CommunityCurationProtocol

From WikiPathways

Revision as of 17:59, 14 May 2008 by Thomas (Talk | contribs)
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In the coming weeks, we are going to review all pathways on WikiPathways to make them more usable for computational analysis. The main improvements we want to make are:

  • Provide a proper graph representation by connecting all lines and arrows that represent an interaction
  • Group complexes and other elements that act together
  • Check the annotation of gene-products and metabolites

Protocol

The following steps could help in reviewing and improving a pathway.

  • Identify stacked datanodes and group them (CTRL-G)

TODO: Example

  • Find labels that span multiple lines. If multiple labels are used to represent a single block of text, convert them to a single multi-line label

TODO: Example

  • Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode
Before After
label2datanode_before.png label2datanode_after.png
  • Replace multiple line segments with a single connector

TODO: Example

  • Replace arc/arrowhead combinations with curved connectors

TODO: Example

  • Link lines between elements. You can press CTRL-R to reveal all unlinked line ends.

TODO: Example

  • ...

Problems

Please use the talk page to discuss problematic pathways.

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