Skip to main content
SpringerLink
Log in
Book cover

International Conference on Evaluation of Novel Approaches to Software Engineering

ENASE 2018: Evaluation of Novel Approaches to Software Engineering pp 314–333Cite as

GenesLove.Me 2.0: Improving the Prioritization of Genetic Variations

  • Conference paper
  • First Online:

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1023))

Abstract

The objective of this research work is to present the advances obtained in the development of the prototype called “VarSearch” (now called “GenesLove.Me 2.0”), which aims to manage large amounts of genomic information for further exploitation through of genomic reports that allow enhancing the highly acclaimed “Personalized Medicine”. This software project is considered from the perspective of Information Systems Engineering (ISE) applied to the genomic domain, this with the goal of eradicating or reducing the problems and challenges present in the so-called “genomic data chaos”. GenesLove.Me 2.0 (GLM 2.0) is based on the Conceptual Model of the Human Genome (CMHG), which allows to improve the understanding and reduce the complexity of the domain. Currently, it has new phenotypes studied, which integrate within the methodology used a data quality criteria that contribute to the management of curated data. Therefore, providing a software tool based on conceptual models for the generation of genomic reports is a breakthrough that improves the working methods and techniques of all stakeholders (e.g., geneticists, researchers, clinical laboratories) in the genomic and clinical context.

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   64.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   84.99
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

Notes

  1. 1.

    http://www.pros.webs.upv.es/.

  2. 2.

    https://www.ncbi.nlm.nih.gov/.

  3. 3.

    https://www.python.org/.

  4. 4.

    www.hospital-lafe.com/.

References

  1. Mardis, E.R.: The $1,000 genome, the $100,000 analysis? Genome Med. 2(11), 84 (2010)

    Article  Google Scholar 

  2. Grosso, L.A.: Precision medicine and cardiovascular diseases. Rev. Colomb. Cardiol. 23(2), 73–76 (2016). https://doi.org/10.1016/j.rccar.2016.01.026

    Article  Google Scholar 

  3. Olivé, A.: Conceptual Modeling of Information Systems. Springer, Heidelberg (2007). https://doi.org/10.1007/978-3-540-39390-0

    Book  MATH  Google Scholar 

  4. Reyes Román, J.F., Pastor, Ó., Casamayor, J.C., Valverde, F.: Applying conceptual modeling to better understand the human genome. In: Comyn-Wattiau, I., Tanaka, K., Song, I.Y., Yamamoto, S., Saeki, M. (eds.) ER 2016. LNCS, vol. 9974, pp. 404–412. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46397-1_31

    Chapter  Google Scholar 

  5. Pastor López, Ó., Palacio, A.L., Reyes Román, J.F., Casamayor, J.C.: 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, pp. 25–40. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-67271-7_3

    Chapter  Google Scholar 

  6. Reyes Román, J.F.: Diseño y Desarrollo de un Sistema de Información Genómica basado en un Modelo Conceptual holístico del Genoma Humano. Universitat Politècnica de València (2018). https://doi.org/10.4995/thesis/10251/99565

  7. Reyes Román, J.F., Roldán Martínez, D., García Simón, A., Rueda, U., Pastor, Ó.: VarSearch: annotating variations using an e-genomics framework. In: Proceedings of the 13th International Conference on Evaluation of Novel Approaches to Software Engineering - Volume 1: ENASE, pp. 328–334 (2018). https://doi.org/10.5220/0006781103280334. ISBN 978-989-758-300-1

  8. Reyes Román, J.F., Iñiguez-Jarrín, C., Pastor López, Ó.: GenesLove.Me: a model-based web-application for direct-to-consumer genetic tests. In: Proceedings of the 12th International Conference on Evaluation of Novel Approaches to Software Engineering - Volume 1: ENASE, pp. 133–143 (2017). https://doi.org/10.5220/0006340201330143. ISBN 978-989-758-250-9

  9. Reyes Román, J.F., Iñiguez-Jarrín, C., Pastor, Ó.: Genomic tools*: web-applications based on conceptual models for the genomic diagnosis. In: Damiani, E., Spanoudakis, G., Maciaszek, L. (eds.) ENASE 2017. CCIS, vol. 866, pp. 48–69. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-94135-6_3

    Chapter  Google Scholar 

  10. Stephens, Z.D., et al.: Big data: astronomical or genomical? PLOS Biol. 13(7), e1002195 (2015). https://doi.org/10.1371/journal.pbio.1002195

