CommunityCurationProtocol

From WikiPathways

Join us in this Community Curation effort!

During the week of May 19-23, we are going to review all pathways on WikiPathways to make them more robust and amenable to computational analysis. The main improvements we want to make are:

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

Sign-up for particular pathways you would like to review and refer to the protocol below. See the discussion mailing list for more details about this event.

--> Pathway Sign-up Table <--

Protocol

Things to look for and change in reviewing and improving a pathway.

• Group stacked DataNodes
  • Find a group of stacked datanodes
  • Select them all
  • Group them by pressing CTRL-G, or choosing 'group' in the right-click menu
• Merge multi line labels
  • Find labels that span multiple lines or labels that are very long
  • If multiple labels are used to represent a single block of text, convert them to a single multi-line label
  • Double click on the label to get the text area where you can type the text over multiple lines
• Convert label/shape combination to a label with outline
  • Find labels with a shape around them that mimic a label with an outline
  • Remove the shape
  • Set the label outline by choosing 'Rectangle' or 'RoundedRectangle' from the 'Outline' field in the properties panel
• Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode
  • Create a DataNode for the label
  • Double click the DataNode to fill in the textlabel, identifier and database
• Replace multiple line segments with a single connector
  • Choose 'Curved' or 'Elbow' for 'Line type' in the right-click menu to get a multi segment connector.
  • Drag the blue segment handles to adjust the position of individual segments
• Replace arc/arrowhead combinations with curved connectors
• Link lines between elements. You can press CTRL-L to reveal all unlinked line ends.

Problems

Please use the talk page to discuss general problems (e.g. how to graphically represent something). For pathway specific problems, please use the talk page of the pathway (by pressing the 'discussion' tab on the pathway page).

If you find any bugs in the software, please report them to our bug tracker.

Participants

Alexander Pico, Kristina Hanspers, Susan Coort, Patrick Ahles, Thomas Kelder, Michiel Adriaens, Martijn van Iersel, Ed Hsiao