[Bioperl-l] xml sequence download from ncbi

[Lapointe, David]

Lewis,

Great stuff!!  Two things I  had a problem with. First IE5 wanted to
download to viewer.cgi so I wonder if the mime type is not set ( is there an
xml mime type? hmmm?). I downloaded anyway
and the file ( entrez.xml) had some errors.

Here are the first few lines as returned
<--?xml version="1.0"?>
<!DOCTYPE Seq---entry PUBLIC "-//NCBI//NCBI Seqset/EN" "NCBI_Seqset.dtd">
<Seq-entry>

The first line should be
<?xml version="1.0"?>

In the second line there are two many '-' in Seq---entry, which should be
<!DOCTYPE Seq-entry PUBLIC "-//NCBI//NCBI Seqset/EN" "NCBI_Seqset.dtd">

to match the root element
<Seq-entry>

Also I had a problem resolving "NCBI_Seqset.dtd" . Shouldn't there be a
DTD-URL something like

<!DOCTYPE Seq-entry PUBLIC "-//NCBI//NCBI Seqset/EN"  
                 "http://www.ncbi.nlm.nih.gov/../NCBI_Seqset.dtd">

/../ being some appropriate path.


> -----Original Message-----
> From: Geer, Lewis (NLM) [mailto:lewisg@mail.nih.gov]
> Sent: Thursday, August 24, 2000 9:08 AM
> To: Bioperl
> Subject: [Bioperl-l] xml sequence download from ncbi
> 
> 
> 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.

We'd be interested in seeing comments!

Lewis
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