[DAS2] FYI: Arabidopsis DAS at PlantGDB

[Ann Loraine]

Hi,

This is an update on Arabidopsis DAS sites:

Iowa State hosts a plant DAS site, but so far I haven't been able to get IGB to
talk to it.

It fails with this error:

     [java] DAS request1:
http://www.plantgdb.org/cgi-bin/das/ATGDB151_das/features?segment=4:15849536,15854959;type=EST_alignment%3AGeneSeqer_cognate;type=cDNA_alignment%3AGeneSeqer_cognate
     [java] Attempting to load data from URL:
http://www.plantgdb.org/cgi-bin/das/ATGDB151_das/features?segment=4:15849536,15854959;type=EST_alignment%3AGeneSeqer_cognate;type=cDNA_alignment%3AGeneSeqer_cognate
     [java] [Fatal Error] :14:83: The reference to entity "dbid" must
end with the ';' delimiter.
     [java] Problem parsing DAS XML data: The reference to entity
"dbid" must end with the ';' delimiter.

The problem appears to be lines such as:

<LINK href="http://www.plantgdb.org/AtGDB-cgi/findRecord.pl?id=23308168&dbid=1">23308168</LINK>

which include "&" symbols that don't signal the start of an entity.

I have written to PlantGDB to ask about this...I'll keep you posted!

It might be useful to add a few links to trusted on-line XML
validators to the upcoming re-done bioDAS Web site to make it easier
for DAS providers to check their XML well-formedness.

Here's one I just now used: http://validator.aborla.net/

Many people who implement DAS services are likely to be beginning
programmers...or programmers like me who don't do it full-time & can
use refreshers :-)

Yours,

Ann

PS If this doesn't get posted to the list, could some-one post it for me?


-- 
Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org