Net operating income is the property, not the deal
Start with the rent for a full year, subtract the vacancy and collection loss you expect, and you have the money the property actually collects. Then subtract the costs of running it: property tax, landlord insurance, maintenance and repairs, management, HOA dues and everything else the owner pays before the mortgage.
What is left is net operating income. It ignores the loan on purpose, which is what makes it comparable between two properties and between two buyers. Divide it by the purchase price and you have the cap rate: the return the property would produce for an all-cash buyer.