[Bioperl-l] Re: Bio::DB::WebSeqDB and Bio::DB::GenBank

Geer, Lewis (NCBI) lewisg@mail.nih.gov
Tue, 12 Dec 2000 09:56:16 -0500

The sequence XML DTD is derived algorithmically from the ASN.1
specification, so barring bugs, the XML DTD should be as stable as the ASN.1
specification.  However, brand-new XML DTDs, like the simplified BLAST
output in standalone BLAST, are not based on a existing ASN.1 specification
and can change at a faster clip.  If you want to know which XML DTD is new
and which is not, send email or post.


> -----Original Message-----
> From: Paul Gordon [mailto:gordonp@niji.imb.nrc.ca]
> Sent: Tuesday, December 12, 2000 8:56 AM
> To: Bioperl
> Subject: Re: [Bioperl-l] Re: Bio::DB::WebSeqDB and Bio::DB::GenBank
> > ASN.1 has been NCBI's format of choice for years, long 
> before they even
> > thought about adopting XML. Their ASN.1 schema is probably also much
> > stabler than the XML equivalent. If we only had a parser 
> for it. There
> > is even a module out on CPAN:
> > 
> http://search.cpan.org/doc/GBARR/Convert-ASN1-0.07/lib/Convert
> /ASN1.pod
> > 
> > I don't know how useful this could be. Any people on the list with
> > experience or feelings in this regard?
> I've tried it previously, albeit not in _great_ detail, but 
> it didn't seem
> to handle the comprehensive NCBI ASN.1 specification and is a 
> bit hackish 
> in dealing with macros (or whatever the ASN.1 term is that I can't
> remember).  I don't know if it would be easy to rescue or not...
> ______________________________________________________________
> __________
> Paul Gordon                                     Paul.Gordon@nrc.ca
> Genomic Technologies				http://maggie.cbr.nrc.ca
> Institute for Marine Biosciences
> National Research Council Canada
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