Researchers are faced with the challenge of integrating on the basis of a common Semantic Web framework the information on biological functions resulting from genomic and proteomic experimental studies. Researchers would also like to integrate the biological functions' roles in larger biomedical conditions, which will support automated analysis and reasoning on the Semantic Web. We address these challenges by proposing the IGIPI framework, standing for "Integrating Gene Interactions and Protein Interactions". IGIPI views different experimental studies as pieces of a puzzle that if positioned properly will contribute to a more complete representation of a biological function or biomedical condition. This framework allows representing the relative time points of events. The IGIPI framework involves integrating different ontologies and vocabularies, including the Gene Ontology, MGED Ontology and UMLS Unified Medical Language System. Researchers can semantically markup their websites through reusing and refining IGIPI representations in the OWL Web Ontology Language. We applied IGIPI to yeast and cancer information.

Keywords: integration, gene, protein, interaction, ontology, biomedical, information.

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