General Elements¶
Document Layout¶
NineML documents must be enclosed within an NineML element, which should be in the ’http://nineml.net/9ML/1.0’ XML namespace.
NineML¶
| Attribute | Type/Format | Required |
|---|---|---|
| xmlns | ‘http://nineml.net/9ML/1.0’ | yes |
| Children | Multiplicity | Required |
|---|---|---|
| Component | set | no |
| ComponentClass | set | no |
| Unit | set | no |
| Dimension | set | no |
| Population | set | no |
| Projection | set | no |
| Selection | set | no |
Seven document-level elements are allowed to reside directly within NineML elements: Component, ComponentClass, Unit, Dimension, Population, Projection and Selection. Each element should be uniquely identified by its name attribute within the scope of the document (see ).
Unit and Dimension elements must be defined within the document they are referenced, whereas the remaining element types can also be referenced from other NineML documents (see Reference and Definition).
Xmlns attribute¶
The xmlns attribute is required and should refer to the URLcorresponding to the correct NineML version, which for version 1.0 is ‘http://nineml.net/9ML/1.0’ (see http://www.w3.org/TR/REC-xml-names/).
Units and Dimensions¶
Dimensions are associated with parameters, analog ports and state variables in component class definitions. Each dimension can give rise to a family of unit declarations, each of which has the same dimensionality but a different multiplier. For example, typical units for a quantity with dimensionality voltage include millivolts (multiplier = \(10^{-3}\)), microvolts (multiplier = \(10^{-6}\)) and volts (multiplier = 1). To express a dimensional quantity both a numerical factor and a unit are required.
Except where physical constants are required, abstraction layer definitions generally only contain references to dimensions and are independent of any particular choice of units. Conversely, the user layer only refers to units. Internally, dimensional quantities are to be understood as rich types with a numerical factor and exponents for each of the base dimensions. They are independent of the particular choice of units by which they are assigned.
Note
The format for units and dimensions is the same as is used for LEMS/NeuroML v2.0 (http://www.neuroml.org) [Cannon2014].
Dimension¶
| Attribute | Type/Format | Required |
|---|---|---|
| name | identifier | yes |
| m | integer |
no |
| l | integer |
no |
| t | integer |
no |
| i | integer |
no |
| n | integer |
no |
| k | integer |
no |
| j | integer |
no |
Dimension objects are constructed values from the powers for each of the seven SI base units: length (l), mass (m), time (t), electric current (i), temperature (k), luminous intensity (l) and amount of substance (n). For example, acceleration has dimension \(lt^{-2}\) and voltage is \(ml^2t^3i^{-1}\). Dimension objects must be declared in the top-level scope of the NineML document where they are referenced.
Name attribute¶
Each Dimension requires a name attribute, which should be a valid and uniquely identify the Dimension in current the scope.
M attribute¶
The m attribute specifies the power of the mass dimension in the Dimension. If omitted the power is zero.
L attribute¶
The l attribute specifies the power of the length dimension in the Dimension. If omitted the power is zero.
T attribute¶
The t attribute specifies the power of the time dimension in the Dimension. If omitted the power is zero.
I attribute¶
The i attribute specifies the power of the current dimension in the Dimension. If omitted the power is zero.
N attribute¶
The n attribute specifies the power of the amount-of-substance dimension in the Dimension. If omitted the power is zero.
Unit¶
| Attribute | Type/Format | Required |
|---|---|---|
| symbol | string |
yes |
| dimension | Dimension.name | yes |
| power | integer |
no |
| offset | integer |
no |
Unit objects specify the dimension multiplier and the offset of a unit with respect to a defined Dimension object. Unit objects must be declared in the top-level scope of the NineML documents where they are referenced.
Symbol attribute¶
Each Unit requires a symbol attribute, which should be a valid and uniquely identify the Unit in current the scope.
Dimension attribute¶
Each Unit requires a dimension attribute. This attribute specifies the dimension of the units and should refer to the name of a Dimension element in the document scope.
Annotating Elements¶
Annotations are provided to add semantic information about the model, preserving structure that is lost during conversion from an extended format to core NineML, and provide suggestions for the simulation of the model. It is highly recommended to add references to all publications on which the model or property values are based in the annotations. For adding semantic structure to the model it is recommended to use the Resource Description Framework (RDF) although it is not a strict requirement.
In order to be compliant with the NineML specification any tool handling NineML descriptions must preserve all existing annotations, except where a user explicitly edits/deletes them. In future versions of this section will be expanded to include suggested formats for commonly used annotations.
Annotations¶
| Children | Multiplicity | Required |
|---|---|---|
| * | set | no |
The Annotations element is the top-level of the annotations attached to a NineML element. They can be included within any NineML element (User Layer and Abstraction Layer) and any valid XML is allowed within them.
| [Cannon2014] | Cannon, R.~C., Gleeson, P., Crook, S., Ganapathy, G., Marin, B., Piasini, E., and Silver, R.~A. (2014). LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Frontiers in neuroinformatics, 8(September):79. |