See: http://www.oasis-open.org/cover/sgml-xml.html

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B. XML Schema for SBML

The following is a first draft of an XML Schema definition for the Systems Biology Markup Language.
Example applications of this XML Schema are presented in Appendix A.

The schema below is well-formed and compiles with the XML Schema standard. However,the use of unique
and keyref elements in this schema has not been fully validated. The other elements have been fully
validated. In practice, the unique and keyref elements may either need to be commented out or will be
ignored, because they are not supported by most XML parsers.

<?xml version="1.0"encoding="UTF-8"?>
<!DOCTYPE xsd:schema PUBLIC "-//W3C//DTD XMLSCHEMA 19991216//EN"""[
<!ENTITY %p 'xsd:'>
<!ENTITY %s ':xsd '>]>
<xsd:schema xmlns:xsd="http://www.w3.org/1999/XMLSchema">
<xsd:annotation>
<xsd:documentation>
File name :sbml.xsd
Description :XML Schema for the Systems Biology Markup Language
Organization:Caltech ERATO Kitano
Version :1
Modified :2000-09-12 10:58 PDT
</xsd:documentation>
</xsd:annotation>
<!--Name -->
<xsd:simpleType base="xsd:string"name="Name">
<xsd:pattern value="(_|[a-z ]|[A-Z ])(_|[a-z ]|[A-Z ]|[0-9 ])*"/>
</xsd:simpleType>
<!--Identifed -->
<xsd:complexType name="Identified"abstract="true">
<xsd:element name="notes"maxOccurs="1"minOccurs="0">
<xsd:complexType>
<xsd:any namespace="http://www.w3.org/1999/xhtml"
maxOccurs="unbounded"minOccurs="1"processContents="skip"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="annotation"maxOccurs="1"minOccurs="0">
<xsd:complexType>
<xsd:any maxOccurs="*"minOccurs="1"processContents="skip"/>
</xsd:complexType>
</xsd:element>
<xsd:attribute name="id"type="xsd:ID"use="optional"/>
<xsd:attribute name="simpleNotes"type="xsd:string"use="optional"/>
</xsd:complexType>
<!--listOfParameters -->
<xsd:element name="listOfParameters">
<xsd:complexType>
<xsd:element name="parameter"type="Parameter"minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<!--listOfUnits-->
<xsd:element name="listOfUnits">
<xsd:complexType>
<xsd:element name="unit"type="Unit"minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<!--specieReference -->
<xsd:element name="specieReference"type="SpecieReference"
minOccurs="1"maxOccurs="unbounded"/>
<!--Model -->
<xsd:complexType name="Model"base="Identified"derivedBy="extension">
<xsd:element name="listOfCompartments"minOccurs="1"maxOccurs="1">
<xsd:complexType>
<xsd:element name="compartment"type="Compartment"
minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="listOfGeometries"minOccurs="0"maxOccurs="1">
<xsd:complexType>
<xsd:element name="geometry"type="Geometry"
minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="listOfMappings"minOccurs="0"maxOccurs="1">
<xsd:complexType>
<xsd:element name="mapping"type="Mapping"
minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="listOfSpecies"minOccurs="1"maxOccurs="1">
<xsd:complexType>
<xsd:element name="specie"type="Specie"
minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="listOfParameters"minOccurs="0"maxOccurs="1"/>
<xsd:element name="listOfRules"minOccurs="0"maxOccurs="1">
<xsd:complexType>
<xsd:choice maxOccurs="unbounded"minOccurs="1">
<xsd:element name="compartmentRule"type="CompartmentRule"
minOccurs="0"maxOccurs="1"/>
<xsd:element name="specieRule"type="SpecieRule"
minOccurs="0"maxOccurs="1"/>
<xsd:element name="parameterRule"type="ParameterRule"
minOccurs="0"maxOccurs="1"/>
</xsd:choice>
</xsd:complexType>
</xsd:element>
<xsd:element name="listOfReactions"minOccurs="1"maxOccurs="1">
<xsd:complexType>
<xsd:element name="reaction"type="Reaction"
minOccurs="1"maxOccurs="unbounded">
<xsd:unique name="parameters">
<xsd:selector>listOfParameters/parameter</xsd:selector>
<xsd:field>@name</xsd:field>
</xsd:unique>
</xsd:element>
</xsd:complexType>
</xsd:element>
<xsd:attribute name="name"type="Name"use="optional"/>
<xsd:attribute name="substanceScale"type="xsd:integer"use="default"value="0"/>
