zorder
Indicates the zorder of the object in the pathway.
fontDecoration
Deprecated: Not in use.
Deprecated: Not in use.
RequiresCurationAttention
biopaxRef
Reuse of references defined by BioPAX.
y
The y-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.
Boolean property for the existence of an Attribute class associated with a given object.
hasAttribute
The typographic style or font face applied to displayed text, e.g., Arial.
fontStyle
Currently just a placeholder -- not used.
InfoBox
The hexidecimal color value used to paint the area of an object, not including its border.
fillColor
Middle of a pathway element in the x-direction.
centerX
Specifies the datasource for the identifier provided as an Xref. Equivalent to http://vocabularies.bridgedb.org/ops#DataSource conventional name .
database
The x-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.
x
The identifier of a PublicationXref or Xref object.
id
boardWidth
Range minimum is zero.
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.
href
The hyperlink optionally specified in a Label.
fontWeight
Thickness of the font used, e.g a bold font would have more weight. Used for DataNodes, Labels and Shapes.
Boolean property for the existence of a PublicationXref associated with a given object.
hasPublicationXref
Deprecated: Not in use.
fontStrikethru
hasInteraction
Boolean property for the existence of an Interaction in a given pathway.
A particular condition, mode or modification of an entity, e.g., phosphorylated, activated, mutated, SNP, etc.
State
lineThickness
The pixel value for the width of a given line, interaction or border.
fontName
The name of the set of printable text characters to be used for visualization.
TextLabel of an object (DataNode, Group, Label, Shape, State).
textlabel
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).
style
The type of Group, e.g., Complex.
hasComment
Boolean property for the existence of a Comment class associated with a given object.
Specifies the type of an object (DataNode, GraphicalLine, Interaction).
type
Boolean property for the existence of a DataNode in a given pathway.
hasDataNode
rotation
The degree value of angular offset relative to the center of a given object.
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
Point
A location in 2-dimensional space defined by x and y coordinates.
Boolean property for the existence of a Group in a given pathway.
hasGroup
WikiPathways GPML Vocabulary
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.
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."
arrowHead
Specifies the glyph at the ends of lines and interactions.
hasLegend
Boolean property for the existence of a Legend in a given pathway.
Vertical alignment of displayed text, e.g., Top, Middle, Bottom.
valign
height
The pixel value for the y-dimensional length of a given object.
email
Deprecated: An electronic mail address. Used to reference the author or maintainer of a pathway prior to WikiPathways.
The visual appearance of a line or border, e.g., Solid or Broken.
lineStyle
Attribute
Element used to specify key/value paired information for a given object.
hasPoint
Boolean property for the existence of a Point in a given line or interaction.
version
The version of a Pathway (currently not used in WP).
Boolean property for the existence of a Label in a given pathway.
hasLabel
The color to be used for visualization.
color
boardHeight
Range minimum is zero.
A free text field to describe the nature or category of a given state.
stateType
hasInfoBox
Boolean property for the existence of an InfroBox in a given pathway.
connectorType
Specifies a set of rules to govern layout of Graphical Lines and Interactions. PathVisio (Java): Line Type and GPML: ConnectorType
hasBiopax
Boolean property for the existence of a BioPax class associated with a given pathway.
centerY
Middle of a pathway element in the y-direction.
value
Value of the key/value pair in the Attribute class.
Shape can refer to two different things in GPML, both of which are associated with graphical elements.
Shape
key
Key of the key/value pair in the Attribute class.
hasXref
Boolean property for the existence of an Xref associated with a given object.
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 subclasses of wp:DataNode or the wpTypes vocabulary defined for use in applications..
A graph diagram representing a biological process as a set of interactions and relationships among genes, proteins, metabolites, and other factors in the context of cellular compartments, tissues and organisms.
Pathway
The date of the last modification of the pathway.
last-Modified
Label
A text field which can be used to annotate any aspect of a pathway.
Deprecated: Not in use.
data-Source
Elements used to provide descriptions and arbitrary notes for a given object.
Comment
The visual representation of an anchor, e.g., Circle or None.
shape
Horizontal alignment of displayed text, e.g., Left, Center, Right.
align
Boolean property for the existence of an Anchor on a given line or interaction.
hasAnchor
Boolean property for the existence of a GraphicalLine in a given pathway.
hasGraphicalLine
The person who created or edited the pathway in question.
author
width
The pixel value for the x-dimensional length of a given object.
A collection of structurally or functionally similar or related pathway elements.
Group
The point value for the size of the font.
fontSize
Interaction
Defines the biochemical relationship between DataNodes or with Anchors on other Interactions. An Xref can be specified for Interactions (in contrast to GraphicalLines).
name
The name of a pathway.
Element used to embed Biopax (namespace: http://www.biopax.org/release/biopax-level3.owl) content in a GPML document.
Biopax
hasState
Boolean property for the existence of a State in a given pathway.
Reference to a database entry that matches the node
in the pathway. It is a combination of an identifier of the entity and an
identifier of the database in which the entity is found.
Xref
The scientific name (e.g., Homo sapiens) of the species being described by the pathway.
organism
Uniquely identifies a gpml:Group in a gpml:Pathway.
groupId
Boolean property for the existence of a Shape in a given pathway.
hasShape
The license of a pathway.
license
PublicationXref
Defines a literature reference. Refers to a BioPAX definition.
Proportional distance of an anchor along the line it belongs to, between 0 and 1.
position
A connection point on a graphical line or an interaction, where another graphical line or interaction can be connected.
Anchor
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
maintainer
The maintainer of the pathway. Currently not used in WP.
The author, reference or category of a comment. Used to help parse pathway-level comments, e.g., the descriptions displayed at WikiPathways.org are comments with source="WikiPathways-description".
source
GraphicalLine
A visual annotation, often used to partition space or connect other annotation, e.g., Shapes. An Xref can not be specified for GraphicalLines (in contrast to Interactions).
An explanatory list of the colors used for visualizing data on the pathway. Not currently used.
Legend