GPML2017.xsd

<?xml version="1.0" encoding="utf-8"?>
<xsd:schema targetNamespace="http://pathvisio.org/GPML/2017" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:gpml="http://pathvisio.org/GPML/2017" elementFormDefault="qualified">

	<!-- Graphical Pathway Markup Language version 2017 -->

	<!-- 
	     Type Definitions 
         This block declares all the properties which would then be attached
         to elements in the GPML hierarchy, most of them are intuitive
         like FontAttributes, RotationType, ColorType
    -->


	<xsd:attributeGroup name="FontAttributes">
		<xsd:attribute name="fontName" default="Arial" type="xsd:string">
			<xsd:annotation>
				<xsd:documentation>
					The name of the set of printable text characters to be used for visualization.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="fontStyle" default="Normal">
			<xsd:annotation>
				<xsd:documentation>
					The typographic style or font face applied to displayed text, e.g., Arial.
				</xsd:documentation>
			</xsd:annotation>
			<xsd:simpleType>
				<xsd:restriction base="xsd:string">
					<xsd:enumeration value="Normal"/>
					<xsd:enumeration value="Italic"/>
				</xsd:restriction>
			</xsd:simpleType>
		</xsd:attribute>
		<xsd:attribute name="fontWeight" default="Normal">
			<xsd:annotation>
				<xsd:documentation>
					Thickness of the font used, e.g a bold font would
					have more weight. Used for DataNodes, Labels and Shapes.
				</xsd:documentation>
			</xsd:annotation>
			<xsd:simpleType>
				<xsd:restriction base="xsd:string">
					<xsd:enumeration value="Normal"/>
					<xsd:enumeration value="Bold"/>
				</xsd:restriction>
			</xsd:simpleType>
		</xsd:attribute>
		<xsd:attribute name="fontSize" type="xsd:nonNegativeInteger" default="12">
			<xsd:annotation>
				<xsd:documentation>
					The point value for the size of the font.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="align" default="Center">
			<xsd:annotation>
				<xsd:documentation>
					Horizontal alignment of displayed text, e.g., Left, Center, Right.
				</xsd:documentation>
			</xsd:annotation>
			<!-- Horizontal alignment -->
			<xsd:simpleType>
				<xsd:restriction base="xsd:string">
					<xsd:enumeration value="Left"/>
					<xsd:enumeration value="Center"/>
					<xsd:enumeration value="Right"/>
				</xsd:restriction>
			</xsd:simpleType>
		</xsd:attribute>
		<xsd:attribute name="vAlign" default="Top">
			<!-- Vertical alignment -->
			<xsd:simpleType>
				<xsd:restriction base="xsd:string">
					<xsd:enumeration value="Top"/>
					<xsd:enumeration value="Middle"/>
					<xsd:enumeration value="Bottom"/>
				</xsd:restriction>
			</xsd:simpleType>
		</xsd:attribute>
	</xsd:attributeGroup>

	<xsd:attributeGroup name="CenterAttributes">
		<xsd:attribute name="centerX" type="xsd:float" use="required">
			<xsd:annotation>
				<xsd:documentation>
					Middle of a pathway element in the x-direction.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>

		<xsd:attribute name="centerY" type="xsd:float" use="required">
			<xsd:annotation>
				<xsd:documentation>
					Middle of a pathway element in the y-direction.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
	</xsd:attributeGroup>

	<xsd:attributeGroup name="DimensionAttributes">
		<xsd:attribute name="width" type="gpml:Dimension" use="required" >
			<xsd:annotation>
				<xsd:documentation>
					The pixel value for the x-dimensional length of a given object.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="height" type="gpml:Dimension" use="required" >
			<xsd:annotation>
				<xsd:documentation>
					The pixel value for the y-dimensional length of a given object.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
	</xsd:attributeGroup>

	<xsd:attributeGroup name="RectAttributes">
		<xsd:attributeGroup ref="gpml:CenterAttributes" />
		<xsd:attributeGroup ref="gpml:DimensionAttributes" />
	</xsd:attributeGroup>

	<xsd:attributeGroup name="LineAttributes">
		<xsd:attribute name="lineStyle" type="gpml:StyleType" default="Solid" >
			<xsd:annotation>
				<xsd:documentation>
					The visual appearance of a line or border, e.g., Solid or Broken.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="lineThickness" type="xsd:float" default="1.0" >
			<xsd:annotation>
				<xsd:documentation>
					The pixel value for the width of a given line, interaction or border.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
	</xsd:attributeGroup>

