Portal:CPTAC/Hallmark Curation

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This brief tutorial will describe how to go about collecting and defining cancer hallmark pathways for the CPTAC project.


Step 1: Access

  • If you are a member of the CPTAC consortium but do not have a WikiPathways account, then start by creating a new account (see links in upper right corner).
  • Then contact Alex Pico to request access to edit the CPTAC portal.
  • You will need to be logged in to complete the later steps of this tutorial. Feel free to work through the other steps in the meantime.

Step 2: Learning

  • Navigate back to the main page and begin by familiarizing yourself with the current set of hallmark categories. Each category displays a representative pathway that rotates through a set of pathways collected so far.
  • Click on the pathway image to navigate to a dedicate page with all the descriptions and annotations for that pathway.
  • Click on the title of the hallmark category to view the current list of pathways collected in each category.
Notice the format for each pathway entry: * <pathway link> <pathway name>
  • If you are logged in, you can click edit at the top of the hallmark category page and see the syntax used to make these lists, e.g.,

Step 3: Collecting

  • Now with a particular category in mind, go to the home page of WikiPathways and try a couple strategies for finding new content:

Search

  • You can type in keywords, gene names, etc into the search field and comb the results for new entries
  • Do you have expert knowledge about a particular gene or process? Search for it and see if the results you'd expect are returned.
  • Keep notes (or browser tabs) for any pathways you'd want to add to a hallmark category. Keep the WPID (e.g., WP3972) and the title.

Browse

  • Go to the Browse page
  • By default, the list shows featured human pathways. You can expand the viewable content by choosing Collection: Approved version
  • Do any of these titles or thumbnails catch your eye? Click on them to investigator further.
  • Keep notes (or browser tabs) for any pathways you'd want to add to a hallmark category. Keep the WPID (e.g., WP3972) and the title.

Step 4: Curating

  • Now return to the CPTAC portal
  • Click on the hallmark category you want to edit
  • Click edit and enter in your newly collected pathways in the same format as the other entries
  • If there are entire categories that are missing, you can attempt adding a new one by following the same syntax patterns as existing one. If this feels too advanced (or you get stuck), you can easily revert/undo any edits via the history tab and then contact Alex Pico for assistance.

Step 5: New Pathways

  • And, of course, if you know of a pathway that belong in our hallmark collection and it isn't already in WikiPathway, then you can either request it to be added using our Request Form or draw it yourself using our free and open tools. If you are new to pathway editing, we recommend starting with WikiPathways Academy.


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