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