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 and 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.