Help:Guidelines EditorPalette

From WikiPathways

Revision as of 19:35, 15 April 2014 by Khanspers (Talk | contribs)
Jump to: navigation, search

This guide describes the most common uses of various 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
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
Image:Dashed_MultiStep.png

T-bar

The T-bar is used to denote inhibition.

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 Image:Elbow2.png Image:Segmented.png

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 should be used for any gene product.
  • Metabolite: Should be used for any metabolite, drug or small molecule.
  • Pathway: Should be used instead of a label to denote a connection to another pathway.
  • RNA: Should be used for any data node that represents RNA, for example miRNA.
  • Protein: Could be used as a more specific way of denoting protein gene products.
GeneProduct, Metabolite, Pathway RNA Protein
Image:DataNodes.png Image:DataNode-RNA.png [[Image:]]

Graphical elements

Label

Line

Arc

Rectangle

Cellular compartments

Cell

Nucleus

Vesicle