forked from PathVisio/GPML
/
GPML2013a-fuller.xsd
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GPML2013a-fuller.xsd
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<?xml version="1.0" encoding="utf-8"?>
<xs:schema targetNamespace="http://pathvisio.org/GPML/2013a"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#"
xmlns:gpml="http://pathvisio.org/GPML/2013a"
elementFormDefault="qualified"
>
<!-- Graphical Pathway Markup Language version 2013a, more fully and accurately specified than GPML2013.xsd -->
<!--
==============================================================
Includes and Imports
==============================================================
-->
<xs:import namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#" schemaLocation="./rdf.xsd"/>
<xs:import namespace="http://www.biopax.org/release/biopax-level3.owl#" schemaLocation="./GPML2013a-BioPAX.xsd"/>
<!-- Type Definitions -->
<xs:attributeGroup name="FontAttributes">
<xs:attribute name="FontName" default="Arial"
type="xs:string"/>
<xs:attribute name="FontStyle" default="Normal">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Normal"/>
<xs:enumeration value="Italic"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="FontDecoration" default="Normal">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Normal"/>
<xs:enumeration value="Underline"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="FontStrikethru" default="Normal">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Normal"/>
<xs:enumeration value="Strikethru"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="FontWeight" default="Normal">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Normal"/>
<xs:enumeration value="Bold"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="FontSize" type="xs:nonNegativeInteger"
default="12"/>
<xs:attribute name="Align" default="Center">
<!-- Horizontal alignment -->
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Left"/>
<xs:enumeration value="Center"/>
<xs:enumeration value="Right"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="Valign" default="Top">
<!-- Vertical alignment -->
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Top"/>
<xs:enumeration value="Middle"/>
<xs:enumeration value="Bottom"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
</xs:attributeGroup>
<xs:attributeGroup name="RectAttributes">
<xs:attribute name="CenterX" type="xs:float" use="required"/>
<xs:attribute name="CenterY" type="xs:float" use="required"/>
<xs:attribute name="Width" type="gpml:Dimension" use="required" />
<xs:attribute name="Height" type="gpml:Dimension" use="required" />
</xs:attributeGroup>
<xs:attributeGroup name="ShapeStyleAttributes">
<xs:attribute name="Color" type="gpml:ColorType" default="Black"/>
<xs:attribute name="LineStyle" type="gpml:StyleType" default="Solid" />
<xs:attribute name="LineThickness" type="xs:float" default="1.0" />
</xs:attributeGroup>
<!-- a rotation is either a float value or a string for each of the four right angles !-->
<xs:simpleType name="RotationType">
<xs:union>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Top"/> <!-- rotation of 0.0 !-->
<xs:enumeration value="Right"/> <!-- rotation of 1/2 pi !-->
<xs:enumeration value="Bottom"/> <!-- rotation of 1 pi !-->
<xs:enumeration value="Left"/> <!-- rotation of 3/2 pi !-->
</xs:restriction>
</xs:simpleType>
<xs:simpleType>
<xs:restriction base="xs:float"/> <!-- rotation is always measured in radians !-->
</xs:simpleType>
</xs:union>
</xs:simpleType>
<xs:simpleType name="ColorType">
<xs:union>
<xs:simpleType>
<xs:restriction base="xs:hexBinary"/>
</xs:simpleType>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="Aqua"/>
<xs:enumeration value="Black"/>
<xs:enumeration value="Blue"/>
<xs:enumeration value="Fuchsia"/>
<xs:enumeration value="Gray"/>
<xs:enumeration value="Green"/>
<xs:enumeration value="Lime"/>
<xs:enumeration value="Maroon"/>
<xs:enumeration value="Navy"/>
<xs:enumeration value="Olive"/>
<xs:enumeration value="Purple"/>
<xs:enumeration value="Red"/>
<xs:enumeration value="Silver"/>
<xs:enumeration value="Teal"/>
<xs:enumeration value="White"/>
<xs:enumeration value="Yellow"/>
