From Ontology-Based Gene Function to Physiological Model

Ajay      Shiv Sharma; Hari      Om Gupta; Petar      M. Mitrasinovic

doi:10.2174/157489312803901054

Abstract

Designing ontology to represent gene function is of vital importance for meeting the major challenge of integrating sequence data with the increasing amount of data from functional analyses of genes. Given that genes are expressed in temporally and spatially characteristic patterns, their products quite often reside in specific cellular compartments and may be part of one or more multi-component complexes. Genes may have more than one product and the products are functionally distinct. An overall strategy elucidating how an ontology-based gene function may be implemented using genomic databases is herein dissected. Knowing that gene products possess one or more biochemical, physiological or structural functions, the present strategy is suggested to lead towards physiological models. A review of the features of the currently available software tools for the implementation of the considered strategy is presented.

Keywords: Database, functional genomics, gene expression, gene ontology, physiology, systems biology, Model Structure Markup Language, physiology, cellular component ontology, International Nucleotide Sequence Database Collaboration