Current PPI databases do not offer sophisticated queryinginterfaces and especially do not integrate existing informationabout proteins. Current algorithms for PIN analysis use onlytopological information, while emerging approaches attempt toexploit the biological knowledge related to proteins and kinds ofinteraction, e.g. protein function, localization, structure,described in Gene Ontology or PDB. The book discussestechnologies, standards and databases for, respectively,generating, representing and storing PPI data. It also describesmain algorithms and tools for the analysis, comparison andknowledge extraction from PINs. Moreover, some case studies andapplications of PINs are also discussed.