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