<?xml version="1.0" encoding="UTF-8"?>

<xs:schema targetNamespace="http://morphml.org/biophysics/schema"
    xmlns:xs="http://www.w3.org/2001/XMLSchema"
    xmlns="http://morphml.org/biophysics/schema"
    xmlns:meta="http://morphml.org/metadata/schema"
elementFormDefault="qualified" attributeFormDefault="unqualified">
    
<!--
    This file specifies a number of elements needed by NeuroML v1.4 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
    
-->
      <xs:annotation>
        <xs: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</xs:documentation>
         </xs:annotation>

    <xs:element name="biophysics" type="Biophysics">
        <xs:annotation>
            <xs:documentation>The root element. All other complex/simple elements will be children of this.</xs:documentation>
        </xs:annotation>
    </xs:element>
        
    <xs:complexType name="Biophysics">
        <xs:annotation>
            <xs:documentation>Description of biophysical properties of a cell.</xs:documentation>
        </xs:annotation>
        <xs:sequence>
            <xs:element name="mechanism" type="Mechanism" minOccurs="1" maxOccurs="unbounded"/>
            <xs:element name="specificCapacitance" type="SpecCapacitance"/>
            <xs:element name="specificAxialResistance" type="SpecAxialResistance"/>
            <xs:element name="initialMembPotential" type="InitialMembPotential" minOccurs="0"/>
            <xs:element name="ionProperties" type="IonProperties" minOccurs="0"/>
        </xs:sequence>
                
                 <xs:attribute name="units" type="Units" use="required">
                    <xs:annotation>
                        <xs:documentation>Unit system of all quantities.</xs:documentation>
                    </xs:annotation>
                </xs:attribute>  
    </xs:complexType>
        
          
        
        
        
         <xs:complexType name="Mechanism">
        <xs:annotation>
            <xs:documentation>Definition of placement of a single electrophysiological mechanism (e.g. channel mechanism)
                        on a group of cables of a cell</xs:documentation>
        </xs:annotation>
        <xs:sequence>
            <xs:element name="parameter" type="NamedParameter" minOccurs="0" maxOccurs="unbounded"/>
            <xs:element name="variableParameter" type="VariableNamedParameter" minOccurs="0" maxOccurs="unbounded"/>
        </xs:sequence>
        <xs:attribute name="name" type="xs:string" use="required"/>
        <xs:attribute name="type" type="MechanismType" use="required"/>
    </xs:complexType>  
        
        
        
         <xs:complexType name="SpecCapacitance">
        <xs:annotation>
                    <xs:appinfo>
                        <meta:units>F/m2</meta:units>
                    </xs:appinfo>
                    <xs:documentation>Capacitance per unit area of a group of sections</xs:documentation>
        </xs:annotation>
        <xs:sequence>
            <xs:element name="parameter" type="UnnamedParameter" minOccurs="0" maxOccurs="unbounded"/>
            <xs:element name="variableParameter" type="VariableParameter" minOccurs="0" maxOccurs="unbounded"/>
        </xs:sequence>
    </xs:complexType>  
        
        
         <xs:complexType name="SpecAxialResistance">
        <xs:annotation>
                    <xs:appinfo>
                        <meta:units>ohm m</meta:units>
                    </xs:appinfo>
            <xs:documentation>Specific axial resistance of a group of sections</xs:documentation>
        </xs:annotation>
        <xs:sequence>
            <xs:element name="parameter" type="UnnamedParameter" minOccurs="0" maxOccurs="unbounded"/>
            <xs:element name="variableParameter" type="VariableParameter" minOccurs="0" maxOccurs="unbounded"/>
        </xs:sequence>
    </xs:complexType>  
        
        
         <xs:complexType name="InitialMembPotential">
        <xs:annotation>
                    <xs:appinfo>
                        <meta:units>V</meta:units>
                    </xs:appinfo>
            <xs:documentation>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</xs:documentation>
        </xs:annotation>
        <xs:sequence>
            <xs:element name="parameter" type="UnnamedParameter" minOccurs="0" maxOccurs="unbounded"/>
            <xs:element name="variableParameter" type="VariableParameter" minOccurs="0" maxOccurs="unbounded"/>
        </xs:sequence>
    </xs:complexType>  
        
        
        
         <xs:complexType name="IonProperties">
        <xs:annotation>
            <xs:documentation>Some properties accociated with an ion type which takes part in the mechanisms on the cell</xs:documentation>
        </xs:annotation>
        <xs:sequence>
            <xs:element name="parameter" type="NamedParameter" minOccurs="0" maxOccurs="unbounded"/>
        </xs:sequence>
        <xs:attribute name="name" type="xs:string" use="required"/>
    </xs:complexType>  
        
        
        
         <xs:complexType name="NamedParameter">
        <xs:annotation>
            <xs:documentation>Definition of a value for a quantity and the associated groups of cables
                        which have this value</xs:documentation>
        </xs:annotation>
        <xs:sequence>
                            <xs:element name="group" type="xs:string" maxOccurs="unbounded"/>
        </xs:sequence>
        <xs:attribute name="name" type="xs:string" use="required"/>
        <xs:attribute name="value" type="xs:double" use="required"/>
    </xs:complexType>  
        
         <xs:complexType name="VariableParameter">
        <xs:annotation>
            <xs:documentation>Definition of a value for a quantity which varies over a given group of cables</xs:documentation>
        </xs:annotation>
        <xs:sequence>
                            <xs:element name="group" type="xs:string" maxOccurs="unbounded"/>
                            <xs:element name="inhomogeneous_value" maxOccurs="unbounded"/>
        </xs:sequence>
        <xs:attribute name="name" type="xs:string"/>
    </xs:complexType>  
        
         <xs:complexType name="VariableNamedParameter">
        <xs:annotation>
            <xs:documentation>Definition of a value for a quantity which varies over a given group of cables</xs:documentation>
        </xs:annotation>
        <xs:sequence>
                            <xs:element name="group" type="xs:string" maxOccurs="unbounded"/>
                            <xs:element name="inhomogeneous_value" type="InhomogeneousValue" maxOccurs="unbounded"/>
        </xs:sequence>
        <xs:attribute name="name" type="xs:string" use="required"/>
    </xs:complexType>  
        
        
         <xs:complexType name="InhomogeneousValue">
        <xs:annotation>
            <xs:documentation>How a value changes over the cable group</xs:documentation>
        </xs:annotation>
        <xs:attribute name="param_name" type="xs:string" use="required">
                    <xs:annotation>
                        <xs:documentation>Name used in the inhomogeneous_param element in the cable group</xs:documentation>
                    </xs:annotation>
        </xs:attribute>
        <xs:attribute name="value" type="xs:string" use="required">
                    <xs:annotation>
                        <xs:documentation>Equation showing how parameter changes as function of variable attribute in inhomogeneous_param element</xs:documentation>
                    </xs:annotation>
        </xs:attribute>
                
    </xs:complexType>        
        
        <!--
         <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> -->
        
        
        
         <xs:complexType name="UnnamedParameter">
        <xs:annotation>
            <xs: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</xs:documentation>
        </xs:annotation>

        <xs:sequence>
            <xs:element name="group" type="xs:string" maxOccurs="unbounded"/>
        </xs:sequence>
        <xs:attribute name="value" type="xs:double" use="required"/>
    </xs:complexType>  
    
    
          <!-- Definition of MechanismType follows. -->
        <xs:simpleType name="MechanismType">
            <xs:annotation>
                <xs:documentation>Specifies the type of cellular mechanism. Note could be used for any type of electrophysiological
                property of a section of a cell</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:string">
                <xs:enumeration value="Channel Mechanism">
                    <xs:annotation>
                        <xs:documentation>Voltage and/or conductance dependent membrane conductance</xs:documentation>
                    </xs:annotation>
                </xs:enumeration>
                <xs:enumeration value="Ion Concentration">
                    <xs:annotation>
                        <xs:documentation>Mechanism which alters the oncentration of a specific ion</xs:documentation>
                    </xs:annotation>
                </xs:enumeration>
                <!--
                <xs:enumeration value="Potential Synaptic Connection Location">
                    <xs:annotation>
                        <xs:documentation>Specifies that a synapse of the named type is allowed on this section</xs:documentation>
                    </xs:annotation>
                </xs:enumeration>
                <xs:enumeration value="Specific Axial Resistance">
                    <xs:annotation>
                        <xs:documentation>Spec Axial resistance of the section</xs:documentation>
                    </xs:annotation>
                </xs:enumeration>
                <xs:enumeration value="Specific Capacitance">
                    <xs:annotation>
                        <xs:documentation>Spec Capacitance of membrane</xs:documentation>
                    </xs:annotation>
                </xs:enumeration>
                <xs:enumeration value="Initial Membrane Potential">
                    <xs:annotation>
                        <xs:documentation>Default starting potential for simulations</xs:documentation>
                    </xs:annotation>
                </xs:enumeration>-->
            </xs:restriction>
        </xs:simpleType>
        
