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

wpTypes:Interaction

An Interaction between DataNode(s) on the diagram.

SubClasses

GeneProduct node

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

wpTypes:Pathway

This class is a subclass of wpTypes:DataNode.

Protein node

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

wpTypes:Unknown

This class is a subclass of wpTypes:DataNode.

Arrow interaction

wpTypes:Arrow

This class is a subclass of wpTypes:Interaction.

Broken Arrow interaction

wpTypes:BrokenArrow

This class is a subclass of wpTypes:Interaction.

Broken Line interaction

wpTypes:BrokenLine

This class is a subclass of wpTypes:Interaction.

Curved interaction

wpTypes:Curved

This class is a subclass of wpTypes:Interaction.

Elbow interaction

wpTypes:Elbow

This class is a subclass of wpTypes:Interaction.

Line interaction

wpTypes:Line

This class is a subclass of wpTypes:Interaction.

TBar interaction

wpTypes:TBar

This class is a subclass of wpTypes:Interaction.

Mim-Binding interaction

wpTypes:MimBinding

This class is a subclass of wpTypes:Interaction.

Mim-Branching-Left interaction

wpTypes:MimBranchingLeft

This class is a subclass of wpTypes:Interaction.

Mim-Branching-Right interaction

wpTypes:MimBranchingRight

This class is a subclass of wpTypes:Interaction.

Mim-Catalysis interaction

wpTypes:MimCatalysis

This class is a subclass of wpTypes:Interaction.

Mim-Cleavage interaction

wpTypes:MimCleavage

This class is a subclass of wpTypes:Interaction.

Mim-Conversion interaction

wpTypes:MimConversion

This class is a subclass of wpTypes:Interaction.

Mim-Covalent-Bond interaction

wpTypes:MimCovalentBond

This class is a subclass of wpTypes:Interaction.

Mim-Gap interaction

wpTypes:MimGap

This class is a subclass of wpTypes:Interaction.

Mim-Inhibition interaction

wpTypes:MimInhibition

This class is a subclass of wpTypes:Interaction.

Mim-Modification interaction

wpTypes:MimModification

This class is a subclass of wpTypes:Interaction.

Mim-Necessary-Stimulation interaction

wpTypes:MimNecessaryStimulation

This class is a subclass of wpTypes:Interaction.

Mim-Stimulation interaction

wpTypes:MimStimulation

This class is a subclass of wpTypes:Interaction.

Mim-Transcription-Translation interaction

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.