Indicates the zorder of the object in the pathway.
zorder
database
Equivalent to http://www.biopax.org/release/biopax-level3.owl#db .
shape
Shape of an anchor.
groupRef
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.
lineStyle
The line style of a GraphicalLine or Interaction as well as the line style of a border of a DataNode, Label, Shape or State.
The maintainer of the pathway. Currently not used in WP.
maintainer
Biopax
Element used to embed Biopax (namespace: http://www.biopax.org/release/biopax-level3.owl) content in a GPML document.
Rotation of a shape.
rotation
color
Range minimum is zero.
boardWidth
Currently just a placeholder -- not used..
InfoBox
height
The height of a DataNode, Label, Shape or State object.
hasInteraction
Links the interaction to the parent pathway.
fontStrikethru
Font Strikethru of the objects (DataNode, Label, Shape).
Thickness of the font used, e.g a bold font would have more weight. Used for DataNodes, Labels and Shapes.
fontWeight
Label
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..
lineThickness
The Thickness of a GraphicalLine or Interaction as well as the border Thickness of a DataNode, Label, Shape or State.
Uniquely identifies a gpml:Group in a gpml:Pathway.
groupId
key
Key of the key/value pair in the Attribute class.
Value of the key/value pair in the Attribute class.
value
Definition: Specifies a set of rules to govern layout of Graphical Lines and Interactions. PathVisio (Java): Line Type and GPML: ConnectorType
connectorType
hasComment
Links a comment to its parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).
The type of a State.
stateType
hasShape
Links a Shape to the pathway.
license
The license of a pathway.
fontStyle
The font style of the pathway element (DataNode, Label, Shape).
The identifier of a PublicationXref or Xref object.
id
An interaction or graphical line that has a point.
hasPoint
position
Position of an anchor on the line it belongs to.
The width of an object (DataNode, Label, Shape, State).
width
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.
Links a Xref to its parent object (DataNode, Interaction, State).
hasXref
A pathway linking to a BioPAX object.
hasBiopax
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
centerY
Middle of a pathway element in the y-direction.
Legend
An explanatory list of the colors used for visualizing data on the pathway. Currently just a placeholder element -- not used.
fontDecoration
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.
hasGraphicalLine
Links the graphicalLine to the parent pathway.
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
biopaxRef
Refers to a biopax:PublicationXref.
style
The style of a group.
The source of a comment.
source
hasPublicationXref
Links a publicationXref to its parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).
An interaction or graphicalLine that has an anchor.
hasAnchor
fontName
Point
The x-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.
x
Middle of a pathway element in the x-direction.
centerX
Here comes the description on: email.
email
TextLabel of an object (DataNode, Group, Label, Shape, State).
textlabel
fillColor
hasInfoBox
Links an InfoBox object to a pathway.
hasLegend
Links a Legend to the pathway.
Defines the relationship between the two entities it connects. The entities can be DataNodes or Anchors..
Interaction
Vertical alignment of a datanode, shape or label.
valign
Shape
Shape can refer to two different things in GPML, both of which are associated with graphical elements.
hasLabel
Links the labels to the pathway.
Xref
organism
The organism of the pathway. Latin name usually provided by BridgeDb.
data-Source
See http://www.biopax.org/release/biopax-level3.owl#dataSource .
Attribute
author
The person who created or edited the pathway in question.
Links the attribute to the parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).
hasAttribute
Links the groups to the pathway.
hasGroup
relX
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).
The version of a Pathway (currently not used in WP).
version
Links a State to the pathway.
hasState
RequiresCurationAttention
PublicationXref
Group
A collection of structurally or functionally similar or related pathway elements..
last-Modified
The date of the last modification of the pathway.
y
The y-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.
arrowHead
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
The possible hyperlink in a Label in a pathway.
href
The name of a pathway.
name
type
Specifies the type of an object (DataNode, GraphicalLine, Interaction).
WikiPathways GPML Vocabulary
align
GraphicalLine
A connector between graphical shapes or between a graphical shape and a biopax:Entity..
Comment
Links the dataNode to the parent pathway.
hasDataNode
fontSize
Anchor
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.
State
boardHeight
Range minimum is zero.
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.