<xsd:attribute name="timeScale"type="xsd:integer"use="default"value="0"/>
<xsd:attribute name="volumeScale"type="xsd:integer"use="default"value="0"/>
<xsd:attribute name="lengthScale"type="xsd:integer"use="default"value="-6"/>
<xsd:attribute name="substanceIsNumberOfMolecules"type="xsd:boolean"
use="default"value="false"/>
</xsd:complexType>
<!--Compartment -->
<xsd:complexType name="Compartment"base="Identified"derivedBy="extension">
<xsd:attribute name="name"type="Name"use="required"/>
<xsd:attribute name="volume"type="xsd:float"use="default"value="1"/>
</xsd:complexType>
<!--Geometry -->
<xsd:complexType name="Geometry"base="Identified"derivedBy="extension">
<xsd:element name="listOfPoints"minOccurs="0"maxOccurs="1">
<xsd:complexType>
<xsd:element name="point"type="Point"minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<xsd:attribute name="name"type="Name"use="required"/>
<xsd:attribute name="length"type="xsd:float"use="optional"/>
<xsd:attribute name="surfaceArea"type="xsd:float"use="optional"/>
<xsd:attribute name="volume"type="xsd:float"use="optional"/>
<xsd:attribute name="lengthScale"type="xsd:integer"use="optional"/>
</xsd:complexType>
<xsd:complexType name="Point"base="Identified"derivedBy="extension">
<xsd:attribute name="x"type="xsd:float"use="required"/>
<xsd:attribute name="y"type="xsd:float"use="required"/>
</xsd:complexType>
<!--Mapping-->
<xsd:complexType name="Mapping"base="Identified"derivedBy="extension">
<xsd:attribute name="compartment"type="Name"use="required"/>
<xsd:attribute name="geometry"type="Name"use="required"/>
</xsd:complexType>
<!--Specie -->
<xsd:complexType name="Specie"base="Identified"derivedBy="extension">
<xsd:attribute name="name"type="Name"use="required"/>
<xsd:attribute name="compartment"type="Name"use="required"/>
<xsd:attribute name="initialAmount"type="xsd:float"use="required"/>
<xsd:attributeGroup ref="substanceUnits"/>
<xsd:attribute name="boundaryCondition"type="xsd:boolean"use="default"value="false"/>
<xsd:attribute name="charge"type="xsd:integer"use="optional"/>
</xsd:complexType>
<!--Parameter -->
<xsd:complexType name="Parameter"base="Identified"derivedBy="extension">
<xsd:element ref="listOfUnits"minOccurs="0"maxOccurs="1"/>
<xsd:attribute name="value"type="xsd:float"use="required"/>
<xsd:attribute name="scale"type="xsd:integer"use="default"value="0"/>
<xsd:attribute name="name"type="Name"use="required"/>
</xsd:complexType>
<xsd:simpleType base="xsd:string"name="UnitKind">
<xsd:enumeration value="mole"/>
<xsd:enumeration value="litre"/>
<xsd:enumeration value="second"/>
<xsd:enumeration value="metre"/>
<xsd:enumeration value="gram"/>
<xsd:enumeration value="ampere"/>
<xsd:enumeration value="kelvin"/>
<xsd:enumeration value="centigrade"/>
<xsd:enumeration value="candela"/>
<xsd:enumeration value="radian"/>
<xsd:enumeration value="streadian"/>
<xsd:enumeration value="hertz"/>
<xsd:enumeration value="newton"/>
<xsd:enumeration value="joule"/>
<xsd:enumeration value="calorie"/>
<xsd:enumeration value="watt"/>
<xsd:enumeration value="coulomb"/>
<xsd:enumeration value="volt"/>
<xsd:enumeration value="farad"/>
<xsd:enumeration value="ohm"/>
<xsd:enumeration value="weber"/>
<xsd:enumeration value="tesla"/>
<xsd:enumeration value="henry"/>
<xsd:enumeration value="lumen"/>
<xsd:enumeration value="lux"/>
<xsd:enumeration value="pascal"/>
<xsd:enumeration value="siemens"/>
<xsd:enumeration value="becquerel"/>
<xsd:enumeration value="gray"/>
</xsd:simpleType>
<xsd:complexType name="Unit"base="Identified"derivedBy="extension">
<xsd:attribute name="type"type="UnitKind"use="required"/>
<xsd:attribute name="power"type="xsd:integer"use="default"value="1"/>
</xsd:complexType>
<!--Rule -->
<xsd:complexType name="Rule"base="Identified"derivedBy="extension"abstract="true">
<xsd:attribute name="formula"type="xsd:string"use="required"/>
</xsd:complexType>
<xsd:complexType name="CompartmentRule"base="Rule"derivedBy="extension">
<xsd:attribute name="compartment"type="Name"use="required"/>
</xsd:complexType>
