Recent progress in proteomics, computational biology, and ontology development has presented an opportunity to investigate protein data sources from a unique perspective that is, examining protein data sources through structure and hierarchy of Protein Ontology (PO). Various data mining algorithms and mathematical models provide methods for analyzing protein data sources; however, there are two issues that need to be addressed: (1) the need for standards for defining protein data description

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... exchange and (2) eliminating errors which arise with the data integration methodologies for complex queries. Protein Ontology is designed to meet these needs by providing a structured protein data specification for Protein Data Representation. Protein Ontology is a standard for representing protein data in a way that helps in defining data integration and data mining models for Protein Structure and Function. We report here our development of PO; a semantic heterogeneity framework based on relationships between PO concepts; and analysis of resultant PO Data of Human Proteins. We also talk in this paper briefly about our ongoing work of designing a trustworthy framework around PO.