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