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SBML Level 3 Core (August 2009 Draft)

Contents

A draft of the SBML Level 3 Version 1 Core specification is now available for downloading. This copy lacks validation rules and XML Schemas, but is otherwise complete. The SBML Editors very much welcome feedback. Please discuss the specification on the sbml-discuss list or by emailing the editors directly.

This page provides a detailed and, we believe, complete summary of the changes in SBML Level 3 Core relative to previous levels of SBML. Although we may discover additional changes need to be made while we implement the changes listed here (for example, we may discover an unforeseen interaction or implication), the changes described here represent our best attempt to list what will change in Level 3 Core. In addition to the specific changes below, a separate page provides descriptions of some of the general principles we tried to follow during the design of Level 3.

This list of changes superedes all other descriptions and in-person discussions of the planned changes for SBML Level 3 Core, as well as in-progress descriptions provided at the SBML Forums and Hackathons in 2007–2009.

Global changes

The following is a list of changes in Level 3 that are global in nature and not limited to one particular component type. (See the next section for changes that are specific to individual SBML components.)

Summary of change Detailed explanation
Attributes and other entities that previously had default values will no longer have default values No default values
Introduction of new primitive types SIdRef and UnitSIdRef New types for id references
All "listOf" lists are optional, not only some ListOf lists are optional
No ordering restrictions on elements within components No ordering restrictions
Clearer interpretation of the notion of a reaction and its generalization to non-biochemical models Generalizing the concept of reactions
New global unit definition for reaction extent Modifications to the unit system
New base unit avogadro Modifications to the unit system
New MathML csymbol for Avogadro's number Modifications to the unit system
Replacement of "built-in" unit symbols such as substance by different scheme Modifications to the unit system
Allowing a new attribute units on MathML cn elements Units attribute on MathML cn elements
Allowing MIRIAM history annotations on any element History annotations allowed anywhere

Changes to specific SBML components

The following is a list of changes in Level 3 that are specific to particular components. (See the section above for changes that are more global to SBML Level 3.)

Summary of change Detailed explanation
The charge attribute on Species will be removed No charge attribute
The outside attribute on Compartment will be removed No outside attribute
Restrictions on Compartment sizes will be removed No restrictions on Compartment's spatialDimensions values
Restrictions on Unit exponent values will be removed No restrictions on Unit's exponent values
SpeciesType and CompartmentType will be removed Removal of CompartmentType and SpeciesType
New construct on the <sbml> element for Level 3 package inclusion Package mechanism
New attribute for conversion factor on Species Changes to Species
New attributes for global units on Model Changes to Model
New attribute for global conversion factor on Model Changes to Model
Access to SpeciesReference's stoichiometry attribute and removal of StoichiometryMath Changes to Reaction
New object type for local parameters in reactions Changes to Reaction
Addition of optional compartment attribute to Reaction Changes to Reaction

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