        

        <!-- Definition of Units follows. -->
        <xs:simpleType name="Units">
            <xs:annotation>
                <xs:documentation>Enumeration of unit scheme used. Initially only SI or physiological units allowed</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:string">
                <xs:enumeration value="Physiological Units"/>
                <xs:enumeration value="SI Units"/>
            </xs:restriction>
        </xs:simpleType>
        
        
        
        
            

        <xs:simpleType name="SynapticDelayValue">
            <xs:annotation>
                <xs:appinfo>
                    <meta:units>s</meta:units>
                    <meta:typical_value>0.005</meta:typical_value>
                </xs:appinfo>
                <xs:documentation>Units of a delay associated with a synaptic connection</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:double">
                <xs:minInclusive value="0"/>
            </xs:restriction>
        </xs:simpleType>
            

        <xs:simpleType name="TimeConstantValue">
            <xs:annotation>
                <xs:appinfo>
                    <meta:units>s</meta:units>
                    <meta:typical_value>0.005</meta:typical_value>
                </xs:appinfo>
                <xs:documentation>Units of any time constant</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:double">
                <xs:minExclusive value="0"/>
            </xs:restriction>
        </xs:simpleType>


        <xs:simpleType name="ConductanceValue">
            <xs:annotation>
                <xs:appinfo>
                    <meta:units>S</meta:units>
                    <meta:typical_value>1e-8</meta:typical_value>
                </xs:appinfo>
                <xs:documentation>Units of conductance</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:double">
                <xs:minInclusive value="0"/>
            </xs:restriction>
        </xs:simpleType>

        <xs:simpleType name="LengthValue">
            <xs:annotation>
                <xs:appinfo>
                    <meta:units>m</meta:units>
                    <meta:typical_value>1e-6</meta:typical_value>
                </xs:appinfo>
                <xs:documentation>Units of length</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:double">
            </xs:restriction>
        </xs:simpleType>


        <xs:simpleType name="ConcentrationValue">
            <xs:annotation>
                <xs:appinfo>
                    <meta:units>mM</meta:units>
                    <meta:typical_value>1e-5</meta:typical_value>
                </xs:appinfo>
                <xs:documentation>Units of concentration</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:double">
                <xs:minInclusive value="0"/>
            </xs:restriction>
        </xs:simpleType>

        <xs:simpleType name="ReversalPotentialValue">
            <xs:annotation>
                <xs:documentation>Units of reversal potential</xs:documentation>
            </xs:annotation>
            <xs:restriction base="VoltageValue"/>
        </xs:simpleType>

        <xs:simpleType name="VoltageValue">
            <xs:annotation>
                <xs:appinfo>
                    <meta:units>V</meta:units>
                    <meta:typical_value>-0.07</meta:typical_value>
                </xs:appinfo>
                <xs:documentation>Units of voltage</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:double"/>
        </xs:simpleType>

        <xs:simpleType name="TemperatureValue">
            <xs:annotation>
                <xs:appinfo>
                    <meta:units>deg C</meta:units>
                    <meta:typical_value>32</meta:typical_value>
                </xs:appinfo>
                <xs:documentation>Units of temperature</xs:documentation>
            </xs:annotation>
            <xs:restriction base="xs:double">
                <xs:minExclusive value="0"/>
            </xs:restriction>
        </xs:simpleType>
        
</xs:schema>