	<xsd:attributeGroup name="LineGraphicAttributes">
		<xsd:attributeGroup ref="gpml:LineAttributes" />
		<xsd:attribute name="color" type="gpml:ColorType" default="Black">
			<xsd:annotation>
				<xsd:documentation>
					The color to be used for visualization.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="connectorType" type="xsd:string" use="optional" default="Straight">
			<xsd:annotation>
				<xsd:documentation>
					Specifies a set of rules to govern layout of Graphical Lines and Interactions.
					PathVisio (Java): Line Type and GPML: ConnectorType
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="zOrder" type="xsd:integer" use="optional"/>
	</xsd:attributeGroup>

	<xsd:attributeGroup name="ShapeStyleAttributes">
		<xsd:attribute name="color" type="gpml:ColorType" default="Black">
			<xsd:annotation>
				<xsd:documentation>
					The color to be used for visualization.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attributeGroup ref="gpml:LineAttributes" />
		<xsd:attribute name="fillColor" type="gpml:ColorType" default="Transparent">
			<xsd:annotation>
				<xsd:documentation>
					The hexidecimal color value used to paint the area of an object, not including its border.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="shapeType" type="xsd:string" default="None"/>
		<xsd:attribute name="zOrder" type="xsd:integer" use="optional"/>
	</xsd:attributeGroup>

	<xsd:attributeGroup name="IdentifierGroup">
		<xsd:attribute name="elementID" type="xsd:ID" use="required">
			<xsd:annotation>
				<xsd:documentation>
					A elementID is a unique identifier for a pathway element within the pathway,
					such as DataNode, Interaction, GraphicalLine, Label, Point, Group, Shape, State and Anchor.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
	</xsd:attributeGroup>

	<xsd:attributeGroup name="IdentifierRefGroup">
		<xsd:attributeGroup ref="gpml:IdentifierGroup" />
		<xsd:attribute name="groupRef" type="xsd:string" use="optional">
			<xsd:annotation>
				<xsd:documentation>
					A GroupRef indicates that its element is part of the gpml:Group
					with the specified GroupId. DataNode, GraphicalLine, Group, Interaction,
					Label and Shape can be part of a group.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="textLabel" type="xsd:string" use="optional">
			<xsd:annotation>
				<xsd:documentation>
					TextLabel of an object (DataNode, Group, Label, Shape, State).
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
	</xsd:attributeGroup>

	<xsd:attributeGroup name="RelativeCoordinates">
			<!-- relX and relY are the coordinates used when
		a point is linked to another object (when elementRef
		is defined). They represent he coordinates of the
		point relative to the object that it's linked to, where
		0,0 lies at the center of the object and 1,1 at the bottom-right
		corner -->
		<xsd:attribute name="relX" type="xsd:float" use="required">
			<xsd:annotation>
				<xsd:documentation>
					RelX is the x-coordinate used when a point or state is linked to
					an another object - relative coordinate to the object that
					it is linked to (0,0 - center, 1,1 - bottom-right).
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="relY" type="xsd:float" use="required">
			<xsd:annotation>
				<xsd:documentation>
					RelY is the y-coordinate used when a point or state is linked to
					an another object - relative coordinate to the object that
					it is linked to (0,0 - center, 1,1 - bottom-right).
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
	</xsd:attributeGroup>
	<xsd:attributeGroup name="RelativeCoordinatesOptional">
		<xsd:attribute name="relX" type="xsd:float" use="optional" />
		<xsd:attribute name="relY" type="xsd:float" use="optional" />
	</xsd:attributeGroup>
	<!-- a rotation is either a float value or a string for each of the four right angles !-->
	<xsd:simpleType name="RotationType">
		<xsd:union>
			<xsd:simpleType>
				<xsd:restriction base="xsd:string">
					<xsd:enumeration value="Top"/> <!-- rotation of 0.0 !-->
					<xsd:enumeration value="Right"/> <!-- rotation of 1/2 pi !-->
					<xsd:enumeration value="Bottom"/> <!-- rotation of 1 pi !-->
					<xsd:enumeration value="Left"/> <!-- rotation of 3/2 pi !-->
				</xsd:restriction>
			</xsd:simpleType>
			<xsd:simpleType>
				<xsd:restriction base="xsd:float"/> <!-- rotation is always measured in radians !-->
			</xsd:simpleType>
		</xsd:union>

