[Bioperl-l] xml sequence download from ncbi
Thu, 24 Aug 2000 10:58:25 -0300 (ADT)
> Sequence download using an xml format derived from our asn.1 standard format
> is now available from Entrez. For an example, try
> 15 where val is the sequence gi number. Note that this xml output is based
That's great! A few minor points though...
<!DOCTYPE Seq---entry PUBLIC "-//NCBI//NCBI Seqset/EN" "NCBI_Seqset.dtd">
According to the XML spec, the doctype name and the root element must have
the same name (see
Also, can we get the DTD NCBI_Seqset.dtd? I was not able to find it
http://www.ncbi.nlm.nih.gov/entrez/NCBI_Seqset.dtd and environs...
> 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.
Paul Gordon Paul.Gordon@nrc.ca
Genomic Technologies http://maggie.cbr.nrc.ca
Institute for Marine Biosciences
National Research Council Canada