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.
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References
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)
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
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)
Olivé, A.: Conceptual Modeling of Information Systems, 1st edn. Springer, Heidelberg (2007)
Aguilera, D., Gómez, C., Olivé, A.: Enforcement of Conceptual Schema Quality Issues in Current Integrated Development Environments, pp. 626–640. Springer, Heidelberg (2013)
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_31
Mirnezami, R., Nicholson, J., Darzi, A.: Preparing for precision medicine. N. Engl. J. Med. 6(366), 489–491 (2012)
Middleton, A.: Society and personal genome data. Hum. Mol. Genet. 27(R1), R8–R13 (2018)
Coll, V.B.: Gestión de mutaciones en ambientes genómicos: una perspectiva basada en Modelos Conceptuales (2012)
Cabot, J., Gómez, C., Pastor, O., Sancho, M.R., Teniente, E. (Eds.): Conceptual Modeling Perspectives. Springer, Heidelberg (2017)
Mylopoulos, J., Chung, L., Nixon, B.: Representing and using nonfunctional requirements: a process-oriented approach. IEEE Trans. Softw. Eng. 18(6), 483–497 (1992)
Thalheim, B.: The Theory of Conceptual Models, The Theory of Conceptual Modelling and Foundations of Conceptual Modelling, pp. 543–577. Springer, Heidelberg (2011)
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)
Muller, G.: System and context modeling - the role of time-boxing and multi-view interaction. Syst. Res. Forum 3, 139–152 (2009)
Ludewig, J.: Models in software engineering–an introduction. Softw. Syst. Model. 2(1), 5–14 (2003)
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)
Bourne, P.: Will a biological database be different from a biological journal? PLoS Comput. Biol. 1(3), 179–181 (2005)
Oxford University: NAR Database Summary Paper. Oxford University Press (2014). www.oxfordjournals.org
National Center for Biotechnology Information, “All resources,” National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/
University of Pittsburgh, “search.HSLS.OBRC,” The Health Sciences Library System 2014 (2018). https://www.hsls.pitt.edu/obrc/
Health Sciences Library Systems, “OBRC: Online Bioinformatics Resources Collections,” University of Pittsburgh (2014). https://www.hsls.pitt.edu/obrc/
Human Genome Variation Society, “Databases & Tools,” HGVS (2018). http://www.hgvs.org/content/databases-tools
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.
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Solis, C.V., León, P.A., Pastor Lopez, O. (2020). Genomic Databases Exploration Using Conceptual Models. In: Fosenca C, E., Rodríguez Morales, G., Orellana Cordero, M., Botto-Tobar, M., Crespo Martínez, E., Patiño León, A. (eds) Information and Communication Technologies of Ecuador (TIC.EC). TICEC 2019. Advances in Intelligent Systems and Computing, vol 1099. Springer, Cham. https://doi.org/10.1007/978-3-030-35740-5_6
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