Comparing journal and paper level classifications of science

•Comparison of the classification system of science between the journal level and the paper level from the same data set.•In the journal classification system, 46.0% of articles were not contributed from their journal’s discipline(s).•In a paper classification system, 51.1% of papers were not published in journals of the same discipline(s).•The difference between these two levels varies by discipline and the methodology constructing the classification system.