GPML
2014-11-17
http://vocabularies.wikipathways.org/gpml#
gpml
Andra Waagmeester
Maastricht University
mim-covalent-bond
Equivalent to http://purl.bioontology.org/ontology/MIM#CovalentIrreversibleBinding
mim-stimulation
Equivalent to http://identifiers.org/biomodels.sbo/SBO:0000170
mim-conversion
Presumably equivalent to http://identifiers.org/biomodels.sbo/SBO:0000182
mim-necessary-stimulation
Equivalent to http://identifiers.org/biomodels.sbo/SBO:0000171
mim-modification
Equivalent to http://identifiers.org/biomodels.sbo/SBO:0000210
mim-cleavage
Equivalent to http://identifiers.org/biomodels.sbo/SBO:0000178
mim-inhibition
Equivalent to http://identifiers.org/biomodels.sbo/SBO:0000169
mim-catalysis
Equivalent to http://identifiers.org/biomodels.sbo/SBO:0000172
mim-degradation
Equivalent to http://identifiers.org/biomodels.sbo/SBO:0000179
mim-transcription-translation
Related to http://www.biopax.org/release/biopax-level3.owl#TemplateReaction
requiresCurationAttention
Legend
An explanatory list of the colors used for visualizing data on the pathway. Currently just a placeholder element -- not used.
Pathway
A graph diagram representing a biological process. Nodes of which represent genes, proteins, metabolites etc and the edges connecting two nodes represent the relationship between them, i.e how the two nodes interact.
Biopax
Element used to embed <a href="http://www.biopax.org/owldoc/Level3/">Biopax</a> (namespace: <a href="http://www.biopax.org/release/biopax-level3.owl">http://www.biopax.org/release/biopax-level3.owl</a>) content in a GPML document.
State
The particular condition that biological entity is in at a specific time, e.g a protein may be phosphorylated or not, so phosphorylation is a state that a protein may have.
InfoBox
Currently just a placeholder -- not used.
Label
A label is a text box which can be used to describe the elements of a pathway. It is mostly used as a name tag, to describe datanodes, interactions or cellular compartments in a pathway.
Shape
Shape can refer to two different things in GPML, both of which are associated with graphical elements.
Group
A collection of structurally or functionally similar or related pathway elements.
DataNode
denotes a biological entity that forms a node in a pathway and has some biological meaning associated with it. For a list of the gpml:DataNode types supported at WikiPathways, see the range for <a href="http://vocabularies.wikipathways.org/gpml#Type">gpml:Type</a>.
mim-branching-left
Deprecated in the GPML vocabulary. Equivalent to http://purl.bioontology.org/ontology/MIM#BranchingLeft
Point
Anchor
mim-gap
Presumably equivalent to http://identifiers.org/go/GO:0005921
Interaction
defines the relationship between the two entities it connects. The entities can be DataNodes or Anchors.
Line
A marker of type Line indicates an interaction input or of undirected interaction.
Arrow
A marker of type Arrow indicates a directed interaction with no inhibiting function.
TBar
A marker of type TBar indicates a directed interaction with inhibiting function.
Graphical Line
A connector between graphical shapes or between a graphical shape and a biopax:Entity.
Elbow
Describes connectors composed of only horizontal and/or vertical segments.
Straight
Describes connectors with only two Points.
Curved
Describes connectors that follow a curve.
Segmented
Describes connectors that are composed of one or more straight line segments.
mim-binding
Equivalent to http://purl.bioontology.org/ontology/MIM#NonCovalentReversibleBinding
mim-branching-right
Deprecated in the GPML vocabulary. Equivalent to http://purl.bioontology.org/ontology/MIM#BranchingRight
fontstyle
fontattributes
linethickness
GroupRef
A GroupRef indicates that its element is part of the gpml:Group with the specified GroupId.
fontsize
Version
Deprecated. From GenMAPP.
license
Here comes the description on: license
fontname
GroupId
Uniquely identifies a gpml:Group in a gpml:Pathway. It has no purpose for existing in parallel with GraphId and should be replaced with GraphId.
align
Data-Source
See http://www.biopax.org/release/biopax-level3.owl#dataSource
Graph Identifier
A GraphId is a unique (per Pathway) identifier for a pathway element, such as a DataNode, Interaction or Anchor.
email
Here comes the description on: email
Organism
See http://www.biopax.org/release/biopax-level3.owl#organism
Color
This would be easier to work with if it had a hash "#" at the beginning to be consistent with CSS.
CenterY
Middle of a pathway element in the y-direction.
maintainer
Here comes the description on: maintainer
valign
last-modified
Here comes the description on: last-modified
Author
The person who created or edited the pathway in question.
fontweight
Thickness of the font used, e.g a bold font would have more weight.
BiopaxRef
Refers to a biopax:PublicationXref.
fontdecoration
fontstrikethru
height
href
Here comes the description on: href
style
Here comes the description on: style
linestyle
Name
Name is the title for a pathway.
CenterX
Middle of a pathway element in the x-direction.
Graph Ref
A GraphRef indicates a "depends on" or child/parent relationship between two Pathway elements. The element with the GraphRef is the child, and the element referred to by the GraphRef is the parent. The parent's GraphId will be specified by the child's GraphRef.
textlabel
Here comes the description on: textlabel
RelX
RelY
width
ID
Equivalent to http://www.biopax.org/release/biopax-level3.owl#id
Database
Equivalent to http://www.biopax.org/release/biopax-level3.owl#db
Graphics
Is Graphics a class or a property? In GPML, it's an element.
fillcolor
zorder
gpml Notes
homologyConvert
wikiPathwaysDescription
genmappremarks
arrowTowards
arrowHead
anchorPosition
Shape Type
Currently: Specifies the glyph (graphical representation) to use for GPML elements, except Anchors.
Proposed: Expand it to also describe Anchors. It should replace the term currently used to specify the graphical representation of an Anchor. The current term is "Shape," which conflicts with the GPML element named "Shape." See details for term "Shape."
pointOrder
X
Y
Connector Type
<p>
<b>Definition:</b> Specifies a set of rules to govern layout of Graphical Lines and Interactions.
</p>
<ul>
<li>PathVisio (Java): Line Type</li>
<li>GPML: ConnectorType</li>
</ul>
Solid
Broken
Double
Type
Specifies the biological role of a gpml:DataNode. See the Range for a list of gpml:Types supported at WikiPathways.