The WikiPathways GPML Vocabulary

This page describes the GPML ontology for WikiPathways (http://vocabularies.wikipathways.org/gpml#). Make sure to visit our homepage!

This ontology is written by (in random order) Andra Waagmeester, Martina Kutmon, Egon Willighagen, and Ryan Miller.

Namespaces

@prefix gpml: <http://vocabularies.wikipathways.org/gpml#> .

@prefix biopax: <http://www.biopax.org/release/biopax-level3.owl#> .

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd:< http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .

Classes

Anchor

gpml:Anchor

An anchor is a connection point on a graphical line or an interaction, where another graphical line or interaction can be connected.

Attribute

gpml:Attribute

Biopax

gpml:Biopax

Element used to embed Biopax (namespace: http://www.biopax.org/release/biopax-level3.owl) content in a GPML document.

Comment

gpml:Comment

DataNode

gpml: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..

GraphicalLine

gpml:GraphicalLine

A connector between graphical shapes or between a graphical shape and a biopax:Entity.

InfoBox

gpml:InfoBox

Currently just a placeholder -- not used.

Group

gpml:Group

A collection of structurally or functionally similar or related pathway elements.

Interaction

gpml:Interaction

Defines the relationship between the two entities it connects. The entities can be DataNodes or Anchors.

Label

gpml: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.

Legend

gpml:Legend

An explanatory list of the colors used for visualizing data on the pathway. Currently just a placeholder element -- not used.

Pathway

gpml: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.

Point

gpml:Point

A position in 2-dimensional space defined by x and y coordinates.

PublicationXref

gpml:PublicationXref

RequiresCurationAttention

gpml:RequiresCurationAttention

Shape

gpml:Shape

Shape can refer to two different things in GPML, both of which are associated with graphical elements.

State

gpml: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.

Xref

gpml:Xref

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.

Object Properties

hasAnchor

gpml:hasAnchor

An interaction or graphicalLine that has an anchor.

This property has gpml:GraphicalLine and gpml:Interaction as domain and gpml:Anchor as range.

hasAttribute

gpml:hasAttribute

Links the attribute to the parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Group, gpml:Interaction, gpml:Label, gpml:Pathway, gpml:Shape, and gpml:State as domain and gpml:Attribute as range.

hasBiopax

gpml:hasBiopax

A pathway linking to a BioPAX object.

This property has gpml:Pathway as domain and gpml:Biopax as range.

hasComment

gpml:hasComment

Links a comment to its parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Group, gpml:Interaction, gpml:Label, gpml:Pathway, gpml:Shape, and gpml:State as domain and gpml:Comment as range.

hasDataNode

gpml:hasDataNode

Links the dataNode to the parent pathway.

This property has gpml:Pathway as domain and gpml:DataNode as range.

hasGraphicalLine

gpml:hasGraphicalLine

Links the graphicalLine to the parent pathway.

This property has gpml:Pathway as domain and gpml:GraphicalLine as range.

hasGroup

gpml:hasGroup

Links the groups to the pathway.

This property has gpml:Pathway as domain and gpml:Group as range.

hasInfoBox

gpml:hasInfoBox

Links an InfoBox object to a pathway.

This property has gpml:Pathway as domain and gpml:InfoBox as range.

hasInteraction

gpml:hasInteraction

Links the interaction to the parent pathway.

This property has gpml:Pathway as domain and gpml:Interaction as range.

hasLabel

gpml:hasLabel

Links the labels to the pathway.

This property has gpml:Pathway as domain and gpml:Label as range.

hasLegend

gpml:hasLegend

Links a Legend to the pathway.

This property has gpml:Pathway as domain and gpml:Legend as range.

hasPoint

gpml:hasPoint

An interaction or graphical line that has a point.

This property has gpml:GraphicalLine and gpml:Interaction as domain and gpml:Point as range.

hasPublicationXref

gpml:hasPublicationXref

Links a publicationXref to its parent object (DataNode, GraphicalLine, Group, Interaction, Label, Pathway, Shape, State).

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Group, gpml:Interaction, gpml:Label, gpml:Pathway, gpml:Shape, and gpml:State as domain and gpml:PublicationXref as range.

hasShape

gpml:hasShape

Links a Shape to the pathway.

This property has gpml:Pathway as domain and gpml:Shape as range.

hasState

gpml:hasState

Links a State to the pathway.

This property has gpml:Pathway as domain and gpml:State as range.

hasXref

gpml:hasXref

Links a Xref to its parent object (DataNode, Interaction, State).

