Skip to main content
SpringerLink
Log in
Book cover

International Joint Conference on Knowledge Discovery, Knowledge Engineering, and Knowledge Management

IC3K 2010: Knowledge Discovery, Knowledge Engineering and Knowledge Management pp 23–37Cite as

Improving the Semantics of a Conceptual Schema of the Human Genome by Incorporating the Modeling of SNPs

  • Conference paper

  • 819 Accesses

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 272))

Abstract

In genetic research, the concept known as SNP, or single nucleotide polymorphism, plays an important role in detection of genes associated with complex ailments and detection of hereditary susceptibility of an individual to a specific trait. Discussing the issue, as it surfaced in the development of a conceptual schema for the human genome, it became clear a high degree of conceptual ambiguity surrounds the term. Solving this ambiguity has lead to the main research question: What makes a genetic variation, classified as a SNP different from genetic variations, not classified as SNP?. For optimal biological research to take place, an unambiguous conceptualization is required. Our main contribution is to show how conceptual modeling techniques applied to human genome concepts can help to disambiguate and correctly represent the relevant concepts in a conceptual schema, thereby achieving a deeper and more adequate understanding of the domain.

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

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

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Scherren, K., Jost, J.: Gene and genon concept: coding versus regulation. Theory in Biosciences 126(2-3), 65–113 (2007)

    Article  Google Scholar 

  2. Gerstein, M.B., Bruce, C., Rozowosky, J., Zheng, D., Du, J., Korbel, J., Emanuelson, O., Zhang, Z., Weissman, S., Snyder, M.: What is a gene, post-ENCODE? Genome Research 17(6), 669–681 (2007)

    Article  Google Scholar 

  3. Pearson, H.: Genetics: What is a gene? Nature 441(7092), 398–402 (2006)

    Article  Google Scholar 

  4. Risch, N., Merikangas, K.: The future of genetic studies of complex human diseases. Science 273, 1516–1517 (1996)

    Article  Google Scholar 

  5. Li, W.-H., Wu, C.-I., Luo, C.-C.: Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. Journal of Molecular Evolution 21, 58–71 (1984)

    Article  Google Scholar 

  6. Zhao, Z., Boerwinkle, E.: Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome. Genome Research 12, 1679–1686 (2002)

    Article  Google Scholar 

  7. Kaessmann, H., Heißig, F., von Haeseler, A., Pääbo, S.: DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Natural Genetics 22, 78–81 (1999)

    Article  Google Scholar 

  8. Zhao, Z., Li, J., Fu, Y.-X., et al.: Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proceedings of the National Academy of Sciences USA 97, 11354–11358 (2000)

    Article  Google Scholar 

  9. Jorde, L.B., Watkins, W.S., Bamshad, M.J.: Population genomics: a bridge from evolutionary history to genetic medicine. Human Molecular Genetics 10, 2199–2207 (2001)

    Article  Google Scholar 

  10. Schwarz, D.F., Hädicke, O., Erdmann, J., Ziegler, A., Bayer, D., Möller, S.: SNPtoGO: characterizing SNPs by enriched GO terms. Bioinformatics 24(1), 146 (2008)

    Article  Google Scholar 

  11. Selic, B.: The Pragmatics of Model-Driven Development. IEEE Software 20(5), 19–26 (2003)

    Article  Google Scholar 

  12. Pastor, O.: Conceptual Modeling Meets the Human Genome. In: Li, Q., Spaccapietra, S., Yu, E., Olivé, A. (eds.) ER 2008. LNCS, vol. 5231, pp. 1–11. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  13. Pastor, O., Levin, A.M., Celma, M., Casamayor, J.C., Eraso Schattka, L.E., Villanueva, M.J., Perez-Alonso, M.: Enforcing Conceptual Modeling to Improve the Understanding of the Human Genome. In: Procs. of the IVth Int. Conference on Research Challenges in Information Science, RCIS 2010, Nice, France. IEEE Press (2010) ISBN #978-1-4244-4840-1

    Google Scholar 

  14. Venter, C., Adams, M.D., Myers, E.W., et al.: The Sequence of the Human Genome. Science 291(5507), 1304–1351 (2000)

    Article  Google Scholar 

  15. Pastor, O., Molina, J.C.: Model-driven architecture in practice: a software production environment based on conceptual modeling. Springer, Heidelberg (2007)

    Google Scholar 

  16. Alberts, B., Bray, D., Hopkin, K., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Essential Cell Biology. Zayatz, E., Lawrence, E. (eds.), 2nd edn., Garland Science USA (2003)

    Google Scholar 

  17. Zhao, Z., Fu, Y.-X., Hewett-Emmett, D., Boerwinkle, E.: Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 312, 207–213 (2003)

    Article  Google Scholar 

  18. Vignal, A., Milan, D., SanCristobal, M., Eggen, A.: A review on SNP and other types of molecular markers and their use in animal genetics. Genetics, Selection, Evolution 34(3), 275 (2002)

    Article  Google Scholar 

  19. dbSNP, http://www.ncbi.nlm.nih.gov/projects/SNP/

  20. National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/

  21. Yue, P., Moult, J.: Identification and analysis of deleterious human SNPs. Journal of Molecular Biology 356(5), 1263–1274 (2006)

    Article  Google Scholar 

  22. Shastry, B.S.: SNPs: Impact on gene function and phenotype. Methods in Molecular Biology 578, 3–22 (2009)

    Article  Google Scholar 

  23. Devlin, B., Risch, N.: A comparison of Linkage Disequilibrium measures for fine-scale mapping. Genomics 29(2), 311–322 (1995)

