Network Working Group B. Kovitz
Request for Comments: 3823 Caltech
Category: Informational June 2004
Network Working Group B. Kovitz
Request for Comments: 3823 Caltech
Category: Informational June 2004
MIME Media Type for the Systems Biology Markup Language (SBML)
系统生物学标记语言（SBML）的MIME媒体类型
Status of this Memo
本备忘录的状况
This memo provides information for the Internet community. It does not specify an Internet standard of any kind. Distribution of this memo is unlimited.
本备忘录为互联网社区提供信息。它没有规定任何类型的互联网标准。本备忘录的分发不受限制。
Copyright Notice
版权公告
Copyright (C) The Internet Society (2004).
版权所有（C）互联网协会（2004年）。
Abstract
摘要
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.
本文档注册MIME子类型application/sbml+xml，这是系统生物学标记语言sbml的一种媒体类型。SBML是由加利福尼亚理工学院的SBML团队和系统生物学界感兴趣的成员定义的。
SBML is an XML format for representing and exchanging models of biochemical reaction networks used in systems biology. SBML:
SBML是一种XML格式，用于表示和交换系统生物学中使用的生化反应网络模型。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 使系统生物学研究人员能够在单个模型上使用多种工具，如模拟器、编辑器、微分方程求解器和可视化工具，而无需为每个工具重写模型；
o enables researchers and publishers to make models available on-line to other researchers even if they use a different software environment;
o 使研究人员和出版商能够在线向其他研究人员提供模型，即使他们使用不同的软件环境；
o enables models, and the intellectual effort put into them, to survive beyond the lifetime of the software tools used to create them.
o 使模型及其智力投入能够在用于创建模型的软件工具的生命周期之外继续存在。
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
目前，大约有60个软件应用程序使用SBML，研究人员正在使用这些应用程序开发定量和定性计算模型，主要是在细胞生物学中。此外，一些财团和联盟已经将SBML标准化为他们的模型
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.
定义语言。SBML社区希望，标准化的MIME媒体类型将有助于研究人员更大规模地共享模型，更多地利用万维网的功能。
A detailed exposition of SBML and its uses within the systems biology community is available in references [HUCKA2003], [FINNEY2003], and [HUCKA2004].
参考文献[HUCKA2003]、[FINNEY2003]和[HUCKA2004]详细阐述了SBML及其在系统生物学界的应用。
This section registers application/sbml+xml as a MIME media type according to the parameters set forth in [RFC2048].
本节根据[RFC2048]中规定的参数将application/sbml+xml注册为MIME媒体类型。
MIME media type name: application
MIME媒体类型名称：应用程序
MIME subtype name: sbml+xml
MIME子类型名称：sbml+xml
Required parameters: none.
所需参数：无。
Optional parameters: none.
可选参数：无。
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].
没有字符集参数。字符处理的语义与省略“application/xml”媒体类型的charset参数的情况相同，如[RFC3023]第3.2节所述。注意，SBML级别2定义为UTF-8编码[SBML2-1，第4.1节]。
Encoding considerations:
编码注意事项：
Same as described in section 3.2 of [RFC3023].
与[RFC3023]第3.2节所述相同。
Security considerations:
安全考虑：
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.
[RFC3470]第7节中描述的安全注意事项都可能适用于sbml+xml文档。特别是，sbml+xml文档可能包含其所有者可能希望保密的专有生物学研究结果。
The XML schema for sbml+xml provides for no active or executable content.
sbml+XML的XML模式不提供活动或可执行内容。
Interoperability considerations:
互操作性注意事项：
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.
sbml+xml文档中的信息描述了生化反应的抽象模型。它与任何特定的软件应用程序无关，实际上，SBML的主要目的是使这些模型能够被许多不同的软件应用程序读取和写入。
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.