<xsd:complexType name="SpecieRule"base="Rule"derivedBy="extension">
<xsd:attribute name="species"type="Name"use="required"/>
</xsd:complexType>
<xsd:complexType name="ParameterRule"base="Rule"derivedBy="extension">
<xsd:element ref="listOfUnits"minOccurs="0"maxOccurs="1"/>
<xsd:attribute name="name"type="Name"use="required"/>
<xsd:attribute name="scale"type="xsd:integer"use="default"value="0"/>
</xsd:complexType>
<!--Reaction -->
<xsd:complexType name="Reaction"base="Identified"derivedBy="extension">
<xsd:element name="listOfReactants"minOccurs="1"maxOccurs="1">
<xsd:complexType>
<xsd:element ref="specieReference"minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="listOfProducts"minOccurs="1"maxOccurs="1">
<xsd:complexType>
<xsd:element ref="specieReference"minOccurs="1"maxOccurs="unbounded"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="kineticLaw"type="KineticLaw"minOccurs="0"maxOccurs="1"/>
<xsd:attribute name="name"type="Name"use="required"/>
<xsd:attribute name="reversible"type="xsd:boolean"use="default"value="false"/>
</xsd:complexType>
<xsd:complexType name="KineticLaw"base="Identified"derivedBy="extension">
<xsd:element ref="listOfParameters"minOccurs="0"maxOccurs="1"/>
<xsd:attribute name="formula"type="xsd:string"use="required"/>
<xsd:attributeGroup ref="substanceUnits"/>
<xsd:attribute name="timeScale"type="xsd:integer"use="optional"/>
</xsd:complexType>
<xsd:complexType name="SpecieReference"base="Identified"derivedBy="extension">
<xsd:attribute name="specie"type="xsd:string"use="required"/>
<xsd:attribute name="stoichiometry"type="xsd:integer"use="default"value="1"/>
<xsd:attribute name="denominator"type="xsd:integer"use="default"value="1"/>
</xsd:complexType>
<!--substanceUnits -->
<xsd:attributeGroup name="substanceUnits">
<xsd:attribute name="substanceScale"type="xsd:integer"use="optional"/>
<xsd:attribute name="substanceIsNumberOfMolecules"type="xsd:boolean"use="optional"/>
</xsd:attributeGroup>
<!--Top-level elements allowed in an sbml document.-->
<xsd:complexType name="sbmlDocument">
<xsd:element name="model"minOccurs="1"maxOccurs="1"type="Model">
<xsd:unique name="compartments">
<xsd:selector>listOfComparments/compartment</xsd:selector>
<xsd:field>@name</xsd:field>
</xsd:unique>
<xsd:unique name="geometries">
<xsd:selector>listOfGeometries/geometry</xsd:selector>
<xsd:field>@name</xsd:field>
</xsd:unique>
<xsd:unique name="species">
<xsd:selector>listOfSpecies/specie</xsd:selector>
<xsd:field>@name</xsd:field>
</xsd:unique>
<xsd:unique name="reactions">
<xsd:selector>listOfReactions/reaction</xsd:selector>
<xsd:field>@name</xsd:field>
</xsd:unique>
<xsd:unique name="globalSymbols">
<xsd:selector>*/*[self::compartment or self::parameter
or self::species or self::parameterRule ]</xsd:selector>
<xsd:field>@name</xsd:field>
</xsd:unique>
<xsd:keyref name="mappingToCompartment"refer="compartments">
<xsd:selector>listOfMappings/mapping</xsd:selector>
<xsd:field>@compartment</xsd:field>
</xsd:keyref>
<xsd:keyref name="mappingToGeometry"refer="geometries">
<xsd:selector>listOfMappings/mapping</xsd:selector>
<xsd:field>@geometry</xsd:field>
</xsd:keyref>
<xsd:keyref name="specieToCompartment"refer="compartments">
<xsd:selector>listOfSpecies/specie</xsd:selector>
<xsd:field>@compartment</xsd:field>
</xsd:keyref>
<xsd:keyref name="specieReferenceToSpecie"refer="species">
<xsd:selector>listOfReactions/reaction/*/specieReference</xsd:selector>
<xsd:field>@specie</xsd:field>
</xsd:keyref>
<xsd:keyref name="specieRuleToSpecie"refer="species">
<xsd:selector>llistOfRules/specieRule</xsd:selector>
<xsd:field>@specie</xsd:field>
</xsd:keyref>
<xsd:keyref name="compartmentRuleToComparment"refer="compartment">
<xsd:selector>llistOfRules/compartmentRule</xsd:selector>
<xsd:field>@compartment</xsd:field>
</xsd:keyref>
</xsd:element>
<xsd:attribute name="xmlns"/>
<xsd:attribute name="version"type="xsd:positiveInteger"use="required"/>
</xsd:complexType>
<xsd:element name="sbml"type="sbml:sbmlDocument"minOccurs="1"maxOccurs="1"/>
<!--The end.-->
</xsd:schema>