	</xsd:simpleType>

	<xsd:simpleType name="ColorType">
		<xsd:union>
			<xsd:simpleType>
				<xsd:restriction base="xsd:hexBinary"/>
			</xsd:simpleType>
			<xsd:simpleType>
				<xsd:restriction base="xsd:string">
					<xsd:enumeration value="Aqua"/>
					<xsd:enumeration value="Black"/>
					<xsd:enumeration value="Blue"/>
					<xsd:enumeration value="Fuchsia"/>
					<xsd:enumeration value="Gray"/>
					<xsd:enumeration value="Green"/>
					<xsd:enumeration value="Lime"/>
					<xsd:enumeration value="Maroon"/>
					<xsd:enumeration value="Navy"/>
					<xsd:enumeration value="Olive"/>
					<xsd:enumeration value="Purple"/>
					<xsd:enumeration value="Red"/>
					<xsd:enumeration value="Silver"/>
					<xsd:enumeration value="Teal"/>
					<xsd:enumeration value="White"/>
					<xsd:enumeration value="Yellow"/>
					<xsd:enumeration value="Transparent"/>
				</xsd:restriction>
			</xsd:simpleType>
		</xsd:union>
	</xsd:simpleType>

	<xsd:simpleType name="StyleType">
		<xsd:restriction base="xsd:string">
			<xsd:enumeration value="Solid"/>
			<xsd:enumeration value="Broken"/>
		</xsd:restriction>
	</xsd:simpleType>

	<!-- use Dimension for width and height, they can't be negative !-->
	<xsd:simpleType name="Dimension">
		<xsd:restriction base="xsd:float">
			<xsd:minInclusive value="0" />
		</xsd:restriction>
	</xsd:simpleType>

	<!--TODO: Rename group since it bundles `Attribute`, `CitationRef`
		- How about CommonGroup, since it is that way in code too..
		  mapCommon, updateCommon
	-->
    <!-- One or more comments bundled together !-->
	<xsd:group name="CommentGroup">
		<xsd:sequence>
			<xsd:element name="Comment" minOccurs="0" maxOccurs="unbounded">
				<xsd:annotation>
					<xsd:documentation>
						Elements used to provide descriptions and arbitrary notes for a given object.
					</xsd:documentation>
				</xsd:annotation>
				<xsd:complexType>
					<xsd:simpleContent>
						<xsd:extension base="xsd:string">
							<xsd:attribute name="source" type="xsd:string"/>
						</xsd:extension>
					</xsd:simpleContent>
				</xsd:complexType>
			</xsd:element>
			<!-- Additional information can be added as attribute key value pairs 
				 can be used or ignored by readers -->
			<xsd:element name="Attribute" minOccurs="0" maxOccurs="unbounded">
				<xsd:annotation>
					<xsd:documentation>
						Element used to specify key/value paired information for a given object.
					</xsd:documentation>
				</xsd:annotation>
				<xsd:complexType>
					<xsd:attribute name="key" type="xsd:string" use="required">
						<xsd:annotation>
							<xsd:documentation>
								Key of the key/value pair in the Attribute class.
							</xsd:documentation>
						</xsd:annotation>
					</xsd:attribute>
					<xsd:attribute name="value" type="xsd:string" use="required">
						<xsd:annotation>
							<xsd:documentation>
								Value of the key/value pair in the Attribute class.
							</xsd:documentation>
						</xsd:annotation>
					</xsd:attribute>
				</xsd:complexType>
			</xsd:element>

			<!--Citation References for Pathway Elements-->

			<xsd:element name="CitationRef" minOccurs="0" maxOccurs="unbounded">
				<xsd:annotation>
					<xsd:documentation>
						Reuse of references defined by Citations.
					</xsd:documentation>
				</xsd:annotation>
				<xsd:complexType>
					<xsd:attribute name="citationID" type="xsd:string" use="required"/>
				</xsd:complexType>
			</xsd:element>
		</xsd:sequence>
	</xsd:group>

	<!-- End: Type Definitions -->

	<!-- ###################################################################### -->

	<!-- 
		Pathway 
        This is the root element of the structure, it encloses
        a complex type sequence of Comment, Graphics, DataNode,
        Interaction, Line, Label, Link, Shape, Group, InfoBox,
        Legend, Biopax
	-->

