The WikiPathways WP Ontology

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

This ontology is written by (in random order) Andra Waagmeester, Alexander Pico, Martina Kutmon, Susan Coort, Anwesha Bohler, Egon Willighagen, and Ryan Miller.

Namespaces

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

@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

Binding

wp:Binding

A binding interaction between two physical entities resulting in the formation of an explicit complex that is reversible without an external factor (e.g. protein complexes). Subclass of wp:DirectedInteraction.

Catalysis

wp:Catalysis

A catalysis. Subclass of wp:DirectedInteraction.

Complex

A physically bound combination of two or more biological entities.

wp:Complex

A Complex of compounds. Subclass of wp:DataNode.

ComplexBinding

wp:ComplexBinding

Subclass of wp:Binding.

Conversion

A process in which a biological entity gets converted into another entity. This could be a metabolic conversion where compound gets chemical modified.

wp:Conversion

Subclass of wp:DirectedInteraction.

DataNode

wp:DataNode

DirectedInteraction

wp:DirectedInteraction

Subclass of wp:Interaction.

GeneProduct

wp:GeneProduct

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.

Subclass of wp:DataNode. The BioPax class biopax:Dna is a subclass of wp:GeneProduct. The BioPax class biopax:Gene is a subclass of wp:GeneProduct. The BioPax class biopax:Rna is a subclass of wp:GeneProduct. The BioPax class biopax:Protein is a subclass of wp:GeneProduct.

Inhibition

wp:Inhibition

Subclass of wp:DirectedInteraction.

Interaction

wp:Interaction

Metabolite

Any chemical compound taking part in a pathway. Unlike true metabolites, this node is also used for compounds which are not the product or substrate of a metabolic conversion.

wp:Metabolite

Subclass of wp:DataNode.

Pathway

wp:Pathway

Protein

wp:Protein

Subclass of wp:GeneProduct.

PublicationReference

wp:PublicationReference

A reference to a published article, book or other citable material. Most commonly a primary literature reference that is indexed by PubMed.

Rna

wp:Rna

Subclass of wp:DataNode.

Stimulation

wp:Stimulation

Subclass of wp:DirectedInteraction.

Transcription Translation

wp:TranscriptionTranslation

Subclass of wp:DirectedInteraction.

Object Properties

BridgeDb ChEBI link

wp:bdbChEBI

A variable URL to the ChEBI data source.

This property has wp:Metabolite as domain and rdfs:Resource as range.

BridgeDb ChemSpider link

wp:bdbChemspider

A variable URL to the Chemspider data source.

This property has wp:Metabolite as domain and rdfs:Resource as range.

BridgeDb Ensembl link

wp:bdbEnsembl

A variable URL to the Ensembl data source.

This property has rdfs:Resource as range.

BridgeDb Entrez Gene link

wp:bdbEntrezGene

A variable URL to the NCBI Gene data source.

This property has rdfs:Resource as range.

BridgeDb HMDB link

wp:bdbHmdb

A variable URL to the Human Metabolome Database (HMDB) data source.

This property has wp:Metabolite as domain and rdfs:Resource as range.

BridgeDb HGNC link

wp:bdbHgncSymbol

A variable URL to the HUGO Gene Nomenclature Committee (HGNC) data source.

This property has rdfs:Resource as range.

BridgeDb PubChem link

wp:bdbPubChem

A variable URL to the PubChem data source (Compound identifiers).

This property has wp:Metabolite as domain and rdfs:Resource as range.

BridgeDb UniProt link

wp:bdbUniprot

A variable URL to the UniProt data source.

This property has rdfs:Resource as range.

cell type ontology tag

A term from the Cell Type ontology available on the NCBO's BioPortal (http://bioportal.bioontology.org/ontologies/CL).

wp:celltypeOntologyTag

This property has wp:Pathway as domain, rdfs:Resource as range, and is subproperty of wp:ontologyTag.

disease ontology tag

A term from the Human Disease Ontology available on the NCBO's BioPortal (http://bioportal.bioontology.org/ontologies/DOID).

wp:diseaseOntologyTag

This property has wp:Pathway as domain, rdfs:Resource as range, and is subproperty of wp:ontologyTag.

participants

wp:participants

pathway ontology tag

A term from the Pathway Ontology ontology available at NCBO's BioPortal (http://bioportal.bioontology.org/ontologies/PW).

wp:pathwayOntologyTag

This property has wp:Pathway as domain, rdfs:Resource as range, and is subproperty of wp:ontologyTag.

source

wp:source

This property has wp:DirectedInteraction as domain and wp:DataNode as range and is subproperty of wp:participants.

target

wp:target

This property has wp:DirectedInteraction as domain and is subproperty of wp:participants.

ontology tag

A term from an ontology or controlled vocabulary.

wp:ontologyTag

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

Data Properties

is about

wp:isAbout

organism

wp:organism

This property has wp:Pathway as domain and rdfs:Class as range. The property biopax:organism is a subproperty of wp:organism.

organism name

Latin name of the organsm in which this pathway takes place.

wp:organismName

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

Technical notes

The conversion of wp#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.