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Network Working Group A. Miller
Request for Comment: 4708 The University of Auckland
Category: Informational October 2006
CellML Media Type
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 (2006).
Abstract
This document standardises a new media type -- application/cellml+xml
-- for use in exchanging mathematical models represented in a CellML
Umbrella 1.0 compliant markup language.
1. Introduction
The CellML Umbrella format is a standardised markup meta-language for
the interchange of mathematical models. The CellML Umbrella format
provides a common base that is supported by a number of specific
formats used in the interchange of mathematical models. The CellML
Umbrella format provides enough information to determine which
specific language is used to express the model. The syntax and
semantics of the CellML Umbrella format are defined by
[CELLML-UMBRELLA].
The CellML Umbrella format is an actual media format. Although
CellML Umbrella documents contain elements in namespaces defined by
other specifications such as [RDF] and [MATHML], the elements in
these namespaces do not contain sufficient information to define a
mathematical model, and so CellML provides the information required
to interconnect the different CellML components, as well as the
information required to link CellML components to their metadata. As
such, CellML Umbrella documents are more than just a collection of
entities defined elsewhere, and so a new media type is required to
identify CellML.
As all well-formed CellML Umbrella documents are also well-formed XML
documents, the convention described in Section 7 of [RFC3023] has
been observed by use of the +xml suffix.
Miller Informational [Page 1]
RFC 4708 CellML Media Type October 2006 The information in CellML Umbrella documents cannot be interpreted without understanding the semantics of the XML elements used to mark up the model structure. Therefore, the application top-level type is used instead of the text top-level type. 2. Notational Conventions The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in [RFC2119]. The terms "element" and "document element" in this document are to be interpreted as in [XML]. The term "XML namespace" is to be interpreted as in [NAMESPACES]. 3. Media Type Registration for CellML Umbrella MIME media type name: application MIME subtype name: cellml+xml Mandatory parameters: none Optional parameters: charset The charset parameter of application/cellml+xml is handled in the same fashion as for application/xml, as specified in Section 3.2 of [RFC3023]. However, per conformance rule 4 of [CELLML-UMBRELLA], valid CellML Umbrella documents MUST be in the UTF-8 character set. If the charset parameter is present, it MUST take the value "utf-8". CellML processing software SHOULD check the charset field, and if it is present but not equal to "utf-8", MAY attempt to recover from the error by processing the document in the specified character set. Encoding considerations: As per Section 3.2 of [RFC3023]. Security considerations: As per Section 5 of this document. Interoperability considerations: As per Section 4.1 of this document. Published specification: CellML Umbrella Specification [CELLML-UMBRELLA]. Applications that use this media type: As per Section 4.2 of this document. Miller Informational [Page 2]
RFC 4708 CellML Media Type October 2006 Additional information: Magic number(s): None. XML processing software can identify CellML Umbrella documents as XML documents that contain a document element with the local name "model". File extension(s): The RECOMMENDED file extension for CellML Umbrella documents is .cellml Some older software uses the file extension .xml. Software vendors have also used the non-standard extension .cml. In contexts where the MIME type is available, or where the type has already been determined as CellML, implementations SHOULD allow files to be opened regardless of the extension. Implementations transferring models to an environment that uses file extensions SHOULD use the .cellml extension. Macintosh File Type Code(s): "TEXT" Person & email address to contact for further information: See the Author's Address section of this document. Intended usage: COMMON Author/Change controller: The CellML Umbrella 1.0 specification was authored by Andrew Miller. The CellML Umbrella 1.0 specification itself will not change. However, the umbrella specification defines the process for new specific formats to be registered. The Bioengineering Institute at The University of Auckland, with input from the CellML Community via the cellml-discussion@cellml.org mailing list, has control over the CellML Umbrella Format Registry. 4. Interoperability and Usage 4.1. Interoperability Considerations The interoperability considerations in Section 3.1 of [RFC3023] also apply to CellML Umbrella documents. CellML Umbrella documents contain XML elements defined by each specific format, all of which are published specifications. In addition to the ability to parse XML, user agents require software support for the semantics of [RDF] and/or part or all of a specific format. As efforts are made to keep Miller Informational [Page 3]