    Article  Google Scholar 

  24. HUGO Gene Nomenclature Committee, http://www.genenames.org/

  25. Maglott, D., Ostell, J., Pruitt, K.D., Tatusova, T.: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research 35, 26–32 (2006)

    Article  Google Scholar 

  26. Stenson, P.D., Mort, M., Ball, E.V., Howells, K., Phillips, A.D., Thomas, N.S.T., Cooper, D.N.: The Human Gene Mutation Database: 2008 update. Genome Medicine 1, 13 (2009)

    Article  Google Scholar 

  27. Mooney, S.D., Altman, R.B.: MutDB: annotating human variation with functionally relevant data. Bioinformatics 19, 1858–1860 (2003)

    Article  Google Scholar 

  28. Szabo, C., Masiello, A., Ryan, J.F., Brody, L.C.: The Breast Cancer Information Core: Database design, structure, and scope. Human Mutation 16, 123–131 (2000)

    Article  Google Scholar 

  29. Povey, S., Lovering, R., Bruford, E., Wright, M., Lush, M., Wain, H.: The HUGO Gene Nomenclature Committee (HGNC). Human Genetics 109, 678–680 (2001)

    Article  Google Scholar 

  30. The HapMap project, http://www.hapmap.org

  31. International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–862 (2007)

    Google Scholar 

  32. Gibbs, R.A., Belmont, J.W., Hardenbol, P., Willis, T.D., Yu, F., et al.: The International HapMap project. Nature 426, 789–796 (2003)

    Article  Google Scholar 

  33. Stoesser, G., Tuli, M.A., Lopez, R., Sterk, P.: The EMBL Nucleotide Sequence Database. Nucleic Acids Research 27, 18–24 (1999)

    Article  Google Scholar 

  34. Okayama, T., Tamura, T., Gojobori, T., Tateno, Y., Ikeo, K., Miyazaki, S., Fukami-Kobayashi, K., Sugawara, H.: Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library. Bioinformatics 14(6), 472 (1998)

    Article  Google Scholar 

  35. Chen, I.M.A., Markowitz, V.: Modeling scientific experiments with an object data model. In: Proceedings of the SSDBM, pp. 391–400. IEEE Press (1995)

    Google Scholar 

  36. Medigue, C., Rechenmann, F., Danchin, A., Viari, A.: Imagene, an integrated computer environment for sequence annotation and analysis. Bioinformatics 15(1), 2 (1999)

    Article  Google Scholar 

  37. Paton, N.W., Khan, S.A., Hayes, A., Moussouni, F., Brass, A., Eilbeck, K., Goble, C.A., Hubbard, S.J., Oliver, S.G.: Conceptual modeling of genomic information. Bioinformatics 16(6), 548–557 (2000)

    Article  Google Scholar 

  38. Pastor, M.A., Burriel, V., Pastor, O.: Conceptual Modeling of Human Genome Mutations: A Dichotomy Between What we Have and What we Should Have. BIOSTEC Bioinformatics, 160–166 (2010) ISBN: 978-989-674-019-1

    Google Scholar 

  39. Ashburner, M., Ball, C.A., Blake, J.A.: Gene Ontology: tool for the unification of biology. Nature Genetics 25(1), 25–30 (2000)

    Article  Google Scholar 

  40. Schwarz, D.F., Hdicke, O., Erdmann, J., Ziegler, A., Bayer, D., Mller, S.: SNPtoGO: characterizing SNPs by enriched GO terms. Bioinformatics 24(1), 146 (2008)

    Article  Google Scholar 

  41. Coulet, A., Smaïl-Tabbone, M., Benlian, P., Napoli, A., Devignes, M.-D.: SNP-Converter: An Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies. In: Leser, U., Naumann, F., Eckman, B. (eds.) DILS 2006. LNCS (LNBI), vol. 4075, pp. 82–93. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  42. Guarino, N.: Formal Ontology in Information Systems. In: Bennett, B., Fellbaum, C. (eds.) Proceedings of the Fourth International Conference (FOIS 2006), vol. 150. IOS Press (1998/2006)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Centro de Investigación en Métodos de Producción de Software -PROS, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022, Valencia, Valencia, Spain

    Óscar Pastor, Matthijs van der Kroon, Ana M. Levin, Matilde Celma & Juan Carlos Casamayor

Authors
  1. Óscar Pastor
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Matthijs van der Kroon
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ana M. Levin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Matilde Celma
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Juan Carlos Casamayor
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. IST - Technical University of Lisbon, Av.Rovisco Pais, 1, 1049-001, Lisbon, Portugal

    Ana Fred

  2. Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands

    Jan L. G. Dietz

  3. Informatics Research Centre, University of Reading, UK

    Kecheng Liu

  4. Departament of Systems and Informatics, Polytechnic Institute of Setúbal – INSTICC, Rua do Vale de Chaves - Estefanilha, 2910-761, Setúbal, Portugal

    Joaquim Filipe

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Pastor, Ó., van der Kroon, M., Levin, A.M., Celma, M., Casamayor, J.C. (2013). Improving the Semantics of a Conceptual Schema of the Human Genome by Incorporating the Modeling of SNPs. In: Fred, A., Dietz, J.L.G., Liu, K., Filipe, J. (eds) Knowledge Discovery, Knowledge Engineering and Knowledge Management. IC3K 2010. Communications in Computer and Information Science, vol 272. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29764-9_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-29764-9_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-29763-2

  • Online ISBN: 978-3-642-29764-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation