MIME Media Type for the Systems Biology Markup Language (SBML)
RFC 3823

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Network Working Group                                          B. Kovitz
Request for Comments: 3823                                       Caltech
Category: Informational                                        June 2004

     MIME Media Type for the Systems Biology Markup Language (SBML)

Status of this Memo

   This memo provides information for the Internet community.  It does
   not specify an Internet standard of any kind.  Distribution of this
   memo is unlimited.

Copyright Notice

   Copyright (C) The Internet Society (2004).

Abstract

   This document registers the MIME sub-type application/sbml+xml, a
   media type for SBML, the Systems Biology Markup Language.  SBML is
   defined by The SBML Team at the California Institute of Technology
   and interested members of the systems biology community.

1.  Introduction

   SBML is an XML format for representing and exchanging models of
   biochemical reaction networks used in systems biology.  SBML:

   o  enables researchers in systems biology to use multiple tools, such
      as simulators, editors, differential-equation solvers, and
      visualizers, on a single model without rewriting the model for
      each tool;

   o  enables researchers and publishers to make models available on-
      line to other researchers even if they use a different software
      environment;

   o  enables models, and the intellectual effort put into them, to
      survive beyond the lifetime of the software tools used to create
      them.

   Currently, about 60 software applications use SBML, and researchers
   are using these applications to develop quantitative and qualitative
   computational models, mostly in cell biology.  In addition, several
   consortia and alliances have standardized SBML as their model

Kovitz                       Informational                      [Page 1]
RFC 3823         Systems Biology Markup Language (SBML)        June 2004

   definition language.  The SBML community hopes that a standardized
   MIME media type will help researchers share models on a larger scale,
   drawing more heavily on the capabilities of the world-wide web.

   A detailed exposition of SBML and its uses within the systems biology
   community is available in references [HUCKA2003], [FINNEY2003], and
   [HUCKA2004].

2.  IANA Registration

   This section registers application/sbml+xml as a MIME media type
   according to the parameters set forth in [RFC2048].

   MIME media type name: application

   MIME subtype name: sbml+xml

   Required parameters: none.

   Optional parameters: none.

      There is no charset parameter.  Character handling has identical
      semantics to the case where the charset parameter of the
      "application/xml" media type is omitted, as described in section
      3.2 of [RFC3023].  Note that SBML level 2 is defined to have UTF-8
      encoding [SBML2-1, section 4.1].

   Encoding considerations:

      Same as described in section 3.2 of [RFC3023].

   Security considerations:

      The security considerations described in section 7 of [RFC3470]
      all potentially apply to sbml+xml documents.  In particular,
      sbml+xml documents might contain the results of proprietary
      biological research that their owner may wish to keep private.

   The XML schema for sbml+xml provides for no active or executable
   content.

   Interoperability considerations:

      The information in an sbml+xml document describes an abstract
      model of biochemical reactions.  It is not tied to any particular
      software application, and indeed the primary purpose of SBML is to
      make these models readable and writable by many different software
      applications.

Kovitz                       Informational                      [Page 2]
RFC 3823         Systems Biology Markup Language (SBML)        June 2004

      This might seem to make sbml+xml more appropriate for the "Model"
      primary content type [RFC2077], but SBML models are not guaranteed
      to have the required three orthogonal dimensions.  SBML models,
      rather, involve interacting entities that exist within
      compartments.  However, ideally, browsers and other software that
      reads sbml+xml would give a human reader multiple choices of how
      to view the document: in a data-visualization tool, in a model
      editor, in a differential-equation analyzer, etc.

      The systems biology community has and will continue to release new
      levels and versions of the SBML schema and semantics.  New
      versions attempt to be backward compatible with old versions, but
      sometimes small incompatibilities are introduced.  Every sbml+xml
      document contains its level and version; programs that read
      sbml+xml should read this information to be sure they correctly
      interpret the remainder of the document.

   Published specification:

      A list of all current SBML specifications and related documents is
      maintained at: