GPML
2015-05-22
http://vocabularies.wikipathways.org/gpml#
gpml
Andra Waagmeester
Maastricht University
Martina Kutmon
Comment
Attribute
requiresCurationAttention
Legend
An explanatory list of the colors used for visualizing data on the pathway. Currently just a placeholder element -- not used.
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.
Biopax
Element used to embed <a href="http://www.biopax.org/owldoc/Level3/">Biopax</a> (namespace: <a href="http://www.biopax.org/release/biopax-level3.owl">http://www.biopax.org/release/biopax-level3.owl</a>) content in a GPML document.
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.
InfoBox
Currently just a placeholder -- not used.
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.
Shape
Shape can refer to two different things in GPML, both of which are associated with graphical elements.
Group
A collection of structurally or functionally similar or related pathway elements.
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 <a href="http://vocabularies.wikipathways.org/gpml#Type">gpml:Type</a>.
Point
Anchor
Interaction
defines the relationship between the two entities it connects. The entities can be DataNodes or Anchors.
Graphical Line
A connector between graphical shapes or between a graphical shape and a biopax:Entity.
Xref
PublicationXref
hasXref
Links a Xref to its parent object (DataNode, Interaction, State)
hasShape
Links a shape to the pathway.
hasDataNode
Links the dataNode to the parent pathway.
hasState
Links the state object to the parent pathway.
value
Value of the key/value pair in the Attribute class.
source
The source of a comment.
rotation
Rotation of a shape.
hasInteraction
Links the interaction to the parent pathway.
key
Key of the key/value pair in the Attribute class.
hasInfoBox
Links an InfoBox object to a Pathway.
hasGroup
Links the groups to the pathway.
hasLabel
Links the labels to the pathway.
boardHeight
Range minimum is zero
fontStyle
The font style of the pathway element (DataNode, Label, Shape).
fontAttributes
Collection of different font attributes.
lineThickness
The thickness of a GraphicalLine or Interaction as well as the border thickness for DataNodes, Labels, Shapes and States.
hasBiopax
A pathway linking to a BioPAX object.
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.
fontSize
version
The version of a Pathway (currently not used in WP).
license
The license of a pathway.
fontName
groupId
Uniquely identifies a gpml:Group in a gpml:Pathway.
align
data-Source
See http://www.biopax.org/release/biopax-level3.owl#dataSource
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.
email
Here comes the description on: email
organism
The organism of the pathway. Latin name usually provided by BridgeDb.
color
This would be easier to work with if it had a hash "#" at the beginning to be consistent with CSS.
centerY
Middle of a pathway element in the y-direction.
maintainer
The maintainer of the pathway. Currently not used in WP.
valign
Vertical alignment of a datanode, shape or label.
last-Modified
The date of the last modification of the pathway.
author
The person who created or edited the pathway in question.
fontWeight
Thickness of the font used, e.g a bold font would have more weight. Used for DataNodes, Labels and Shapes.
biopaxRef
Refers to a biopax:PublicationXref.
fontDecoration
fontStrikethru
Font Strikethru of the objects (DataNode, Label, Shape).
height
The height of a DataNode, Label, Shape or State object
href
The possible hyperlink in a Label in a pathway.
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.
name
The name of a pathway.
centerX
Middle of a pathway element in the x-direction.
graph Ref
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.
textlabel
TextLabel of an object (DataNode, Group, Label, Shape, State).
relX
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).
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).
width
The width of an object (DataNode, Label, Shape, State).
id
The identifier of a PublicationXref or Xref object.
database
Equivalent to http://www.biopax.org/release/biopax-level3.owl#db
graphics
Graphics is a collection of properties. We think the elements should specify the subproperties directly but it is still good to keep the superproperty in as well.
fillColor
zorder
Indicates the zorder of the object in the pathway.
shapeStyleAttributes
arrowHead
position
Position of an anchor on the line it belongs to.
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."
hasGraphicalLine
Links the graphicalLine to the parent pathway.
hasAnchor
An interaction or graphicalLine that has an anchor.
hasComment
Links a comment to its parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State)
x
The x-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.
y
The y-coordinate of a point in the 2-dimensional plane a pathway is drawn.
connector Type
<p>
<b>Definition:</b> Specifies a set of rules to govern layout of Graphical Lines and Interactions.
</p>
<ul>
<li>PathVisio (Java): Line Type</li>
<li>GPML: ConnectorType</li>
</ul>
hasPublicationXref
Links a publicationXref to its parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State)
boardWidth
Range minimum is zero
rectAttributes
hasAttribute
Links the attribute to the parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State)
stateType
The type of a State.
hasPoint
An interaction or graphical line that has a point.
shape
Shape of an anchor.
type
Specifies the type of an object (DataNode, GraphicalLine, Interaction)
hasLegend
Links a Legend to the Pathway.