GPML2013a Schema Documentation

GPML2013a Schema Documentation

Table of Contents

top

Schema Document Properties

Target Namespace http://pathvisio.org/GPML/2013a
Element and Attribute Namespaces
  • Global element and attribute declarations belong to this schema's target namespace.
  • By default, local element declarations belong to this schema's target namespace.
  • By default, local attribute declarations have no namespace.

Declared Namespaces

Prefix Namespace
xml http://www.w3.org/XML/1998/namespace
xsd http://www.w3.org/2001/XMLSchema
gpml http://pathvisio.org/GPML/2013a
Schema Component Representation
<xsd:schema targetNamespace="http://pathvisio.org/GPML/2013a" elementFormDefault="qualified">
...
</xsd:schema>
top

Global Declarations

Element: Pathway

Name Pathway
Type Locally-defined complex type
Nillable no
Abstract no
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.
XML Instance Representation
<gpml:Pathway
Name="xsd:string [1] ?"
Organism="xsd:string [0..1] ?"
Data-Source="xsd:string [0..1]"
Version="xsd:string [0..1] ?"
Author="xsd:string [0..1] ?"
Maintainer="xsd:string [0..1] ?"
Email="xsd:string [0..1]"
License="xsd:string [0..1] ?"
Last-Modified="xsd:string [0..1] ?"
BiopaxRef="xsd:string [0..1]">
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
<gpml:Graphics
BoardWidth="gpml:Dimension [1]"
BoardHeight="gpml:Dimension [1]"/> [0..1]
<gpml:DataNode> ... </gpml:DataNode> [0..*]
<gpml:State> ... </gpml:State> [0..*]
<gpml:Interaction> ... </gpml:Interaction> [0..*]
<gpml:GraphicalLine> ... </gpml:GraphicalLine> [0..*]
<gpml:Label> ... </gpml:Label> [0..*]
<gpml:Shape> ... </gpml:Shape> [0..*]
<gpml:Group> ... </gpml:Group> [0..*]
<gpml:InfoBox> ... </gpml:InfoBox> [1]
<gpml:Legend> ... </gpml:Legend> [0..1]
<gpml:Biopax> ... </gpml:Biopax> [0..1]
</gpml:Pathway>
Schema Component Representation
<xsd:element name="Pathway">
<xsd:complexType>
<xsd:sequence>
<xsd:group ref="gpml:CommentGroup"/>
<xsd:element name="Graphics" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="BoardWidth" type="gpml:Dimension" use="required"/>
<xsd:attribute name="BoardHeight" type="gpml:Dimension" use="required"/>
</xsd:complexType>
</xsd:element>
<xsd:element ref="gpml:DataNode" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gpml:State" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gpml:Interaction" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gpml:GraphicalLine" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gpml:Label" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gpml:Shape" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gpml:Group" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element ref="gpml:InfoBox" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="gpml:Legend" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="gpml:Biopax" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute name="Name" type="xsd:string" use="required">
<-- GenMAPP Pathway Title -->
</xsd:attribute>
<xsd:attribute name="Organism" type="xsd: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. -->
</xsd:attribute>
<xsd:attribute name="Data-Source" type="xsd: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. Deprecated in 2017 version -->
</xsd:attribute>
<xsd:attribute name="Version" type="xsd:string" use="optional">
<-- GenMAPP version, use for export of maps from GenMAPP only. -->
</xsd:attribute>
<xsd:attribute name="Author" type="xsd:string" use="optional"/>
<xsd:attribute name="Maintainer" type="xsd:string" use="optional"/>
<xsd:attribute name="Email" type="xsd:string" use="optional"/>
<xsd:attribute name="License" type="xsd:string" use="optional"/>
<xsd:attribute name="Last-Modified" type="xsd:string" use="optional"/>
<xsd:attribute name="BiopaxRef" type="xsd:string" use="optional"/>
</xsd:complexType>
</xsd:element>
top

