1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
|
<pre>Network Working Group B. Kovitz
Request for Comments: 3823 Caltech
Category: Informational June 2004
<span class="h1">MIME Media Type for the Systems Biology Markup Language (SBML)</span>
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.
<span class="h2"><a class="selflink" id="section-1" href="#section-1">1</a>. Introduction</span>
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
<span class="grey">Kovitz Informational [Page 1]</span></pre>
<hr class='noprint'/><!--NewPage--><pre class='newpage'><span id="page-2" ></span>
<span class="grey"><a href="./rfc3823">RFC 3823</a> Systems Biology Markup Language (SBML) June 2004</span>
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 [<a href="#ref-HUCKA2003" title=""The Systems Biology Markup Language (SBML): a Medium for Representation and Exchange of Biochemical Network Models"">HUCKA2003</a>], [<a href="#ref-FINNEY2003" title=""Systems Biology Markup Language: Level 2 and Beyond"">FINNEY2003</a>], and
[<a href="#ref-HUCKA2004" title=""Evolving a Lingua Franca and Associated Software Infrastructure for Computational Systems Biology: The Systems Biology Markup Language (SBML) Project"">HUCKA2004</a>].
<span class="h2"><a class="selflink" id="section-2" href="#section-2">2</a>. IANA Registration</span>
This section registers application/sbml+xml as a MIME media type
according to the parameters set forth in [<a href="./rfc2048" title=""Multipurpose Internet Mail Extensions (MIME) Part Four: Registration Procedures"">RFC2048</a>].
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 <a href="./rfc3023#section-3.2">section</a>
<a href="./rfc3023#section-3.2">3.2 of [RFC3023]</a>. Note that SBML level 2 is defined to have UTF-8
encoding [SBML2-1, <a href="#section-4.1">section 4.1</a>].
Encoding considerations:
Same as described in <a href="./rfc3023#section-3.2">section 3.2 of [RFC3023]</a>.
Security considerations:
The security considerations described in <a href="./rfc3470#section-7">section 7 of [RFC3470]</a>
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.
<span class="grey">Kovitz Informational [Page 2]</span></pre>
<hr class='noprint'/><!--NewPage--><pre class='newpage'><span id="page-3" ></span>
<span class="grey"><a href="./rfc3823">RFC 3823</a> Systems Biology Markup Language (SBML) June 2004</span>
This might seem to make sbml+xml more appropriate for the "Model"
primary content type [<a href="./rfc2077" title=""The Model Primary Content Type for Multipurpose Internet Mail Extensions"">RFC2077</a>], 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:
<a href="http://sbml.org/documents">http://sbml.org/documents</a>
Current specifications are:
SBML level 2, version 1
<a href="http://sbml.org/specifications/sbml-level-2-v1.ps">http://sbml.org/specifications/sbml-level-2-v1.ps</a>
<a href="http://sbml.org/specifications/sbml-level-2-v1.pdf">http://sbml.org/specifications/sbml-level-2-v1.pdf</a>
SBML level 1, version 2
<a href="http://sbml.org/specifications/sbml-level-1-v2.ps">http://sbml.org/specifications/sbml-level-1-v2.ps</a>
<a href="http://sbml.org/specifications/sbml-level-1-v2.pdf">http://sbml.org/specifications/sbml-level-1-v2.pdf</a>
SBML level 1, version 1
<a href="http://sbml.org/specifications/sbml-level-1-v1.ps">http://sbml.org/specifications/sbml-level-1-v1.ps</a>
<a href="http://sbml.org/specifications/sbml-level-1-v1.pdf">http://sbml.org/specifications/sbml-level-1-v1.pdf</a>
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
<span class="grey">Kovitz Informational [Page 3]</span></pre>
<hr class='noprint'/><!--NewPage--><pre class='newpage'><span id="page-4" ></span>
<span class="grey"><a href="./rfc3823">RFC 3823</a> Systems Biology Markup Language (SBML) June 2004</span>
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
<span class="grey">Kovitz Informational [Page 4]</span></pre>
<hr class='noprint'/><!--NewPage--><pre class='newpage'><span id="page-5" ></span>
<span class="grey"><a href="./rfc3823">RFC 3823</a> Systems Biology Markup Language (SBML) June 2004</span>
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 <a href="http://sbml.org">http://sbml.org</a>.
