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On how to generalize specie-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome

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On how to generalize specie-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome

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García-Simón, A.; Casamayor Rodenas, JC. (2021). On how to generalize specie-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome. BMC Bioinformatics. 22(13):1-26. https://doi.org/10.1186/s12859-021-04237-x

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Título: On how to generalize specie-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome
Autor: García-Simón, Alberto Casamayor Rodenas, Juan Carlos
Entidad UPV: Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació
Fecha difusión:
Resumen:
[EN] Background Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and ...[+]
Palabras clave: Conceptual modeling , Genomics , Bioinformatics
Derechos de uso: Reconocimiento (by)
Fuente:
BMC Bioinformatics. (issn: 1471-2105 )
DOI: 10.1186/s12859-021-04237-x
Editorial:
Springer (Biomed Central Ltd.)
Versión del editor: https://doi.org/10.1186/s12859-021-04237-x
Coste APC: 2000 €
Código del Proyecto:
info:eu-repo/grantAgreement/AGENCIA ESTATAL DE INVESTIGACION//TIN2016-80811-P//UN METODO DE PRODUCCION DE SOFTWARE DIRIGIDO POR MODELOS PARA EL DESARROLLO DE APLICACIONES BIG DATA/
info:eu-repo/grantAgreement/GENERALITAT VALENCIANA//PROMETEO%2F2018%2F176//GISPRO-GENOMIC INFORMATION SYSTEMS PRODUCTION/
Agradecimientos:
This work was supported by the Spanish Ministry of Science and Innovation through Project DataME (ref: TIN2016-80811-P) and the Generalitat Valenciana through project GISPRO (PROMETEO/2018/176).
Tipo: Artículo

References

Mylopoulos J. Conceptual modelling and Telos. 1992;49–68.

Delcambre L, Liddle S, Pastor O, Storey V. A reference framework for conceptual modeling: focusing on conceptual modeling research. Technical report, Portland State University; 2018. https://doi.org/10.13140/RG.2.2.33041.07521.

Pearson H. What is a gene? Nat Publ Group. 2006. https://doi.org/10.1038/441398a. [+]
Mylopoulos J. Conceptual modelling and Telos. 1992;49–68.

Delcambre L, Liddle S, Pastor O, Storey V. A reference framework for conceptual modeling: focusing on conceptual modeling research. Technical report, Portland State University; 2018. https://doi.org/10.13140/RG.2.2.33041.07521.

Pearson H. What is a gene? Nat Publ Group. 2006. https://doi.org/10.1038/441398a.

Smirnov A, Schneider C, Hör J, Vogel J. Discovery of new RNA classes and global RNA-binding proteins. Elsevier; 2017. https://doi.org/10.1016/j.mib.2017.11.016.

Palacio AL, Fernández IP, López OP. Genomic Information Systems applied to precision medicine: genomic data management for Alzheimer’s disease treatment. In: International conference on information systems development (ISD); 2018. https://aisel.aisnet.org/isd2014/proceedings2018/eHealth/6.

Palacio AL, López Ó P. Towards an effective medicine of precision by using conceptual modelling of the genome. In: Proceedings of the international conference on software engineering. New York: IEEE Computer Society; 2018. p. 14–7. https://doi.org/10.1145/3194696.3194700.

Román JFR, López ÓP. Use of GeIS for early diagnosis of alcohol sensitivity. In: BIOINFORMATICS 2016—7th International conference on bioinformatics models, methods and algorithms, proceedings; part of 9th international joint conference on biomedical engineering systems and technologies, BIOSTEC. SCITEPRESS-Science and and Technology Publications; 2016. p. 284–9. https://doi.org/10.5220/0005822902840289.

León Palacio A, García Giménez A, Casamayor Ródenas JC, Reyes Román JF. Genomic data management in big data environments: the colorectal cancer case. In: Woo C, Lu J, Li Z, Ling TW, Li G, Lee ML, editors. Advances in conceptual modeling, Lecture notes in computer science, vol. 11158. Cham: Springer; 2018. p. 319–29. https://doi.org/10.1007/978-3-030-01391-2_36. Accessed 16 Feb 2021.

Navarrete-Hidalgo M, Reyes Román JF, Pastor López O. 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. SCITEPRESS—Science and Technology Publications, Funchal, Madeira; 2018. p. 267–74. https://doi.org/10.5220/0006705802670274. Accessed Feb 16 2021.

Reyes Román JF, García A, Rueda U, Pastor O. GenesLove.Me 2.0: improving the prioritization of genetic variations. In: Damiani E, Spanoudakis G, Maciaszek LA, editors. Evaluation of novel approaches to software engineering, Communications in computer and information science, vol 1023. Cham: Springer; 2019. p. 314–33. https://doi.org/10.1007/978-3-030-22559-9_14. Accessed 16 Feb 2021.

Reyes Román JF, Roldán Martínez D, García Simón A, Rueda U, Pastor O. VarSearch: annotating variations using an e-Genomics Framework:. In: Proceedings of the 13th international conference on evaluation of novel approaches to software engineering. SCITEPRESS—Science and Technology Publications, Funchal, Madeira, Portugal; 2018. p. 328–34. https://doi.org/10.5220/0006781103280334. Accessed 16 Feb 2021.

