[MOBY] Re: [MOBY-l] XML namespaces

[Paul Gordon]

The "" prefix in this document does not map to any namespace.  There is 
no default namespace, so CrossReference is not attached to any DTD or 
Schema.  In order for this document to be semantically correct as a MOBY 
document, it requires the root element to have a default namespace 
declaration:

<MOBY xmlns='http://www.biomoby.org/moby-s' xmlns:moby='http://www.biomoby.org/moby-s'>

so that all the tags, with and without the "moby:" are part recognized as MOBY data.

This would be the case even if you had included a doctype declaration saying it's a moby document.  When you code XHTML with a doctype declaration, the root HTML element still requires the xmlns="http://www.w3.org/1999/xhtml" default namespace attribute.

><?xml version='1.0' encoding='UTF-8'?>
><moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>
><moby:Query>
>  <moby:queryInput>
>    <moby:Simple>
>      <moby:AminoAcidSequence namespace='AGI_LocusCode' id='At3g19100' moby:articleName='seqA'>
>        <moby:Integer namespace='' id='' articleName='Length'>947</moby:Integer>
>        <moby:String  namespace='' id='' articleName='SequenceString'>
>	  <CrossReference>
>	    <Object namespace='taxon' id='9913'/>
>	    <Object namespace='Global_Keyword' id='Bos taurus'/>
>	    <Object namespace='NCBI_Acc' id='M80838'/>
>	  </CrossReference>
>	  sequence a
>	</moby:String>
>      </moby:AminoAcidSequence>
>    </moby:Simple>
>  </moby:queryInput>
>  <moby:queryInput>
>    <moby:Simple>
>      <moby:AminoAcidSequence namespace='NCBI_gi' id='At3g19101' moby:articleName='seqB'>
>        <moby:Integer namespace='' id='' articleName='Length'>947</moby:Integer>
>        <moby:String  namespace='' id='' articleName='SequenceString'>sequence b</moby:String>
>      </moby:AminoAcidSequence>
>    </moby:Simple>
>  </moby:queryInput>
></moby:Query>
></moby:MOBY>
>
>
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