Additional information:
For further information, contact:
Michael Hucka
mhucka@caltech.edu
Andrew Finney
afinney@cds.caltech.edu
The SBML Team
<a href="http://sbml.orgsbml-team@caltech.edu">http://sbml.org</a>
<a href="http://sbml.orgsbml-team@caltech.edu">sbml-team@caltech.edu</a>
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:
<a href="http://sbml.org/workshops">http://sbml.org/workshops</a>
<span class="grey">Kovitz Informational [Page 5]</span></pre>
<hr class='noprint'/><!--NewPage--><pre class='newpage'><span id="page-6" ></span>
<span class="grey"><a href="./rfc3823">RFC 3823</a> Systems Biology Markup Language (SBML) June 2004</span>
<span class="h2"><a class="selflink" id="section-3" href="#section-3">3</a>. Security Considerations</span>
Security considerations for sbml+xml are discussed in the "Security
Considerations" heading in the IANA registration in <a href="#section-2">section 2</a>.
<span class="h2"><a class="selflink" id="section-4" href="#section-4">4</a>. Contributors</span>
The following people contributed to the content of this document:
Michael Hucka (Caltech), Andrew Finney (University of Hertfordshire).
<span class="h2"><a class="selflink" id="section-5" href="#section-5">5</a>. References</span>
<span class="h3"><a class="selflink" id="section-5.1" href="#section-5.1">5.1</a>. Normative References</span>
[<a id="ref-SBML2-1">SBML2-1</a>] 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: <a href="http://sbml.org/specifications/sbml-level-2-v1.pdf">http://sbml.org/specifications/sbml-</a>
<a href="http://sbml.org/specifications/sbml-level-2-v1.pdf">level-2-v1.pdf</a>
[<a id="ref-SBML1-2">SBML1-2</a>] 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:
<a href="http://sbml.org/specifications/sbml-level-1-v2.pdf">http://sbml.org/specifications/sbml-level-1-v2.pdf</a>
<span class="h3"><a class="selflink" id="section-5.2" href="#section-5.2">5.2</a>. Informative References</span>
[<a id="ref-FINNEY2003">FINNEY2003</a>] Finney, A. and Hucka, M., "Systems Biology Markup
Language: Level 2 and Beyond", Biochemical Society
Transactions 31:1472-1473, December, 2003.
[<a id="ref-HUCKA2003">HUCKA2003</a>] 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.
<span class="grey">Kovitz Informational [Page 6]</span></pre>
<hr class='noprint'/><!--NewPage--><pre class='newpage'><span id="page-7" ></span>
<span class="grey"><a href="./rfc3823">RFC 3823</a> Systems Biology Markup Language (SBML) June 2004</span>
[<a id="ref-HUCKA2004">HUCKA2004</a>] 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.
[<a id="ref-RFC2048">RFC2048</a>] Freed, N., Klensin, J. and J. Postel, "Multipurpose
Internet Mail Extensions (MIME) Part Four: Registration
Procedures", <a href="https://www.rfc-editor.org/bcp/bcp13">BCP 13</a>, <a href="./rfc2048">RFC 2048</a>, November 1996.
[<a id="ref-RFC2077">RFC2077</a>] Nelson, S. and C. Parks, "The Model Primary Content Type
for Multipurpose Internet Mail Extensions", <a href="./rfc2077">RFC 2077</a>,
January 1997.
[<a id="ref-RFC3023">RFC3023</a>] Murata, M., St. Laurent, S. and D. Kohn, "XML Media
Types", <a href="./rfc3023">RFC 3023</a>, January 2001.
[<a id="ref-RFC3470">RFC3470</a>] Hollenbeck, S., Rose, M. and L. Masinter, "Guidelines
for the Use of Extensible Markup Language (XML) within
IETF Protocols", <a href="https://www.rfc-editor.org/bcp/bcp70">BCP 70</a>, <a href="./rfc3470">RFC 3470</a>, January 2003.
<span class="h2"><a class="selflink" id="section-6" href="#section-6">6</a>. Author's Address</span>
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
<span class="grey">Kovitz Informational [Page 7]</span></pre>
<hr class='noprint'/><!--NewPage--><pre class='newpage'><span id="page-8" ></span>
<span class="grey"><a href="./rfc3823">RFC 3823</a> Systems Biology Markup Language (SBML) June 2004</span>
<span class="h2"><a class="selflink" id="section-7" href="#section-7">7</a>. Full Copyright Statement</span>
Copyright (C) The Internet Society (2004). This document is subject
to the rights, licenses and restrictions contained in <a href="https://www.rfc-editor.org/bcp/bcp78">BCP 78</a>, 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 <a href="https://www.rfc-editor.org/bcp/bcp78">BCP 78</a> and <a href="https://www.rfc-editor.org/bcp/bcp79">BCP 79</a>.
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
<a href="http://www.ietf.org/ipr">http://www.ietf.org/ipr</a>.
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]
</pre>
|
