Help:Guidelines EditorPalette

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Revision as of 04:46, 5 July 2014

This guide describes the recommended uses of the most commonly used elements of the WikiPathways editor palette. Examples are taken directly from the WikiPathways archives. If you have questions about specific cases, contact the discussion mailing list.

For each figure, the original pathway is linked to from the image header.

Contents

Basic Interactions

Line / Arrow

The solid line and arrow are used to denote a variety of processes, including conversion, translocation, activation, binding and modification.

Conversion Receptor binding Translocation between compartments Activation by cAMP
Image:Arrow.png Image:Arrow_binding.png Image:Arrow_translocation.png Image:Arrow_activation.png

Dashed line / dashed arrow

The dashed line and arrow are used to denote an uncertain process or a process that involves additional steps not outlined in the current diagram.

Multi-step process without details

T-bar

The T-bar is used to denote inhibition.

Inhibition by transcriptional regulation
Image:Inhibition.png

Line types

Any interaction can have a line style of either straight, curved, elbow or segmented. The default style is straight, and is shown in the examples above. The other three line styles are used primarily to increase readability of complex pathways.

Curved Elbow Segmented
Image:Curved.png

MIM Interactions - Molecular Interaction Maps

The WikiPathways editor includes a set of MIM interaction types, based on the Molecular Interaction Maps notation. Refer to the MIM specification for details on recommended usage.

Necessary stimulation Binding Conversion
Image:MIM-Necessary-Stimulation.png Image:MIM-Conversion2.png
Stimulation Catalysis Transcription-Translation
Image:MIM-Stimulation2.png Image:MIM-Catalysis.png Image:Transcription.png

Data nodes

  • GeneProduct: Default data node and used for genes, RNA and/or proteins.
  • Metabolite: Used for any metabolite, drug or small molecule.
  • Pathway: Used instead of a label to denote a connection to another pathway.
  • Protein: Used specifically for proteins.
  • RNA: Used specifically for RNA, for example miRNA.
GeneProduct Metabolite Pathway
Image:Metabolite.png Image:Pathway.png
Protein RNA
Image:DataNode-Protein.png

Graphical elements

Graphical elements are purely graphical, meaning they do not have a meaning in the network graph that defines nodes and interactions.

Label

Labels are used to describe locations, entities, processes or context:

Labels used to indicate cell type and event Labels used to describe complexes
Image:Labels2.png

Line

Lines can be used to denote cellular structures such as membranes.


Arc

The arc is typically used to denote a cellular or molecular structure.

Rectangle

The rectangle is typically used to enclose a set of entities or annotations:

Cellular compartments

Cellular compartment shapes are used to specify the cellular location of processes. Using the defined cellular compartment shapes also ensures that this information is encoded in the gpml.

Cell Nucleus Vesicle Mitochondria
Image:Cell.png Image:Nucleus.png Image:Vesicle.png Image:Mitochondria.jpg