boardWidth
Range minimum is zero.
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.
groupRef
An interaction or graphicalLine that has an anchor.
hasAnchor
Currently: Specifies the glyph (graphical representation) to use for GPML elements (DataNode, Label, Shape, State).
Proposed: Expand it to also describe Anchors. It should replace the term currently used to specify the graphical representation of an Anchor. The current term is "Shape," which conflicts with the GPML element named "Shape." See details for term "Shape."
shapeType
arrowHead
Links a Shape to the pathway.
hasShape
Here comes the description on: email.
email
TextLabel of an object (DataNode, Group, Label, Shape, State).
textlabel
color
align
Legend
An explanatory list of the colors used for visualizing data on the pathway. Currently just a placeholder element -- not used.
Biopax
Element used to embed Biopax (namespace: http://www.biopax.org/release/biopax-level3.owl) content in a GPML document.
hasDataNode
Links the dataNode to the parent pathway.
stateType
The type of a State.
data-Source
See http://www.biopax.org/release/biopax-level3.owl#dataSource .
Group
A collection of structurally or functionally similar or related pathway elements..
The height of a DataNode, Label, Shape or State object.
height
biopaxRef
Refers to a biopax:PublicationXref.
hasBiopax
A pathway linking to a BioPAX object.
fontDecoration
A label is a text box which can be used to describe the elements of a pathway. It is mostly used as a name tag, to describe datanodes, interactions or cellular compartments in a pathway..
Label
Definition: Specifies a set of rules to govern layout of Graphical Lines and Interactions. PathVisio (Java): Line Type and GPML: ConnectorType
connectorType
WikiPathways GPML Vocabulary
Links the attribute to the parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).
hasAttribute
A graph diagram representing a biological process. Nodes of which represent genes, proteins, metabolites etc and the edges connecting two nodes represent the relationship between them, i.e how the two nodes interact.
Pathway
hasPublicationXref
Links a publicationXref to its parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).
Value of the key/value pair in the Attribute class.
value
Rotation of a shape.
rotation
hasComment
Links a comment to its parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).
fontWeight
Thickness of the font used, e.g a bold font would have more weight. Used for DataNodes, Labels and Shapes.
Middle of a pathway element in the y-direction.
centerY
zorder
Indicates the zorder of the object in the pathway.
Defines the relationship between the two entities it connects. The entities can be DataNodes or Anchors..
Interaction
RelX is the x-coordinate used when a point or state is linked to a another object - relative coordinate to the object that it is linked to (0,0 - center, 1,1 - bottom-right).
relX
fontSize
The person who created or edited the pathway in question.
author
Currently just a placeholder -- not used..
InfoBox
fillColor
hasState
Links a State to the pathway.
valign
Vertical alignment of a datanode, shape or label.
hasLegend
Links a Legend to the pathway.
Attribute
The name of a pathway.
name
hasInteraction
Links the interaction to the parent pathway.
Uniquely identifies a gpml:Group in a gpml:Pathway.
groupId
Comment
hasGroup
Links the groups to the pathway.
fontStrikethru
Font Strikethru of the objects (DataNode, Label, Shape).
Middle of a pathway element in the x-direction.
centerX
The identifier of a PublicationXref or Xref object.
id
State
The particular condition that biological entity is in at a specific time, e.g a protein may be phosphorylated or not, so phosphorylation is a state that a protein may have.
Links a Xref to its parent object (DataNode, Interaction, State).
hasXref
The width of an object (DataNode, Label, Shape, State).
width
The date of the last modification of the pathway.
last-Modified
Key of the key/value pair in the Attribute class.
key
graphId
A GraphId is a unique (per Pathway) identifier for a pathway element, such as DataNode, Interaction, GraphicalLine, Label, Point, Group, Shape, State and Anchor.
The maintainer of the pathway. Currently not used in WP.
maintainer
Position of an anchor on the line it belongs to.
position
The style of a group.
style
The line style of a GraphicalLine or Interaction as well as the line style of a border of a DataNode, Label, Shape or State.
lineStyle
RelY is the y-coordinate used when a point or state is linked to a another object - relative coordinate to the object that it is linked to (0,0 - center, 1,1 - bottom-right).
relY
An interaction or graphical line that has a point.
hasPoint
The font style of the pathway element (DataNode, Label, Shape).
fontStyle
The organism of the pathway. Latin name usually provided by BridgeDb.
organism
The Thickness of a GraphicalLine or Interaction as well as the border Thickness of a DataNode, Label, Shape or State.
lineThickness
hasLabel
Links the labels to the pathway.
version
The version of a Pathway (currently not used in WP).
PublicationXref
y
The y-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.
boardHeight
Range minimum is zero.
RequiresCurationAttention
type
Specifies the type of an object (DataNode, GraphicalLine, Interaction).
database
Equivalent to http://www.biopax.org/release/biopax-level3.owl#db .
Shape can refer to two different things in GPML, both of which are associated with graphical elements.
Shape
The x-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.
x
hasInfoBox
Links an InfoBox object to a pathway.
Point
hasGraphicalLine
Links the graphicalLine to the parent pathway.
graphRef
A GraphRef indicates a \"depends on\" or child/parent relationship between two Pathway elements. The element with the GraphRef is the child, and the element referred to by the GraphRef is the parent. The parent's GraphId will be specified by the child's GraphRef.
The source of a comment.
source
href
The possible hyperlink in a Label in a pathway.
Shape of an anchor.
shape
license
The license of a pathway.
fontName
A connector between graphical shapes or between a graphical shape and a biopax:Entity..
GraphicalLine
Xref
DataNode
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 the range for gpml:Type.
Anchor