I have a sore knee from running. Hurts on the middle especially when held in a flexion position for a while like seated. Painful to run and ride- walking is okay to a certain extent.

Patellar Tendonitis. It sounds like you may have patellar tenodinitis. This will feel more painful with the knee in flexed position because the patellar tendon is extended. Normally is painful also with walking up and down stairs. Ibuprofen will normally work for this but if it does not it may need a steroid injection. Please follow up with your primary doctor if symptoms persist for a prolonged period of time.