This property has gpml:DataNode, gpml:Interaction, and gpml:State as domain and gpml:Xref as range.

Data Properties

align

gpml:align

This property has gpml:DataNode, gpml:Label, and gpml:Shape as domain and xsd:string as range.

arrowHead

gpml:arrowHead

This property has gpml:Point as domain and xsd:string as range.

author

gpml:author

The person who created or edited the pathway in question.

This property has gpml:Pathway as domain and xsd:string as range.

biopaxRef

gpml:biopaxRef

Reuse of references defined by BioPAX.

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Group, gpml:Interaction, gpml:Label, gpml:Pathway, gpml:Shape, and gpml:State as domain and xsd:string as range.

Refers to a biopax:PublicationXref.

boardHeight

gpml:boardHeight

Range minimum is zero.

This property has gpml:Pathway as domain and xsd:float as range.

boardWidth

gpml:boardWidth

Range minimum is zero.

This property has gpml:Pathway as domain and xsd:float as range.

centerX

gpml:centerX

Middle of a pathway element in the x-direction.

This property has gpml:DataNode, gpml:InfoBox, gpml:Label, gpml:Legend, and gpml:Shape as domain and xsd:float as range.

centerY

gpml:centerY

Middle of a pathway element in the y-direction.

This property has gpml:DataNode, gpml:InfoBox, gpml:Label, gpml:Legend, and gpml:Shape as domain and xsd:float as range.

color

gpml:color

The color to be used for visualization.

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Label, gpml:Interaction, gpml:Shape, and gpml:State as domain and xsd:hexBinary as range.

connectorType

gpml:connectorType

Specifies a set of rules to govern layout of Graphical Lines and Interactions. PathVisio (Java): Line Type and GPML: ConnectorType

This property has gpml:GraphicalLine and gpml:Interaction as domain and xsd:string as range.

data-Source

gpml:data-Source

This property has gpml:Pathway as domain and xsd:string as range.

See biopax:dataSource.

database

gpml:database

Equivalent to http://www.biopax.org/release/biopax-level3.owl#db .

This property has gpml:PublicationXref and gpml:Xref as domain and xsd:string as range.

Equivalent to biopax:db.

email

gpml:email

An electronic mail address. Used to reference the author or maintainer of a pathway prior to WikiPathways.

Here comes the description on: email.

This property has gpml:Pathway as domain and xsd:string as range.

fillColor

gpml:fillColor

This property has gpml:DataNode, gpml:Label, gpml:Shape, and gpml:State as domain and xsd:hexBinary as range.

fontDecoration

gpml:fontDecoration

This property has gpml:Label and gpml:Shape as domain and xsd:string as range.

fontName

gpml:fontName

The name of the set of printable text characters to be used for visualization.

This property has gpml:Label and gpml:Shape as domain and xsd:string as range.

fontSize

gpml:fontSize

This property has gpml:Label and gpml:Shape as domain and xsd:nonNegativeInteger as range.

fontStrikethru

gpml:fontStrikethru

Font Strikethru of the objects (DataNode, Label, Shape).

This property has gpml:DataNode, gpml:Label and gpml:Shape as domain and xsd:string as range.

fontStyle

gpml:fontStyle

The typographic style or font face applied to displayed text, e.g., Arial.

The font style of the pathway element (DataNode, Label, Shape).

This property has gpml:DataNode, gpml:Label and gpml:Shape as domain and xsd:string as range.

fontWeight

gpml:fontWeight

Thickness of the font used, e.g a bold font would have more weight. Used for DataNodes, Labels and Shapes.

This property has gpml:DataNode, gpml:Label and gpml:Shape as domain and xsd:string as range.

graphId

gpml: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.

This property has gpml:Anchor, gpml:DataNode, gpml:GraphicalLine, gpml:Group, gpml:Interaction, gpml:Label, gpml:Point, gpml:Shape and gpml:State as domain and xsd:string as range.

graphRef

gpml: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.

This property has gpml:Point and gpml:State as domain and xsd:string as range.

groupId

gpml:groupId

Uniquely identifies a gpml:Group in a gpml:Pathway.

This property has gpml:Group as domain and xsd:string as range.

groupRef

gpml: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.

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Group, gpml:Interaction, gpml:Label and gpml:Shape as domain and xsd:string as range.

height

gpml:height

The height of a DataNode, Label, Shape or State object.

This property has gpml:DataNode, gpml:Label, gpml:Shape, and gpml:State as domain and xsd:float as range.

href

gpml:href

The possible hyperlink in a Label in a pathway.