<xs:enumeration value="Transparent"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType>
<xs:simpleType name="StyleType">
<xs:restriction base="xs:string">
<xs:enumeration value="Solid"/>
<xs:enumeration value="Broken"/>
</xs:restriction>
</xs:simpleType>
<!-- use Dimension for width and height, they can't be nagative !-->
<xs:simpleType name="Dimension">
<xs:restriction base="xs:float">
<xs:minInclusive value="0" />
</xs:restriction>
</xs:simpleType>
<xs:group name="CommentEtcGroup">
<xs:sequence>
<!-- One or more comments - bundles GenMAPP notes and GenMAPP remarks together !-->
<xs:element name="Comment" minOccurs="0"
maxOccurs="unbounded">
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="Source" type="xs:string"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
</xs:element>
<xs:element name="PublicationXref" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="ID" type="xs:string" use="required"/>
<xs:attribute name="Database" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="BiopaxRef" minOccurs="0"
maxOccurs="unbounded">
<xs:complexType>
<xs:simpleContent>
<xs:extension base="xs:string"/>
</xs:simpleContent>
</xs:complexType>
</xs:element>
<xs:element name="Attribute" minOccurs="0"
maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="Key" type="xs:string" use="required"/>
<xs:attribute name="Value" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:group>
<!-- EdgeGraphics -->
<xs:complexType name="EdgeGraphicsType">
<xs:sequence>
<xs:element name="Point" minOccurs="2" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="X" type="xs:float" use="required" />
<xs:attribute name="Y" type="xs:float" use="required" />
<!-- relX and relY are the coordinates used when
a point is linked to another object (when GraphRef
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 -->
<xs:attribute name="RelX" type="xs:float" use="optional" />
<xs:attribute name="RelY" type="xs:float" use="optional" />
<xs:attribute name="GraphRef" type="xs:IDREF" use="optional" />
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
<!-- Note: only the ArrowHead attribute on first and last points are used, the rest is ignored. !-->
<xs:attribute name="ArrowHead" default="Line" type="xs:string" />
</xs:complexType>
</xs:element>
<xs:element name="Anchor" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="Position" type="xs:float" use="required" />
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
<xs:attribute name="Shape" default="None" type="xs:string" />
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="Color" type="gpml:ColorType" default="Black" />
<xs:attribute name="LineThickness" type="xs:float"/>
<xs:attribute name="LineStyle" type="gpml:StyleType" default="Solid" />
<xs:attribute name="ConnectorType" type="xs:string" use="optional" default="Straight"/>
<xs:attribute name="ZOrder" type="xs:integer" use="optional"/>
</xs:complexType>
<!-- End: EdgeGraphics -->
<!-- DataNode -->
<!-- DataNode is the old GeneProduct, a gene in GenMAPP
terminology. -->
<xs:complexType name="DataNodeType">
<xs:sequence>
<xs:group ref="gpml:CommentEtcGroup"/>
<xs:element name="Graphics" minOccurs="1" maxOccurs="1">
<xs:complexType>
<xs:attributeGroup ref="gpml:RectAttributes"/>
<xs:attributeGroup ref="gpml:FontAttributes"/>
<xs:attributeGroup ref="gpml:ShapeStyleAttributes"/>
<xs:attribute name="FillColor" type="gpml:ColorType" default="White"/>
<xs:attribute name="ShapeType" type="xs:string" default="Rectangle"/>
<xs:attribute name="ZOrder" type="xs:integer" use="optional"/>
</xs:complexType>
</xs:element>
<xs:element name="Xref" minOccurs="1" maxOccurs="1">
<xs:complexType>
<xs:attribute name="Database" type="xs:string" use="required"/>
<xs:attribute name="ID" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
<xs:attribute name="GroupRef" type="xs:string" use="optional" />
<xs:attribute name="TextLabel" use="required" type="xs:string"/>
<xs:attribute name="Type" default="Unknown">
<xs:simpleType>
<xs:union>
<xs:simpleType>
<xs:restriction base="xs:string">
<!--
These are the values used at WikiPathways.
You can use any string, but we recommend
that you use these values whenever possible.
