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rfc:rfc3823

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:
    http://sbml.org/documents
    Current specifications are:
    SBML level 2, version 1
    http://sbml.org/specifications/sbml-level-2-v1.ps
    http://sbml.org/specifications/sbml-level-2-v1.pdf
    SBML level 1, version 2
    http://sbml.org/specifications/sbml-level-1-v2.ps
    http://sbml.org/specifications/sbml-level-1-v2.pdf
    SBML level 1, version 1
    http://sbml.org/specifications/sbml-level-1-v1.ps
    http://sbml.org/specifications/sbml-level-1-v1.pdf
    All specifications are authored by and available in hardcopy form
    from The SBML Team (see below for mailing information).
 Applications which use this media type:
    The following application and database projects read and/or write
    models in sbml+xml format.  Currently, most do not encode or
    decode MIME-format messages.  Hopefully the registration of

Kovitz Informational [Page 3] RFC 3823 Systems Biology Markup Language (SBML) June 2004

    sbml+xml will make it easier for these projects to connect through
    a broader infrastructure, such as the creation of repositories of
    models on the world-wide web.
       BALSA
       BASIS
       BioCharon
       biocyc2SBML
       BioGrid
       BioNetGen
       Bio Sketch Pad
       BioSpreadsheet
       BioUML
       BSTLab
       CADLIVE
       CellDesigner
       Cellerator
       Cellware
       COPASI
       Cytoscape
       DBsolve
       Dizzy
       E-CELL
       ecellJ
       ESS
       Gepasi
       Jarnac
       JDesigner
       JigCell
       JSIM
       JWS
       Karyote
       KEGG2SBML
       Kinsolver (planned)
       libSBML
       MathSBML
       MMT2
       Modesto
       MOMA (planned)
       Monod
       NetBuilder
       PathArt
       PathScout
       PaVESy
       PathwayBuilder
       ProcessDB (planned)
       SBW
       SCIpath

Kovitz Informational [Page 4] RFC 3823 Systems Biology Markup Language (SBML) June 2004

       SigPath
       SigTran
       Simpathica
       SimWiz
       StochSim
       STOCKS
       Trelis
       Virtual Cell
       VLX Suite
       WinSCAMP
    A list of SBML-enabled applications, along with URLs for more
    information about them, is maintained at http://sbml.org.
 Additional information:
    For further information, contact:
       Michael Hucka
       mhucka@caltech.edu
       Andrew Finney
       afinney@cds.caltech.edu
       The SBML Team
       http://sbml.org
       sbml-team@caltech.edu
       Control and Dynamical Systems, MC 107-81
       California Institute of Technology
       Pasadena, CA  91125
       USA
 Intended usage: LIMITED USE
 Author/Change Controller:
    The SBML specification is a free, open, community effort organized
    and edited by The SBML Team.  The SBML Team has change control
    over the specification.
    The SBML Team and interested members of the systems biology
    community meet regularly at the "Workshops on Software Platforms
    for Systems Biology".  Information about past and planned
    workshops is maintained at:
       http://sbml.org/workshops

Kovitz Informational [Page 5] RFC 3823 Systems Biology Markup Language (SBML) June 2004

3. Security Considerations

 Security considerations for sbml+xml are discussed in the "Security
 Considerations" heading in the IANA registration in section 2.

4. Contributors

 The following people contributed to the content of this document:
 Michael Hucka (Caltech), Andrew Finney (University of Hertfordshire).

5. References

5.1. Normative References

 [SBML2-1]    Finney, A. and Hucka, M., "Systems Biology Markup
              Language (SBML) Level 2: Structures and Facilities for
              Model Definitions", June 28, 2003.  Available from The
              SBML Team at: http://sbml.org/specifications/sbml-
              level-2-v1.pdf
 [SBML1-2]    Hucka, M., Finney, A., Sauro, H. and Bolouri, H.,
              "Systems Biology Markup Language (SBML) Level 1:
              Structures and Facilities for Basic Model Definitions",
              August 28, 2003.  Available from The SBML Team at:
              http://sbml.org/specifications/sbml-level-1-v2.pdf

