





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.



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   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.



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   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





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   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.



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   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.







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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










































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Full Copyright Statement

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