We are a single service desk for the entire organization. We would like to report on requests created by department, but I can't find a way to do that out of the box? What are the best practices out there for tracking departments of users and their requests?
Reporting depends on how you want to report.
If you simply want to see what department (organization) owns the issues then a filtered list that includes Organization column would provide that view.
If you want to create a report for each department then a JQL like:
project = ABC and assignee in organizationMembers("organization")
you can even leave off project if your orgs span projects.
you can also display these on dashboards if desired.
if this isn't helping please provide more details of what your goal is.
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