Help:Guidelines EditorPalette

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__NOTOC__
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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 [https://groups.google.com/forum/#!forum/wikipathways-discuss|WikiPathways discussion mailing list].  
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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 [https://groups.google.com/forum/#!forum/wikipathways-discuss|WikiPathways discussion mailing list].
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= Interactions =
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For each figure, the original pathway is linked to from the image header.
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= MIM Interactions - Molecular Interaction Maps =
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The WikiPathways editor includes a set of MIM interaction types, based on the [http://discover.nci.nih.gov/mim/ Molecular Interaction Maps] notation. Refer to the [http://discover.nci.nih.gov/mim/formal_mim_spec.pdf formal MIM specification] for details on recommended usage.
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==== Line / Arrow ====
 
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The solid line and arrow are used to denote a variety of processes, including <b>conversion</b>, <b>translocation</b>, <b>activation</b>, <b>binding</b> and <b>modification</b>.
 
{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  !Enzymatic conversion
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  ![[Pathway:WP2272|Necessary stimulation]]
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  !Receptor binding
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  ![[Pathway:WP58|Binding]]
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  !Translocation between compartments
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  ![[Pathway:WP550|Conversion and Catalysis]]
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  !Activation by cAMP
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  ![[Pathway:WP554|Inhibition]]
  |-
  |-
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  |[[Image:Arrow.png]]
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  |[[Image:MIM-Necessary-Stimulation.png|border]]
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  |[[Image:Arrow_binding.png]]
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  |[[Image:MIM-Binding.png|250px|border]]
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  |[[Image:Arrow_translocation.png]]
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  |[[Image:Arrow.png|border]]
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  |[[Image:Arrow_activation.png]]
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  |[[Image:mim-inhibition.png|border|300px]]
|}
|}
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==== Dashed line / dashed arrow ====
 
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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.
 
