Advertisement

Genomic Databases Exploration Using Conceptual Models

  • C. Vanessa SolisEmail author
  • P. Ana León
  • Oscar Pastor Lopez
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 1099)

Abstract

The modeling of the human genome is a fundamental part that allows us to consider the involved entities and their relationships. For this reason, the present work incorporates a conceptual model under a mapping with different existing genomic databases, establishing links between the information genomic databases contrasted with each of the elements of the Conceptual Schema of the Human Genome (CSHG). This work presents the development of the exploration of genomic databases found in lists endorsed by research institutes in the genomic area, as a basis for a later construction of an information system oriented to the genomic field. It states the verification process of the found sites, since some have suffered changes in the servers or have simply stopped working. Also, exposes generated depuration tasks, because each of the genomic databases have different structures, information organization, or even in some cases unusual nomenclature was used. Subsequently, the mapping of each genomic database with the elements of the CSHG is presented. Finally, the results obtained are shown with statistics established in the exploration of the genomic databases.

Keywords

Conceptual schema of the human genome (CSHG) Genomic data bases Human genome Genomic information system Conceptual schema (CM) 

Notes

Acknowledges

The authors wish to thank the members of the Genome Group of the PROS Research Center for the fruitful discussions on the application of conceptual modeling in the field of medicine. This work has been supported by the Ministry of Science and Innovation of Spain through the DataME project (ref: TIN2016-80811-P) and the Research and Development Assistance Program (PAID-01-16) of the Universitat Politècnica de València under the FPI 2137 grant.

References

  1. 1.
    Cook, C.E., Bergman, M.T.C.G., Apweiler, R., Birney, E.: The European bioinformatics institute in 2017: data coordination and integration. Nucleic Acids Res. 46, D21–D29 (2017)CrossRefGoogle Scholar
  2. 2.
    UK government, Strategy for UK life sciences: one year on (2012). https://www.gov.uk/government/publications/strategy-for-uk-life-sciences-one-year-on
  3. 3.
    Tao, C., Embley, D.: Seed-based generation of personalized bio-ontologies for information extraction. In: Advances in Conceptual Modeling–Foundations and Applications, pp. 74–84 (2007)Google Scholar
  4. 4.
    Olivé, A.: Conceptual Modeling of Information Systems, 1st edn. Springer, Heidelberg (2007)zbMATHGoogle Scholar
  5. 5.
    Aguilera, D., Gómez, C., Olivé, A.: Enforcement of Conceptual Schema Quality Issues in Current Integrated Development Environments, pp. 626–640. Springer, Heidelberg (2013)Google Scholar
  6. 6.
    Reyes Román, J.F., Pastor, Ó., Casamayor, J.C., Valverde, F.: Applying conceptual modeling to better understand the human genome. In: ER 2016 Concept Model, pp. 404–412. Springer, Gifu (2016).  https://doi.org/10.1007/978-3-319-46397-1_31CrossRefGoogle Scholar
  7. 7.
    Mirnezami, R., Nicholson, J., Darzi, A.: Preparing for precision medicine. N. Engl. J. Med. 6(366), 489–491 (2012)CrossRefGoogle Scholar
  8. 8.
    Middleton, A.: Society and personal genome data. Hum. Mol. Genet. 27(R1), R8–R13 (2018)CrossRefGoogle Scholar
  9. 9.
    Coll, V.B.: Gestión de mutaciones en ambientes genómicos: una perspectiva basada en Modelos Conceptuales (2012)Google Scholar
  10. 10.
    Cabot, J., Gómez, C., Pastor, O., Sancho, M.R., Teniente, E. (Eds.): Conceptual Modeling Perspectives. Springer, Heidelberg (2017)Google Scholar
  11. 11.
    Mylopoulos, J., Chung, L., Nixon, B.: Representing and using nonfunctional requirements: a process-oriented approach. IEEE Trans. Softw. Eng. 18(6), 483–497 (1992)CrossRefGoogle Scholar
  12. 12.
    Thalheim, B.: The Theory of Conceptual Models, The Theory of Conceptual Modelling and Foundations of Conceptual Modelling, pp. 543–577. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  13. 13.
    Cabot, J., Gómez, C., Sancho, M.R., Teniente, E.: 30 years of contributions to conceptual. In: Conceptual Modeling Perspectives, pp. 7–20. Springer, Heidelberg (2017)CrossRefGoogle Scholar
  14. 14.
    Muller, G.: System and context modeling - the role of time-boxing and multi-view interaction. Syst. Res. Forum 3, 139–152 (2009)CrossRefGoogle Scholar
  15. 15.
    Ludewig, J.: Models in software engineering–an introduction. Softw. Syst. Model. 2(1), 5–14 (2003)CrossRefGoogle Scholar
  16. 16.
    Reyes Román, J.F.: Diseño y Desarrollo de un Sistema de Información Genómica Basado en un Modelo Conceptual Holístico del Genoma Humano (Doctoral dissertation), Valencia: Tesis Doctoral (2018)Google Scholar
  17. 17.
    Bourne, P.: Will a biological database be different from a biological journal? PLoS Comput. Biol. 1(3), 179–181 (2005)CrossRefGoogle Scholar
  18. 18.
    Oxford University: NAR Database Summary Paper. Oxford University Press (2014). www.oxfordjournals.org
  19. 19.
    National Center for Biotechnology Information, “All resources,” National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/
  20. 20.
    University of Pittsburgh, “search.HSLS.OBRC,” The Health Sciences Library System 2014 (2018). https://www.hsls.pitt.edu/obrc/
  21. 21.
    Health Sciences Library Systems, “OBRC: Online Bioinformatics Resources Collections,” University of Pittsburgh (2014). https://www.hsls.pitt.edu/obrc/
  22. 22.
    Human Genome Variation Society, “Databases & Tools,” HGVS (2018). http://www.hgvs.org/content/databases-tools

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • C. Vanessa Solis
    • 1
    Email author
  • P. Ana León
    • 1
  • Oscar Pastor Lopez
    • 1
  1. 1.Research Center on Software Production Methods (PROS)Universitat Politècnica de ValènciaValenciaSpain

Personalised recommendations