The WikiPathways WP Types Ontology

This page describes the WP Types ontology for WikiPathways (http://vocabularies.wikipathways.org/wpTypes#). 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 wpTypes: <http://vocabularies.wikipathways.org/wpTypes#> .

@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

Datanode

wpTypes:Datanode

A DataNode on the diagram.

Interaction

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..

wpTypes:Interaction

An Interaction between DataNode(s) on the diagram.

SubClasses

GeneProduct node

An entity representing any product of a given gene, including DNA, RNA and Protein. This is the most generic representation of a gene-based biomolecule and is useful when more than one representation might be useful in the given context.

wpTypes:GeneProduct

This class is a subclass of wpTypes:DataNode.

Metabolite node

An entity representing a metabolite, including chemical compounds that participate in or are produced by metabolic reactions, but also other chemical compounds that participate in a pathway otherwise.

wpTypes:Metabolite

This class is a subclass of wpTypes:DataNode.

Pathway node

A biological process representing a set of interactions and relationships among genes, proteins, metabolites, and other factors in the context of cellular compartments, tissues and organisms.

wpTypes:Pathway

This class is a subclass of wpTypes:DataNode.

Protein node

A biomolecular polymer of amino acids, translated from mRNA.

wpTypes:Protein

This class is a subclass of wpTypes:DataNode.

RNA node

An entity representing an RNA peptide, including mRNA, miRNA, etc. This is commonly used to explicitly represent mRNA transcripts (excluding DNA or protein forms) or other RNA species, like miRNA, exRNA, lncRNA, etc.

wpTypes:Rna

This class is a subclass of wpTypes:DataNode.

Unknown node

An unspecified biological entity or factor. Should only be used if the type is truly unknown or is different from the ones covered by other data node types.

wpTypes:Unknown

This class is a subclass of wpTypes:DataNode.

Arrow interaction

A style of line or interaction that includes a glyph at the terminus.

wpTypes:Arrow

This class is a subclass of wpTypes:Interaction.

Broken Arrow interaction

A style of line or interaction with a glyph at the terminus that allows for regular gaps in their paths.

wpTypes:BrokenArrow

This class is a subclass of wpTypes:Interaction.

Broken Line interaction

A style of line or interaction that allows for regular gaps in their paths.

wpTypes:BrokenLine

This class is a subclass of wpTypes:Interaction.

Curved interaction

A style of line or interaction that allows for smooth arcs and bends in their paths.

wpTypes:Curved

This class is a subclass of wpTypes:Interaction.

Elbow interaction

A style of line or interaction that allows for 90 degree bends in their paths.

wpTypes:Elbow

This class is a subclass of wpTypes:Interaction.

Line interaction

A visual annotation, often used to partition space or connect other annotations.

wpTypes:Line

This class is a subclass of wpTypes:Interaction.

TBar interaction

An interaction in which the source entity has an inhibitory effect on the target entity or interaction.

wpTypes:TBar

This class is a subclass of wpTypes:Interaction.

Mim-Binding interaction

MIM Specification

wpTypes:MimBinding

This class is a subclass of wpTypes:Interaction.

Mim-Branching-Left interaction

MIM Specification

wpTypes:MimBranchingLeft

This class is a subclass of wpTypes:Interaction.

Mim-Branching-Right interaction

MIM Specification

wpTypes:MimBranchingRight

This class is a subclass of wpTypes:Interaction.

Mim-Catalysis interaction

MIM Specification

wpTypes:MimCatalysis

This class is a subclass of wpTypes:Interaction.

Mim-Cleavage interaction

MIM Specification

wpTypes:MimCleavage

This class is a subclass of wpTypes:Interaction.

Mim-Conversion interaction

MIM Specification

wpTypes:MimConversion

This class is a subclass of wpTypes:Interaction.

Mim-Covalent-Bond interaction

MIM Specification

wpTypes:MimCovalentBond

This class is a subclass of wpTypes:Interaction.

Mim-Gap interaction

MIM Specification

wpTypes:MimGap

This class is a subclass of wpTypes:Interaction.

Mim-Inhibition interaction

MIM Specification

wpTypes:MimInhibition

This class is a subclass of wpTypes:Interaction.

Mim-Modification interaction

MIM Specification

wpTypes:MimModification

This class is a subclass of wpTypes:Interaction.

Mim-Necessary-Stimulation interaction

MIM Specification

wpTypes:MimNecessaryStimulation

This class is a subclass of wpTypes:Interaction.

Mim-Stimulation interaction

MIM Specification

wpTypes:MimStimulation

This class is a subclass of wpTypes:Interaction.

Mim-Transcription-Translation interaction

MIM Specification

wpTypes:MimTranscriptionTranslation

This class is a subclass of wpTypes:Interaction.

Object Properties

Data Properties

Technical notes

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