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Does anyone have any knowledge about how I would add a workflow condition based on context in system notes? I'd like to have a transition field in our workflow where if the context is web services it will skip the workflow but I'm not able to find where the record or field would be in the conditions

Create a saved search and set it as a condition in the workflow. In the saved search you can access the system notes.

caution here - you wouldn't be able to have your workflow set stuff during record create.

Can you not just edit the contexts on the workflow definition to exclude web services?

(you'd have to manually define all the contexts you want it to run on, as opposed to "de" selecting the one you don't want it to be)