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