MIME Media Type for the Systems Biology Markup Language (SBML)
RFC 3823
Document | Type |
RFC - Informational
(June 2004; No errata)
Was draft-sbml-media-type (individual in app area)
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Author | Ben Kovitz | ||
Last updated | 2015-10-14 | ||
Stream | IETF | ||
Formats | plain text html pdf htmlized bibtex | ||
Stream | WG state | (None) | |
Document shepherd | No shepherd assigned | ||
IESG | IESG state | RFC 3823 (Informational) | |
Consensus Boilerplate | Unknown | ||
Telechat date | |||
Responsible AD | Ned Freed | ||
Send notices to | (None) |
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:Show full document text