Bioperl: Re: Extensible XML

[Paul Gordon]

Thanks for the note! I think I may have been misunderstood. The BIOML
servers out there reference a *flavor* of the original proposal.  My
problem was that they were doing this instead of using the original DTD
and properly extending it in the markup declaration part of the <!DOCTYPE>
declaration (W3C's REC-xml BNF rule 28).  That's the key to the "X" 
in XML! Because of this they didn't get past my parser, so I need to write
my own server...

Yes, I was a confusing in my original post.  I meant that if they
aren't going to declare the additions that they should store
the additional data in processing instructions with targets recognized by
their browsers, or something of the sort.  In that way no 'errors' occur.
In any case you are very right, it's not fatal, but the purist in me likes
to see properly formatted documents. :)

> The XML 1.0 standard 
> allows for markup which does not fit the DTD. This is an 'error' which is
> not 'fatal' and may
> be ignored or otherwise handled by a parser. 
<snip>
> *	treat the markup they understand
> *	fail only if required markup is missing
> *	ignore markup they don't understand, and hence allow for extensible
> markup
<snip>
> > Call me a purist, but I'm against adding attributes that are not part of
> > the DTD.  As tempting as it is to add attributes to suit the application
> > (which seems to be the case for both BIOML servers mentioned here), I
> > think it will lead to problems like their are in HTML (browser
> > compatibility, etc).  Extra data markup is probably better kept in
> > processing instructions and externally resolved entities in XML.
> > 
> > Regards, 
> > 	Paul Gordon
> > > In reply to Paul Gordon's post, there is a CGI program that serves 
> > > BIOML at
> > > 
> > > http://198.139.168.101/prowl-cgi/bioml.exe?name=XXX
> > <snip> 
> > > Ronald Beavis


Regards,
	Paul Gordon
	Institute for Marine Biosciences
	National Research Council of Canada


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