The WikiPathways GPML Vocabulary

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

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#> .

Classes

Anchor

gpml:Anchor

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

Attribute

gpml:Attribute

Element used to specify key/value paired information for a given object.

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

Elements used to provide descriptions and arbitrary notes for a given object.

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 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).

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 biochemical relationship between DataNodes or with Anchors on other Interactions. An Xref can be specified for Interactions (in contrast to GraphicalLines).

Label

gpml:Label

A text field which can be used to annotate any aspect of a pathway.

Legend

gpml:Legend

An explanatory list of the colors used for visualizing data on the pathway. Not currently used.

Pathway

gpml: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.

Point

gpml:Point

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

PublicationXref

gpml:PublicationXref

Defines a literature reference. Refers to a BioPAX definition.

RequiresCurationAttention

gpml:RequiresCurationAttention

Deprecated: Not in use.

Shape

gpml:Shape

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

State

gpml:State

A particular condition, mode or modification of an entity, e.g., phosphorylated, activated, mutated, SNP, etc.

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

Boolean property for the existence of an Anchor on a given line or interaction.

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

hasAttribute

gpml:hasAttribute

Boolean property for the existence of an Attribute class associated with a given object.

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

Boolean property for the existence of a BioPax class associated with a given pathway.

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

hasComment

gpml:hasComment

Boolean property for the existence of a Comment class associated with a given object.

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

Boolean property for the existence of a DataNode in a given pathway.

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

hasGraphicalLine

gpml:hasGraphicalLine

Boolean property for the existence of a GraphicalLine in a given pathway.

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

hasGroup

gpml:hasGroup

Boolean property for the existence of a Group in a given pathway.

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

hasInfoBox

gpml:hasInfoBox

Boolean property for the existence of an InfroBox in a given pathway.

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

hasInteraction

gpml:hasInteraction

Boolean property for the existence of an Interaction in a given pathway.

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

hasLabel

gpml:hasLabel

Boolean property for the existence of a Label in a given pathway.

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

hasLegend

gpml:hasLegend

Boolean property for the existence of a Legend in a given pathway.

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

hasPoint

gpml:hasPoint

Boolean property for the existence of a Point in a given line or interaction.

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

hasPublicationXref

gpml:hasPublicationXref

Boolean property for the existence of a PublicationXref associated with a given object.

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

Boolean property for the existence of a Shape in a given pathway.

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

hasState

gpml:hasState

Boolean property for the existence of a State in a given pathway.

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

hasXref

gpml:hasXref

Boolean property for the existence of an Xref associated with a given object.

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

Data Properties

align

gpml:align

Horizontal alignment of displayed text, e.g., Left, Center, Right.

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

arrowHead

gpml:arrowHead

Specifies the glyph at the ends of lines and interactions.

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

Deprecated: Not in use.

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

database

gpml:database

Specifies the datasource for the identifier provided as an Xref. Equivalent to http://vocabularies.bridgedb.org/ops#DataSource conventional name .

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

Equivalent to BridgeDb:DataSource.

email

gpml:email

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

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

fillColor

gpml:fillColor

The hexidecimal color value used to paint the area of an object, not including its border.

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

fontDecoration

gpml:fontDecoration

Deprecated: Not in use.

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

The point value for the size of the font.

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

fontStrikethru

gpml:fontStrikethru

Deprecated: Not in use.

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.

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 pixel value for the y-dimensional length of a given object.

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

href

gpml:href

The hyperlink optionally specified in a Label.

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

The visual appearance of a line or border, e.g., Solid or Broken.

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 pixel value for the width of a given line, interaction or border.

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 scientific name (e.g., Homo sapiens) of the species being described by the pathway.

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.

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

The degree value of angular offset relative to the center of a given object.

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

shape

gpml:shape

The visual representation of an anchor, e.g., Circle or None.

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 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".

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

stateType

gpml:stateType

A free text field to describe the nature or category of a given state.

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

style

gpml:style

The type of Group, e.g., Complex.

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

Vertical alignment of displayed text, e.g., Top, Middle, Bottom.

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 pixel value for the x-dimensional length of a given object.

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 and contributor history are available from the WpVocabularies repository at GitHub. The original ontology was constructed by Andra Waagmeester, Martina Kutmon and Alexander Pico. The OWL ontology can be extracted here.