Abstract: Methods and systems for filtering data in a protein-protein interaction network are provided, which can be used to identify potential food-drug interactions. A method of filtering data in protein-protein interaction network includes mapping proteins associated with a plurality of chemicals of a first type (e.g drugs) and proteins associated with one or more chemicals of a second type (e.g., foods). The method further includes determining proximities of proteins associated with the plurality of chemicals of the first type and proteins associated with the one or more chemicals of the second type and generating a reduced dataset of proteins within the protein-protein interaction network. The reduced dataset includes proteins associated with a subset of the plurality of chemicals of the first type based on the determined proximities.