Database
[{"name":"abc","linked_data":{"sheet 1":["7d387e05d3f8180a","8534sfjog904395"],"sheet 2":["7d387e05d3f8180a","54647sgdsevey67r34"]}}]
Query
db.collection.aggregate([{"$set":{"linked_data":{"$objectToArray":"$linked_data"}}},{$set:{linked_data:{"$filter":{"input":"$linked_data","as":"ld","cond":{"$in":["8534sfjog904395","$$ld.v"]}}}}},{"$set":{"linked_data":{"$arrayToObject":"$linked_data"}}},{$match:{linked_data:{$ne:{}}}}])