This property has gpml:Label as domain and xsd:string as range.

id

gpml:id

The identifier of a PublicationXref or Xref object.

This property has gpml:PublicationXref and gpml:Xref as domain and xsd:string as range.

Equivalent to biopax:id.

key

gpml:key

Key of the key/value pair in the Attribute class.

This property has gpml:Attribute as domain and xsd:string as range.

last-Modified

gpml:last-Modified

The date of the last modification of the pathway.

This property has gpml:Pathway as domain and xsd:string as range.

license

gpml:license

The license of a pathway.

This property has gpml:Pathway as domain and xsd:string as range.

lineStyle

gpml:lineStyle

Describes how the line is visualized.

The line style of a GraphicalLine or Interaction as well as the line style of a border of a DataNode, Label, Shape or State.

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Interaction, gpml:Label, gpml:Shape, and gpml:State as domain and xsd:string as range.

lineThickness

gpml:lineThickness

The Thickness of a GraphicalLine or Interaction as well as the border Thickness of a DataNode, Label, Shape or State.

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Interaction, gpml:Label, gpml:Shape, and gpml:State as domain and xsd:string as range.

maintainer

gpml:maintainer

The maintainer of the pathway. Currently not used in WP.

This property has gpml:Pathway as domain and xsd:string as range.

name

gpml:name

The name of a pathway.

This property has gpml:Pathway as domain and xsd:string as range.

organism

gpml:organism

The organism of the pathway. Latin name usually provided by BridgeDb.

This property has gpml:Pathway as domain and xsd:string as range.

position

gpml:position

Proportional distance of an anchor along the line it belongs to, between 0 and 1.

Position of an anchor on the line it belongs to.

This property has gpml:Anchor as domain and xsd:float as range.

relX

gpml: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).

This property has gpml:Point and gpml:State as domain and xsd:float as range.

relY

gpml: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).

This property has gpml:Point and gpml:State as domain and xsd:float as range.

rotation

gpml:rotation

Rotation of a shape.

This property has gpml:Shape as domain and xsd:float as range.

shape

gpml:shape

Shape of an anchor.

This property has gpml:Anchor as domain and xsd:string as range.

shapeType

gpml: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."

This property has gpml:DataNode, gpml:Label, gpml:Shape, and gpml:State as domain and xsd:string as range.

source

gpml:source

The source of a comment.

This property has gpml:Anchor as domain and xsd:string as range.

stateType

gpml:stateType

The type of a State.

This property has gpml:State as domain and xsd:string as range.

style

gpml:style

The style of a group.

This property has gpml:Group as domain and xsd:string as range.

textlabel

gpml:textlabel

TextLabel of an object (DataNode, Group, Label, Shape, State).

This property has gpml:DataNode, gpml:Group, gpml:Label, gpml:Shape, and gpml:State as domain and xsd:string as range.

type

gpml:type

Specifies the type of an object (DataNode, GraphicalLine, Interaction).

This property has gpml:DataNode, gpml:GraphicalLine, and gpml:Interaction as domain and xsd:string as range.

valign

gpml:valign

Alignment of displayed text in the vertical dimension, either Top, Middle or Bottom.

Vertical alignment of a datanode, shape or label.

This property has gpml:DataNode, gpml:Label, and gpml:Shape as domain and xsd:string as range.

value

gpml:value

Value of the key/value pair in the Attribute class.

This property has gpml:Attribute as domain and xsd:string as range.

version

gpml:version

The version of a Pathway (currently not used in WP).

This property has gpml:Pathway as domain and xsd:string as range.

width

gpml:width

The width of an object (DataNode, Label, Shape, State).

This property has gpml:DataNode,gpml:Label, gpml:Shape, and gpml:State as domain and xsd:float as range.

x

gpml:x

The x-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.

This property has gpml:Point as domain and xsd:float as range.

y

gpml:y

The y-coordinate of a point in the 2-dimensional plane in which a pathway is drawn.

This property has gpml:Point as domain and xsd:float as range.

zorder

gpml:zorder

Indicates the zorder of the object in the pathway.

This property has gpml:DataNode, gpml:GraphicalLine, gpml:Interaction, gpml:Label, gpml:Shape, and gpml:State as domain and xsd:integer as range.

Technical notes

The conversion of gpml#foo to index.html#foo is done with .htaccess and a RewriteRule. The source code is available from the WpVocabularies repository at GitHub. The OWL ontology can be extracted here.