WP
2014-10-29
http://vocabularies.wikipathways.org/wp#
wp
Andra Waagmeester
Maastricht University
UtilityClass
Author
Definition: An author is creator, editor, or curator of a pathway. The author is known by a unique WikiPathways username.
Reference
Xref in BioPAX
PublicationReference
PublicationXref in Biopax
DatasourceReference
UnificationXref in BioPAX
Interaction
<br><b>An interaction is a generic biological interaction between two or more pathway elements.</b><br>
* GPML: Line (ArrowHead = none or all others)<br>
* BioPAX: Interaction
PathwayVersion
Pathway
Pathway in BioPAX
Protein
Protein in BioPAX
<br><b>Definition:</b> A molecule composed of polymers of amino acids joined together by peptide bonds.
<br>ref: www.biology-online.org/dictionary
Metabolite
SmallMolecule in BioPAX
GeneProduct
Superclass for each of the following:
biopax:Dna
biopax:Gene
biopax:Rna
biopax:Protein
Unknown
PathwayAnnotation
no corresponding element in BioPAX
Label
no corresponding element in BioPAX
GPML:Label
Compartment
no corresponding elements in BioPAX and GPML
Cell
Definition: A Cell is a shape in a pathway that represents the basic structural and functional unit of the organism on which this pathways is topical.
Extracellular
no corresponding elements in BioPAX and GPML (might be nice to add functionality to define extracellular space in a pathway)
<br><b>Defintion: </b> Occurring or being (situated) outside the cell or cells. (www.biology-online.org/dictionary)
See ExtracellularRegion. This is an available CellularComponent from GPML/Pathvisio-Java.
Vesicle
Shape in GPML, no corresponding element in BioPAX
<br><b>Defintion: </b> A bubble-like membranous structure that stores and transports cellular products, and digests metabolic wastes within the cell.
<br>ref: www.biology-online.org/dictionary
SarcoplasmicReticulum
Shape in GPML, no corresponding element in BioPAX
<br><b>Definition:</b> The special type of smooth endoplasmic reticulum found in smooth and striated muscle fibers whose function is to store and release calcium ions.
<br> ref:www.biology-online.org/dictionary
Organelle
Shape in GPML, no corresponding element in BioPAx
Group
Nucleus
Shape in GPML, no corresponding element in BioPAX
Mitochondria
Shape in GPML, no element in BioPAX
GolgiApparatus
Shape in GPML, no corresponding element in BioPAX
<br><b> Definition: </b>An organelle composed of membrane-bound stacks known as cisternae
<br><b> Function: </b>Involved in glycosylation (i.e. adding carbohydrate to a protein), packaging of molecules like proteins into vesicles for secretion, transport of lipids around the cell, and the creation of lysosomes
<br> ref:www.biology-online.org/dictionary
EndoplasmicReticulum
<br><b>Defintion: </b> A membrane-bounded organelle that occurs as labyrinthine, interconnected flattened sacs or tubules that is connected to the nuclear membrane, runs through the cytoplasm, and may well extend into the cell membrane. (ref: www.biology-online.org/dictionary)
Complex
NecessaryStimulation
<br><b>Description: </b>An interaction where the controller entity is necessary for the controlled interaction to proceed.
<br>
<b>Properties: </b><br>
- participant (DataNodes or Interactions)<br>
- controller (DataNodes)<br>
- controlled (DataNodes or Interactions)<br>
<b>GPML: </b>Line with one Point having an arrowhead "mim-necessary-stimulation". The Point without the arrowhead cannot be an interaction.
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.
Conversion
<br><b>Description: </b>An interaction in which one entity is transformed into one or more other entities (e.g. the conversion of ATP to cyclical-AMP).
<br>
<b>Properties:</b> <br>
- participant - one or more DataNodes<br>
- source - one or more DataNodes<br>
- target - one or more DataNodes<br>
<b>GPML:</b> Line with one Point having a "conversion" arrowhead (if both Points have a conversion arrowhead then we are actually talking about two interactions and they should be split up in the pathway).
Stimulation
<br><b>Description: </b>Enhancement of the velocity or extent of a reaction or contingency by the controller entity.
<br>
<b>Properties: </b><br>
- participant (DataNodes or Interactions)<br>
- controller (DataNodes)<br>
- controlled (DataNodes or Interactions)<br>
<b>GPML: </b>Line with one Point having an arrowhead "mim-stimulation". The Point without the arrowhead cannot be an interaction.
MIMModificiation
<br>
<b>Description: </b>An asymmetric covalent non-reversible binding reaction (e.g. phosphorylation and acetylation) where one of the substrates must be a modifier physical entity. <br>
<b>Properties:</b><br>
- participant (one or more DataNodes)<br>
- source (one or more DataNodes)<br>
- target (one or more DataNodes)<br>
<b>GPML: </b>A Line with one Point having an arrowhead "mim-modification".
