Request for advice: sbml+xml Media Type
Ben Kovitz
bkovitz at caltech.edu
Sat Jul 5 05:22:00 CEST 2003
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
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