A system and computer-based method is provided for decomposing and storing a markup based document into a relational database. For a schema of a markup based document a user identifies multiple items mapping into a same database table-column pair, creates a logical table and associates the logical table to each item and a corresponding database table. Next, a user creates a mapping document of the markup based document with mapping annotations defining mapping of the items into columns of the logical tables. Decomposition of each item into a corresponding logical table column is accomplished by collecting the item content from the markup based document and storing it in the corresponding row column.