Element: DataNode

Name DataNode
Type Locally-defined complex type
Nillable no
Abstract no
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.
XML Instance Representation
<gpml:DataNode
BiopaxRef="xsd:string [0..1]"
GraphId="xsd:ID [0..1]"
GroupRef="xsd:string [0..1]"
TextLabel="xsd:string [1]"
Type="xsd:string [0..1] ?">
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
<gpml:Graphics
CenterX="xsd:float [1] ?"
CenterY="xsd:float [1] ?"
Width="gpml:Dimension [1] ?"
Height="gpml:Dimension [1] ?"
FontName="xsd:string [0..1] ?"
FontStyle="xsd:string (value comes from list: {'Normal'|'Italic'}) [0..1] ?"
FontDecoration="xsd:string (value comes from list: {'Normal'|'Underline'}) [0..1] ?"
FontStrikethru="xsd:string (value comes from list: {'Normal'|'Strikethru'}) [0..1] ?"
FontWeight="xsd:string (value comes from list: {'Normal'|'Bold'}) [0..1] ?"
FontSize="xsd:nonNegativeInteger [0..1] ?"
Align="xsd:string (value comes from list: {'Left'|'Center'|'Right'}) [0..1] ?"
Valign="xsd:string (value comes from list: {'Top'|'Middle'|'Bottom'}) [0..1] ?"
Color="gpml:ColorType [0..1] ?"
LineStyle="gpml:StyleType [0..1] ?"
LineThickness="xsd:float [0..1] ?"
FillColor="gpml:ColorType [0..1]"
ShapeType="xsd:string [0..1]"
ZOrder="xsd:integer [0..1]"/> [1]
<gpml:Xref
Database="xsd:string [1]"
ID="xsd:string [1]"/> [1]
</gpml:DataNode>
Schema Component Representation
<xsd:element name="DataNode">
<-- DataNode is the old GeneProduct, a gene in GenMAPP terminology. DataNode represents all possible biological entities in a pathway like GeneProduct, Metabolite, Pathway, Protein, RNA, Unknown. -->
<xsd:complexType>
<xsd:sequence>
<xsd:group ref="gpml:CommentGroup"/>
<-- Graphics related attributes-->
<xsd:element name="Graphics" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attributeGroup ref="gpml:RectAttributes"/>
<xsd:attributeGroup ref="gpml:FontAttributes"/>
<xsd:attributeGroup ref="gpml:ShapeStyleAttributes"/>
<xsd:attribute name="FillColor" type="gpml:ColorType" default="White"/>
<xsd:attribute name="ShapeType" type="xsd:string" default="Rectangle"/>
<xsd:attribute name="ZOrder" type="xsd:integer" use="optional"/>
</xsd:complexType>
</xsd:element>
<-- End Graphics related attributes-->
<xsd:element name="Xref" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="Database" type="xsd:string" use="required"/>
<xsd:attribute name="ID" type="xsd:string" use="required"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="BiopaxRef" type="xsd:string" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<xsd:attribute name="GroupRef" type="xsd:string" use="optional"/>
<xsd:attribute name="TextLabel" type="xsd:string" use="required"/>
<xsd:attribute name="Type" type="xsd:string" default="Unknown">
<-- Old versions of GPML only allowed these values for Type: It's recommended that you use these values as often as possible. -->
</xsd:attribute>
</xsd:complexType>
</xsd:element>
top

Element: State

Name State
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Always linked to a DataNode representing a specific state of the biological entity (e.g. phosphorylation, genetic variants, etc)
XML Instance Representation
<gpml:State
BiopaxRef="xsd:string [0..1]"
GraphId="xsd:ID [0..1]"
GraphRef="xsd:IDREF [0..1]"
TextLabel="xsd:string [1]"
StateType="xsd:string [0..1]">
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
<gpml:Graphics
RelX="xsd:float [1]"
RelY="xsd:float [1]"
Width="gpml:Dimension [1]"
Height="gpml:Dimension [1]"
Color="gpml:ColorType [0..1] ?"
LineStyle="gpml:StyleType [0..1] ?"
LineThickness="xsd:float [0..1] ?"
FillColor="gpml:ColorType [0..1]"
ShapeType="xsd:string [0..1]"
ZOrder="xsd:integer [0..1]"/> [1]
<gpml:Xref
Database="xsd:string [1]"
ID="xsd:string [1]"/> [0..1]
</gpml:State>
Schema Component Representation
<xsd:element name="State">
<xsd:complexType>
<xsd:sequence>
<xsd:group ref="gpml:CommentGroup"/>
<-- Graphics related attributes-->
<xsd:element name="Graphics" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="RelX" type="xsd:float" use="required"/>
<xsd:attribute name="RelY" type="xsd:float" use="required"/>
<xsd:attribute name="Width" type="gpml:Dimension" use="required"/>
<xsd:attribute name="Height" type="gpml:Dimension" use="required"/>
<xsd:attributeGroup ref="gpml:ShapeStyleAttributes"/>
<xsd:attribute name="FillColor" type="gpml:ColorType" default="White"/>
<xsd:attribute name="ShapeType" type="xsd:string" default="Rectangle"/>
<xsd:attribute name="ZOrder" type="xsd:integer" use="optional"/>
</xsd:complexType>
</xsd:element>
<-- End Graphics related attributes-->
<xsd:element name="Xref" minOccurs="0" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="Database" type="xsd:string" use="required"/>
<xsd:attribute name="ID" type="xsd:string" use="required"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="BiopaxRef" type="xsd:string" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<xsd:attribute name="GraphRef" type="xsd:IDREF" use="optional"/>
<xsd:attribute name="TextLabel" type="xsd:string" use="required"/>
<xsd:attribute name="StateType" type="xsd:string" default="Unknown"/>
<-- Biological modification type. suggested values: Phosphorylated, Glycosylated, Activated, ... !-->
</xsd:complexType>
</xsd:element>
top

