From WikiPathways

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Revision as of 22:27, 5 May 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.

Interactions

Line / Arrow

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

Enzymatic conversion	Receptor binding	Translocation between compartments	Activation by cAMP

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

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

Interactions - Molecular Interaction Maps (MIM)

The WikiPathways editor includes a set of MIM interaction types, based on the Molecular Interaction Maps notation.

Necessary stimulation

Binding

Conversion

Stimulation

Catalysis

Transcription-Translation

Data nodes

• GeneProduct: Default data node and used for any gene product.
• Metabolite: Used for any metabolite, drug or small molecule.
• Pathway: Used instead of a label to denote a connection to another pathway.
• RNA: Used for any data node that represents RNA, for example miRNA.
• Protein: Can be used as a more specific way of denoting protein gene products.

GeneProduct, Metabolite, Pathway	RNA	Protein

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

Line

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

Arc

Rectangle

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