5.2. Informative References

 [FINNEY2003] Finney, A. and Hucka, M., "Systems Biology Markup
              Language: Level 2 and Beyond", Biochemical Society
              Transactions 31:1472-1473, December, 2003.
 [HUCKA2003]  Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle,
              J.C., Kitano, H., Arkin, A.P., Bornstein, B.J., Bray,
              D., Cornish-Bowden, A., Cuellar, A.A., Dronov, S.,
              Gilles, E.D., Ginkel, M., Gor, V., Goryanin, I.I.,
              Hedley, W.J., Hodgman, T.C., Hofmeyr, J.-H., Hunter,
              P.J., Juty, N.S., Kasberger, J.L., Kremling, A., Kummer,
              U., Le Novere, N., Loew, L.M., Lucio, D., Mendes, P.,
              Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R.,
              Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro,
              B.E., Shimizu, T.S., Spence, H.D., Stelling, J.,
              Takahashi, K., Tomita, M., Wagner, J., Wang, J., "The
              Systems Biology Markup Language (SBML): a Medium for
              Representation and Exchange of Biochemical Network
              Models", Bioinformatics 19(4):524-531, 2003.

Kovitz Informational [Page 6] RFC 3823 Systems Biology Markup Language (SBML) June 2004

 [HUCKA2004]  Hucka, M., Finney, A., Bornstein, B. J., Keating, S. M.,
              Shapiro, B. E., Matthews, M., Kovitz, B. L., Schilstra,
              M. J., Funahashi, A., Doyle, J. C., and Kitano, H.,
              "Evolving a Lingua Franca and Associated Software
              Infrastructure for Computational Systems Biology: The
              Systems Biology Markup Language (SBML) Project", Systems
              Biology, Vol. 1, 2004.
 [RFC2048]    Freed, N., Klensin, J. and J. Postel, "Multipurpose
              Internet Mail Extensions (MIME) Part Four: Registration
              Procedures", BCP 13, RFC 2048, November 1996.
 [RFC2077]    Nelson, S. and C. Parks, "The Model Primary Content Type
              for Multipurpose Internet Mail Extensions", RFC 2077,
              January 1997.
 [RFC3023]    Murata, M., St. Laurent, S. and D. Kohn, "XML Media
              Types", RFC 3023, January 2001.
 [RFC3470]    Hollenbeck, S., Rose, M. and L. Masinter, "Guidelines
              for the Use of Extensible Markup Language (XML) within
              IETF Protocols", BCP 70, RFC 3470, January 2003.

6. Author's Address

 Ben Kovitz
 Control and Dynamical Systems, MC 107-81
 California Institute of Technology
 Pasadena, CA  91125
 USA
 Phone: +1 626 395-6911
 EMail: bkovitz@caltech.edu

Kovitz Informational [Page 7] RFC 3823 Systems Biology Markup Language (SBML) June 2004

7. Full Copyright Statement

 Copyright (C) The Internet Society (2004).  This document is subject
 to the rights, licenses and restrictions contained in BCP 78, and
 except as set forth therein, the authors retain all their rights.
 This document and the information contained herein are provided on an
 "AS IS" basis and THE CONTRIBUTOR, THE ORGANIZATION HE/SHE REPRESENTS
 OR IS SPONSORED BY (IF ANY), THE INTERNET SOCIETY AND THE INTERNET
 ENGINEERING TASK FORCE DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED,
 INCLUDING BUT NOT LIMITED TO ANY WARRANTY THAT THE USE OF THE
 INFORMATION HEREIN WILL NOT INFRINGE ANY RIGHTS OR ANY IMPLIED
 WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

Intellectual Property

 The IETF takes no position regarding the validity or scope of any
 Intellectual Property Rights or other rights that might be claimed to
 pertain to the implementation or use of the technology described in
 this document or the extent to which any license under such rights
 might or might not be available; nor does it represent that it has
 made any independent effort to identify any such rights.  Information
 on the procedures with respect to rights in RFC documents can be
 found in BCP 78 and BCP 79.
 Copies of IPR disclosures made to the IETF Secretariat and any
 assurances of licenses to be made available, or the result of an
 attempt made to obtain a general license or permission for the use of
 such proprietary rights by implementers or users of this
 specification can be obtained from the IETF on-line IPR repository at
 http://www.ietf.org/ipr.
 The IETF invites any interested party to bring to its attention any
 copyrights, patents or patent applications, or other proprietary
 rights that may cover technology that may be required to implement
 this standard.  Please address the information to the IETF at ietf-
 ipr@ietf.org.

Acknowledgement

 Funding for the RFC Editor function is currently provided by the
 Internet Society.

Kovitz Informational [Page 8]

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