	<xsd:element name="Pathway">
		<xsd:annotation>
			<xsd:documentation>
				A graph diagram representing a biological process as a set of interactions
				and relationships among genes, proteins, metabolites, and other factors in
				the context of cellular compartments, tissues and organisms.
			</xsd:documentation>
		</xsd:annotation>
		<xsd:complexType>
			<xsd:sequence>
				<!-- pathways can have xrefs -->
				<xsd:element name="Xref" type="gpml:Xref" minOccurs="0" maxOccurs="1"/>
				
				<!--TODO rename element name? conflicts with Citations.Citation.Author-->
				<xsd:element name="Author" minOccurs="0" maxOccurs="1">
					<xsd:annotation>
						<xsd:documentation>
							The people who created or edited the pathway in question.
						</xsd:documentation>
					</xsd:annotation>
					<xsd:complexType>
						<xsd:attribute name="name" type="xsd:string" use="required"/>
 					</xsd:complexType>
				</xsd:element>

				<xsd:group ref="gpml:CommentGroup"/>

				<xsd:element name="OntologyTermRef" minOccurs="0" maxOccurs="unbounded">
					<xsd:complexType>
						<xsd:attribute name="ontologyTermID" type="xsd:string" use="required"/>
					</xsd:complexType>
				</xsd:element>

				<xsd:element name="DataNode" type="gpml:DataNode" minOccurs="0" maxOccurs="unbounded"/>

				<xsd:element name="State" type="gpml:State" minOccurs="0" maxOccurs="unbounded"/>

				<xsd:element name="Interaction" type="gpml:Interaction" minOccurs="0" maxOccurs="unbounded"/>

				<xsd:element name="GraphicalLine" type="gpml:GraphicalLine" minOccurs="0" maxOccurs="unbounded"/>

				<xsd:element name="Label" type="gpml:Label" minOccurs="0" maxOccurs="unbounded"/>

				<xsd:element name="Shape" type="gpml:Shape" minOccurs="0" maxOccurs="unbounded"/>

				<xsd:element name="Group" type="gpml:Group" minOccurs="0" maxOccurs="unbounded"/>

				<xsd:element name="InfoBox" type="gpml:InfoBox" minOccurs="1" maxOccurs="1" />

				<xsd:element name="Legend" type="gpml:Legend" minOccurs="0" maxOccurs="1"/>

				<xsd:element name="Citations" type="gpml:Citations" minOccurs="0" maxOccurs="1"/>

				<xsd:element name="OntologyTerms" type="gpml:OntologyTerms" minOccurs="0" maxOccurs="1"/>

			</xsd:sequence>

			<!-- Metadata for the pathway -->
			<xsd:attribute name="name" type="xsd:string" use="required">
				<xsd:annotation>
					<xsd:documentation>
						The name of a pathway.
					</xsd:documentation>
				</xsd:annotation>
			</xsd:attribute>

			<xsd:attribute name="organism" type="xsd:string" use="optional">
				<xsd:annotation>
					<xsd:documentation>
						The scientific name (e.g., Homo sapiens) of the
						species being described by the pathway.
					</xsd:documentation>
				</xsd:annotation>
			</xsd:attribute>

			<!--TODO conflicts with Xref.dataSource -->
			<xsd:attribute name="dataSource" type="xsd:string" use="optional">
				<xsd:annotation>
					<xsd:documentation>
						Deprecated: Not in use.
					</xsd:documentation>
				</xsd:annotation>
			</xsd:attribute>

			<xsd:attribute name="revision" type="xsd:string" use="optional">
				<xsd:annotation>
					<xsd:documentation>
						The version of a Pathway (currently not used in WP).
					</xsd:documentation>
				</xsd:annotation>
			</xsd:attribute>

			<xsd:attribute name="license" type="xsd:string" use="optional">
				<xsd:annotation>
					<xsd:documentation>
						The license of a pathway.
					</xsd:documentation>
				</xsd:annotation>
			</xsd:attribute>

			<!-- Not separate elements but a reference to the elements at the end of the GPML -->

			<!-- Graphics related attributes-->
			<xsd:attributeGroup ref="gpml:DimensionAttributes"/>
			<!-- End Graphics related attributes-->

		</xsd:complexType>
	</xsd:element>
	<!-- End: Pathway -->

	<!-- ###################################################################### -->

	<!-- 
		Data Node 
        These are the elements with biological context
        forming the basis of the biological pathway
    -->

