[DAS2] hrefs and xml:base

Ed Erwin ed_erwin at affymetrix.com
Wed May 4 23:55:11 UTC 2005

Andrew Dalke wrote:
> In a related topic, the TYPES example we have says
>      xmlns="http://www.biodas.org/ns/das/genome/2.00"
>      xmlns:xlink="http://www.w3.org/1999/xlink"
>      xmlns:bg="http://www.bioperl.org/biographics/properties"
>      xmlns:das="http://www.biodas.org/ns/das/genome/2.00"
>      xml:base="http://www.wormbase.org/das/genome/volvox/1/type/">
> ...
>     <PROP key="bg:glyph"     value="box" />
>     <PROP key="bg:bgcolor"   value="white" />
>     <PROP key="bg:fgcolor"   value="black" />
>     <PROP key="bg:key"       value="tRNAs" />
>     <PROP key="bg:citation"  value="tRNA predictions made using Sean 
> Eddy's tRNAscan program." />
>     <PROP key="bg:fontcolor" value="slateblue" />
>     <PROP key="bg:height"    value="3" />
> Is the "bg" in the XML namespace "bg" supposed to be inserted
> into the key name as a string?  If so, how?  Using universal
> names ( http://www.jclark.com/xml/xmlns.htm ) like
>  "{http://www.bioperl.org/biographics/properties}height"
> Or is the xmlns:bg definition there in error?

I also wondered about this.

I assumed that the "bg:" is a mistake, because later there is an example 
of this feature type request:


Here, ".../citation" is used, rather than ".../bg:citation", but it is 
my understanding that the <PROP> key is supposed to literally map to the 
name used in constructing that type request URL.

I have two other question/comments on that document ( 
http://biodas.org/documents/das2/das2_get.html ):

 > <FORMAT>   (zero or more)
 >  indicates which representations are available for objects
 >  within the given namespace.

Does this mean *all* objects in the given namespace will be available in 
*all* of the given format ? or that *some* will be available in each of 
the listed formats ?

In the example response to this query, the "sequence-ontology" header is 
commented-out for no good reason:


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