[DAS] DSN DTD

[Ethan Cerami]

Hello again,

This is another picky, little question, but I just
want to make sure that I have it right.

When one issues a dsn request, the server is required
to return a document which adheres to dasdsn.dtd.

This DTD looks like this:

<!ELEMENT DASDSN (DSN+)>
<!ELEMENT DSN (SOURCE, DESCRIPTION?, MAPMASTER)>
<!ELEMENT SOURCE (#PCDATA)>
<!ATTLIST SOURCE id CDATA #REQUIRED>
<!ATTLIST SOURCE version CDATA #IMPLIED>
<!ELEMENT DESCRIPTION (#PCDATA)>
<!ATTLIST DESCRIPTION href CDATA #IMPLIED>
<!ELEMENT MAPMASTER (#PCDATA)>

However, just about every server that I have tried
returns data like this:

<?xml version='1.0' standalone='no' ?>
<!DOCTYPE DASDSN SYSTEM 'dasdsn.dtd' >
<DASDSN>
  <DSN>
    <SOURCE id="CNBs" version="1.0">CNBs</SOURCE>
<MAPMASTER>http://servlet.sanger.ac.uk:8080/das/ensembl729</MAPMASTER>
    <DESCRIPTION>Conserved Noncoding
Blocks</DESCRIPTION>
  </DSN>
...

The DTD requires that DESCRIPTION appear before
MAPMASTER, but in this document, MAPMASTER appears
after, meaning that the DAS server has returned an
invalid document.  Just to doublecheck, I validated
the document using JDOM and got the following error:

JDOM Exception:  Error on line 8 of document
file:/C:/xmlbio/examples/classes/..
/dsn.xml: The content of element type "DSN" must match
"(SOURCE,DESCRIPTION?,MAP
MASTER)".

I checked wormbase, ucsc, and ensembl, and they all
seem to return the same invalid documents.

Can any confirm that this is correct, or do I perhaps
have an older version of the DTD?

Thanks,

Ethan

p.s.  I probably should have introduce myself in the
last email.  I am basically co-writing a book with
Brian Gilman on "XML and Bioinformatics", and we are
planning on including a DAS chapter.  Hence, my many
questions.  Thanks...

__________________________________________________
Do you Yahoo!?
New DSL Internet Access from SBC & Yahoo!
http://sbc.yahoo.com