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 |