Your Mission

The pathway is now almost complete, and we can make some final additions and adjustments to it. We will add a cell object to ass location context. While it's not obvious from the figure in the paper, the pathway is relevant for hepatocytes; we can add this as a label on the cell object. We will also add a reference for the publication, and make adjustments to the pathway layout.

    Add a cell object.

  • Select the Cell object from the Object panel and place it on the board.
  • Adjust the size and placement of the cell shape to fit the pathway. Importantly, make sure the INSR and SLC2A2 nodes (representing receptor and transporter) are aligned with the cell membrane at the top of the pathway.
  • Select the cell object, and in the Text Label field in the Properties tab, enter "Hepatocyte", to label the cell.
  • Update the Vertical Alignment to "Bottom", to move the cell label to the bottom.

    • 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: 38504356
  • Click Query PubMed. When the results are loaded, click OK.

    • Adjust layout and check for unconnected interactions

  • Review the layout of your pathway, and make any adjustment to node/interaction placement to minimize white space and to make sure the pathway is clear and easy to understand.
  • 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.
  • The overall layout of a pathway in terms of node spacing, placement on the board etc is important to the readability of the pathway at default zoom levels. As a final step in the creation of your pathway model, consider the following aspects of your pathway and adjust the layout accordingly:
    • Minimize white space by using a space efficient and compact layout.
    • Place the pathway diagram in the upper left of the pathway drawing board
    • Use consistent font size (12 or larger)

    To see a showcase gallery of representative pathway models with efficient and clear layout, visit the WikiPathways Help page.

    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 description.

    • 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.