Element: GraphicalLine

Name GraphicalLine
Type Locally-defined complex type
Nillable no
Abstract no
Documentation A visual annotation, often used to partition space or connect other annotation, e.g., Shapes. GrapicalLine are graphical annotations without semantic meaning An Xref cannot be specified for GraphicalLines (in contrast to Interactions).
XML Instance Representation
<gpml:GraphicalLine
GroupRef="xsd:string [0..1]"
BiopaxRef="xsd:string [0..1]"
GraphId="xsd:ID [0..1]"
Type="xsd:string [0..1]">
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
<gpml:Graphics
Color="gpml:ColorType [0..1]"
LineThickness="xsd:float [0..1]"
LineStyle="gpml:StyleType [0..1]"
ConnectorType="xsd:string [0..1]"
ZOrder="xsd:integer [0..1]"> [1]
<gpml:Point
X="xsd:float [1]"
Y="xsd:float [1]"
RelX="xsd:float [0..1]"
RelY="xsd:float [0..1]"
GraphRef="xsd:IDREF [0..1]"
GraphId="xsd:ID [0..1]"
ArrowHead="xsd:string [0..1]"/> [2..*]
<gpml:Anchor
Position="xsd:float [1]"
GraphId="xsd:ID [0..1]"
Shape="xsd:string [0..1]"/> [0..*]
</gpml:Graphics>
</gpml:GraphicalLine>
Schema Component Representation
<xsd:element name="GraphicalLine">
<xsd:complexType>
<xsd:sequence>
<xsd:group ref="gpml:CommentGroup"/>
<-- Graphics related attributes-->
<xsd:element name="Graphics" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="Point" minOccurs="2" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="X" type="xsd:float" use="required"/>
<xsd:attribute name="Y" type="xsd: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 -->
<xsd:attribute name="RelX" type="xsd:float" use="optional"/>
<xsd:attribute name="RelY" type="xsd:float" use="optional"/>
<xsd:attribute name="GraphRef" type="xsd:IDREF" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<-- Note: only the ArrowHead attribute on first and last points are used, the rest is ignored. !-->
<xsd:attribute name="ArrowHead" type="xsd:string" default="Line"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="Anchor" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Position" type="xsd:float" use="required"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<xsd:attribute name="Shape" type="xsd:string" default="ReceptorRound"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Color" type="gpml:ColorType" default="Black"/>
<xsd:attribute name="LineThickness" type="xsd:float"/>
<xsd:attribute name="LineStyle" type="gpml:StyleType" default="Solid"/>
<xsd:attribute name="ConnectorType" type="xsd:string" use="optional" default="Straight"/>
<xsd:attribute name="ZOrder" type="xsd:integer" use="optional"/>
</xsd:complexType>
</xsd:element>
<-- End Graphics related attributes-->
</xsd:sequence>
<xsd:attribute name="GroupRef" type="xsd:string" use="optional"/>
<xsd:attribute name="BiopaxRef" type="xsd:string" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<xsd:attribute name="Type" type="xsd:string" use="optional"/>
</xsd:complexType>
</xsd:element>
top