	<xsd:complexType name="DataNode">
		<!-- DataNode represents all possible biological entities in a pathway
			 like GeneProduct, Metabolite, Pathway, Protein, RNA, Unknown. -->
		<xsd:annotation>
			<xsd:documentation>
				Denotes a biological entity that forms a node in a pathway and
				has some biological meaning associated with it. For a list of
				the gpml:DataNode types supported at WikiPathways, see subclasses
				of wp:DataNode or the wpTypes vocabulary defined for use in applications.
			</xsd:documentation>
		</xsd:annotation>
		<xsd:sequence>
			<xsd:group ref="gpml:CommentGroup"/>
			<xsd:element name="Xref" type="gpml:Xref" minOccurs="1" maxOccurs="1"/>
		</xsd:sequence>

		<!-- Graphics related attributes-->
		<xsd:attributeGroup ref="gpml:RectAttributes"/>
		<xsd:attributeGroup ref="gpml:FontAttributes"/>
		<xsd:attributeGroup ref="gpml:ShapeStyleAttributes"/>

		<xsd:attribute name="backgroundImage" type="xsd:string"/>
		<!-- End Graphics related attributes-->


		<xsd:attributeGroup ref="gpml:IdentifierRefGroup" />

		<xsd:attribute name="type" default="Unknown">
			<!-- Basic GPML types are:
				"Protein", "Rna", "GeneProduct", "Metabolite", "Pathway" and "Unknown".
				It's recommended that you use these values as often as possible. -->
			<xsd:simpleType>
				<xsd:union>
					<xsd:simpleType>
						<xsd:restriction base="xsd:string">
							<xsd:enumeration value="Unknown"/>
							<xsd:enumeration value="Rna"/>
							<xsd:enumeration value="Protein"/>
							<xsd:enumeration value="Complex"/>
							<xsd:enumeration value="GeneProduct"/>
							<xsd:enumeration value="Metabolite"/>
							<xsd:enumeration value="Pathway"/>
						</xsd:restriction>
					</xsd:simpleType>
					<xsd:simpleType>
						<xsd:restriction base="xsd:string"/>
					</xsd:simpleType>
				</xsd:union>
			</xsd:simpleType>
		</xsd:attribute>
	</xsd:complexType>
	<!-- End: DataNode -->

	<!-- ###################################################################### -->

	<!-- 
		State 
        Always linked to a DataNode representing a specific state of the biological 
		entity (e.g. phosphorylation, genetic variants, etc)
    -->

	<xsd:complexType name="State">
		<xsd:annotation>
			<xsd:documentation>
				A particular condition, mode or modification of an entity,
				e.g., phosphorylated, activated, mutated, SNP, etc.
			</xsd:documentation>
		</xsd:annotation>

		<xsd:sequence>
			<xsd:group ref="gpml:CommentGroup"/>
			<xsd:element name="Xref" type="gpml:Xref" minOccurs="0" maxOccurs="1"/>

		</xsd:sequence>

		<xsd:attributeGroup ref="gpml:RelativeCoordinates" />
		<!-- Graphics related attributes-->
		<xsd:attributeGroup ref="gpml:DimensionAttributes"/>
		<xsd:attributeGroup ref="gpml:FontAttributes" />
		<xsd:attributeGroup ref="gpml:ShapeStyleAttributes"/>
		<!-- End Graphics related attributes-->

		<xsd:attributeGroup ref="gpml:IdentifierGroup" />

		<xsd:attribute name="elementRef" type="xsd:IDREF" use="required" />

		<xsd:attribute name="stateType" type="xsd:string" default="Unknown"/>
		<!-- Biological modification type. suggested values: Phosphorylated, Glycosylated, Activated, ... !-->

	</xsd:complexType>
	<!-- End: State -->

	<!-- ###################################################################### -->

	<!-- 
		Grapical Line, Interaction  
        These are the only elements which can be used to connect data nodes, for
        implementing any kind of connections or interactions.
		Interactions represent biological relation between entities - should always be attached
		to DataNodes
		GraphicalLines are graphical annotations without semantic meaning
    -->

	<xsd:complexType name="GraphicalLine">
		<xsd:annotation>
			<xsd:documentation>
				A visual annotation, often used to partition space or connect other annotation,
				e.g., Shapes. An Xref can not be specified for GraphicalLines
				(in contrast to Interactions).
			</xsd:documentation>
		</xsd:annotation>
		<xsd:sequence>

			<xsd:group ref="gpml:CommentGroup" />

			<xsd:element name="Point" type="gpml:Point" minOccurs="2" maxOccurs="unbounded" />