-->
<xs:enumeration value="Unknown"/>
<xs:enumeration value="Rna"/>
<xs:enumeration value="Protein"/>
<xs:enumeration value="Complex"/>
<xs:enumeration value="GeneProduct"/>
<xs:enumeration value="Metabolite"/>
<xs:enumeration value="Pathway"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType>
<xs:restriction base="xs:string"/>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:attribute>
</xs:complexType>
<!-- End: DataNode -->
<!-- State -->
<xs:complexType name="StateType">
<xs:sequence>
<xs:group ref="gpml:CommentEtcGroup"/>
<xs:element name="Graphics" minOccurs="1" maxOccurs="1">
<xs:complexType>
<xs:attribute name="RelX" type="xs:float" use="required"/>
<xs:attribute name="RelY" type="xs:float" use="required"/>
<xs:attribute name="Width" type="gpml:Dimension" use="required" />
<xs:attribute name="Height" type="gpml:Dimension" use="required" />
<xs:attributeGroup ref="gpml:ShapeStyleAttributes"/>
<xs:attribute name="FillColor" type="gpml:ColorType" default="White"/>
<xs:attribute name="ShapeType" type="xs:string" default="Rectangle"/>
<xs:attribute name="ZOrder" type="xs:integer" use="optional"/>
</xs:complexType>
</xs:element>
<xs:element name="Xref" minOccurs="0" maxOccurs="1">
<xs:complexType>
<xs:attribute name="Database" type="xs:string" use="required"/>
<xs:attribute name="ID" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
<xs:attribute name="GraphRef" type="xs:IDREF" use="optional" />
<xs:attribute name="TextLabel" use="required" type="xs:string"/>
<xs:attribute name="StateType" type="xs:string" default="Unknown"/>
<!-- Biological modification type. suggested values: Phosphorylated, Glycosylated, Activated, ... !-->
</xs:complexType>
<!-- End: State -->
<!-- Graphical Line -->
<xs:complexType name="GraphicalLineType">
<xs:sequence>
<xs:group ref="gpml:CommentEtcGroup" />
<xs:element name="Graphics" type="gpml:EdgeGraphicsType" minOccurs="1" maxOccurs="1" />
</xs:sequence>
<xs:attribute name="GroupRef" type="xs:string" use="optional" />
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
<xs:attribute name="Type" type="xs:string" use="optional" />
</xs:complexType>
<!-- End: Graphical Line -->
<!-- Interaction -->
<xs:complexType name="InteractionType">
<xs:sequence>
<xs:group ref="gpml:CommentEtcGroup" />
<xs:element name="Graphics" type="gpml:EdgeGraphicsType" minOccurs="1" maxOccurs="1" />
<xs:element name="Xref" minOccurs="1" maxOccurs="1">
<xs:complexType>
<xs:attribute name="Database" type="xs:string" use="required"/>
<xs:attribute name="ID" type="xs:string" use="required"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="GroupRef" type="xs:string" use="optional" />
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
<xs:attribute name="Type" type="xs:string" use="optional" />
</xs:complexType>
<!-- End: Interaction -->
<!-- Label -->
<xs:complexType name="LabelType">
<!-- This is text on a GenMAPP map that
can have associated comments. -->
<xs:sequence>
<xs:group ref="gpml:CommentEtcGroup"/>
<xs:element name="Graphics" minOccurs="1" maxOccurs="1">
<xs:complexType>
<xs:attributeGroup ref="gpml:RectAttributes"/>
<xs:attributeGroup ref="gpml:FontAttributes" />
<xs:attributeGroup ref="gpml:ShapeStyleAttributes" />
<xs:attribute name="FillColor" type="gpml:ColorType" default="Transparent"/>
<xs:attribute name="ShapeType" type="xs:string" default="None"/>
<xs:attribute name="ZOrder" type="xs:integer" use="optional"/>
</xs:complexType>
</xs:element>
</xs:sequence>
<!-- for a reference to a url !-->
<xs:attribute name="Href" use="optional" type="xs:string" />
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
<xs:attribute name="GroupRef" type="xs:string" use="optional" />
<xs:attribute name="TextLabel" use="required" type="xs:string"/>
</xs:complexType>
<!-- End: Label -->
<!-- Shape -->
<xs:complexType name="ShapeType">
<xs:sequence>
<xs:group ref="gpml:CommentEtcGroup" />
<xs:element name="Graphics" minOccurs="1" maxOccurs="1">
<xs:complexType>
<xs:attributeGroup ref="gpml:RectAttributes"/>
<xs:attributeGroup ref="gpml:FontAttributes" />
<xs:attributeGroup ref="gpml:ShapeStyleAttributes" />
<xs:attribute name="FillColor" type="gpml:ColorType" default="Transparent"/>
<xs:attribute name="ShapeType" type="xs:string" use="required"/>
