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A cognitive subroutine was a subroutine that allowed Soong-type androids and holograms to think.

In 2376, a Hirogen used a micro-tunneling sensor to tap into the cognitive subroutines of The Doctor. He observed what he believed was everything that was happening around The Doctor on the USS Voyager, only to later realize that he was actually observing his daydreams. (VOY: "Tinker Tenor Doctor Spy")

In 2379, Data only activated the cognitive and communication subroutines of B-4. When B-4 asked him why he was unable to move, Data explained what he had done, adding that it was because B-4 posed a danger to the USS Enterprise-E. (Star Trek Nemesis)

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