Element: Interaction

Name Interaction
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Defines the biochemical relationship between DataNodes or with Anchors on other Interactions. An Xref can be specified for Interactions (in contrast to GraphicalLines).
XML Instance Representation
<gpml:Interaction
GroupRef="xsd:string [0..1]"
BiopaxRef="xsd:string [0..1]"
GraphId="xsd:ID [0..1]"
Type="xsd:string [0..1]">
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
<gpml:Graphics
Color="gpml:ColorType [0..1]"
LineThickness="xsd:float [0..1]"
LineStyle="gpml:StyleType [0..1]"
ConnectorType="xsd:string [0..1]"
ZOrder="xsd:integer [0..1]"> [1]
<gpml:Point
X="xsd:float [1]"
Y="xsd:float [1]"
RelX="xsd:float [0..1]"
RelY="xsd:float [0..1]"
GraphRef="xsd:IDREF [0..1]"
GraphId="xsd:ID [0..1]"
ArrowHead="xsd:string [0..1]"/> [2..*]
<gpml:Anchor
Position="xsd:float [1]"
GraphId="xsd:ID [0..1]"
Shape="xsd:string [0..1]"/> [0..*]
</gpml:Graphics>
<gpml:Xref
Database="xsd:string [1]"
ID="xsd:string [1]"/> [1]
</gpml:Interaction>
Schema Component Representation
<xsd:element name="Interaction">
<xsd:complexType>
<xsd:sequence>
<xsd:group ref="gpml:CommentGroup"/>
<-- Graphics related attributes-->
<xsd:element name="Graphics" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="Point" minOccurs="2" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="X" type="xsd:float" use="required"/>
<xsd:attribute name="Y" type="xsd: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 -->
<xsd:attribute name="RelX" type="xsd:float" use="optional"/>
<xsd:attribute name="RelY" type="xsd:float" use="optional"/>
<xsd:attribute name="GraphRef" type="xsd:IDREF" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<-- Note: only the ArrowHead attribute on first and last points are used, the rest is ignored. !-->
<xsd:attribute name="ArrowHead" type="xsd:string" default="Line"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="Anchor" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Position" type="xsd:float" use="required"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<xsd:attribute name="Shape" type="xsd:string" default="ReceptorRound"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="Color" type="gpml:ColorType" default="Black"/>
<xsd:attribute name="LineThickness" type="xsd:float"/>
<xsd:attribute name="LineStyle" type="gpml:StyleType" default="Solid"/>
<xsd:attribute name="ConnectorType" type="xsd:string" use="optional" default="Straight"/>
<xsd:attribute name="ZOrder" type="xsd:integer" use="optional"/>
</xsd:complexType>
</xsd:element>
<-- End Graphics related attributes-->
<xsd:element name="Xref" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attribute name="Database" type="xsd:string" use="required"/>
<xsd:attribute name="ID" type="xsd:string" use="required"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="GroupRef" type="xsd:string" use="optional"/>
<xsd:attribute name="BiopaxRef" type="xsd:string" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<xsd:attribute name="Type" type="xsd:string" use="optional"/>
</xsd:complexType>
</xsd:element>
top

Element: Label

Name Label
Type Locally-defined complex type
Nillable no
Abstract no
Documentation A text field which can be used to annotate any aspect of a pathway.
XML Instance Representation
<gpml:Label
Href="xsd:string [0..1] ?"
BiopaxRef="xsd:string [0..1]"
GraphId="xsd:ID [0..1]"
GroupRef="xsd:string [0..1]"
TextLabel="xsd:string [1]">
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
<gpml:Graphics
CenterX="xsd:float [1] ?"
CenterY="xsd:float [1] ?"
Width="gpml:Dimension [1] ?"
Height="gpml:Dimension [1] ?"
FontName="xsd:string [0..1] ?"
FontStyle="xsd:string (value comes from list: {'Normal'|'Italic'}) [0..1] ?"
FontDecoration="xsd:string (value comes from list: {'Normal'|'Underline'}) [0..1] ?"
FontStrikethru="xsd:string (value comes from list: {'Normal'|'Strikethru'}) [0..1] ?"
FontWeight="xsd:string (value comes from list: {'Normal'|'Bold'}) [0..1] ?"
FontSize="xsd:nonNegativeInteger [0..1] ?"
Align="xsd:string (value comes from list: {'Left'|'Center'|'Right'}) [0..1] ?"
Valign="xsd:string (value comes from list: {'Top'|'Middle'|'Bottom'}) [0..1] ?"
Color="gpml:ColorType [0..1] ?"
LineStyle="gpml:StyleType [0..1] ?"
LineThickness="xsd:float [0..1] ?"
FillColor="gpml:ColorType [0..1]"
ShapeType="xsd:string [0..1]"
ZOrder="xsd:integer [0..1]"/> [1]
</gpml:Label>
Schema Component Representation
<xsd:element name="Label">
<xsd:complexType>
<-- This is text on a GenMAPP map that can have associated comments. -->
<xsd:sequence>
<xsd:group ref="gpml:CommentGroup"/>
<-- Graphics related attributes-->
<xsd:element name="Graphics" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attributeGroup ref="gpml:RectAttributes"/>
<xsd:attributeGroup ref="gpml:FontAttributes"/>
<xsd:attributeGroup ref="gpml:ShapeStyleAttributes"/>
<xsd:attribute name="FillColor" type="gpml:ColorType" default="Transparent"/>
<xsd:attribute name="ShapeType" type="xsd:string" default="None"/>
<xsd:attribute name="ZOrder" type="xsd:integer" use="optional"/>
</xsd:complexType>
</xsd:element>
<-- End Graphics related attributes-->
</xsd:sequence>
<xsd:attribute name="Href" type="xsd:string" use="optional"/>
<xsd:attribute name="BiopaxRef" type="xsd:string" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<xsd:attribute name="GroupRef" type="xsd:string" use="optional"/>
<xsd:attribute name="TextLabel" type="xsd:string" use="required"/>
</xsd:complexType>
</xsd:element>
top

Element: Shape

Name Shape
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Shape can refer to two different things in GPML, both of which are associated with graphical elements.
XML Instance Representation
<gpml:Shape
BiopaxRef="xsd:string [0..1]"
GraphId="xsd:ID [0..1]"
GroupRef="xsd:string [0..1]"
TextLabel="xsd:string [0..1]">
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
<gpml:Graphics
CenterX="xsd:float [1] ?"
CenterY="xsd:float [1] ?"
Width="gpml:Dimension [1] ?"
Height="gpml:Dimension [1] ?"
FontName="xsd:string [0..1] ?"
FontStyle="xsd:string (value comes from list: {'Normal'|'Italic'}) [0..1] ?"
FontDecoration="xsd:string (value comes from list: {'Normal'|'Underline'}) [0..1] ?"
FontStrikethru="xsd:string (value comes from list: {'Normal'|'Strikethru'}) [0..1] ?"
FontWeight="xsd:string (value comes from list: {'Normal'|'Bold'}) [0..1] ?"
FontSize="xsd:nonNegativeInteger [0..1] ?"
Align="xsd:string (value comes from list: {'Left'|'Center'|'Right'}) [0..1] ?"
Valign="xsd:string (value comes from list: {'Top'|'Middle'|'Bottom'}) [0..1] ?"
Color="gpml:ColorType [0..1] ?"
LineStyle="gpml:StyleType [0..1] ?"
LineThickness="xsd:float [0..1] ?"
FillColor="gpml:ColorType [0..1]"
ShapeType="xsd:string [1]"
ZOrder="xsd:integer [0..1]"
Rotation="gpml:RotationType [0..1]"/> [1]
</gpml:Shape>
Schema Component Representation
<xsd:element name="Shape">
<xsd:complexType>
<xsd:sequence>
<xsd:group ref="gpml:CommentGroup"/>
<-- Graphics related attributes-->
<xsd:element name="Graphics" minOccurs="1" maxOccurs="1">
<xsd:complexType>
<xsd:attributeGroup ref="gpml:RectAttributes"/>
<xsd:attributeGroup ref="gpml:FontAttributes"/>
<xsd:attributeGroup ref="gpml:ShapeStyleAttributes"/>
<xsd:attribute name="FillColor" type="gpml:ColorType" default="Transparent"/>
<xsd:attribute name="ShapeType" type="xsd:string" use="required"/>
<xsd:attribute name="ZOrder" type="xsd:integer" use="optional"/>
<xsd:attribute name="Rotation" type="gpml:RotationType" default="Top"/>
</xsd:complexType>
</xsd:element>
<-- End Graphics related attributes-->
</xsd:sequence>
<xsd:attribute name="BiopaxRef" type="xsd:string" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
<xsd:attribute name="GroupRef" type="xsd:string" use="optional"/>
<xsd:attribute name="TextLabel" type="xsd:string" use="optional"/>
</xsd:complexType>
</xsd:element>
top

Element: Group

Name Group
Type Locally-defined complex type
Nillable no
Abstract no
Documentation A collection of structurally or functionally similar or related pathway elements.
XML Instance Representation
<gpml:Group
BiopaxRef="xsd:string [0..1]"
GroupId="xsd:string [1]"
GroupRef="xsd:string [0..1]"
Style="xsd:string [0..1]"
TextLabel="xsd:string [0..1]"
GraphId="xsd:ID [0..1]">
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
</gpml:Group>
Schema Component Representation
<xsd:element name="Group">
<xsd:complexType>
<xsd:sequence>
<xsd:group ref="gpml:CommentGroup"/>
</xsd:sequence>
<xsd:attribute name="BiopaxRef" type="xsd:string" use="optional"/>
<xsd:attribute name="GroupId" type="xsd:string" use="required"/>
<xsd:attribute name="GroupRef" type="xsd:string" use="optional"/>
<xsd:attribute name="Style" type="xsd:string" default="None"/>
<xsd:attribute name="TextLabel" type="xsd:string" use="optional"/>
<xsd:attribute name="GraphId" type="xsd:ID" use="optional"/>
</xsd:complexType>
</xsd:element>
top

