[Bioperl-l] [Gmod-schema] beginning work on SeqIO::chadoxml

Scott Cain cain.cshl at gmail.com
Fri Feb 2 11:03:16 EST 2007

Hi Hilmar,

That is a good idea; when I started down this road, it felt like there
would only be a few things that I might want to allow to be different,
but I think you are right that having one standard implementation that
can be subclassed for legacy systems is a good thing.


On Fri, 2007-02-02 at 10:09 -0500, Hilmar Lapp wrote:
> On Feb 1, 2007, at 2:55 PM, Scott Cain wrote:
> > The second main change was to introduce a -flybase_compat argument  
> > when
> > initializing the Bio::SeqIO writer, so that 'old style' cv and cvterms
> > (that are compatable with flybase) will be used, but now the default
> > will be to use current standards:
> Just my $0.02 ... obviously, Flybase may be the only organization  
> that uses an 'old style' or any other way not compliant with 'current  
> standards' (presumably SO), but if it's not the only one then this  
> approach won't scale.
> Also, an argument -flybase_compat suggests to the unsuspecting that  
> this is an endorsed flavor of the standard and fine to use for  
> everyone else too.
> If Flybase is idiosyncratic in this way, why not make chadoxml.pm  
> compliant with the standard as we all want it, keep it free from  
> litter caused by usage of old versions of SO, and create a second  
> module fb-chadoxml.pm that inherits from the first and merely  
> overrides a few things so that it works for Flybase. This way, other  
> organizations with similar needs can follow the path and create their  
> own xyz-chadoxml.pm, rather than having to muck around in the  
> chadoxml.pm that comes with the distribution.
> I'm not sure I fully grasp the underlying issue, so I may not make  
> much sense here. Apologies if that's the case ...
> 	-hilmar
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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