Catalysis
<br />
<b>Description</b>: An interaction where the controller entity increases the rate of the controlled reaction.<br />
<b>Properties</b>:<br />
- participant<br />
- controller<br />
- controlled<br />
<b>GPML</b>: A line with one point with arrowhead terminating on an anchor; the other point does not have an arrowhead and terminates on a datanode or group.
MIMInhibition
<br><b>Description: </b> An interaction where a controller entity causes a decrease in the velocity or extent of controlled reaction or contingency; the probability of the controlled interaction occurring remains greater than 0.
<br>
<b>Properties:</b><br>
- participant (DataNodes or Interactions)<br>
- controller (DataNodes)<br>
- controlled (DataNodes or Interactions)<br>
<b>GPML: </b> Line with one Point having an arrowhead "conversion". The Point without the arrowhead cannot be an interaction.
Cleavage
<br /><b>Description: </b>The scission of a covalent bond or the separation of connections between entity features.
<br />
<b>Properties:</b> <br />
- participant - one or more DataNodes<br />
- source - one or more DataNodes<br />
- target - one or more DataNodes<br />
<b>GPML:</b> Line with one Point having a "cleavage" arrowhead on a datanode; the other Point has no arrowhead and is also on a datanode.
CovalentBond
<br /><b>Description: </b>An asymmetric covalent non-reversible binding reaction (e.g. phosphorylation and acetylation)
where one of the substrates must be a modifier physical entity.
<br />
<b>Properties:</b> <br />
- participant - one or more DataNodes<br />
- source - one or more DataNodes<br />
- target - one or more DataNodes<br />
<b>GPML:</b> Line with a Point having a "mim-covalent-bond" arrowhead on a datanode; and the Point with no arrowhead on a datanode.
BranchingLeft
<br />
<b>Description</b>:A connection point for two interaction lines, stylized to indicate left directionality or flow, but not biologically meaningful.<br />
<b>Properties</b>:<br />
- participant
<br />
<b>GPML</b>: A line with a point with branching glyph terminating on an anchor; the other point can have another arrowhead type and terminate on a datanode or group.
BranchingRight
<br />
<b>Description</b>:A connection point for two interaction lines, stylized to indicate right directionality or flow, but not biologically meaningful.<br />
<b>Properties</b>:<br />
- participant
<br />
<b>GPML</b>: A line with a point with branching glyph terminating on an anchor; the other point can have another arrowhead type and terminate on a datanode or group.
TranscriptionTranslation
<br>
<b>Description: </b>A type of production without loss that involves a template (e.g. the polymerization of a nucleic acid macromolecule from a nucleic acid macromolecule template). <br>
<b>Properties:</b><br>
- particpant (two or more DataNodes)<br>
- template (one or more DataNodes) <br>
- product (one or more DataNodes)<br>
<b>GPML: </b>Line with one Point having an arrowhead "mim-transcription-translation". Cannot be reversible!
Gap
BasicInteraction
<br><b>A BasicInteraction is a generic biological interaction between two or more pathway elements that is not identified with a MIM type.</b><br>
* GPML: Line (ArrowHead = none, "Line", "Arrow" or "TBar")<br>
* BioPAX: Interaction
RNA
Rna in Biopax, DataNode in GPML
Why does this say "DataNode in GPML" but other DataNode Types like Protein don't have this annotation?
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
Catalyst
<br><b>Definition: </b> A substance capable of initiating or speeding up a chemical reaction.
(ref: www.biology-online.org/dictionary)
Unspecified
<p>
<b>Definition:</b> indicates some relationship between the data nodes that are connected, but we do not know what that interaction is.
</p>
<ul>
<li>PathVisio (Java): Line Type option "Line"</li>
<li>GPML: ArrowHead="Line", or no ArrowHead property present</li>
</ul>
Activity
<p>
<b>Definition:</b> Any kind of conversion or other activity occurring between two data nodes.
</p>
<ul>
<li>PathVisio (Java): Line Type option "Arrow"</li>
<li>GPML: ArrowHead="Arrow"</li>
</ul>
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>
Reaction
Corresponds to gpml:Anchor
Degradation
Represented in GPML as ShapeType mim-degradation.
MembraneRegion
CytosolRegion
ExtracellularRegion
Is this a duplicate of Extracellular? Where do we put the CellularComponents from GPML/PathVisio-Java?
Lysosome
Vacuole
Nucleolus
username
Links to FOAF, Sciencepeople
realName
Links to FOAF
email
revision
DCidentifier
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
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>