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.
@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/> . @prefix obo: <http://purl.obolibrary.org/obo/> .
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.
wp:Catalysis
A process where a chemical reaction is enhanced by the action of a catalyst.
Subclass of wp:DirectedInteraction.A physically bound combination of two or more biological entities.
wp:Complex
A Complex of compounds. Subclass of wp:DataNode.
A binding interaction that specifically leads to the formation of a complex.
wp:ComplexBinding
Subclass of wp:Binding.
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.
Superclass; deprecated; do not use.
wp:DataNode
Defines a biochemical relationship from a source biological entity to a target biological entity.
wp:DirectedInteraction
Subclass of wp:Interaction.
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.
A process in which one biological entity restrains, blocks, or suppresses another biological entity or interaction.
wp:Inhibition
Subclass of wp:DirectedInteraction.
Defines the biochemical relationship between biological entities.
wp:Interaction
Any chemical compound taking part in a pathway. Unlike true metabolites, this node is also used for chemical compounds which are not the product or substrate of a metabolic conversion.
wp:Metabolite
Subclass of wp:DataNode.
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.
wp:Pathway
A biomolecular polymer of amino acids, translated from mRNA.
wp:Protein
Subclass of wp:GeneProduct.
wp:PublicationReference
A reference to a published article, book or other citable material. Most commonly a primary literature reference that is indexed by PubMed.
A biomolecular polymer of ribonucleic acids, transcibed from DNA.
wp:Rna
Subclass of wp:DataNode.
An interaction in which the source entity enhances the raate or extent of another reaction or entity.
wp:Stimulation
Subclass of wp:DirectedInteraction.
An interaction in which the source entity regulates or influences in the transcription or translation of a target entity. Also referred to as a Template Reaction.
wp:TranscriptionTranslation
Subclass of wp:DirectedInteraction.
A process in which a biological entity moves from one cellular location to another.
wp:Translocation
Subclass of wp:DirectedInteraction.
wp:bdbChEBI
A variable URL to the ChEBI data source.
This property has wp:Metabolite as domain and rdfs:Resource as range.
wp:bdbChemspider
A variable URL to the Chemspider data source.
This property has wp:Metabolite as domain and rdfs:Resource as range.
wp:bdbEnsembl
A variable URL to the Ensembl data source.
This property has rdfs:Resource as range.
wp:bdbEntrezGene
A variable URL to the NCBI Gene data source.
This property has rdfs:Resource as range.
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.
wp:bdbHgncSymbol
A variable URL to the HUGO Gene Nomenclature Committee (HGNC) data source.
This property has rdfs:Resource as range.
wp:bdbPubChem
A variable URL to the PubChem data source (Compound identifiers).
This property has wp:Metabolite as domain and rdfs:Resource as range.
wp:bdbRhea
A variable URL to the Rhea data source.
This property has rdfs:Resource as range.
wp:bdbUniprot
A variable URL to the UniProt data source.
This property has rdfs:Resource as range.
wp:bdbWikidata
A variable URL to the Wikidata data source.
This property has rdfs:Resource as range.
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.
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.
wp:participants
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.
The beginning terminus of an interaction.
wp:source
This property has wp:DirectedInteraction as domain and wp:DataNode as range and is subproperty of wp:participants.
The ending terminus of an interaction.
wp:target
This property has wp:DirectedInteraction as domain and is subproperty of wp:participants.
A term from an ontology or controlled vocabulary.
wp:ontologyTag
This property has wp:Pathway as domain and xsd:string as range.
It is the link between the biological entity and the gpml entity. Used in cases of interactions, complexes and groups.
wp:isAbout
The scientific name (e.g., Homo sapiens) of the species being described by the pathway.
wp:organism
This property has wp:Pathway as domain and rdfs:Class as range. The property biopax:organism is a subproperty of wp:organism.
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.
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 downloaded here.