Transforming XML file: NeuroMLFiles/Schemata/v1.6/Level2/Biophysics_v1.6.xsd
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NeuroMLFiles/Schemata/XSDtoRNG.xsl
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Converting the file: Biophysics_v1.6.xsd
<?xml version="1.0" encoding="UTF-8"?>
<rng:grammar xmlns:a="http://relaxng.org/ns/compatibility/annotations/1.0" xmlns:rng="http://relaxng.org/ns/structure/1.0" xmlns="http://morphml.org/biophysics/schema" xmlns:meta="http://morphml.org/metadata/schema" ns="http://morphml.org/biophysics/schema" datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes">
<!--
This file specifies a number of elements needed by NeuroML v1.6 Level 2 compliant files
This file has been developed as part of the neuroConstruct and NeuroML initiatives
Funding for this work has been received from the Medical Research Council
Author: Padraig Gleeson
-->
<rng:include href="../Level1/Metadata_v1.6.rng" ns="http://morphml.org/metadata/schema"/>
<a:documentation>
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
</a:documentation>
<rng:start combine="choice">
<rng:ref name="biophysics"/>
</rng:start>
<rng:define combine="choice" name="biophysics">
<rng:element name="biophysics">
<rng:ref name="Biophysics"/>
<a:documentation>
The root element. All other complex/simple elements will be children of this.
</a:documentation>
</rng:element>
</rng:define>
<rng:define combine="choice" name="Biophysics">
<a:documentation>
Description of biophysical properties of a cell.
</a:documentation>
<rng:oneOrMore>
<rng:element name="mechanism">
<rng:ref name="Mechanism"/>
</rng:element>
</rng:oneOrMore>
<rng:element name="specificCapacitance">
<rng:ref name="SpecCapacitance"/>
</rng:element>
<rng:element name="specificAxialResistance">
<rng:ref name="SpecAxialResistance"/>
</rng:element>
<rng:optional>
<rng:element name="initialMembPotential">
<rng:ref name="InitialMembPotential"/>
</rng:element>
</rng:optional>
<rng:optional>
<rng:element name="ionProperties">
<rng:ref name="IonProperties"/>
</rng:element>
</rng:optional>
<rng:attribute name="units">
<rng:ref name="Units"/>
<a:documentation>
Unit system of all quantities.
</a:documentation>
</rng:attribute>
</rng:define>
<rng:define combine="choice" name="Mechanism">
<a:documentation>
Definition of placement of a single electrophysiological mechanism (e.g. channel mechanism)
on a group of cables of a cell
</a:documentation>
<rng:zeroOrMore>
<rng:element name="parameter">
<rng:ref name="NamedParameter"/>
</rng:element>
</rng:zeroOrMore>
<rng:zeroOrMore>
<rng:element name="variableParameter">
<rng:ref name="VariableNamedParameter"/>
</rng:element>
</rng:zeroOrMore>
<rng:attribute name="name">
<rng:data type="string"/>
</rng:attribute>
<rng:attribute name="type">
<rng:ref name="MechanismType"/>
</rng:attribute>
</rng:define>
<rng:define combine="choice" name="SpecCapacitance">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">F/m2</meta:units>
Capacitance per unit area of a group of sections
</a:documentation>
<rng:zeroOrMore>
<rng:element name="parameter">
<rng:ref name="UnnamedParameter"/>
</rng:element>
</rng:zeroOrMore>
<rng:zeroOrMore>
<rng:element name="variableParameter">
<rng:ref name="VariableParameter"/>
</rng:element>
</rng:zeroOrMore>
</rng:define>
<rng:define combine="choice" name="SpecAxialResistance">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">ohm m</meta:units>
Specific axial resistance of a group of sections
</a:documentation>
<rng:zeroOrMore>
<rng:element name="parameter">
<rng:ref name="UnnamedParameter"/>
</rng:element>
</rng:zeroOrMore>
<rng:zeroOrMore>
<rng:element name="variableParameter">
<rng:ref name="VariableParameter"/>
</rng:element>
</rng:zeroOrMore>
</rng:define>
<rng:define combine="choice" name="InitialMembPotential">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">V</meta:units>
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
</a:documentation>
<rng:zeroOrMore>
<rng:element name="parameter">
<rng:ref name="UnnamedParameter"/>
</rng:element>
</rng:zeroOrMore>
<rng:zeroOrMore>
<rng:element name="variableParameter">
<rng:ref name="VariableParameter"/>
</rng:element>
</rng:zeroOrMore>
</rng:define>
<rng:define combine="choice" name="IonProperties">
<a:documentation>
Some properties accociated with an ion type which takes part in the mechanisms on the cell
</a:documentation>
<rng:zeroOrMore>
<rng:element name="parameter">
<rng:ref name="NamedParameter"/>
</rng:element>
</rng:zeroOrMore>
<rng:attribute name="name">
<rng:data type="string"/>
</rng:attribute>
</rng:define>
<rng:define combine="choice" name="NamedParameter">
<a:documentation>
Definition of a value for a quantity and the associated groups of cables
which have this value
</a:documentation>
<rng:oneOrMore>
<rng:element name="group">
<rng:data type="string"/>
</rng:element>
</rng:oneOrMore>
<rng:attribute name="name">
<rng:data type="string"/>
</rng:attribute>
<rng:attribute name="value">
<rng:data type="double"/>
</rng:attribute>
</rng:define>
<rng:define combine="choice" name="VariableParameter">
<a:documentation>
Definition of a value for a quantity which varies over a given group of cables
</a:documentation>
<rng:oneOrMore>
<rng:element name="group">
<rng:data type="string"/>
</rng:element>
</rng:oneOrMore>
<rng:oneOrMore>
<rng:element name="inhomogeneous_value">
<rng:ref name="InhomogeneousValue"/>
</rng:element>
</rng:oneOrMore>
<rng:attribute name="name">
<rng:data type="string"/>
</rng:attribute>
</rng:define>
<rng:define combine="choice" name="VariableNamedParameter">
<a:documentation>
Definition of a value for a quantity which varies over a given group of cables
</a:documentation>
<rng:oneOrMore>
<rng:element name="group">
<rng:data type="string"/>
</rng:element>
</rng:oneOrMore>
<rng:oneOrMore>
<rng:element name="inhomogeneous_value">
<rng:ref name="InhomogeneousValue"/>
</rng:element>
</rng:oneOrMore>
<rng:attribute name="name">
<rng:data type="string"/>
</rng:attribute>
</rng:define>
<rng:define combine="choice" name="InhomogeneousValue">
<a:documentation>
How a value changes over the cable group. Implementation here based on NEURON inhomogeneous parameter specification.
