Background

In this task, you will finalize the pathway layout, complete a quality control checklist and add a literature reference.

Your Mission

Make final adjustments to pathway layout, go through the checklist and add a literature reference. For this task, ideally you should start with your own draft from the previous step. Alternatively, you can use the starter pathway.

  • Launch PathVisio and open the your draft pathway file via File > Open.

    • Adjust layout and check for unconnected interactions

  • Starting at the top of the pathway, make sure the first 4 metabolites are aligned.
  • Similarly, align the three sets of metabolites on each side of the Krebs cycle.
  • Make sure each data node size is adjusted so that the text label is readable.
  • To check if all interactions are properly connected, type Ctrl+L (Command+L on Mac). This will highlight all unconnected ends of interactions in green. Connect any unconncted interactions before proceeding.

    • Add a literature reference

  • Right-click on the Pathway Information Area and select Literature > Add literature reference.
  • In the Literature reference properties window, type in the PMID for the original article: 26536169
  • Click Query PubMed. When the results are loaded, click OK. Congratulations! You have converted your first pathway model from the scientific literature.

    • Pick a pathway title and indicate organism

  • Check your pathway title against our pathway title guidelines.
  • Make sure to select the correct species for your pathway. Highlight the Pathway Information area in the top left and review the Organism entry in the Properties tab. It should be "Homo sapiens".

    • Draft a Description

  • Before your pathway is considered complete and ready to be submitted to WikiPathways, it must have a description. Create your description in a separate text editor; you will need if you decide to upload your pathway to WikiPathways (optional step below). For more information about creating a description, see WikiPathways: Add a descption.

    • Final checklist

    Any pathway that you plan to submit to WikiPathways must meet a set of content requirements in order to be accepted:

    Criteria for pathways to be approved:

    1. No unconnected interactions.
    2. Most (>90%) of datanodes must be annotated with database references.
    3. The pathway must have a complete description, meaning a 2-3 sentence summary of the process that the pathway describes.
    4. Minimum of one literature reference.
    5. Minimum of one pathway ontology tag. Ontology tags can be added AFTER the pathway is uploaded to WikiPathways.
    6. Overall, the pathway model should be useful for data visualization and analysis.

    Submit your pathway to WikiPathways

  • Your pathway is now ready to be submitted to WikiPathways. See WikiPathways - Publish Pathway for details.
  • Save your work as a GPML file under File > Save As.
  • Drag-and-drop the GPML file below to check if it is correct.