    Article  Google Scholar 

  11. León Palacio, A., Pastor López, Ó.: From big data to smart data: a genomic information systems perspective. In: 2018 12th International Conference on Research Challenges in Information Science (RCIS), pp. 1–11 (2018). https://doi.org/10.1109/rcis.2018.8406658

  12. Navarrete-Hidalgo, M., Reyes Román, J.F., Pastor López, Ó.: Design and implementation of a GeIS for the genomic diagnosis using the SILE methodology. Case Study: Congenital Cataract. In Proceedings of the 13th International Conference on Evaluation of Novel Approaches to Software Engineering – Vol. 1: ENASE, pp. 267–274 (2018). https://doi.org/10.5220/0006705802670274. ISBN 978-989-758-300-1

  13. Bornberg-Bauer, E., Paton, N.W.: Conceptual data modelling for bioinformatics. Briefings Bioinform. 3(2), 166–180 (2002). https://doi.org/10.1093/bib/3.2.166

    Article  Google Scholar 

  14. Gray, R.E., Grasso, D.G., Maxwell, R.J., Finnegan, P.M., Nagley, P., Devenish, R.J.: Identification of a 66 KDa protein associated with yeast mitochondrial ATP synthase as heat shock protein hsp60. FEBS Lett. 268(1), 265–268 (1990)

    Article  Google Scholar 

  15. Ram, S., Wei, W.: Modeling the semantics of 3D protein structures. In: Atzeni, P., Chu, W., Lu, H., Zhou, S., Ling, T.-W. (eds.) ER 2004. LNCS, vol. 3288, pp. 696–708. Springer, Heidelberg (2004). https://doi.org/10.1007/978-3-540-30464-7_52

    Chapter  Google Scholar 

  16. 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). https://doi.org/10.1007/978-3-540-87877-3_1

    Chapter  Google Scholar 

  17. Pastor, M.Á., Burriel, V., Pastor, O.: Conceptual modeling of human genome mutations - a dichotomy between what we have and what we should have. In: Bioinformatics, pp. 160–166 (2010)

    Google Scholar 

  18. Reyes Román, J.F., León Palacio, A., Pastor López, Ó.: 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 - Volume 1: ENASE, pp. 301–307 (2017). https://doi.org/10.5220/0006368203010307. ISBN 978-989-758-250-9

  19. Pastor, O., Reyes Román, J.F., Valverde, F.: Conceptual Schema of the Human Genome (CSHG). Technical report (2016). http://hdl.handle.net/10251/67297

  20. León, A., Reyes, J., Burriel, V., Valverde, F.: Data quality problems when integrating genomic information. In: Link, S., Trujillo, J. (eds.) ER 2016. LNCS, vol. 9975, pp. 173–182. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-47717-6_15

    Chapter  Google Scholar 

  21. León Palacio, A., Pastor López, Ó.: Towards an effective medicine of precision by using conceptual modelling of the genome: short paper. In: Proceedings of the International Workshop on Software Engineering in Healthcare Systems, pp. 14–17. ACM (2018)

    Google Scholar 

  22. Rouse, M.: A data lake is a large object-based storage repository that holds data in its native format until it is needed (2014)

    Google Scholar 

  23. Breul, J.D.: Cyber Society, Big Data, and Evaluation: Comparative Policy Evaluation. Transaction Publishers, Piscataway (2017)

    Google Scholar 

  24. Rigden, D.J., Fernández, X.M.: The 2018 nucleic acids research database issue and the online molecular biology database collection. Nucleic Acids Res. 46(D1), D1–D7 (2017)

    Article  Google Scholar 

  25. Alexov, E.: Navigating through genomics data to deliver testable predictions. Hum. Mutat. 36(2), v (2015)

    Article  Google Scholar 

  26. Landrum, M.J.: ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 44(D1), D862–D868 (2015)

    Article  Google Scholar 

  27. Nasko, D.J., Koren, S., Phillippy, A.M., Treangen, T.J.: RefSeq database growth influences the accuracy of k-mer-based species identification. bioRxiv, p. 304972 (2018)

