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