[Bioperl-l] RE: GenBank XML report format & DTD

[Geer, Lewis (NCBI)]

Hilmar,

It's not documented, unfortunately.  Please send mail to
info@ncbi.nlm.nih.gov if you would like to see documentation.  The form of
the url is given below:
http://www.ncbi.nlm.nih.gov/entrez/viewer.cgi?val=5174476&db=Nucleotide&dopt
=xml&txt=on
where val is the gi of the sequence.  viewer.cgi is the program used by the
entrez query engine, query.fcgi, to display sequence records.  There is a
new version of viewer.cgi that takes accessions as an argument, but I am
unsure of its development status.

The DTDs can be found at ftp://ncbi.nlm.nih.gov/toolbox/xmlspecs/  

Lewis

> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp@gmx.net]
> Sent: Tuesday, December 12, 2000 1:56 PM
> To: Geer, Lewis (NCBI)
> Cc: 'Paul Gordon'; Bioperl
> Subject: GenBank XML report format & DTD

> First, I have difficulties figuring out how to make the NCBI 
> query tools
> to report sequences in XML format. The documentation pages I 
> was able to
> find on NCBI's website
> (http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html,
> http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html) 
> only mention
> GenBank/GenPept, FASTA, and ASN.1 report format options, and 
> if you try,
> dopt=XML indeed yields an error. What did I miss? If we could retrieve
> XML other than through the HTML forms, we can certainly use that.
> Assuming the XML DTD evolves independent from the ASN.1 was of course
> stupid from me.
> 
> Second, yes, a pointer to the most recent DTD would help, 
> otherwise we'd
> have to find a way through the website (assuming that it's documented
> there at some place). Thanks for the post.
> 
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> -----------------------------------------------------------------
>