    Google Scholar 

  28. NCBI Resource Coordinators: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 44(Database issue), D7 (2016)

    Google Scholar 

  29. NCBI Resource Coordinators: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 45(Database issue), D12 (2017)

    Google Scholar 

  30. Zerbino, D.R., et al.: Ensembl 2018. Nucleic Acids Res. 46(D1), D754–D761 (2017)

    Article  Google Scholar 

  31. Bhagwat, M.: Searching NCBI’s dbSNP database. Current Protoc. Bioinform. 32(1), 1–19 (2010)

    Google Scholar 

  32. Kinoshita, J., Clark, T.: Alzforum. Neuroinformatics, pp. 365–381. Humana Press, New York (2007)

    Google Scholar 

  33. Reyes Román, J.F., Pastor López, Ó.: Use of GeIS for early diagnosis of alcohol sensitivity. In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: Bioinformatics (BIOSTEC 2016), pp. 284–289 (2016). https://doi.org/10.5220/0005822902840289. ISBN 978-989-758-170-0

  34. Zhou, H., Yang, D., Xu, Y.: An ETL strategy for real-time data warehouse. In: Wang, Y., Li, T. (eds.) Practical Applications of Intelligent Systems Advances in Intelligent and Soft Computing, vol. 124. Springer, Heidelberg (2011). https://doi.org/10.1007/978-3-642-25658-5_41

    Chapter  Google Scholar 

  35. Van Der Kroon, M.: Conceptual Modeling Applied to Genomics: Challenges Faced in Data Loading. Universitat Politècnica de València (2012). http://hdl.handle.net/10251/16993

  36. Navarrete Hidalgo, M., Pastor, Ó., Reyes Román, J.F.: Diseño e Implementación de un Sistema de Información Genómico para el Diagnóstico de la Catarata Congénita utilizando la Metodología SILE. Universitat Politècnica de València (2017). http://hdl.handle.net/10251/90234

  37. Claverie, J.M., Notredame, C.: Bioinformatics for Dummies. Wiley, New York (2011)

    Google Scholar 

  38. Miller, J.J.: Graph database applications and concepts with Neo4j. In: Proceedings of the Southern Association for Information Systems Conference, Atlanta, GA, USA, vol. 2324, p. 36 (2013)

    Google Scholar 

  39. Burriel, V., Reyes Román, J.F., Casanoves, A.H., Iñiguez-Jarrín, C., León Palacio, A.: GeIS based on conceptual models for the risk assessment of neuroblastoma. In: 2017 11th International Conference on Research Challenges in Information Science (RCIS), pp. 451–452. IEEE (2017). https://doi.org/10.1109/rcis.2017.7956581

Download references

Acknowledgements

This work was supported by the Generalitat Valenciana through the Spanish Ministry of Science and Innovation through Project DataME (ref: TIN2016-80811-P) and the Generalitat Valenciana through the GISPRO project (PROMETEO / 2018/176).

The authors are grateful to Ana León Palacio, Carlos Iñiguez-Jarrín, Sipan Arevshatyan and Manuel Navarrete Hidalgo for their valuable assistance.

Author information

Authors and Affiliations

  1. PROS Research Center, Universitat Politècnica de València, Camino Vera S/N. 46022, Valencia, Spain

    José Fabián Reyes Román, Alberto García, Urko Rueda & Óscar Pastor

  2. Department of Engineering Sciences, Universidad Central del Este (UCE), Ave. Francisco Alberto Caamaño Deñó, 21000, San Pedro de Macorís, Dominican Republic

    José Fabián Reyes Román

Authors
  1. José Fabián Reyes Román
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alberto García
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Urko Rueda
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Óscar Pastor
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to José Fabián Reyes Román .

Editor information

Editors and Affiliations

  1. Khalifa University, Abu Dhabi, United Arab Emirates

    Ernesto Damiani

  2. City University London, London, UK

    George Spanoudakis

  3. Wrocław University of Economics, Wroclaw, Poland

    Leszek A. Maciaszek

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Reyes Román, J.F., García, A., Rueda, U., Pastor, Ó. (2019). GenesLove.Me 2.0: Improving the Prioritization of Genetic Variations. In: Damiani, E., Spanoudakis, G., Maciaszek, L. (eds) Evaluation of Novel Approaches to Software Engineering. ENASE 2018. Communications in Computer and Information Science, vol 1023. Springer, Cham. https://doi.org/10.1007/978-3-030-22559-9_14

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-22559-9_14

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-22558-2

  • Online ISBN: 978-3-030-22559-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation