Organisational/Department Setup

What is the best way to setup JIRA in order to differentiate / keep projects completely seperate. i.e. different departments must not share any data across projects.

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You need to take advantage of the project permission schemes. Following might be a good starting point.

1. Create different groups of each organization, may be even different groups for different roles in the orgs

2. Use the groups in the project role of the relevant projects

3. Use project roles in the permission schemes, notifications, workflows etc.

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