Advertisement

Ontological Foundation for Protein Data Models

  • Amandeep S. Sidhu
  • Tharam S. Dillon
  • Elizabeth Chang
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3762)

Abstract

In this paper we proposed a Protein Ontology to integrate protein data and information from various Protein Data Sources. Protein Ontology provides the technical and scientific infrastructure and knowledge to allow description and analysis of relationships between various proteins. Protein Ontology uses relevant protein data sources of information like PDB, SCOP, and OMIM. Protein Ontology describes: Protein Sequence and Structure Information, Protein Folding Process, Cellular Functions of Proteins, Molecular Bindings internal and external to Proteins, and Constraints affecting the Final Protein Conformation. We also created a database of 10 Major Prion Proteins available in various Protein data sources, based on the vocabulary provided by Protein Ontology. Details about Protein Ontology are available online at http://www.proteinontology.info/.

Keywords

Protein Data Bank Prion Protein Description Logic Class Hierarchy Nucleic Acid Research 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Weissiga, H., Bourne, P.E.: Protein structure resources. Biological Crystallography 58, 908–915 (2002)CrossRefGoogle Scholar
  2. 2.
    Westbrook, J., Feng, Z., et al.: The Protein Data Bank: unifying the archive. Nucleic Acid Research 30(1), 245–248 (2002)CrossRefGoogle Scholar
  3. 3.
    Bhat, T.N., Bourne, P.E., et al.: The PDB data uniformity project. Nucleic Acid Research 29(1), 214–218 (2001)CrossRefGoogle Scholar
  4. 4.
    Bernstein, F.C., Koetzle, T.F., et al.: The Protein Data Bank: a computer-based archival file for macromolecular structures. Journal of Molecular Biology 112(3), 535–542 (1977)CrossRefGoogle Scholar
  5. 5.
    Conte, L.L., Ailey, B., et al.: SCOP: a Structural Classification of Proteins database. Nucleic Acids Research 28(1), 257–259 (2000)CrossRefGoogle Scholar
  6. 6.
    Murzin, A.G., Brenner, S.E., et al.: SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology 247, 536–540 (1995)Google Scholar
  7. 7.
    Mckusick, V. A.: Online Mendelian Inheritance in Man, OMIM. Baltimore, MD, Johns Hopkins University, National Center for Biotechnology Information, and National Library of Medicine (2000)Google Scholar
  8. 8.
    Schulze-Kremer, S.: Ontologies for Molecular Biology. In: Proceedings of Third Pacific Symposium on Biocomputing, Hawaii, AAAI Press, pp. 693–704. AAAI Press, Hawaii (1998)Google Scholar
  9. 9.
    Karp, P., Riley, M., et al.: Ecocyc: Electronic Encyclopedia of E.coli genes and metabolism. Nucleic Acids Research 26, 50 (1998)CrossRefGoogle Scholar
  10. 10.
    Borgida, A.: Description Logics in Data Management. IEEE Transactions on Knowledge and Data Engineering 7, 671–682 (1995)CrossRefGoogle Scholar
  11. 11.
    GO. Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11, 1425–1433 (2001) Google Scholar
  12. 12.
    G.: Gene Ontology: looking backwards and forwards. Genome Biology 6(1) 103, 103.1-103.4 (2004)Google Scholar
  13. 13.
    Altmann, R.B., Bada, M., et al.: riboweb: An Ontology-Based System for Collaborative Molecular Biology. IEEE Intelligent Systems 76, 68–76 (1999)CrossRefGoogle Scholar
  14. 14.
    Westbrook, J., Ito, N., et al.: PDBML: The Representation of Archival Macromolecular Structure Data in XML. Bioinformatics 21(7), 988–992 (2005)CrossRefGoogle Scholar
  15. 15.
    Mani, I., Hu, Z., et al.: PRONTO: A Large-scale Machine-induced Protein Ontology. In: 2nd Standards and Ontologies for Functional Genomics Conference, UK (SOFG 2004)Google Scholar
  16. 16.
    Sidhu, A.S., Dillon, T.S., et al.: An Ontology for Protein Data Models. In: 27th annual international conference of the ieee engineering in medicine and biology society 2005 (IEEE EMBC 2005), Shanghai, China, IEEE Press, Los Alamitos (2005)Google Scholar
  17. 17.
    Sidhu, A.S., Dillon, T.S., et al.: Ontology-based Knowledge Representation of Protein Data. In: 3rd International IEEE Conference on Industrial Informatics, Perth, Australia, IEEE CS Press, Los Alamitos (2005)Google Scholar
  18. 18.
    Sidhu, A.S., Dillon, T.S., et al.: Protein Ontology: Vocabulary for Protein Data. In: 3rd IEEE International Conference on Information Technology and Applications, Sydney, Australia, IEEE CS Press, Los Alamitos (2005)Google Scholar
  19. 19.
    Sidhu, A.S., Dillon, T.S., et al.: A Unified Representation of Protein Structure Databases (Book Section). In: Reddy, M.S., Khanna, S. (eds.) Biotechnological Approaches for Sustainable Development, Mumbai, India, pp. 396–408. Allied Publishers Pvt. Ltd (2004)Google Scholar
  20. 20.
    Sidhu, A.S., Dillon, T.S., et al.: An XML based semantic protein map. In: Zanasi, A., Ebecken, N.F.F., Brebbia, C.A. (eds.) Data Mining 2004, Malaga, Spain, vol. 10, pp. 51–60. WIT Press, Southampton (2004)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Amandeep S. Sidhu
    • 1
  • Tharam S. Dillon
    • 1
  • Elizabeth Chang
    • 2
  1. 1.Faculty of Information TechnologyUniversity of TechnologySydneyAustralia
  2. 2.School of Information SystemsCurtin University of Technical UniversityPerthAustralia

Personalised recommendations