			<xsd:element name="Anchor" type="gpml:Anchor" minOccurs="0" maxOccurs="unbounded" />

		</xsd:sequence>


		<!-- Graphics related attributes-->
		<xsd:attributeGroup ref="gpml:LineGraphicAttributes" />
		<!-- End Graphics related attributes-->

		<xsd:attributeGroup ref="gpml:IdentifierRefGroup" />
	</xsd:complexType>
	<!-- End: Graphical Line -->

	<!-- Interaction -->
	<xsd:complexType name="Interaction">
		<xsd:annotation>
			<xsd:documentation>
				Defines the biochemical relationship between DataNodes
				or with Anchors on other Interactions. An Xref can be
				specified for Interactions (in contrast to GraphicalLines).
			</xsd:documentation>
		</xsd:annotation>
		<xsd:sequence>
			<xsd:group ref="gpml:CommentGroup" />

			<xsd:element name="Xref" type="gpml:Xref" minOccurs="1" maxOccurs="1"/>

			<xsd:element name="Point" type="gpml:Point" minOccurs="2" maxOccurs="unbounded" />

			<xsd:element name="Anchor" type="gpml:Anchor" minOccurs="0" maxOccurs="unbounded" />

		</xsd:sequence>


		<!-- Graphics related attributes-->
		<xsd:attributeGroup ref="gpml:LineGraphicAttributes" />
		<!-- End Graphics related attributes-->

		<xsd:attributeGroup ref="gpml:IdentifierRefGroup" />
	</xsd:complexType>
	<!-- End: Interaction -->

	<!-- ###################################################################### -->

	<!-- 
		Label
        An element to attach simple labels to the pathway
		No semantic meaning - graphical attributes
    -->

	<xsd:complexType name="Label">

		<xsd:annotation>
			<xsd:documentation>
				A text field which can be used to annotate any aspect of a pathway.
			</xsd:documentation>
		</xsd:annotation>

		<xsd:sequence>
			<xsd:group ref="gpml:CommentGroup"/>
		</xsd:sequence>

		<!-- Graphics related attributes-->
		<xsd:attributeGroup ref="gpml:RectAttributes"/>
		<xsd:attributeGroup ref="gpml:FontAttributes" />
		<xsd:attributeGroup ref="gpml:ShapeStyleAttributes" />
		<!-- End Graphics related attributes-->

		<!-- for a reference to a url !-->
		<xsd:attribute name="href" use="optional" type="xsd:string" >
			<xsd:annotation>
				<xsd:documentation>
					The hyperlink optionally specified in a Label.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>

		<xsd:attributeGroup ref="gpml:IdentifierRefGroup" />

	</xsd:complexType>


	<!-- End: Label -->

	<!-- ###################################################################### -->

	<xsd:complexType name="Alias">

		<xsd:annotation>
			<xsd:documentation>
				Description for Alias element
			</xsd:documentation>
		</xsd:annotation>

		<xsd:sequence>
			<xsd:group ref="gpml:CommentGroup"/>
		</xsd:sequence>

		<!-- Graphics related attributes-->
		<xsd:attributeGroup ref="gpml:RectAttributes"/>
		<xsd:attributeGroup ref="gpml:FontAttributes" />

		<xsd:attribute name="color" type="gpml:ColorType" default="Black">
			<xsd:annotation>
				<xsd:documentation>
					The color to be used for visualization.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>

		<xsd:attributeGroup ref="gpml:LineAttributes" />

		<xsd:attribute name="fillColor" type="gpml:ColorType" default="Transparent">
			<xsd:annotation>
				<xsd:documentation>
					The hexidecimal color value used to paint the area of an object, not including its border.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="shapeType" type="xsd:string" default="Hexagon"/>
		<xsd:attribute name="zOrder" type="xsd:integer" use="optional"/>

		<!-- End Graphics related attributes-->

		<xsd:attributeGroup ref="gpml:IdentifierRefGroup" />

		<xsd:attribute name="groupAliasRef" use="required" type="xsd:IDREF"/>
	</xsd:complexType>

	<!--
		Shape
        Graphical elements - shapes with or without a text label
    -->

	<xsd:complexType name="Shape">
		<xsd:annotation>
			<xsd:documentation>
				Shape can refer to two different things in GPML,
				both of which are associated with graphical elements.
			</xsd:documentation>
		</xsd:annotation>

