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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:
+
+ 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
+
+
+
+
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+
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+Kovitz Informational [Page 7]
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+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.
+
+
+
+
+
+
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+Kovitz Informational [Page 8]
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