A method, device, and computer program storage product for generating a query to extract clinical features into a set of electronic medical record (EMR) tables based on clinical knowledge. A knowledge tree is constructed according to a set of clinical knowledge data. An EMR graph corresponding to a set of EMR tables is obtained. The EMR graph comprises at set of table nodes and a set of attribute nodes. The set of table nodes and the set of attribute nodes represent a structure of each EMR table in the set of EMR tables and a reference relationship among attributes of set of EMR tables. A plurality of sub-queries is generated based on the knowledge tree and the EMR graph. At least one query is generated by combining the plurality of sub-queries according to the knowledge tree.