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What is the best way to find all Indicators that use a specific DataElement? Do I have to search for the id in the numerator and denominator strings like this, or is there a better way?

/api/25/indicators?filter=numerator:like:HifxrAyx4sO /api/25/indicators?filter=denominator:like:HifxrAyx4sO

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Yes that is the best way at the moment. We do have primitive support for logical operators (applies to entire query) so you could combine it like

/api/indicators?filter=numerator:like:fbfJHSPpUQD&filter=denominator:like:fbfJHSPpUQD&rootJunction=OR

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