From WikiPathways

Revision as of 18:31, 28 July 2020

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.

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 formal MIM specification for details on recommended usage.

Necessary stimulation	Binding	Conversion and Catalysis	Inhibition

Stimulation	Transcription-Translation

Basic Interactions

Line / Arrow

The solid line and arrow are used to denote a variety of processes when the more specific mim-interactions are not appropriate, including translocation and activation.

Generic arrow	Translocation between compartments	Undefined process

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 to increase readability or to allow for a specific layout.

Curved	Elbow	Segmented

Data nodes

• GeneProduct: The default data node, used for proteins, RNA and genes.
• Metabolite: Used for any metabolite, drug or small molecule.
• Pathway: Used 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 event	Labels used to describe complexes

Line

Lines can be used to create more complicated graphical objects representing biological structures, or to create a pathway legend.

Multiple lines used to represent a sarcomere	Lines used to create a legend

Arc

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

Arcs used to represent a cellular structure	Arcs used to represent an organelle

Rectangle

The rectangle is typically used for headers, to create an 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 instead of simple graphical shapes ensures that the cellular location information is encoded in the gpml. Use the "Text Label" property of the object 9in the Properties panel) to add a title, instead of adding a separate label.

Cell	Nucleus

Vesicle	Mitochondria