Transforming XML file: NeuroMLFiles/Schemata/v1.8.1/Level2/Biophysics_v1.8.1.xsd
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NeuroMLFiles/Schemata/XSD_Readable.xsl
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Converting the file: Biophysics_v1.8.1.xsd
Note: this representation of the contents of the XSD file is intended as a quick reference only.
** The original *.xsd file should be consulted if there
is any doubt regarding data types **
There is also the option to view this file in Relax NG format.
Note this representation is for
reference only (for those who prefer that format). The XSD should be used for final validation.
Conversion of an XSD file into human readable form
| Description |
| Description of the Schema taken from the XSD file |
| Definition of the elements needed for specifying the biophysical properties of cells.
These elements are linked with those in MorphML.xsd and from the ChannelML spec by
the NeuroML.xsd file |
|
Schema info
Information on the namespaces, etc.
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| targetNamespace | http://morphml.org/biophysics/schema |
| elementFormDefault | qualified |
| attributeFormDefault | unqualified |
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Imported Schemas
Other schemas used by this file, with different target namespaces
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| Namespace: http://morphml.org/metadata/schema | Location: ../Level1/Metadata_v1.8.1.xsd |
Elements
| Element: biophysics |
| The root element. All other complex/simple elements will be children of this. |
| Type: Biophysics |
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Simple Types
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Simple Type: MechanismType
Specifies the type of cellular mechanism. Note could be used for any type of electrophysiological
property of a section of a cell
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| Restriction: | Base:
xs:string
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| Allowed values: |
| Channel Mechanism |
(Voltage and/or conductance dependent membrane conductance)
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| Ion Concentration |
(Mechanism which alters the oncentration of a specific ion)
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MechanismType used by:
Mechanism (xs:complexType)
Instances of this element which are used by other elements in this document
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Simple Type: SynapticDelayValue
Units of a delay associated with a synaptic connection
Units in SI: s
Typical value: 0.005 s
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| Restriction: | Base:
xs:double
Minimum value inclusive: 0 |
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Simple Type: TimeConstantValue
Units of any time constant, greater than zero
Units in SI: s
Typical value: 0.005 s
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| Restriction: | Base:
xs:double
Minimum value exclusive: 0 |
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Simple Type: InvTimeConstantValue
Units of the inverse of a time constant
Units in SI: s-1
Typical value: 100 s-1
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| Restriction: | Base:
xs:double
Minimum value inclusive: 0 |
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Simple Type: TimeConstantValueIncZero
Units of any time constant which can have value zero
Units in SI: s
Typical value: 0.005 s
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| Restriction: | Base:
xs:double
Minimum value inclusive: 0 |
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Simple Type: ConductanceDensityValue
Units of conductance density
Units in SI: S m-2
Typical value: 100 S m-2
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| Restriction: | Base:
xs:double
Minimum value inclusive: 0 |
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Complex Types
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Complex Type: Biophysics
Description of biophysical properties of a cell.
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| The following elements must appear in the sequence outlined here.
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| mechanism |
| Definition of placement of a single electrophysiological mechanism (e.g. channel mechanism)
on a group of cables of a cell. Note there should be at least one of these to specify the passive membrane conductance.
Note: elements spec_capacitance, spec_axial_resistance, ion_props etc. should be used in preference to specificCapacitance etc! |
| |
| Only one of the following SUB elements may appear.
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| specificCapacitance | |
| spec_capacitance | |
| Only one of the following SUB elements may appear.
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| specificAxialResistance | |
| spec_axial_resistance | |
| Only one of the following SUB elements may appear.
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| initialMembPotential | |
| init_memb_potential | |
| Only one of the following SUB elements may appear.
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| ionProperties | |
| ion_props | |
| Attributes |
| units |
| Unit system of all quantities. |
| Type:
meta:Units
, Use: required |
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Biophysics used by:
biophysics (xs:element)
Instances of this element which are used by other elements in this document
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Complex Type: Mechanism
Definition of placement of a single electrophysiological mechanism (e.g. channel mechanism)
on a group of cables of a cell
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| The following elements must appear in the sequence outlined here.
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| parameter | |
| variableParameter |
| Note variable_parameter will be the preferred form in v2.0 |
| |
| variable_parameter |
| Note variable_parameter will be the preferred form in v2.0 |
| |
| Attributes |
| name |
| Name of the mechanism. Should refer to a named mechanism in a ChannelML file |
| Type:
xs:string
, Use: required |
| type |
| Specifies the type of cellular mechanism (Channel Mechanism/Ion Concentration). Note could be used for any type of electrophysiological property of a section of a cell |
| Type: MechanismType, Use: required |
| passive_conductance |
| Whether this is a passive/leak conductance. In this case, 2 params, gmax and e should be sufficient to fully specify the
mechanism, independent of any implementation. Useful e.g. for mapping to and from inbuilt mechanisms in simulators (e.g. pas in NEURON, Em/Rm in GENESIS).
NOTE: this attribute will be required in v2.0!! Don't use passiveConductance anymore.
Changed for consistency with ChannelML and NetworkML naming conventions. |
| Type:
xs:boolean
, Use: optional, default: false |
| passiveConductance |
| Whether this is a passive/leak conductance. NOTE: this attribute will be removed in v2.0!! Use passive_conductance instead.
Changed for consistency with ChannelML and NetworkML naming conventions. |
| Type:
xs:boolean
, Use: optional, default: false |
|
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Mechanism used by:
Biophysics (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: SpecCapacitance
Capacitance per unit area of a group of sections
Units in SI: F/m2
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| The following elements must appear in the sequence outlined here.
|
| parameter | |
| variableParameter |
| Note variable_parameter will be the preferred form in v2.0 |
| |
| variable_parameter |
| Note variable_parameter will be the preferred form in v2.0 |
| |
|
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SpecCapacitance used by:
Biophysics (xs:complexType)
Biophysics (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: SpecAxialResistance
Specific axial resistance of a group of sections
Units in SI: ohm m
|
| The following elements must appear in the sequence outlined here.
|
| parameter | |
| variableParameter |
| Note variable_parameter will be the preferred form in v2.0 |
| |
| variable_parameter |
| Note variable_parameter will be the preferred form in v2.0 |
| |
|
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SpecAxialResistance used by:
Biophysics (xs:complexType)
Biophysics (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: InitialMembPotential
This quantity is often required for computational simulations and specifies the potential
difference across the membrane at the start of the simulation. This is an optional field
Units in SI: V
|
| The following elements must appear in the sequence outlined here.
|
| parameter | |
| variableParameter | |
|
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InitialMembPotential used by:
Biophysics (xs:complexType)
Biophysics (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: IonProperties
Some properties accociated with an ion type which takes part in the mechanisms on the cell
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| The following elements must appear in the sequence outlined here.
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| parameter | |
| Attributes |
| name | Type:
xs:string
, Use: required |
|
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IonProperties used by:
Biophysics (xs:complexType)
Biophysics (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: NamedParameter
Definition of a value for a quantity and the associated groups of cables
which have this value. Can have any name, but gmax and e are special...
|
| The following elements must appear in the sequence outlined here.
|
| group | |
| Attributes |
| name |
| 2 names have special meaning: gmax for the maximum conductance density, and e for the reversal potential of a passive channel |
| Type:
xs:string
, Use: required |
| value | Type:
xs:double
, Use: required |
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NamedParameter used by:
Mechanism (xs:complexType)
IonProperties (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: VariableNamedParameter
Definition of a value for a quantity which varies over a given group of cables
|
| The following elements must appear in the sequence outlined here.
|
| group | |
| inhomogeneous_value | |
| Attributes |
| name | Type:
xs:string
, Use: required |
|
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VariableNamedParameter used by:
Mechanism (xs:complexType)
Mechanism (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: InhomogeneousValue
How a value changes over the cable group. Implementation here based on NEURON inhomogeneous parameter specification.
See example for usage of this element
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| Attributes |
| param_name |
| Name used in the inhomogeneous_param element in the cable group |
| Type:
xs:string
, Use: required |
| value |
| Equation showing how parameter changes as function of variable attribute in inhomogeneous_param element |
| Type:
xs:string
, Use: required |
|
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InhomogeneousValue used by:
VariableParameter (xs:complexType)
VariableNamedParameter (xs:complexType)
Instances of this element which are used by other elements in this document
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Complex Type: UnnamedParameter
Definition of a value for a quantity and the associated groups of cables
which have this value. The quantity referred to will be clear from the usage, e.g. InitialMembPotential
|
| The following elements must appear in the sequence outlined here.
|
| group | |
| Attributes |
| value | Type:
xs:double
, Use: required |
|
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UnnamedParameter used by:
SpecCapacitance (xs:complexType)
SpecAxialResistance (xs:complexType)
InitialMembPotential (xs:complexType)
Instances of this element which are used by other elements in this document
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