Mapping

A mapping between CellML 1.1 and a draft of CellML 1.2

Abstract

This document is a mapping between a draft version of CellML 1.2. It is fixed for a particular early unofficial draft of CellML 1.2, without any of the major proposals for CellML 1.2 included (so in other words, a specification which is, more or less, a trimmed down version of CellML 1.1 using slightly more formal language). The intention is that this document will make it easier for the CellML community to comment on and make proposals for CellML 1.2.

Using this document

This document should be read alongside the CellML 1.1 specification and the unofficial draft of the CellML 1.2 Specification available from git as git://repo.or.cz/srv/git/cellml-draft-miller.git commit 160f7655dc73aa90ca7306117560597a78b9797a. For your convenience, a rendered version of this specification is available online. Care should be taken when using this document alongside different drafts, as online minor changes may result in complete renumbering of the specification. Instead, it is recommended that you identify the text from the above draft, and identify the same text in the draft you are interested in.

This document is written as a mapping table listing the section in CellML 1.1, the section in the CellML 1.2 unofficial draft above, along with any comments comments. In many cases, text in CellML 1.1 is not normative (is an example, or is redundant explanatory text, and so it will not have a corresponding entry in the CellML 1.2. These entries are identified using the comment "I", which means that the corresponding text is considered purely informative.


CellML 1.1 CellML 1.2 Comments
Abstract Abstract  
1.1 - I
1.1.1 - I
1.1.2 2.1.1  
1.1.3 1 Terminology has changed a fair bit.
1.2 - I
2.1 - I
2.2.1 3.1  
2.2.2 2.4  
2.2.3 2.5  
2.3 - I
2.4.1 3.1 2.4.1 contradicts itself, the interpretation in the text is preferred over the EBNF one
2.4.2 2.4.1 However, attribute information items with no namespace prefix are no longer placed into the namespace of the parent element, as this doesn't respect the layered approach of building CellML on top of XML.
2.4.3 2.5  
2.4.4 2.4.2  
2.5.1 3.1  
2.5.2 - Attribute information items with no namespace prefix are no longer placed into the namespace of the parent element, as this doesn't respect the layered approach of building CellML on top of XML.
2.5.3 2.5.3 There is no suggestion that software should alert the user to extension elements they don't recognise, but software is required to ignore extension elements they don't recognise.
3.1 - I
3.2.1 4.2  
3.2.2 5.1  
3.2.3 6.1  
3.2.4 7.1, 8, 9  
3.4.1 4.2  
3.4.2.1 5.1.2  
3.4.2.2 5.1.1 In the draft, components also cannot have the same name as any import component.
3.4.2.3 14.1.2  
3.4.2.4 - Unnecessary, 1.2 treats import components as different types of element to normal components, and 14.1.2 relates exclusively to import components.
3.4.3 6.1 It is unnecessary to explicitly mention RDF due to 2.8
3.4.4 7.1  
 3.4.5 8.1
 
3.4.6.1-3
9.1
 
3.4.6.4
18.4.11
  
3.5.1 18.10.4
Performing units conversions at connections is mandatory in the draft
4.1
-
I
4.2.1
2.4.5 Mostly I
4.2.2 5.1.2.b
  
4.2.3 -
The draft has no concept of a CellML Subset
4.2.4
18.10.1
The draft makes it clear the CellML is declarative, rather than saying how not to solve it
 4.2.5 18.10.1
Partly I
4.2.6
18.7, 18.10.5
 
4.2.7 -
I - The draft does not speculate about the inclusion of scripts.
4.3 -
 I
4.4.1 5.1.2.b
 No reaction roles in the draft
4.4.2 18.10.3
Partly I
4.4.3
18.10.5
 Units attributes can also refer to imported units in the draft.
4.4.4 -
The concept of modifying variables is poorly conceived in a declarative language.
4.5.1
18.10.1
 The draft makes it clear the CellML is declarative, rather than saying how not to solve it
4.5.2 18.10.3
 
4.5.3 - I; This is repeating part of the MathML Specification
5.1 - I
5.2.1 18.5.4.d  
5.2.2 18.5-18.6  
5.2.3 18.6.2  
5.2.4 - I
5.2.5 - I
5.2.6 - I
5.2.7 - I
5.3 - I
5.4.1.1 15.1, 16.1  
5.4.1.2 15.1.1, 16.1.1  
5.4.1.3-4 16.1.2  
5.4.2 15.1.2  
5.4.3.1 17.1.2  
5.4.3.2 17.1.1  
5.4.3.3 17.1.2.a  
5.4.3.4 17.1.2.d  
5.4.3.5 17.1.2.c  
5.4.3.6-7 17.1.2.b In the draft, numbers are compared by what they represent and not the underlying string
5.5.1 18.5  
5.5.2 - I (not needed to define CellML itself)
6.1 - I
6.2.1 10.1  
6.2.2 18.4.7-8  
6.2.3 - Containment is allowed as a relationship type but not defined in this draft version - whether to keep containment at all needs further discussion
6.2.4 - Not included as a consequence of the above
6.2.5 18.3 name not defined for now - there is a proposal to only support encapsulation grouping
6.3 - I
6.4.1 10.1  
6.4.2 12.1 Name attribute not currently defined in draft
6.4.3 11.1  
6.5.1-3 - These are constraints on user-defined groups, for which there is a proposal to drop
7 - Reactions are not defined in the draft specification
8 - Mostly I; RDF is allowed due to 2.8, but the interpretation is not defined in the core specification
8.5.1 2.6.1  
9.1 - I
9.2 13.1  
9.3 - I
9.4.1 13.1  
9.5.1 18.9.1 Note that models, not units, become a new instance in the draft
9.5.2 18.9.1-2 Note that models, not components, become a new instance in the draft
A - I
B - Scripting not defined in the draft
C.1 - I
C.2.1 18.6.1-2 The draft achieves the same effect as C.2.1 by distinguishing units elements from units
C.2.2 - Definition not used directly in the draft
C.3.1,C.3.4 18.6.3  
C.3.2-3 - This could be specified in a secondary specification
C.3.5 18.10.4  
C.3.6 - I
C.4 - I
D - I