Copyright © 2005 IEEE

The advances in information and communication technologies coupled with increased knowledge about genes and proteins have opened new perspectives for study of protein complexes. There is a growing need to integrate the knowledge about various protein complexes for effective disease prevention mechanisms, individualized medicines and treatments and other accepts of healthcare. In this paper we propose a Protein Ontology that will handle the following computational challenges in the area Proteomics and systems biology in general: (1) It will provide more accurate interpretations and associations as conclusions are based on Data and Semantics. (2) It will make it possible to study relationships among proteins, protein folding, behaviour of protein under various environments, and most importantly cellular function of protein. This Protein Ontology is a unified terminology description integrating various protein database schemas and will provide a easier way to predict and understand proteins. Index Terms — Protein Ontology, Protein Informatics, Biomedical Ontologies, Biomedical Systems, Data Integration