		<xsd:sequence>
			<xsd:group ref="gpml:CommentGroup" />
		</xsd:sequence>

		<!-- Graphics related attributes-->
		<xsd:attributeGroup ref="gpml:RectAttributes"/>
		<xsd:attributeGroup ref="gpml:FontAttributes" />
		<xsd:attributeGroup ref="gpml:ShapeStyleAttributes" />
		<xsd:attribute name="rotation" type="gpml:RotationType" default="Top" />
		<!-- End Graphics related attributes-->

		<xsd:attributeGroup ref="gpml:IdentifierRefGroup" />

	</xsd:complexType>

	<!-- End: Shape -->

	<!-- ###################################################################### -->

	<!-- 
		Group
		Elements in the pathway can be grouped. 
		Basic GPML group styles are: 
		None, Pathway, Group, Complex
	-->

	<xsd:complexType name="Group">
		<xsd:annotation>
			<xsd:documentation>
				A collection of structurally or functionally similar or related pathway elements.
			</xsd:documentation>
		</xsd:annotation>
		<xsd:sequence>
			<xsd:group ref="gpml:CommentGroup" />
		</xsd:sequence>

		<xsd:attributeGroup ref="gpml:IdentifierRefGroup" />

		<!-- renamed to groupType -->
		<xsd:attribute name="groupType" default="Group">
			<xsd:simpleType>
				<xsd:union>
					<xsd:simpleType>
						<xsd:restriction base="xsd:string">
							<xsd:enumeration value="Group"/>
							<xsd:enumeration value="Complex"/>
							<xsd:enumeration value="Pathway"/>
							<xsd:enumeration value="Analog"/>
							<xsd:enumeration value="Paralog"/>
						</xsd:restriction>
					</xsd:simpleType>
					<xsd:simpleType>
						<xsd:restriction base="xsd:string"/>
					</xsd:simpleType>
				</xsd:union>
			</xsd:simpleType>
		</xsd:attribute>
	</xsd:complexType>
	<!-- End: Group -->

	<!-- ###################################################################### -->

	<!-- 
		InfoBox, Legend
		General properties/annotations of the pathway
	-->

	<xsd:complexType name="InfoBox">
		<xsd:annotation>
			<xsd:documentation>
				Currently just a placeholder -- not used.
			</xsd:documentation>
		</xsd:annotation>
		<!-- InfoBox element holds the coordinates where name and organism are displayed in the pathway -->
		<xsd:attributeGroup ref="gpml:CenterAttributes" />
	</xsd:complexType>
	<!-- End: InfoBox -->

	<!-- Legend -->
	<xsd:complexType name="Legend">
		<xsd:annotation>
			<xsd:documentation>
				An explanatory list of the colors used for visualizing data on the pathway. Not currently used.
			</xsd:documentation>
		</xsd:annotation>

		<xsd:attributeGroup ref="gpml:CenterAttributes" />

	</xsd:complexType>
	<!-- End: Legend -->


	<!-- ###################################################################### -->

	<!-- 
		Citations
		List of all Citations referred in the pathway
	-->

	<xsd:complexType name="Citations">
		<xsd:annotation>
			<xsd:documentation>
				Defines a literature reference.
			</xsd:documentation>
		</xsd:annotation>
		<xsd:sequence>
			<xsd:element name="Citation" minOccurs="0" maxOccurs="unbounded">
				<xsd:complexType>
					<xsd:sequence>
						<xsd:element name="Xref" type="gpml:Xref" minOccurs="0" maxOccurs="1"/>
						<xsd:element name="Author" minOccurs="0" maxOccurs="unbounded">
							<xsd:complexType>
								<xsd:attribute name="name" type="xsd:string" use="required"/>
							</xsd:complexType>
						</xsd:element>
					</xsd:sequence>
					<xsd:attribute name="citationID" type="xsd:ID" use="required" />
					<xsd:attribute name="title" use="required"/>
					<xsd:attribute name="year" use="optional"/>
					<xsd:attribute name="URL" use="required"/>
					<xsd:attribute name="source" use="optional"/>
				</xsd:complexType>
			</xsd:element>
		</xsd:sequence>
	</xsd:complexType>
	<!-- End: Citations -->

	<!-- ###################################################################### -->

	<!-- 
		OntologyTerms
		List of all OntologyTerms used for the pathway
	-->
	<xsd:complexType name="OntologyTerms">
		<xsd:sequence>
			<xsd:element name="OntologyTerm" minOccurs="0" maxOccurs="unbounded">
				<xsd:complexType>
					<xsd:attribute name="term" type="xsd:string" use="required"/>
					<xsd:attribute name="ontology" type="xsd:string" use="required"/>
					<xsd:attribute name="ontologyTermID" type="xsd:string" use="required" />
				</xsd:complexType>
			</xsd:element>
		</xsd:sequence>
	</xsd:complexType>

