

"GenBank" can mean:

The flat file format of GenBank - (Bio/SeqIO/GenBank)

The distributed databases of GenBank, which incidently uses GenBank
format (Bio/Index/GenBank - Index because it uses indexing flat files).

The network accessible GenBank database (Bio/DB/GenBank).


Depending on your bent, the overlaping names are either sensible or not
(I'd prefer different names, but in these cases I am somewhat of a
pedant).

> 
> I find it confusing, but maybe I just forgot that there was a rationale
> behind it?
> 

There is and I think it is pretty sesnsible - people can complain. One of
the biggest mistakes in bioinformatics is to put *anything* to do with the
word 'EMBL' (the format, the flat file distributed database, and network
accessible database, and the EMBL web site) all in the same object/module.
It is classic biological fuzzy thinking... which is a curse and a
blessing.

> Elia
> 
> **************************
> tel:    +44 1223 49 44 31
> mobile: +44 7971 59 03 69
> fax:    +44 1223 49 44 68
> **************************
> 
> 
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------

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