[Bioperl-l] GenBank XML report format & DTD

Hilmar Lapp hlapp@gmx.net
Tue, 12 Dec 2000 10:55:49 -0800

"Geer, Lewis (NCBI)" wrote:
> 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.

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/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 Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757