Element: InfoBox

Name InfoBox
Type Locally-defined complex type
Nillable no
Abstract no
Documentation InfoBox element holds the coordinates on the GenMAPP layout where the Information kept in the Info table will be displayed in the mapp.
XML Instance Representation
<gpml:InfoBox
CenterX="xsd:float [1]"
CenterY="xsd:float [1]"/>
Schema Component Representation
<xsd:element name="InfoBox">
<xsd:complexType>
<xsd:attribute name="CenterX" type="xsd:float" use="required"/>
<xsd:attribute name="CenterY" type="xsd:float" use="required"/>
</xsd:complexType>
</xsd:element>
top

Element: Legend

Name Legend
Type Locally-defined complex type
Nillable no
Abstract no
Documentation An explanatory list of the colors used for visualizing data on the pathway. Not currently used.
XML Instance Representation
<gpml:Legend
CenterX="xsd:float [1]"
CenterY="xsd:float [1]"/>
Schema Component Representation
<xsd:element name="Legend">
<xsd:complexType>
<xsd:attribute name="CenterX" type="xsd:float" use="required"/>
<xsd:attribute name="CenterY" type="xsd:float" use="required"/>
</xsd:complexType>
</xsd:element>
top

Element: Biopax

Name Biopax
Type Locally-defined complex type
Nillable no
Abstract no
Documentation Integration of annotation, references, and ontology from Biopax.
XML Instance Representation
<gpml:Biopax>
Allow any elements from the following namespace(s): http://www.biopax.org/release/biopax-level3.owl# (skip validation). [0..*]
</gpml:Biopax>
Schema Component Representation
<xsd:element name="Biopax">
<xsd:complexType>
<xsd:sequence>
<xsd:any namespace="http://www.biopax.org/release/biopax-level3.owl#" processContents="skip" minOccurs="0" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
top

Global Definitions

Attribute Group: FontAttributes

Name FontAttributes
Documentation Common font properties.
XML Instance Representation
FontName="xsd:string [0..1] ?"
FontStyle="xsd:string (value comes from list: {'Normal'|'Italic'}) [0..1] ?"
FontDecoration="xsd:string (value comes from list: {'Normal'|'Underline'}) [0..1] ?"
FontStrikethru="xsd:string (value comes from list: {'Normal'|'Strikethru'}) [0..1] ?"
FontWeight="xsd:string (value comes from list: {'Normal'|'Bold'}) [0..1] ?"
FontSize="xsd:nonNegativeInteger [0..1] ?"
Align="xsd:string (value comes from list: {'Left'|'Center'|'Right'}) [0..1] ?"
Valign="xsd:string (value comes from list: {'Top'|'Middle'|'Bottom'}) [0..1] ?"
Schema Component Representation
<xsd:attributeGroup name="FontAttributes">
<xsd:attribute name="FontName" type="xsd:string" default="Arial"/>
<xsd:attribute name="FontStyle" default="Normal">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="Normal"/>
<xsd:enumeration value="Italic"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="FontDecoration" default="Normal">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="Normal"/>
<xsd:enumeration value="Underline"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="FontStrikethru" default="Normal">
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="Normal"/>
<xsd:enumeration value="Strikethru"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
<xsd:attribute name="FontWeight" default="Normal">
<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:attribute name="Align" default="Center">
<-- 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>
top

Attribute Group: RectAttributes

Name RectAttributes
Documentation Group of attributes for a pathway element, e.g. rectangular node.
XML Instance Representation
CenterX="xsd:float [1] ?"
CenterY="xsd:float [1] ?"
Width="gpml:Dimension [1] ?"
Height="gpml:Dimension [1] ?"
Schema Component Representation
<xsd:attributeGroup name="RectAttributes">
<xsd:attribute name="CenterX" type="xsd:float" use="required"/>
<xsd:attribute name="CenterY" type="xsd:float" use="required"/>
<xsd:attribute name="Width" type="gpml:Dimension" use="required"/>
<xsd:attribute name="Height" type="gpml:Dimension" use="required"/>
</xsd:attributeGroup>
top

