CellML Media Type
A MIME type for exchanging mathematical models in CellML format
Miller, A., "CellML Media Type", RFC 4708, DOI 10.17487/RFC4708, October 2006, <https://www.rfc-editor.org/info/rfc4708>.
@misc{rfc4708,
series = {Request for Comments},
number = 4708,
howpublished = {RFC 4708},
publisher = {RFC Editor},
doi = {10.17487/RFC4708},
url = {https://www.rfc-editor.org/info/rfc4708},
author = {A. Miller},
title = {{CellML Media Type}},
pagetotal = 7,
year = 2006,
month = oct,
} RFC text
Contents
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.
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.
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
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.
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.
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
Full Copyright Statement
Copyright (C) The Internet Society (2006).
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AI ELI5
On this page
§1Why CellML Needs Its Own Media Type
CellML is a standardized markup language for describing mathematical models, especially of biological systems. CellML Umbrella 1.0 is a meta-language that provides a common base for various specific modeling formats.
Although CellML documents are valid XML and contain elements from other specifications like RDF and MathML, these imported elements do not carry enough information on their own to describe a complete model. CellML adds the connective information that ties components together and links them to their metadata. Therefore, CellML documents are more than just a collection of elements from other standards, and require their own MIME type to be properly identified.
CellML files look like XML files, but they contain special science information that XML alone does not know about. A special label (MIME type) helps software recognize them.
§2The CellML Media Type Registration
The media type is registered as application/cellml+xml. According to RFC 3023, the +xml suffix indicates that the format is based on XML.
CellML Umbrella documents MUST be in UTF-8 encoding. The media type includes an optional charset parameter. If present, it must be set to "utf-8". Software MAY attempt to recover from errors where the charset parameter claims a different encoding, but valid CellML must always be UTF-8.
The recommended file extension for CellML documents is .cellml. Older software may use .xml or the non-standard .cml extension. When a MIME type is available, implementations should open files regardless of extension.
The official label is application/cellml+xml. The files must be stored in a text format called UTF-8, and should have the .cellml ending. This way, different programs can recognize and open CellML files.
§3Interoperability Considerations
CellML Umbrella documents reference elements from RDF and other XML vocabularies. To properly handle these documents, user agents need more than just XML parsing capability; they require software support for the semantics of RDF and the specific formats used within their CellML instances.
The CellML Umbrella Format Registry lists the specific formats currently supported. Implementers SHOULD support all specific formats listed in this registry, as maintaining the number of specific formats small improves overall interoperability. A range of tools already support CellML, including validators, editors, visualization tools, and systems for translating between related specifications, evaluating mathematics, fitting models to data, and archiving models.
Different programs need to understand not just the XML structure, but the scientific meanings inside. There is a list of approved CellML variations that programs should all support.
§4Security Concerns with CellML
Because CellML is an XML-based language, it inherits all the security considerations from RFC 3023. Additionally, CellML documents can contain references to external URLs in several ways: XML schema definitions or DTDs, imports of other models, and user-defined data fields.
Some CellML processing software may automatically attempt to retrieve documents from these URLs. This creates security risks. If a CellML document is received by email and opened, the recipient's system could disclose that fact to the sender without the recipient's knowledge. When a document is transferred to a new location, the original author may be notified. Processing software may also make requests on the recipient's behalf, potentially executing actions with the recipient's privileges without consent.
CellML processors can mitigate these threats by requiring explicit user confirmation before loading any external documents, especially in environments where this is a concern.
A math model file can contain links to other files on the internet. A program opening the file might secretly download those files and tell someone online that you looked at the model. This is risky, so programs should ask you first before fetching anything.
§5Registration with IANA
This document specifies a new media type for IANA registration. The media type name is application, the subtype is cellml+xml, and there are no mandatory parameters. The charset parameter is optional and handled the same way as for application/xml.
The magic number for identifying CellML documents is that they are XML documents with a document element having the local name "model". The intended usage is COMMON, indicating that this media type is expected to be widely used.
The CellML Umbrella 1.0 specification will not change, but the specification defines a process for registering new specific formats. Control over the CellML Umbrella Format Registry is held by the Bioengineering Institute at The University of Auckland, with input from the broader CellML Community.
IANA is the organization that keeps the official list of all media types. This RFC asks them to add cellml+xml to that list. The registry is controlled by the University of Auckland.