这似乎使sbml+xml更适合“模型”主要内容类型[RFC2077]，但sbml模型不能保证具有所需的三个正交维度。相反，SBML模型涉及存在于隔间内的交互实体。然而，理想情况下，浏览器和其他读取sbml+xml的软件将为人类读者提供查看文档的多种选择：在数据可视化工具中，在模型编辑器中，在微分方程分析器中，等等。
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.
系统生物学社区已经并将继续发布新级别和版本的SBML模式和语义。新版本试图与旧版本向后兼容，但有时会引入一些小的不兼容。每个sbml+xml文档都包含其级别和版本；读取sbml+xml的程序应该读取这些信息，以确保它们正确地解释了文档的其余部分。
Published specification:
已发布的规范：
A list of all current SBML specifications and related documents is maintained at:
所有当前SBML规范和相关文件的列表保存在：
http://sbml.org/documents
http://sbml.org/documents
Current specifications are:
目前的规格是：
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 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 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
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).
所有规范均由SBML团队编写并以硬拷贝形式提供（邮寄信息见下文）。
Applications which use this media type:
使用此媒体类型的应用程序：
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
以下应用程序和数据库项目以sbml+xml格式读取和/或写入模型。目前，大多数不编码或解码MIME格式的消息。希望注册
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.
sbml+xml将使这些项目更容易通过更广泛的基础设施进行连接，例如在万维网上创建模型库。
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
BALSA BASIS BioCharon biocyc2SBML BioCharon BioCharon biocyc2SBML BioGrid BioNetGen Bio Sketch Pad BioSpreadsheet BIOBSTLAB CADLIVE CellDesigner Cellrator Cellware COPASI Cytoscape DBsolve Dizzy E-Cells Gepasi Jarnac JDesigner JigCell JSIM JWS核型KEGG2SBML Kinsolver（计划）libSBML MathSBML MMT2 MOMA（计划）Monod NetBuilder PathArt PathScout PaVESy PathwayBuilder ProcessDB（计划）SBW SCIpath
SigPath SigTran Simpathica SimWiz StochSim STOCKS Trelis Virtual Cell VLX Suite WinSCAMP
SigPath SigTran Simpathica SimWiz StochSim STOCKS Trelis虚拟单元VLX套件WinSCAMP
A list of SBML-enabled applications, along with URLs for more information about them, is maintained at http://sbml.org.
启用SBML的应用程序列表以及有关这些应用程序的更多信息的URL都保存在http://sbml.org.
Additional information:
其他信息：
For further information, contact:
有关更多信息，请联系：
Michael Hucka mhucka@caltech.edu
迈克尔·哈卡mhucka@caltech.edu
Andrew Finney afinney@cds.caltech.edu
安德鲁·芬尼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
SBML团队http://sbml.org sbml-team@caltech.edu控制与动力系统，MC 107-81加利福尼亚理工学院帕萨迪纳，加利福尼亚州91125美国
Intended usage: LIMITED USE
预期用途：有限用途
Author/Change Controller:
作者/变更控制员：
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.
SBML规范是由SBML团队组织和编辑的自由、开放的社区工作。SBML团队对规范具有变更控制权。
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:
SBML团队和感兴趣的系统生物学社区成员定期在“系统生物学软件平台研讨会”上会面。关于过去和计划中研讨会的信息保存在：
http://sbml.org/workshops
http://sbml.org/workshops
Security considerations for sbml+xml are discussed in the "Security Considerations" heading in the IANA registration in section 2.
第2节IANA注册中的“安全注意事项”标题讨论了sbml+xml的安全注意事项。
The following people contributed to the content of this document: Michael Hucka (Caltech), Andrew Finney (University of Hertfordshire).
以下人员对本文件的内容做出了贡献：迈克尔·哈卡（加州理工大学）、安德鲁·芬尼（赫特福德大学）。
[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
[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
[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
[FINNEY2003] Finney, A. and Hucka, M., "Systems Biology Markup Language: Level 2 and Beyond", Biochemical Society Transactions 31:1472-1473, December, 2003.
