From WikiPathways

Revision as of 20:34, 29 July 2014

This guide describes the recommended utilization 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.

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

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 diagram.

Undefined process

T-bar

The T-bar is used to denote inhibition.

Inhibition of enzymatic activity by a drug

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

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

Stimulation	Catalysis	Transcription-Translation

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

Protein	RNA

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	Labels used to indicate event	Labels used to describe complexes

Line

Lines can be used to create more complicated graphical objects representing biological structures.

Multiple lines used to represent a sarcomere

Arc

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

Arcs used to represent a cellular structure

Rectangle

The rectangle is typically used for headers, to create and outline for a legend or as a purely graphical object:

Rectangle used as a header border

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