Attribute Group: ShapeStyleAttributes

Name ShapeStyleAttributes
Documentation Group of attributes defining the style (e.g. color, line style) of a pathway element.
XML Instance Representation
Color="gpml:ColorType [0..1] ?"
LineStyle="gpml:StyleType [0..1] ?"
LineThickness="xsd:float [0..1] ?"
Schema Component Representation
<xsd:attributeGroup name="ShapeStyleAttributes">
<xsd:attribute name="Color" type="gpml:ColorType" default="Black"/>
<-- 2017 adds fillColor attribute -->
<xsd:attribute name="LineStyle" type="gpml:StyleType" default="Solid"/>
<xsd:attribute name="LineThickness" type="xsd:float" default="1.0"/>
</xsd:attributeGroup>
top

Simple Type: RotationType

Super-types: None
Sub-types: None
Name RotationType
Content
  • Union of following types:
    • Locally defined type:
      • Base XSD Type: string
      • value comes from list: {'Top'|'Right'|'Bottom'|'Left'}
    • Locally defined type:
      • Base XSD Type: float
Documentation A float value (rotation in radians) or a string (Top, Right, Bottom, Left) for each of the four right angles.
Schema Component Representation
<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>
top

Simple Type: ColorType

Super-types: None
Sub-types: None
Name ColorType
Content
  • Union of following types:
    • Locally defined type:
      • Base XSD Type: hexBinary
    • Locally defined type:
      • Base XSD Type: string
      • value comes from list: {'Aqua'|'Black'|'Blue'|'Fuchsia'|'Gray'|'Green'|'Lime'|'Maroon'|'Navy'|'Olive'|'Purple'|'Red'|'Silver'|'Teal'|'White'|'Yellow'|'Transparent'}
Documentation Color as a hexadecimal number, binary code, or string (enumerated colors).
Schema Component Representation
<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>
top

Simple Type: StyleType

Super-types: xsd:string < StyleType (by restriction)
Sub-types: None
Name StyleType
Content
  • Base XSD Type: string
  • value comes from list: {'Solid'|'Broken'}
Schema Component Representation
<xsd:simpleType name="StyleType">
<xsd:restriction base="xsd:string">
<xsd:enumeration value="Solid"/>
<xsd:enumeration value="Broken"/>
</xsd:restriction>
</xsd:simpleType>
top

Simple Type: Dimension

Super-types: xsd:float < Dimension (by restriction)
Sub-types: None
Name Dimension
Content
  • Base XSD Type: float
  • value >= 0
Documentation Dimension for width and height. Cannot be negative values.
Schema Component Representation
<xsd:simpleType name="Dimension">
<xsd:restriction base="xsd:float">
<xsd:minInclusive value="0"/>
</xsd:restriction>
</xsd:simpleType>
top

Model Group: CommentGroup

Name CommentGroup
Documentation One or more comments, references, and key value attributes.
XML Instance Representation
<gpml:Comment
Source="xsd:string [0..1]"> [0..*] ?
xsd:string
</gpml:Comment>
<gpml:PublicationXref
ID="xsd:string [1]"
Database="xsd:string [1]"/> [0..*]
<gpml:BiopaxRef> ... </gpml:BiopaxRef> [0..*]
<gpml:Attribute
Key="xsd:string [1]"
Value="xsd:string [1]"/> [0..*]
Schema Component Representation
<xsd:group name="CommentGroup">
<xsd:sequence>
<xsd:element name="Comment" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:simpleContent>
<xsd:extension base="xsd:string">
<xsd:attribute name="Source" type="xsd:string"/>
</xsd:extension>
</xsd:simpleContent>
</xsd:complexType>
</xsd:element>
<xsd:element name="PublicationXref" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="ID" type="xsd:string" use="required"/>
<xsd:attribute name="Database" type="xsd:string" use="required"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="BiopaxRef" minOccurs="0" maxOccurs="unbounded"/>
<xsd:element name="Attribute" minOccurs="0" maxOccurs="unbounded">
<xsd:complexType>
<xsd:attribute name="Key" type="xsd:string" use="required"/>
<xsd:attribute name="Value" type="xsd:string" use="required"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:group>
top

Legend

Complex Type:

Schema Component Type

AusAddress

Schema Component Name
Super-types: Address < AusAddress (by extension)
Sub-types:
  • QLDAddress (by restriction)
If this schema component is a type definition, its type hierarchy is shown in a gray-bordered box.
Name AusAddress
Abstract no
The table above displays the properties of this schema component.
XML Instance Representation
<... country="Australia" >
<unitNo> string </unitNo> [0..1]
<houseNo> string </houseNo> [1]
<street> string </street> [1]
Start Choice [1]
<city> string </city> [1]
<town> string </town> [1]
End Choice
<state> AusStates </state> [1]
<postcode> string <<pattern = [1-9][0-9]{3}>> </postcode> [1] ?
</...>

The XML Instance Representation table above shows the schema component's content as an XML instance.