See example for usage of this element
</a:documentation>
<rng:attribute name="param_name">
<rng:data type="string">
<a:documentation>
Name used in the inhomogeneous_param element in the cable group
</a:documentation>
</rng:data>
</rng:attribute>
<rng:attribute name="value">
<rng:data type="string">
<a:documentation>
Equation showing how parameter changes as function of variable attribute in inhomogeneous_param element
</a:documentation>
</rng:data>
</rng:attribute>
</rng:define>
<!--
<xs:complexType name="IonParameter">
<xs:annotation>
<xs:documentation>NamedParameter restricted to params for ions</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:restriction base="NamedParameter">
<xs:sequence>
<xs:element name="group">
<xs:restriction base="xs:string">
<xs:enumeration value="yes"/>
<xs:enumeration value="no"/>
</xs:restriction>
</xs:element>
</xs:sequence>
<xs:attribute name="name" type="xs:string" use="required"/>
<xs:attribute name="value" type="xs:double" use="required"/>
</xs:restriction>
</xs:complexContent>
</xs:complexType> -->
<rng:define combine="choice" name="UnnamedParameter">
<a:documentation>
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
</a:documentation>
<rng:oneOrMore>
<rng:element name="group">
<rng:data type="string"/>
</rng:element>
</rng:oneOrMore>
<rng:attribute name="value">
<rng:data type="double"/>
</rng:attribute>
</rng:define>
<!-- Definition of MechanismType follows. -->
<rng:define combine="choice" name="MechanismType">
<a:documentation>
Specifies the type of cellular mechanism. Note could be used for any type of electrophysiological
property of a section of a cell
</a:documentation>
<rng:choice>
<rng:value>Channel Mechanism</rng:value>
<a:documentation>
Voltage and/or conductance dependent membrane conductance
</a:documentation>
<rng:value>Ion Concentration</rng:value>
<a:documentation>
Mechanism which alters the oncentration of a specific ion
</a:documentation>
</rng:choice>
</rng:define>
<rng:define combine="choice" name="SynapticDelayValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">s</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">0.005</meta:typical_value>
Units of a delay associated with a synaptic connection
</a:documentation>
<rng:data type="double">
<rng:param name="minInclusive">0</rng:param>
</rng:data>
</rng:define>
<rng:define combine="choice" name="TimeConstantValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">s</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">0.005</meta:typical_value>
Units of any time constant
</a:documentation>
<rng:data type="double">
<rng:param name="minExclusive">0</rng:param>
</rng:data>
</rng:define>
<rng:define combine="choice" name="TimeValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">s</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">0.005</meta:typical_value>
Units of any time value, zero or greater
</a:documentation>
<rng:data type="double">
<rng:param name="minInclusive">0</rng:param>
</rng:data>
</rng:define>
<rng:define combine="choice" name="FrequencyValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">Hz</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">50</meta:typical_value>
Units of any frequency, zero or greater
</a:documentation>
<rng:data type="double">
<rng:param name="minInclusive">0</rng:param>
</rng:data>
</rng:define>
<rng:define combine="choice" name="ConductanceValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">S</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">1e-8</meta:typical_value>
Units of conductance
</a:documentation>
<rng:data type="double">
<rng:param name="minInclusive">0</rng:param>
</rng:data>
</rng:define>
<rng:define combine="choice" name="ConductanceDensityValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">S m-2</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">100</meta:typical_value>
Units of conductance density
</a:documentation>
<rng:data type="double">
<rng:param name="minInclusive">0</rng:param>
</rng:data>
</rng:define>
<rng:define combine="choice" name="LengthValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">m</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">1e-6</meta:typical_value>
Units of length
</a:documentation>
<rng:data type="double">
</rng:data>
</rng:define>
<rng:define combine="choice" name="CurrentValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">A</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">1e-11</meta:typical_value>
Units of current
</a:documentation>
<rng:data type="double">
</rng:data>
</rng:define>
<rng:define combine="choice" name="ConcentrationValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">mM</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">1e-5</meta:typical_value>
Units of concentration
</a:documentation>
<rng:data type="double">
<rng:param name="minInclusive">0</rng:param>
</rng:data>
</rng:define>
<rng:define combine="choice" name="VoltageValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">V</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">-0.07</meta:typical_value>
Units of voltage
</a:documentation>
<rng:data type="double"/>
</rng:define>
<rng:define combine="choice" name="TemperatureValue">
<a:documentation>
<meta:units xmlns:xs="http://www.w3.org/2001/XMLSchema">deg C</meta:units>
<meta:typical_value xmlns:xs="http://www.w3.org/2001/XMLSchema">32</meta:typical_value>
Units of temperature
</a:documentation>
<rng:data type="double">
<rng:param name="minExclusive">0</rng:param>
</rng:data>
</rng:define>
</rng:grammar>
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