<xs:attribute name="ZOrder" type="xs:integer" use="optional"/>
<xs:attribute name="Rotation" type="gpml:RotationType" default="Top" />
</xs:complexType>
</xs:element>
</xs:sequence>
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
<xs:attribute name="GroupRef" type="xs:string" use="optional" />
<xs:attribute name="TextLabel" use="optional" type="xs:string"/>
</xs:complexType>
<!-- End: Shape -->
<!-- Group -->
<xs:complexType name="GroupType">
<xs:sequence>
<xs:group ref="gpml:CommentEtcGroup" />
</xs:sequence>
<xs:attribute name="GroupId" type="xs:string" use="required" />
<xs:attribute name="GroupRef" type="xs:string"
use="optional" />
<xs:attribute name="Style" type="xs:string" default="None" />
<xs:attribute name="TextLabel" type="xs:string"
use="optional" />
<xs:attribute name="GraphId" type="xs:ID" use="optional" />
</xs:complexType>
<!-- InfoBox -->
<!-- InfoBox element holds the
coordinates on the GenMAPP layout where the Information kept in the
Info table will be displayed in the mapp. -->
<xs:complexType name="InfoBoxType">
<xs:attribute name="CenterX" type="xs:float" use="required"/>
<xs:attribute name="CenterY" type="xs:float" use="required"/>
</xs:complexType>
<!-- End: InfoBox -->
<!-- Legend -->
<xs:complexType name="LegendType">
<xs:attribute name="CenterX" type="xs:float" use="required"/>
<xs:attribute name="CenterY" type="xs:float" use="required"/>
</xs:complexType>
<!-- End: Legend -->
<!-- Biopax -->
<xs:complexType name="BiopaxType">
<xs:sequence>
<xs:any namespace="http://www.biopax.org/release/biopax-level3.owl#"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element ref="bp:PublicationXref" minOccurs="0" maxOccurs="unbounded"/>
<xs:element ref="bp:openControlledVocabulary" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<!-- End: Biopax -->
<!-- End: Type Definitions -->
<!-- Pathway -->
<xs:element name="Pathway">
<xs:complexType>
<xs:sequence>
<xs:group ref="gpml:CommentEtcGroup"/>
<xs:element name="Graphics" minOccurs="0" maxOccurs="1">
<xs:complexType>
<xs:attribute name="BoardWidth" type="gpml:Dimension"
use="required"/>
<xs:attribute name="BoardHeight" type="gpml:Dimension"
use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="DataNode" type="gpml:DataNodeType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="State" type="gpml:StateType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="Interaction" type="gpml:InteractionType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="GraphicalLine" type="gpml:GraphicalLineType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="Label" type="gpml:LabelType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="Shape" type="gpml:ShapeType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="Group" type="gpml:GroupType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="InfoBox" type="gpml:InfoBoxType" minOccurs="1" maxOccurs="1" />
<xs:element name="Legend" type="gpml:LegendType" minOccurs="0" maxOccurs="1"/>
<xs:element name="Biopax" type="gpml:BiopaxType" minOccurs="0" maxOccurs="1"/>
</xs:sequence>
<xs:attribute name="Name" type="xs:string" use="required">
<!-- GenMAPP Pathway Title -->
</xs:attribute>
<xs:attribute name="Organism" type="xs:string" use="optional">
<!-- Organism is not a field in the
GenMAPP database at this time, but we want to preserve this
information when importing maps, and also when exporting maps.
GenMAPP maps have the organism implied from the
filename. -->
</xs:attribute>
<xs:attribute name="Data-Source" type="xs:string" use="optional">
<!-- On import to GenMAPP,
Data-Source value could be 'KEGG', 'Cytoscape', etc. On export
from GenMAPP, value should be 'GenMAPP' with version
number. -->
</xs:attribute>
<xs:attribute name="Version" type="xs:string" use="optional">
<!-- GenMAPP version, use for export
of maps from GenMAPP only. -->
</xs:attribute>
<xs:attribute name="Author" type="xs:string" use="optional"/>
<xs:attribute name="Maintainer" type="xs:string" use="optional"/>
<xs:attribute name="Email" type="xs:string" use="optional"/>
<xs:attribute name="License" type="xs:string" use="optional"/>
<xs:attribute name="Last-Modified" type="xs:string" use="optional">
<!-- Last modification date, in the form of YYYYMMDD -->
</xs:attribute>
</xs:complexType>
</xs:element>
<!-- End: Pathway -->
</xs:schema>