	<xsd:complexType name="Xref">
		<xsd:annotation>
			<xsd:documentation>
				Reference to a database entry that matches the node in the pathway.
				It is a combination of an identifier of the entity and an identifier
				of the database in which the entity is found.
			</xsd:documentation>
		</xsd:annotation>
		<xsd:attribute name="identifier" type="xsd:string" use="required">
			<xsd:annotation>
				<xsd:documentation>
					The identifier of a PublicationXref or Xref object.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="dataSource" type="xsd:string" use="required">
			<xsd:annotation>
				<xsd:documentation>
					Specifies the datasource for the identifier provided as an Xref.
					Equivalent to http://vocabularies.bridgedb.org/ops#DataSource conventional name .
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
	</xsd:complexType>


	<xsd:complexType name="Point">
		<xsd:annotation>
			<xsd:documentation>
				A location in 2-dimensional space defined by x and y coordinates.
			</xsd:documentation>
		</xsd:annotation>

		<xsd:attribute name="x" type="xsd:float" use="required" />
		<xsd:attribute name="y" type="xsd:float" use="required" />
		<xsd:attributeGroup ref="gpml:RelativeCoordinatesOptional" />
		<xsd:attribute name="elementRef" type="xsd:IDREF" use="optional" >
			<xsd:annotation>
				<xsd:documentation>
					A elementRef indicates a "depends on" or child/parent relationship
					between two Pathway elements. The element with the elementRef is
					the child, and the element referred to by the elementRef is the parent.
					The parent's elementID will be specified by the child's elementRef.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attributeGroup ref="gpml:IdentifierGroup" />
		<!-- Note: only the arrowHead attribute on first and last points are used, the rest is ignored. !-->
		<xsd:attribute name="arrowHead" default="Line">
			<xsd:annotation>
				<xsd:documentation>
					Specifies the glyph at the ends of lines and interactions.
				</xsd:documentation>
			</xsd:annotation>
            <xsd:simpleType>
                <xsd:union>
                    <xsd:simpleType>
                        <xsd:restriction base="xsd:string">
                            <xsd:enumeration value="Line"/>
                            <xsd:enumeration value="Arrow"/>
                            <xsd:enumeration value="TBar"/>
                            <xsd:enumeration value="mim-necessary-stimulation"/>
                            <xsd:enumeration value="mim-binding"/>
                            <xsd:enumeration value="mim-conversion"/>
                            <xsd:enumeration value="mim-stimulation"/>
                            <xsd:enumeration value="mim-catalysis"/>
                            <xsd:enumeration value="mim-modification"/>
                            <xsd:enumeration value="mim-inhibition"/>
                            <xsd:enumeration value="mim-covalent-bond"/>
                            <xsd:enumeration value="mim-transcription-translation"/>
                        </xsd:restriction>
                    </xsd:simpleType>
                    <xsd:simpleType>
                        <xsd:restriction base="xsd:string"/>
                    </xsd:simpleType>
                </xsd:union>
            </xsd:simpleType>
		</xsd:attribute>
	</xsd:complexType>

	<xsd:complexType name="Anchor">
		<xsd:annotation>
			<xsd:documentation>
				A connection point on a graphical line or an interaction, where another graphical line or interaction can be connected.
			</xsd:documentation>
		</xsd:annotation>
		<xsd:attribute name="position" type="xsd:float" use="required">
			<xsd:annotation>
				<xsd:documentation>
					Proportional distance of an anchor along the line it belongs to, between 0 and 1.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
		<xsd:attribute name="x" type="xsd:float" use="optional" />
		<xsd:attribute name="y" type="xsd:float" use="optional" />
		<xsd:attributeGroup ref="gpml:RelativeCoordinatesOptional" />

		<xsd:attributeGroup ref="gpml:IdentifierGroup" />
		<xsd:attribute name="shapeType" default="None" type="xsd:string" >
			<xsd:annotation>
				<xsd:documentation>
					The visual representation of an anchor, e.g., Circle or None.
				</xsd:documentation>
			</xsd:annotation>
		</xsd:attribute>
	</xsd:complexType>
</xsd:schema>