[Bioperl-l] bond() operator

[Heikki Lehvaslaiho]

>From Guenter Stoesser, , EMBL Database Coordinator:

- 'bond' is not a collab feature, and has never been discussed with or 
   mentioned to the collaborators (EMBL & DDBJ)
-  this seems to appear in a Refseq entry - Refseq activities are not 
   part of the collaborative effort and basically NCBI can do there 
   whatever they want - besides the confusion it creates with the user 
   community, since navigating via Entrez does not make it clear to the 
   user that Refseq records are not part of the DDBJ/EMBL/GenBank work 
 
--Guenter


Mey it is time make clearer distinction between GenBank and RefSeq
parsers?

	-Heikki


On Mon, 2003-03-03 at 21:02, Hilmar Lapp wrote:
> On Monday, March 3, 2003, at 08:20  AM, Ewan Birney wrote:
> 
> > Well... is this a bug?
> >
> >
> > http://www.ebi.ac.uk/embl/Documentation/FT_definitions/
> > feature_table.html#operators
> >
> > bond is not in there.
> >
> 
> Right. That's why I sent a grumbling email when this first came up  
> whether Genbank wants to repeat the same mistake (mistake IMHO anyways)  
> it made a while ago with annotating polymorphisms, namely to fold  
> annotation into the location string.
> 
> With polymorphisms, they used the dreaded replace('A', 100) syntax.  
> Meanwhile they corrected this and it's now a feature with key  
> 'variation' and standard location syntax.
> 
> Having annotation and location folded into the same string really  
> creates a whole mess in bioperl with regard to parsing this out in a  
> structured manner, and even worse, round-tripping. So, quite honestly,  
> I do hope that NCBI backs off of that, as they did for replace(). But  
> maybe I'm missing something.
> 
> 	-hilmar
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     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
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