Researchers in biological sciences often face the problem of combining the results of different types of genomic and proteomic studies. Integrating the results of different types of experimental studies using ontologies, could provide researchers with many benefits, such as predicting gene function more reliably and supporting the evolution of current knowledge by integrating it with new genomic data. We address this important genomics problem by proposing the IGIPI ontological framework, standing for “Integrating Gene Interactions with Protein Interactions”, for integrating the results of experimental studies. IGIPI is based on the concept of goals that need to be satisfied in an experiment. IGIPI views different experiments as pieces of a puzzle that if positioned properly will create a more complete model of the cell. Researchers can potentially use IGIPI for semantic markup of web sites that have biomedical content. For semantic markup of web sites, IGIPI-based ontologies in terms of the OWL Web Ontology Language can be used. Section 1 introduces the problem domain and the motivation. Section 2 describes the IGIPI ontological framework and illustrates an example application on yeast.