Proteins in the same protein complexes should highly interact with each other but rarely interact with the other proteins in protein-protein interaction (PPI) networks. All interaction network weighting schemes have been proposed so far in the literature in order to eliminate the noise inherent in interactome data. Visualization representation of data visually and is an important task in scientific research. PPI are discovered using mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. Using Random walk on weighted graphs for identifying the interaction easily between Protein subsets and measuring the evaluation performance of proteins, Graphs for PINs visualizing the high number of nodes and connections, the heterogeneity of nodes (proteins) and edges (interactions), the possibility to annotate proteins and interactions with biological information that enriches the PINs with semantic information, and maintained as a separate databases for easy retrieval information of proteins from various Protein databases.