Bioperl: XML/BioPerl

[David J. States]

I appreciate your comments on sticking to the reference dtd.  There were a 
couple of problems with the original BIOML dtd that prevented us from using 
it as it was.  Specifically, there was no way to specify a structured 
database cross-reference, and the domain types were limited to secondary 
structure elements.

This does point up a need for mechanisms to develop communally useful 
definitions.  One approach is to have a czar in charge of specific data 
type definition.  Suggestions can then be funneled to that person for 
approval and incorporation in the standard.  Ron Beavis 
(beavis@netdirect.net) and Joe Spitnzer (jspitzne@m5.columbus.rr.com) being 
the relevant individuals for BIOML and BSML respectively.  An alternative 
would be to post the definitions on a server like bio.perl.org and allow 
cooperative editing.  While the latter may make it a bit faster to 
incorporate changes, in the long run having a czar is probably a good 
thing.  I have been in touch with Ron about my needs for BIOML, and I think 
we will be able to work something out.

David

----
David J. States, M.D., Ph.D.
Associate Professor and Director
Institute for Biomedical Computing
Washington University in St. Louis
700 S. Euclid Ave.
St. Louis, MO   63110

tel: 314 362 2134
fax: 314 362 0234
email: states@ibc.wustl.edu

-----Original Message-----
From:	Paul Gordon [SMTP:pgordon@cs.dal.ca]
Sent:	Tuesday, January 19, 1999 1:16 PM
To:	vsns-bcd-perl@lists.uni-bielefeld.de
Subject:	RE: Bioperl: XML/BioPerl

It may be of interest to the bioperlers to note that "BIOML" in these
discussions seems to be used in reference to several supersets of said
markup.  I based my parser on BIOML Proposal 19990110, which I presumed to
be the reference for BIOML.

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
	Institute for Marine Biosciences
	National Research Council of Canada

> ...
> 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

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