GPML
2014-10-29
http://vocabularies.wikipathways.org/gpml#
gpml
Andra Waagmeester
Maastricht University
requiresCurationAttention
Legend
An explanatory list of the colours used for visualizing data on the pathway.
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
Here comes the description on: Biopax
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
Here comes the description on: InfoBox
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 datanodes.
Question: does it only include DataNodes? Because it's possible to group other elements in PathVisio-Java, such as Interactions.
DataNode
<strong>Datanode</strong> is a biological entity that forms a node in a pathway and has some biological meaning associated with it; e.g gene, metabolite, protein etc. Types of DataNodes currently recognized by PathVisio are: <ul> <li>GeneProduct,</li> <li>Protein,</li> <li>Metabolite, </li><li>RNA, </li><li>Pathway, </li> and <li>Unknown.</li></ul>
Definition: A datanode is used to denote a biological entity that participates in a pathway. In WikiPathways the following DataNode types can be present in a pathway: GeneProduct, Metabolite, Protein, Complex, Rna, Pathway and Unknown.
PublicationXref
Xref
Constitutes of text representing an identifier and the system code of the database from which the identifier was obtained, e.g: If a metabolite in the pathway is annotated with the identifier HMDB00122 from the database HMDB, it's <strong>xref</strong> would be Ch:HMDB00122. Ch is the system code using which PathVisio identifies the database HMDB.
Point
Anchor
Interaction
An interaction defines the relationship between the two datanodes it connects.
ArrowHeadLine
An arrow head of type line indicates an interaction input or of undirected interaction.
ArrowHeadArrow
An arrow head of type arrow indicates a directed interaction with no inhibiting function.
ArrowHeadTBar
An arrow head of type TBar indicates a directed interaction with inhibiting function.
Graphical Line
A connector between graphical shapes or between a graphical shape and a BiologicalEntity.
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.
Port
Anything that an edge can snap to, including anchors and the 12 spots around every shape.
hasAnchor
fontstyle
fontattributes
linethickness
shapestyleattributes
statetype
Here comes the description on: statetype
groupref
Here comes the description on: groupref
fontsize
Version
Deprecated. From GenMAPP.
license
Here comes the description on: license
fontname
groupid
Here comes the description on: groupid
align
data-source
Database from which the identifier used to annotate the biological entity is obtained, e.g HMDB, Ensembl etc.
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
The organism for which the biological process represented in the pathway is either identified or predicted. Should we lowercase this in GPML?
rectattributes
color
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
Here comes the description on: biopaxref
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. In PathVisio-Java, this term is set as the "Title." In GPML, it is capitalized. Should we lowercase it in GPML?
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
database
graphics
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."
unifiedIdentifier
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 whether a DataNode is a GeneProduct, Metabolite, etc.