WP-old
2015-10-06
http://vocabularies.wikipathways.org/wp-old#
wp-old
Andra Waagmeester
Maastricht University
www.bigcat.unimaas.nl
Alexander Pico
Martina Kutmon
Susan Coort
Anwesha Bohler
Ryan Miller
Author
Definition: An author is creator, editor, or curator of a pathway. The author is known by a unique WikiPathways username.
DatasourceReference
UnificationXref in BioPAX
PathwayVersion
GeneProduct
Gene Product
Superclass for the following BioPAX terms:<br>
http://www.biopax.org/release/biopax-level3.owl#Dna<br>
http://www.biopax.org/release/biopax-level3.owl#Gene<br>
http://www.biopax.org/release/biopax-level3.owl#Rna<br>
http://www.biopax.org/release/biopax-level3.owl#Protein<br>
PathwayAnnotation
no corresponding element in BioPAX
Label
no corresponding element in BioPAX
GPML:Label
Compartment
no corresponding elements in BioPAX and GPML
Group
Binding
<br><b>Description:</b> 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). Binding subclass of Mimbinding
<br>
<b>Properties:</b> <br>
- hasParticipant<br>
<b>GPML:</b> Line with both Points having a "mim-binding" arrowhead.
CurationTag
ControlledVocabulary
<br><b>Defintion: </b>A controlled vocabulary is a vocabulary consisting of a prescribed list of terms or headings each one having an assigned meaning. ref: http://edutechwiki.unige.ch
Metabolic Process
Cellular Process
<br><b>Definition: </b> Any process that is carried out at cellular level.
Molecular Function
Physiological Process
PathwayCategory
Inhibitory Activity
<p>
<b>Definition:</b> Any kind of inhibition or other inhibitory activity.
</p>
<ul>
<li>PathVisio (Java): Line Type option "TBar"</li>
<li>GPML: ArrowHead="TBar"</li>
</ul>
CytosolRegion
DataNode
Pathway
Interaction
Protein
Metabolite
RNA
Complex
PathwayNode
Un-directed Ineraction
Directed Interaction
Inhibition
Conversion
Stimulation
Catalysis
Complex Binding
Binding information for complexes
Transcription-translation
username
Links to FOAF, Sciencepeople
realName
Links to FOAF
email
revision
Equivalent to http://schema.org/version
hasIdentfier
DC.identifier
hasPathway
Indirect
<p>
<b>Definition:</b> Indicates there are one or more steps missing in the interaction from the first data node to the second data node connected by this interaction.
</p>
<ul>
<li>PathVisio (Java): Line Style option "Dashed"</li>
<li>GPML: LineStyle="Broken"</li>
</ul>
organism
category
Indicates the pathway category to which a selected pathway adheres
pathwayOntology
hasParticipant
interactionTarget
unifiedIdentifier
In WikiPathways curators have the liberty to use any identifier they like. We store a unified Identifier to enable integrative approaches recognizing similar object with different identifier patterns. The mapping between original identifiers and the unified Identifier is provided by the same bridgeDb framework as used in WikiPathways.
bdbEnsembl
bdbUniprot
bdbHmdb
bdbChemspider
bdbEntrezGene
interactsWith
Pathway elements can interact among each other. wp:interactsWith is to express a basic interaction.
Direct
<p>
<b>Definition:</b> Indicates there are no steps missing in the interaction from the first data node to the second data node connected by this interaction.
</p>
<ul>
<li>PathVisio (Java): Line Style option "Solid"</li>
<li>GPML: LineStyle="Solid" or LineStyle not specified</li>
</ul>
ID
Organism
OntologyTag
Ontology terms for a pathway
Represents
isPartOf
Ensembl ID
pubmed
Publication information
participants
entrez ID
HGNC ID
Uniprot ID
Chembl ID
Pubchem ID
HMDB ID
ChEBI ID
Source
Target