RFC 3823

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

📅 published June 2004, from ietf

RFC 3823: MIME Media Type for SBML 🧬✨

okay so this one is from June 2004 and it's Informational, which means it's sharing info for the community, not a binding standard 💅. Ben Kovitz from Caltech wrote it, and it doesn't obsolete or update anything. The title is literally MIME Media Type for the Systems Biology Markup Language (SBML) 🎀. Basically it's about giving SBML its own official media type so models can travel around the web 🌸

Status of this Memo 📋

this memo is giving info to the internet community. it doesn't specify an internet standard of any kind, and distribution is unlimited 🫶

Copyright (C) The Internet Society (2004).

Abstract 🦋

this doc registers the MIME sub-type application/sbml+xml, which is a media type for SBML (the Systems Biology Markup Language). SBML is defined by The SBML Team at the California Institute of Technology along with interested members of the systems biology community 💜

1. Introduction 🌈

okay so SBML is an XML format for representing and exchanging models of biochemical reaction networks used in systems biology 🧪 it's giving "one model, many tools" and here's why it's iconic:

  • it lets systems biology researchers use multiple tools (simulators, editors, differential-equation solvers, and visualizers) on a single model without rewriting the model for each tool 🔥
  • it lets researchers and publishers make models available online to other researchers, even if those researchers use a different software environment 🌸
  • it lets models, and the intellectual effort put into them, survive beyond the lifetime of the software tools used to create them 👑

right now about 60 software applications use SBML, and researchers are using them to build quantitative and qualitative computational models, mostly in cell biology 🍓 a bunch of consortia and alliances have also standardized SBML as their model definition language. the SBML community is hoping a standardized MIME media type will help researchers share models on a bigger scale, leaning harder into what the world-wide web can do 🌍✨

a detailed explanation of SBML and how the systems biology community uses it is in references [HUCKA2003], [FINNEY2003], and [HUCKA2004] 📚

2. IANA Registration 📝

this section registers application/sbml+xml as a MIME media type using the parameters set out 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:

🚨 okay this part is SERIOUS bestie. 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. like, your lab's secret research could be sitting in one of these files 😭🔒

the XML schema for sbml+xml provides for no active or executable content 🙌

Interoperability considerations:

the info in an sbml+xml document describes an abstract model of biochemical reactions. it isn't tied to any particular software application, and the whole point of SBML is to make these models readable and writable by lots of different software applications 🦋

this might seem to make sbml+xml a good fit for the "Model" primary content type [RFC2077], but SBML models aren't guaranteed to have the required three orthogonal dimensions 🙈 instead, SBML models involve interacting entities that exist within compartments. ideally though, browsers and other software that reads sbml+xml would give a human reader multiple ways to view the document: in a data-visualization tool, a model editor, a differential-equation analyzer, and so on 💅

the systems biology community has released, and will keep releasing, new levels and versions of the SBML schema and semantics. new versions try to stay backward compatible with old versions, but sometimes small incompatibilities sneak in 😩 every sbml+xml document contains its level and version, so programs that read sbml+xml should read that info to make sure they interpret the rest of the document correctly 🧚

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 The SBML Team and available in hardcopy form from them (see below for mailing info) 📮

Applications which use this media type:

the following application and database projects read and/or write models in sbml+xml format. right now most of them don't encode or decode MIME-format messages, but the hope is that registering sbml+xml will make it easier for these projects to connect through a broader infrastructure, like 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
SigPath
SigTran
Simpathica
SimWiz
StochSim
STOCKS
Trelis
Virtual Cell
VLX Suite
WinSCAMP

a list of SBML-enabled applications, plus URLs for more info 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, and 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". info about past and planned workshops is maintained at:

http://sbml.org/workshops

3. Security Considerations 🔐

security considerations for sbml+xml are discussed under 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) and 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.

[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

the end of this one, bestie! 🌈💖

okay so bestie, this part is the legal fine print 📜💅 it's giving "we own this, but also here's how you can use it" energy. Copyright is claimed by The Internet Society (2004) 🫶, and this document is subject to the rights, licenses and restrictions in BCP 78 🎀. Except as set forth in there, the authors keep all their rights 💜.

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The IETF invites anyone who's interested to bring any copyrights, patents, patent applications, or other proprietary rights that might cover technology needed to implement this standard to its attention 🧚. Send that info to the IETF at ietf-ipr@ietf.org 💖. Bestie, speak up if you spot something 📣.

Acknowledgement 🌸

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