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