{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  !Multi-step process without details
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  ![[Pathway:WP1601|Stimulation]]
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![[Pathway:WP554|Transcription-Translation]]
  |-
  |-
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  |[[Image:Dashed_MultiStep.png|250px]]
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  |[[Image:MIM-Stimulation2.png|border|300px]]
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|[[Image:Transcription.png|border|300px]]
|}
|}
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==== T-bar ====
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= Basic Interactions =
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The T-bar is used to denote <b>inhibition</b>.
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==== Line / Arrow ====
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The solid line and arrow are used to denote a variety of processes when the more specific mim-interactions are not appropriate, including <b>translocation</b> and <b>activation</b>.
{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  !Inhibition by transcriptional regulation
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  ![[Pathway:WP428|Generic arrow]]
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![[Pathway:WP1603|Translocation between compartments]]
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![[Pathway:WP2059|Undefined process]]
  |-
  |-
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  |[[Image:MIM-Inhibition2.png]]
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  |[[Image:PlainArrow.png|border]]
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|[[Image:Arrow_translocation.png|border]]
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|[[Image:DashedArrow.png|border]]
|}
|}
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==== Line types ====
==== Line types ====
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Any interaction can have a line style of either <i>straight</i>, <i>curved</i>, <i>elbow</i> or <i>segmented</i>. 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.
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Any interaction can have a line style of either <i>straight</i>, <i>curved</i>, <i>elbow</i> or <i>segmented</i>. 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.
{|class="prettytable"
{|class="prettytable"
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  |-
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  !Curved
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  ![[Pathway:WP690|Curved]]
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  !Elbow
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  ![[Pathway:WP197|Elbow]]
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  !Segmented
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  ![[Pathway:WP78|Segmented]]
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  |-
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  |[[Image:Curved.png|350px]]
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  |[[Image:Curved.png|border]]
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  |[[Image:Elbow2.png|350px]]
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  |[[Image:Elbow.png|border|300px]]
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  |[[Image:Segmented.png|350px]]
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  |[[Image:Segmented.png|border|300px]]
|}
|}
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= Interactions - Molecular Interaction Maps (MIM) =
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= Data nodes =
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The WikiPathways editor includes a set of MIM interaction types, based on the [http://discover.nci.nih.gov/mim/| Molecular Interaction Maps] notation. Refer to the [http://discover.nci.nih.gov/mim/formal_mim_spec.pdf|formal MIM specification] for details on recommended usage.
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* <b>GeneProduct</b>: The default data node, used for proteins, RNA and genes.  
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* <b>Metabolite</b>: Used for any metabolite, drug or small molecule.
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* <b>Pathway</b>: Used to denote a connection to another pathway.
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* <b>Protein</b>: Used specifically for proteins.
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* <b>RNA</b>: Used specifically for RNA, for example miRNA.
{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  !Necessary stimulation
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  ![[Pathway:WP1246|GeneProduct]]
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  !Binding
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  ![[Pathway:WP1531|Metabolite]]
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  !Conversion
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  ![[Pathway:WP78|Pathway]]
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  |-
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  |[[Image:MIM-Necessary-Stimulation.png]]
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  |[[Image:GeneProduct.png|border]]
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  |[[Image:MIM-Binding.png|250px]]
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  |[[Image:Metabolite.png|border]]
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  |[[Image:MIM-Conversion2.png]]
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  |[[Image:Pathway.png|border]]
|}
|}
{|class="prettytable"
{|class="prettytable"
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  |-
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  !Stimulation
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  ![[Pathway:WP1544|Protein]]
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  !Catalysis
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  ![[Pathway:WP608|RNA]]
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!Transcription-Translation
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  |-
  |-
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  |[[Image:MIM-Stimulation2.png]]
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  |[[Image:Protein.png|border]]
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|[[Image:MIM-Catalysis.png]]
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  |[[Image:DataNode-RNA.png|border]]
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|[[Image:MIM-Transcription-Translation2.png]]
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|}
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= Data nodes =
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* <b>GeneProduct</b>: Default data node and used for any gene product.
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* <b>Metabolite</b>: Used for any metabolite, drug or small molecule.
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* <b>Pathway</b>: Used instead of a label to denote a connection to another pathway.
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* <b>RNA</b>: Used for any data node that represents RNA, for example miRNA.
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* <b>Protein</b>: Can be used as a more specific way of denoting protein gene products.
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{|class="prettytable"
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|-
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!GeneProduct, Metabolite, Pathway
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!RNA
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!Protein
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|-
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|[[Image:DataNodes.png]]
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  |[[Image:DataNode-RNA.png|300px]]
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|[[Image:DataNode-Protein.png]]
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|}
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{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  !Labels used to indicate cell type and event
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  ![[Pathway:WP1603|Labels used to indicate event]]
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  !Labels used to describe complexes  
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  ![[Pathway:WP111|Labels used to describe complexes]]
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  |-
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  |[[Image:Labels1.png|300px]]
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  |[[Image:Label-event.png|border|350px]]
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  |[[Image:Labels2.png]]
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  |[[Image:Label-complex.png|border]]
|}
|}
==== Line ====
==== Line ====
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Lines can be used to denote cellular structures such as membranes.
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Lines can be used to create more complicated graphical objects representing biological structures, or to create a pathway legend.
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[[Image:Line1.png|border|250px]]
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{|class="prettytable"
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|-
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![[Pathway:WP2118|Multiple lines used to represent a sarcomere]]
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![[Pathway:WP339|Lines used to create a legend]]
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|-
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|[[Image:Line.png|border|450px]]
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|[[Image:Legend.png|border]]
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|}
==== Arc ====
==== Arc ====
The arc is typically used to denote a cellular or molecular structure.
The arc is typically used to denote a cellular or molecular structure.
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[[Image:Arc.png|border]]
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{|class="prettytable"
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|-
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![[Pathway:WP2118|Arcs used to represent a cellular structure]]
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![[Pathway:WP4249|Arcs used to represent an organelle]]
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|-
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|[[Image:Arc.png|border]]
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|[[Image:Cilium.png|border]]
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|}
==== Rectangle ====
==== Rectangle ====
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The rectangle is typically used for headers, to create an outline for a legend or as a purely graphical object:
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{|class="prettytable"
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|-
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![[Pathway:WP509|Rectangle used as a header border]]
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|-
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|[[Image:Rectangle2.png|border]]
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|}
= Cellular compartments =
= Cellular compartments =
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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.
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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.
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{|class="prettytable"
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|-
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![[Pathway:WP1531|Cell]]
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![[Pathway:WP1425|Nucleus]]
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|-
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|[[Image:Cell.png|border]]
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|[[Image:Nucleus.png|border]]
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|}
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{|class="prettytable"
{|class="prettytable"
  |-
  |-
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  !Cell
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  ![[Pathway:WP1603|Vesicle]]
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  !Nucleus
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  ![[Pathway:WP2059|Mitochondria]]
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!Vesicle
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  |-
  |-
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  |[[Image:Cell.png]]
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  |[[Image:Vesicle.png|border]]
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  |[[Image:Nucleus.png]]
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  |[[Image:Mitochondria.png|border]]
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|[[Image:Vesicle.png]]
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|}
|}

Current revision

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.

Contents

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
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