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