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