Research in Biomedicine is increasing rapidly day by day and the need for maintaining the biomedical literature is also a tedious task. Data Curators, Doctors, Scientific Researchers have a requirement of analyzing biomedical articles for Scientific discoveries and scholarly knowledge from this vast collection of data to take a proper prediction. Biomedical data includes a collection of genes and protein related information and the mutations of the above which leads to diseases. This kind of hidden knowledge and relationships between above mentioned entities can be mined with proper preprocessing methods. This paper illustrates the comparison of various preprocessing methods used on biomedical data and the best combination of methods can be used for the retrieval of hidden intrinsic knowledge and patterns from Biomedical Literature Data Sources.