  • The minimum and maximum occurrence of elements and attributes are provided in square brackets, e.g. [0..1].
  • Model group information are shown in gray, e.g. Start Choice ... End Choice.
  • For type derivations, the elements and attributes that have been added to or changed from the base type's content are shown in bold.
  • If an element/attribute has a fixed value, the fixed value is shown in green, e.g. country="Australia".
  • Otherwise, the type of the element/attribute is displayed.
    • If the element/attribute's type is in the schema, a link is provided to it.
    • For local simple type definitions, the constraints are displayed in angle brackets, e.g. <<pattern = [1-9][0-9]{3}>>.
  • If a local element/attribute has documentation, it will be displayed in a window that pops up when the question mark inside the attribute or next to the element is clicked, e.g. <postcode>.
Schema Component Representation
<complexType name="AusAddress">
<complexContent>
<extension base="Address">
<sequence>
<element name="state" type="AusStates"/>
<element name="postcode">
<simpleType>
<restriction base="string">
<pattern value="[1-9][0-9]{3}"/>
</restriction>
</simpleType>
</element>
</sequence>
<attribute name="country" type="string" fixed="Australia"/>
</extension>
</complexContent>
</complexType>
The Schema Component Representation table above displays the underlying XML representation of the schema component. (Annotations are not shown.)
top

Glossary

Abstract (Applies to complex type definitions and element declarations). An abstract element or complex type cannot used to validate an element instance. If there is a reference to an abstract element, only element declarations that can substitute the abstract element can be used to validate the instance. For references to abstract type definitions, only derived types can be used.

All Model Group Child elements can be provided in any order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-all.

Choice Model Group Only one from the list of child elements and model groups can be provided in instances. See: http://www.w3.org/TR/xmlschema-1/#element-choice.

Collapse Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32). Then, collapse contiguous sequences of space characters into single space character, and remove leading and trailing space characters.

Disallowed Substitutions (Applies to element declarations). If substitution is specified, then substitution group members cannot be used in place of the given element declaration to validate element instances. If derivation methods, e.g. extension, restriction, are specified, then the given element declaration will not validate element instances that have types derived from the element declaration's type using the specified derivation methods. Normally, element instances can override their declaration's type by specifying an xsi:type attribute.

Key Constraint Like Uniqueness Constraint, but additionally requires that the specified value(s) must be provided. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Key Reference Constraint Ensures that the specified value(s) must match value(s) from a Key Constraint or Uniqueness Constraint. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Model Group Groups together element content, specifying the order in which the element content can occur and the number of times the group of element content may be repeated. See: http://www.w3.org/TR/xmlschema-1/#Model_Groups.

Nillable (Applies to element declarations). If an element declaration is nillable, instances can use the xsi:nil attribute. The xsi:nil attribute is the boolean attribute, nil, from the http://www.w3.org/2001/XMLSchema-instance namespace. If an element instance has an xsi:nil attribute set to true, it can be left empty, even though its element declaration may have required content.

Notation A notation is used to identify the format of a piece of data. Values of elements and attributes that are of type, NOTATION, must come from the names of declared notations. See: http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations.

Preserve Whitespace Policy Preserve whitespaces exactly as they appear in instances.

Prohibited Derivations (Applies to type definitions). Derivation methods that cannot be used to create sub-types from a given type definition.

Prohibited Substitutions (Applies to complex type definitions). Prevents sub-types that have been derived using the specified derivation methods from validating element instances in place of the given type definition.

Replace Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32).

Sequence Model Group Child elements and model groups must be provided in the specified order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-sequence.

Substitution Group Elements that are members of a substitution group can be used wherever the head element of the substitution group is referenced.

Substitution Group Exclusions (Applies to element declarations). Prohibits element declarations from nominating themselves as being able to substitute a given element declaration, if they have types that are derived from the original element's type using the specified derivation methods.

Target Namespace The target namespace identifies the namespace that components in this schema belongs to. If no target namespace is provided, then the schema components do not belong to any namespace.

Uniqueness Constraint Ensures uniqueness of an element/attribute value, or a combination of values, within a specified scope. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

top

Generated by xs3p (old link) . Last modified: