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Classifying biomedical literature is a difficult and challenging task, especially when a large number of biomedical articles should be organized into a hierarchical structure. In this paper, we present an approach for classifying a collection of biomedical text abstracts downloaded from Medline database with the help of ontology alignment. To accomplish our goal, we construct two types of hierarchies, the OHSUMED disease hierarchy and the Medline abstract disease hierarchies from the OHSUMEDdoi:10.5281/zenodo.1080995 fatcat:zjjn3mx6z5ax5jkvvxl72w5suq