RFC 4708 CellML Media Type October 2006 the number of specific formats small, user agents SHOULD implement all specific formats listed in the CellML Umbrella Format Registry at the time they were developed. 4.2. Applications that Use CellML Umbrella Format CellML Umbrella is device-, platform-, and vendor-neutral and is supported by a wide range of CellML processing tools, including those designed to validate, edit, and/or visualise CellML models, extract MathML or RDF, translate to or from other related specifications, evaluate mathematics and ordinary differential equations, fit parameters to models, and serve, archive, and annotate models. 5. Security Considerations As CellML Umbrella is an XML-based markup language, all the security considerations presented in Section 10 of [RFC3023] also apply to CellML Umbrella. Some types of CellML Umbrella documents can refer to other Uniform Resource Locators (URLs) in a number of places: i) References to XML document type definitions or schemas. ii) References to other models using the import features of some specific formats. iii) References to other documents embedded in user-defined data. Some types of CellML processing software may then automatically attempt to access the URL and retrieve the document. This retrieval could have several consequences, specifically, i) if a CellML document is transferred via e-mail, the fact that the recipient has opened the CellML document could be disclosed to the sender without the recipient's knowledge or consent. ii) where the recipient of a document transfers the document to another location using the MIME type defined in this document, the original author of the document may be notified of the second address by the attempted retrieval of further documents. iii) by performing requests on the recipient's behalf, the CellML processing software may cause actions to be performed with privileges granted to the recipient, without the recipient's knowledge or consent. Miller Informational [Page 4]
RFC 4708 CellML Media Type October 2006 CellML processing software can mitigate this threat when running in an environment where it is a concern by requiring explicit confirmation from the user before attempting to load any external documents. 6. IANA Considerations This document specifies a new media type. IANA has added this media type to their media types registry as specified in [RFC4288]. 7. References 7.1. Normative References [CELLML-UMBRELLA] Miller, A.K., "CellML Umbrella Specification 1.0", 20 April 2006, <http://www.cellml.org/ specifications/cellml_umbrella_1.0> [NAMESPACES] Bray, T., et. al., "Namespaces in XML 1.1", 4 February 2004, <http://www.w3.org/TR/xml-names11> [RFC2119] Bradner, S., "Key words for use in RFCs to Indicate Requirement Levels", BCP 14, RFC 2119, March 1997. [RFC3023] Murata, M., St. Laurent, S., and D. Kohn, "XML Media Types", RFC 3023, January 2001. [XML] Bray, T., et. al., "Extensible Markup Language (XML) 1.0 (Fourth Edition)", 29 September 2006, <http://www.w3.org/TR/REC-xml/> 7.2. Informative References [MATHML] Ion, P. and Miner, R.(editors) "Mathematical Markup Language (MathML) 1.01 Specification", 7 July 1999, <http://www.w3.org/TR/REC-MathML/> [RDF] Beckett, D.(editor) "RDF/XML Syntax Specification (Revised)", 10 February 2004, <http://www.w3.org/TR/rdf-syntax-grammar/> [RFC4288] Freed, N. and J. Klensin, "Media Type Specifications and Registration Procedures", BCP 13, RFC 4288, December 2005. Miller Informational [Page 5]
RFC 4708 CellML Media Type October 2006 Author's Address Andrew Miller The Bioengineering Institute at The University of Auckland Level 6, 70 Symonds St Auckland Central Auckland EMail: ak.miller@auckland.ac.nz Miller Informational [Page 6]
RFC 4708 CellML Media Type October 2006 Full Copyright Statement Copyright (C) The Internet Society (2006). 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 provided by the IETF Administrative Support Activity (IASA). Miller Informational [Page 7]