Skip to main content

Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology

  • Conference paper
Biomedical Engineering Systems and Technologies (BIOSTEC 2012)

Abstract

The human oral cavity is a complex ecosystem where multiple interactions occur and whose comprehension is critical in understanding several disease mechanisms. In order to comprehend the composition of the oral cavity at a molecular level, it is necessary to compile and integrate the biological information resulting from specific techniques, especially from proteomic studies of saliva. The objective of this work was to compile and curate a specific group of proteins related to the oral cavity, providing a tool to conduct further studies of the salivary proteome. In this paper we present a platform that integrates in a single endpoint all available information for proteins associated with the oral cavity. The proposed tool allows researchers in biomedical sciences to explore microorganisms, proteins and diseases, constituting a unique tool to analyse meaningful interactions for oral health.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Cherry, J.M., et al.: SGD: Saccharomyces genome database. Nucleic Acids Research 26(1), 73 (1998)

    Article  Google Scholar 

  2. Mering, C., et al.: STRING: a database of predicted functional associations between proteins. Nucleic Acids Research 31(1), 258 (2003)

    Article  Google Scholar 

  3. Maglott, D., et al.: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research 33(suppl. 1), D54 (2005)

    Google Scholar 

  4. Bairoch, A., et al.: The universal protein resource (UniProt). Nucleic Acids Research 33(suppl. 1), D154 (2005)

    Google Scholar 

  5. Humbertclaude, V., et al.: G.P.9.10 Clinical development of the French UMD-DMD database. Neuromuscular Disorders 17(9-10), 817–818 (2007)

    Article  Google Scholar 

  6. Fokkema, I.F.A.C., den Dunnen, J.T., Taschner, P.E.M.: LOVD: Easy creation of a locus specific sequence variation database using an “LSDB in a box” approach. Human Mutation 26(2), 63–68 (2005)

    Article  Google Scholar 

  7. D O’Connor, B., et al.: GMODWeb: a web framework for the Generic Model Organism Database. Genome Biology 9(6), R102 (2008)

    Google Scholar 

  8. Swertz, M., et al.: The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinformatics 11(suppl. 12), S12 (2010)

    Google Scholar 

  9. de Almeida, P.V., et al.: Saliva composition and functions: a comprehensive review. J. Contemp. Dent. Pract. 9(3), 72–80 (2008)

    Google Scholar 

  10. Greabu, M., et al.: Saliva—a diagnostic window to the body, both in health and in disease. J. Med. Life 2, 124–132 (2009)

    Google Scholar 

  11. Nagler, R.M.: Saliva as a tool for oral cancer diagnosis and prognosis. Oral Oncology 45(12), 1006–1010 (2009)

    Article  Google Scholar 

  12. Shpitzer, T., et al.: Salivary analysis of oral cancer biomarkers. British Journal of Cancer 101(7), 1194–1198 (2009)

    Article  Google Scholar 

  13. Rudney, J., Staikov, R., Johnson, J.: Potential biomarkers of human salivary function: a modified proteomic approach. Archives of Oral Biology 54(1), 91–100 (2009)

    Article  Google Scholar 

  14. Gonçalves, L.D.R., et al.: Comparative proteomic analysis of whole saliva from chronic periodontitis patients. Journal of Proteomics 73(7), 1334–1341 (2010)

    Article  Google Scholar 

  15. Streckfus, C.F., et al.: Breast cancer related proteins are present in saliva and are modulated secondary to ductal carcinoma in situ of the breast. Cancer Investigation 26(2), 159–167 (2008)

    Article  Google Scholar 

  16. Hu, S., et al.: Salivary proteomic and genomic biomarkers for primary Sjögren’s syndrome. Arthritis & Rheumatism 56(11), 3588–3600 (2007)

    Article  Google Scholar 

  17. Rao, P.V., et al.: Proteomic identification of salivary biomarkers of type-2 diabetes. Journal of Proteome Research 8(1), 239–245 (2009)

    Article  Google Scholar 

  18. Livnat, G., et al.: Salivary profile and oxidative stress in children and adolescents with cystic fibrosis. Journal of Oral Pathology & Medicine 39(1), 16–21 (2010)

    Article  Google Scholar 

  19. Giusti, L., et al.: Specific proteins identified in whole saliva from patients with diffuse systemic sclerosis. The Journal of Rheumatology 34(10), 2063 (2007)

    Google Scholar 

  20. Seymour, G.J., Cullinan, M.P., Heng, N.C.: Oral Biology: Molecular Techniques and Applications (Methods in Molecular Biology). Humana Press (2010)

    Google Scholar 

  21. Wong, D.T.: Salivary diagnostics powered by nanotechnologies, proteomics and genomics. The Journal of the American Dental Association 137(3), 313 (2006)

    Google Scholar 

  22. Helmerhorst, E., Oppenheim, F.: Saliva: a dynamic proteome. Journal of Dental Research 86(8), 680 (2007)

    Article  Google Scholar 

  23. Chen, T., et al.: The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database: the Journal of Biological Databases and Curation 2010 (2010)

    Google Scholar 

  24. Nelson, K.E., et al.: A catalog of reference genomes from the human microbiome. Science 328(5981), 994–999 (2010)

    Article  Google Scholar 

  25. Xie, H., et al.: Proteomics analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry. Molecular & Cellular Proteomics 7(3), 486 (2008)

    Article  Google Scholar 

  26. Santos, R.J., Bernardino, J.: Real-time data warehouse loading methodology. In: Proceedings of the 2008 International Symposium on Database Engineering & Applications, pp. 49–58. ACM, Coimbra (2008)

    Google Scholar 

  27. Barbosa, A.C.P., Porto, F.A.M., Melo, R.N.: Configurable data integration middleware system. Journal of the Brazilian Computer Society 8(2), 12–19 (2002)

    Article  Google Scholar 

  28. Lopes, P., Dalgleish, R., Oliveira, J.L.: WAVe: web analysis of the variome. Human Mutation (2011)

    Google Scholar 

  29. Lamster, I.B., et al.: The relationship between oral health and diabetes mellitus. The Journal of the American Dental Association 139(suppl. 5), 19S (2008)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Melo, J. et al. (2013). Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology. In: Gabriel, J., et al. Biomedical Engineering Systems and Technologies. BIOSTEC 2012. Communications in Computer and Information Science, vol 357. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38256-7_27

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-38256-7_27

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-38255-0

  • Online ISBN: 978-3-642-38256-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics