CommunityCurationProtocol

From WikiPathways

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

• 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.