[FINNEY2003]Finney，A.和Hucka，M.，“系统生物学标记语言：2级及以上”，生物化学学会学报31:1472-1473，2003年12月。
[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.
[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.，Hedley，W.J.，Hodgeman，T.C.，Hofmeyr，J.-H.，Hunter，P.J.，Juty，N.S.，Kasberger，J.，J.L.，Kremer，Novele，N.，勒夫，L.M.，卢西奥，D.，门德斯，P.，明奇，E.，Mjolsness，E.D.，中山，Y.，纳尔逊，M.R.，尼尔森，P.F.，樱田，T.，沙夫，J.C.，夏皮罗，B.E.，清水，T.S.，斯宾塞，H.D.，斯特林，J.，高桥，K.，富田，M.，瓦格纳，J.，王，J.，“系统生物学标记语言（SBML）：生物化学网络模型的表示和交换媒介”，生物信息学19（4）：524-5312003。
[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.
[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.，和Kitano，H.，“为计算系统生物学发展通用语言和相关软件基础设施：系统生物学标记语言（SBML）项目”，系统生物学，2004年第1卷。
[RFC2048] Freed, N., Klensin, J. and J. Postel, "Multipurpose Internet Mail Extensions (MIME) Part Four: Registration Procedures", BCP 13, RFC 2048, November 1996.
[RFC2048]Freed，N.，Klensin，J.和J.Postel，“多用途互联网邮件扩展（MIME）第四部分：注册程序”，BCP 13，RFC 2048，1996年11月。
[RFC2077] Nelson, S. and C. Parks, "The Model Primary Content Type for Multipurpose Internet Mail Extensions", RFC 2077, January 1997.
[RFC2077]Nelson，S.和C.Parks，“多用途Internet邮件扩展的主要内容类型模型”，RFC 2077，1997年1月。
[RFC3023] Murata, M., St. Laurent, S. and D. Kohn, "XML Media Types", RFC 3023, January 2001.
[RFC3023]Murata，M.，St.Laurent，S.和D.Kohn，“XML媒体类型”，RFC 3023，2001年1月。
[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.
[RFC3470]Hollenbeck，S.，Rose，M.和L.Masinter，“IETF协议中可扩展标记语言（XML）的使用指南”，BCP 70，RFC 3470，2003年1月。
Ben Kovitz Control and Dynamical Systems, MC 107-81 California Institute of Technology Pasadena, CA 91125 USA
Ben Kovitz控制与动力系统，MC 107-81加利福尼亚理工学院帕萨迪纳，加利福尼亚州91125
Phone: +1 626 395-6911
EMail: bkovitz@caltech.edu
Phone: +1 626 395-6911
EMail: bkovitz@caltech.edu
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.
版权所有（C）互联网协会（2004年）。本文件受BCP 78中包含的权利、许可和限制的约束，除其中规定外，作者保留其所有权利。
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.
本文件及其包含的信息是按“原样”提供的，贡献者、他/她所代表或赞助的组织（如有）、互联网协会和互联网工程任务组不承担任何明示或暗示的担保，包括但不限于任何保证，即使用本文中的信息不会侵犯任何权利，或对适销性或特定用途适用性的任何默示保证。
Intellectual Property
知识产权
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.
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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.
向IETF秘书处披露的知识产权副本和任何许可证保证，或本规范实施者或用户试图获得使用此类专有权利的一般许可证或许可的结果，可从IETF在线知识产权存储库获取，网址为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.
IETF邀请任何相关方提请其注意任何版权、专利或专利申请，或其他可能涵盖实施本标准所需技术的专有权利。请将信息发送至IETF的IETF-ipr@ietf.org.
Acknowledgement
确认
Funding for the RFC Editor function is currently provided by the Internet Society.
RFC编辑功能的资金目前由互联网协会提供。