Egyptian clover varieties are part of a very important agricultural family, second only to cereals. In this paper, the materials under the present investigation consisted of three biological datasets, containing different protein characteristics annotated from interpro, prints and quick Godatabasesthey were selected and have been applied to data from XML flat files into a local database of size 10MB in oracle tool which is used throughout the experiments Shimaa A. Badawy(2013).Moreover, in the present study, a new program was designed and applied which showed high flexibility and efficient of mining the hierarchy (Molecular Biology data of T. alexandrinum L.). In addition describe protein characteristics including family of protein, finger print of protein of Trifoliumalexandrinum L.