Request for advice: sbml+xml Media Type

[Ben Kovitz]

Hi,  
  
I work on SBML (Systems Biology Markup Language) at Caltech.  We  
are thinking of proposing a new XML MIME media type.  
  
When learning about the process for getting a new IETF-tree media  
type approved, I was strongly advised to consult the members of  
the ietf-types and ietf-xml-mime discussion lists for advice  
before diving in.  So here I am.  I'll appreciate any advice you  
can give me, especially any that saves us from making some stupid  
mistakes that the biological modeling community will regret for  
years to come.  Please forgive me if I reveal my ignorance in  
some questions below.  
  
  
First, a little background.  SBML is an XML format for  
representing systems of biochemical reactions.  Making it a MIME  
media type would enable browser-based simulation tools to  
conveniently download, run, and edit models.  Work is now  
beginning on a web infrastructure to make it easy for biological  
researchers to share models on the web, download models used in  
published papers, etc.  
  
Two "levels" of SBML have been defined so far.  Specifications,  
including the XML schemas, are at:  
  
http://www.sbw-sbml.org/sbml/docs/papers/sbml-level-1-version-2/sbml-level-1.pdf  
http://www.sbw-sbml.org/sbml/docs/papers/sbml-level-2-version-1/sbml-level-2.pdf  
  
We are thinking that the ideal name would be either:  
  
   application/sbml+xml  
  
or:  
  
   model/sbml+xml  
  
  
Now, here are a few questions.  
  
1. Would it be a bad idea if we used RFC3236 (The  
application/xhtml+xml Media Type) as a model for the document w  
write?  I'm hoping that we don't need to explain the full  
semantics of SBML in the RFC, since there are already some  
weighty papers that do that (referenced above).  At only 8 pages,  
RFC3236 seems like a model of simplicity and clarity that we  
would like to emulate.  Or is it possible to get even simpler?  
Some of the docs I found for XML MIME media types seemed to do  
little more than list the name of the type and who submitted it.  
  
2. We are thinking of including required parameters of "level"  
and "version".  Anything to watch out for here?  Is this a wrong  
idea?  SBML has multiple levels to enable different simulation  
tools to interoperate at different levels of complexity and  
sophistication.  Each level can come in different versions.  More  
levels are planned.  
  
3. Is it completely stupid to even consider model/sbml+xml?  The  
other model/ media types have been for spatial models.  SBML is  
primarily used for spatial models of reactions that occur within  
biological cells, and has some notions of spatial relation, but  
an SBML model does not necessarily have the minimum 3 orthogonal  
dimensions specified in RFC2077.  We're wondering if SBML is  
still within the spirit of the model/ top-level content type,  
though.  RFC2077 speaks of economic models, behavioral models,  
and so on, and seems to encourage a situation where modeling  
tools might work successfully on models from radically different  
domains.  
  
4. Any other advice you'd care to offer?  
  
  
Thanks in advance for your assistance,  
  
Ben  
  
--  
Ben Kovitz  
Systems Biology Workbench (SBW) Development Group, Caltech  
http://www.sbw-sbml.org  
bkovitz at caltech.edu