[BioXML-dev] RE: [Bioperl-l] xml sequence download from ncbi

[Bradley Marshall]

I was planning on writing an xsl sheet from the blast
xml into game, which can then be parsed into bioperl. 
Sound good?

Brad

--- "Geer, Lewis (NLM)" <lewisg@mail.nih.gov> wrote:
> Thanks, Ewan,
> The xml you see is pretty stable as it's based on
> the asn.1 format, which is
> mature.  The only changes ought to be bug fixes.
> 
> You'd have to ask Jim Ostell about the future of
> this, as he is the author
> of much of it as well as Andriy Klymenko.  Jim has
> discussed creating
> another DTD that decouples the XML and ASN.1 as you
> propose -- this might
> have the added benefit of filtering some of the
> complexity that is purely
> historical in nature.  The blast xml was done this
> way.
> 
> If someone does parse the XML and gives comments,
> this would help a great
> deal.
> 
> Lewis
> 
> > -----Original Message-----
> > From: Ewan Birney [mailto:birney@ebi.ac.uk]
> > Sent: Thursday, August 24, 2000 9:21 AM
> > To: Geer, Lewis (NLM)
> > Cc: Bioperl; bioxml-dev@bioxml.org
> > Subject: Re: [Bioperl-l] xml sequence download
> from ncbi
> > 
> > 
> > On Thu, 24 Aug 2000, Geer, Lewis (NLM) wrote:
> > 
> > > Hi, 
> > > 
> > > Sequence download using an xml format derived
> from our 
> > asn.1 standard format
> > > is now available from Entrez.  For an example,
> try
> > > 
> >
>
http://www.ncbi.nlm.nih.gov/entrez/viewer.cgi?cmd&save=on&view
> > =xml&val=18279
> > > 15  where val is the sequence gi number.  Note
> that this 
> > xml output is based
> > > on our asn.1 records which are both complete and
> complex -- 
> > we may end up
> > > making a genbank flatfile-like version,
> especially since 
> > there are small
> > > mismatches between the asn.1 and xml languages
> that make 
> > the xml a bit more
> > > complex than if xml was our native format.
> > 
> > Very interesting. Great stuff. I'm going to
> forward this onto 
> > the bioxml
> > lists as well.
> > 
> > The DTD is clearly very asn based (lots of
> nesting). How 
> > stable are parts
> > of this XML? What is the "going forward" view of
> XML from NCBI (is
> > there one?) Hmmmm. 
> > 
> > 
> > I would actually suggest that there is not a tight
> coupling 
> > if possible
> > between the internal ASN.1 model and the actual
> XML dumped - 
> > I'm trying to
> > prevent the foreseeable problems of NCBI wanting
> to move their ASN.1
> > model: however, of course, someone has to write
> the code for that and
> > manage it, and there are arguments to say that
> this is possibly better
> > done in, say, bioperl and NCBI just should make a
> clear, easy-to-parse
> > data dump...
> > 
> > 
> > Any volunteers for writing the bioperl parser for
> this (?). I suspect
> > we wont know really what comments we have on this
> until someone starts
> > bashing out a parser for it.
> > 
> > 
> > > 
> > > We'd be interested in seeing comments!
> > > 
> > 
> > Thanks for letting us comment. It is great to see
> a NIH person on this
> > list...
> > 
> > 
> > > Lewis
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > > 
> > 
> >
>
-----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44
> 1223 494420
> > <birney@ebi.ac.uk>. 
> >
>
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> > 
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> > 
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