Abstract
Programs are historically the basic notion in Software Engineering, which represents the final artifact to be executed in a machine. These programs have been created by humans, using a silicon-based code, whose final components use a binary code represented by 0s and 1s. If we look at life as a program with a DNA-based genetic code with a final representation that uses four essential units (A, C, G and T), one challenging question emerges. Can we establish a correspondence between life – from a genomic perspective – and programs – from a Software Engineering perspective? This paper assumes a positive answer to this question and shows how genomic can benefit from Information Systems Engineering by applying conceptual modeling to determine those relevant data that life represents in order to manage them accordingly, with special emphasis in the health domain. The main contributions focus on i) a concrete materialization of a Conceptual Schema of the Human Genome, ii) the need of having a method to provide a methodological guidance concerning genome data management, and iii) the importance of assessing data quality for all generated data that are going to be used in critical domains such as health and Precision Medicine.
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References
Olivé, A.: Conceptual Schema-Centric Development: A Grand Challenge for Information Systems Research. In: Pastor O., Falcão e Cunha J. (eds) Advanced Information Systems Engineering. CAiSE 2005. Lecture Notes in Computer Science, vol 3520. Springer, Berlin, Heidelberg (2005)
Askham, N., Cook, D., Doyle, M., Fereday, H., Gibson, M., Landbeck, U., Lee, R., Maynard, C., Palmer, G., Schwarzenbach, J.: The Six Primary Dimensions for Data Quality Assessment. In: DAMA UK Working Group (2013) Available via White Papers. http://bit.ly/2qcimnf
Burriel Coll, V., Pastor, O.: Conceptual Schema of Breast Cancer: The background to design an efficient information system to manage data from diagnosis and treatment of breast cancer patients. In IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI), pp. 432–435. IEEE (2014)
Burriel Coll, V., Reyes Román, J.F., Heredia Casanoves, A., Iñiguez-Jarrín, C., León Palacio, A.: GeIS based on Conceptual Models for the Risk Assessment of Neuroblastoma. In IEEE Eleventh International Conference on Research Challenges in Information Science (RCIS), pp. 1–2 (2017)
Ińiguez, C.: A conceptual modelling-based approach to generate data value through the enduser interactions: A case study in the genomics domain. PoEM Doctoral Consortium, pp. 14–21 (2016)
León, A., Reyes, J.F., Burriel, V., Valverde, F.: Data Quality problems when integrating genomic information. In 3rd. Workshop Quality of Models and Models of Quality (QMMQ 2016) in conjunction with the 35th International Conference on Conceptual Modeling (ER2016). Springer International Publishing pp. 173–182 (2016)
Ogino, S., Gulley, M.L., den Dunnen, J.T., Wilson, R.B., and the Association for Molecular Pathology Training and Education Committee: Standard Mutation Nomenclature in Molecular Diagnostics: Practical and Educational Challenges. The Journal of molecular diagnostics (2016) doi:10.2353/jmoldx.2007.060081.
Olivé, A.: Conceptual modeling of information systems. Springer-Verlag Berlin Heidelberg pp. 1–445 (2007)
Online Mendelian Inheritance in Man Homepage. Available via OMIM. https://www.omim.org/
Pastor, O., Reyes Román, J.F., Valverde, F.: Conceptual Schema of the Human Genome (CSHG). Universitat Politècnica de València (2016) Available via RiuNet. http://hdl.handle.net/10251/67297
Reducing proteome redundancy (2016) Available via UniProt. http://www.uniprot.org/help/proteome_redundancy
Reyes Román, J.F., Pastor, O., Casamayor J.C., Valverde F.: Applying Conceptual Modeling to Better Understand the Human Genome. In The 35th International Conference on Conceptual Modeling, Springer International Publishing, pp. 1–9 (2016)
Reyes Román, J.F., Pastor, O. Use of GeIS for Early Diagnosis of Alcohol Sensitivity. In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016), pp. 284–289 (2016)
Reyes Román, J.F., Pastor, O., Valverde, F., Roldán, D.: Including haplotypes treatment in a Genomic Information Systems Management. In Ibero-American Conference on Software Engineering, pp. 11–24 (2016)
Reyes Román, J.F., Pastor, O., Valverde, F., Roldán, D.: How to deal with Haplotype data?: An Extension to the Conceptual Schema of the Human Genome. Universitat Politècnica de València (2016). Available via RiuNet. https://riunet.upv.es/handle/10251/82704
Reyes Román, J.F., León Palacio, A., Pastor López, O.: Software Engineering and Genomics: The Two Sides of the Same Coin?. In Proceedings of the 12th International Conference on Evaluation of Novel Approaches to Software Engineering (ENASE 2017), pp. 301–307 (2017)
The 24th annual Nucleic Acids Research database issue. Available via Oxford Academic. http://www.oxfordjournals.org/our_journals/nar/database/c/
Reyes Román, J.F., Iñiguez-Jarrín, C., Pastor López, O.: GenesLove.Me: A Model-basedWebapplication for Direct-to-consumer Genetic Tests. In Proceedings of the 12th International Conference on Evaluation of Novel Approaches to Software Engineering (ENASE 2017), pp. 133–143 (2017)
Acknowledgements
The authors are grateful to the members of the PROS Center Genome group for fruitful discussions. This work has been supported by the Ministry of Higher Education, Science and Technology (MESCyT) of the Dominican Republic and also has the support of Generalitat Valenciana through project IDEO (PROMETEOII/2014/039), the Research and Development Aid Program (PAID-01-16) of the UPV under FPI Grant 2137. and Spanish Ministry of Science and Innovation through project DataME (ref: TIN2016-80811-P).
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López, Ó.P., Palacio, A.L., Román, J.F.R., Casamayor, J.C. (2017). Modeling Life: A Conceptual Schema-centric Approach to Understand the Genome. In: Cabot, J., Gómez, C., Pastor, O., Sancho, M., Teniente, E. (eds) Conceptual Modeling Perspectives. Springer, Cham. https://doi.org/10.1007/978-3-319-67271-7_3
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DOI: https://doi.org/10.1007/978-3-319-67271-7_3
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