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PPDB: A Tool for Investigation of Plants Physiology Based on Gene Ontology

  • Ajay Shiv SharmaEmail author
  • Hari Om Gupta
  • Rajendra Prasad
Original Research Article

Abstract

Representing the way forward, from functional genomics and its ontology to functional understanding and physiological model, in a computationally tractable fashion is one of the ongoing challenges faced by computational biology. To tackle the standpoint, we herein feature the applications of contemporary database management to the development of PPDB, a searching and browsing tool for the Plants Physiology Database that is based upon the mining of a large amount of gene ontology data currently available. The working principles and search options associated with the PPDB are publicly available and freely accessible online (http://www.iitr.ac.in/ajayshiv/) through a user-friendly environment generated by means of Drupal-6.24. By knowing that genes are expressed in temporally and spatially characteristic patterns and that their functionally distinct products often reside in specific cellular compartments and may be part of one or more multicomponent complexes, this sort of work is intended to be relevant for investigating the functional relationships of gene products at a system level and, thus, helps us approach to the full physiology.

Keywords

Biology Bioinformatics Database Data mining Functional genomics Gene ontology Gene products Physiology Plant 

Notes

Acknowledgments

We acknowledge the gene ontology consortium and open-source community as the source and inspiration for Plants Physiology Database. The authors also acknowledge AmiGO for the sourced term images on PPDB web site. The authors are thankful to Indian Institute of Technology, Roorkee, for providing the facilities to carry out this work. The authors also recognize contributions made by Dr. Petar M. Mitrasinovic. Ajay Shiv Sharma thanks to All India Council for Technical Education, Ministry of Human Resource Development, Government of India, for providing financial assistance.

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Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Ajay Shiv Sharma
    • 1
    Email author
  • Hari Om Gupta
    • 1
  • Rajendra Prasad
    • 1
  1. 1.Department of Electrical EngineeringIndian Institute of Technology RoorkeeRoorkeeIndia

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