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A unique identifier is how your domain or organisation is identified to service providers when users access resources. They are either a numeric organisation ID or an entityID / scope pair more usually a scope depending on the service provider.

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Sometimes a domain is very large or widespread and has different resource needs for the organisations within it - e.g. sites in different countries. Where this is the case, the organisation can be set to have a its own unique identifier and this allows the users under of that organisation to be seen by service providers as being represented by a different subscription. Specifically they will have their own organisation ID and scope - they will still use the same federation entityID as the domain.

Advantages of a unique identifier for an organisation

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To set a sub-organisation as unique, open their account details, go to the permissions tab and tick both the unique identifier and unique scope boxes and save: