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The goal of cognitive neuroscience is to understand how cognitive functions map onto brain systems, but cognitive neuroscience has largely focused on mapping or decoding task features rather than the cognitive functions that underlie them. I will first discuss the challenge of characterizing cognitive functions, in the context of the Cognitive Atlas ontology. I will then turn to discussing a set of studies that have used ontological frameworks to perform ontology driven decoding. I will conclude by discussing the need to move from folk-psychological to computational cognitive ontologies.