Internet Draft

Intended Status:
Network Working Group                                       A. K. Miller
Request for Comments: nnnn                    The University of Auckland
Standards Track                                               March 2006

                           CellML Media Type

Status of this Memo

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    Copyright (C) The Internet Society (2006).


    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.

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1. Introduction

    CellML Umbrella format is a standardised markup meta-language for the
    interchange of mathematical models. CellML Umbrella Format provides
    a common base which is supported by a number of specific formats
    used in the interchange of mathematical models. 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].

    This document standardises a new media type --
    application/cellml+xml -- for use in exchanging mathematical models
    represented in a specific CellML Umbrella compliant language.

2. Notational Conventions

   The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT",
   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. Discussion

    CellML Umbrella is an XML-based markup meta-language for the
    interchange of mathmatical models.

    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 information 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.

    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.

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4. 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].

    Encoding considerations: As per Section 3.2 of [RFC3023].

    Security considerations: As per Section 6 of this document.

    Interoperability considerations: As per Section 5.1 of this

    Published specification:

      CellML Umbrella Specification[CELLML-UMBRELLA].

    Applications which use this media type: As per Section 5.2 of this

    Additional information:

      Magic number(s): None.
        XML processing software may identify CellML Umbrella documents
        as XML documents which contain a document element with local
        name "model".

      File extension(s):
        The recommended file extension for CellML Umbrella documents is

        Some older software still uses the obsolete file extension .cml

      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

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        at The University of Auckland, with input from the CellML
        Community via the mailing list,
        has control over the CellML Umbrella Format Registry.

5. Interoperability and usage
5.1. 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 the number of specific formats small, user agents SHOULD
    implement all specific formats listed in the registry at the time
    they were developed.

5.2. Applications which 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

6. 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

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      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
      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.

    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

7. IANA Considerations

    This document specifies a new media type. IANA will add this media
    type to the media types registry as specified in [RFC4288].

8. References
8.1. Normative References

    [CELLML-UMBRELLA] Miller, A.K., "CellML Umbrella Specification 1.0",
                      20 April 2006,

    [NAMESPACES]      Bray, T., et. al., "Namespaces in XML 1.1",
                      4 February 2004,

    [RFC2119]         Bradner, S., "Key words for use in RFCs to
                      Indicate Requirement Levels", RFC 2119, BCP 14,
                      March 1997

    [RFC3023]         Murata, M., Simon, S.L., Kohn, D., "XML Media
                      Types", RFC 3023, January 2001

    [XML]             Bray, T., et. al., "Extensible Markup Language
                      (XML) 1.0 (Third Edition)", 4 February 2004,

8.2. Informative References
    [MATHML]          Ion, P. and Miner, R.(editors) "Mathematical
                      Markup Language (MathML) 1.01 Specification", 7
                      July 1999, <>

    [RDF]             Beckett, D.(editor) "RDF/XML Syntax Specification
                      (Revised)", 10 February 2004,

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    [RFC4288]        Freed, N. and Klensin, J.C., "Media Type
                     Specifications and Registration Procedures",
                     RFC 4288, BCP 13, December 2005

Author's Address

    Andrew Miller
    The Bioengineering Institute at The University of Auckland
    Level 6, 70 Symonds St
    Auckland Central


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