Iñiguez-Jarrín C, Alberto GS, Reyes JF, López, Ó P. GenDomus: interactive and collaboration mechanisms for diagnosing genetic diseases. In: ENASE 2017—proceedings of the 12th international conference on evaluation of novel approaches to software engineering. 2017; p. 91–102. https://doi.org/10.5220/0006324000910102.

García SA, Reyes Román JF, Casamayor JC, Pastor O. Towards an effective and efficient management of genome data: an information systems engineering perspective. In: Cappiello C, Ruiz M, editors. Information systems engineering in responsible information systems, lecture notes in business information processing, vol 350. Cham: Springer; 2019. p. 99–110. https://doi.org/10.1007/978-3-030-21297-1_9.

Reyes Román JF. Diseño y Desarrollo de un Sistema de Información Genómica Basado en un Modelo Conceptual Holístico del Genoma Humano. PhD thesis, Universitat Politècnica de València; 2018. https://riunet.upv.es/handle/10251/99565.

Publishing W (ed.): The Genus Citrus. Elsevier; 2020. https://doi.org/10.1016/C2016-0-02375-6. Accessed 16 Feb 2021.

Wu GA, Terol J, Ibanez V, López-García A, Pérez-Román E, Borredá C, Domingo C, Tadeo FR, Carbonell-Caballero J, Alonso R, Curk F, Du D, Ollitrault P, Roose ML, Dopazo J, Gmitter FG, Rokhsar DS, Talon M. Genomics of the origin and evolution of Citrus. Nature. 2018;554(7692):311–6. https://doi.org/10.1038/nature25447.

García S, A, Pastor O. CSCG: Conceptual Schema of the Citrus Genome. Technical report, Polytechnic University of Valencia, Spain; 2020. http://hdl.handle.net/10251/144234.

Cooper GM, Cooper GM. The cell, 2nd edn. Sinauer Associates; 2000.

Eichler EE, Sankoff D. Structural dynamics of eukaryotic chromosome evolution. Science. 2003;301(5634):793–7. https://doi.org/10.1126/science.1086132.

Bell SP, Dutta A. DNA replication in Eukaryotic cells. Annu Rev Biochem. 2002;71(1):333–74. https://doi.org/10.1146/annurev.biochem.71.110601.135425.

Heinzelmann R, et al. Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae. Heredity. 2020;124(6):699–713. https://doi.org/10.1038/s41437-020-0306-z.

Griffiths PE, Tabery J. Behavioral genetics and development: historical and conceptual causes of controversy; Pergamon. 2008. https://doi.org/10.1016/j.newideapsych.2007.07.016.

Meaney MJ. Epigenetics and the biological definition of gene X environment interactions. Wiley; 2010. https://doi.org/10.1111/j.1467-8624.2009.01381.x.

Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Cold Spring Harbor Laboratory Press; 2007.

Yu P, Ma D, Xu M. Nested genes in the human genome. Genomics. 2005;86(4):414–22. https://doi.org/10.1016/j.ygeno.2005.06.008.

Herai RH, Yamagishi MEB. Detection of human interchromosomal trans-splicing in sequence databanks. Brief Bioinfor. 2010;11(2):198–209. https://doi.org/10.1093/bib/bbp041.

Campbell PN, Smith AD, Peters TJ. Biochemistry illustrated: biochemistry and molecular biology in the post-genomic era, 5th edn. Edinburgh: Elsevier; 2005. p. 242.

Ghada B, Amel O, Aymen M, Aymen A, Amel SH. Phylogenetic patterns and molecular evolution among ‘True citrus fruit trees’ group (Rutaceae family and Aurantioideae subfamily). Sci Hortic. 2019;253:87–98. https://doi.org/10.1016/j.scienta.2019.04.011.

Rose AB. Intron-mediated regulation of gene expression. Springer; 2008.

Rose AB. Introns as gene regulators: a brick on the accelerator. Front Genet. 2019;10:672. https://doi.org/10.3389/fgene.2018.00672.

Michael IP, et al. Intron retention: a common splicing event within the human kallikrein gene family. Clin Chem. 2005;51(3):506–15. https://doi.org/10.1373/clinchem.2004.042341.

Zhang D, et al. Intron retention is a hallmark and spliceosome represents a therapeutic vulnerability in aggressive prostate cancer. Nat Commun. 2020;11(1):1–19. https://doi.org/10.1038/s41467-020-15815-7.

Heger A, Holm L. Exhaustive enumeration of protein domain families. J Mol Biol. 2003;328(3):749–67. https://doi.org/10.1016/S0022-2836(03)00269-9.

Whiffin N, et al. Characterising the loss-of-function impact of 5′ untranslated region variants in 15,708 individuals. Nat Commun. 2020;11(1):1–12. https://doi.org/10.1038/s41467-019-10717-9.

Miller JB, Pickett BD, Ridge PG. JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. Bioinformatics. 2019;35(4):546–52. https://doi.org/10.1093/bioinformatics/bty669.

Train CM, Glover NM, Gonnet GH, Altenhoff AM, Dessimoz C. Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. Bioinformatics. 2017;33(14):75–82. https://doi.org/10.1093/bioinformatics/btx229.

Janzen GM, Wang L, Hufford MB. The extent of adaptive wild introgression in crops; 2019. https://doi.org/10.1111/nph.15457.

Belmont JW, et al. A haplotype map of the human genome. Nature. 2005;437(7063):1299–320. https://doi.org/10.1038/nature04226.

Chen C, Gmitter FG. Mining of haplotype-based expressed sequence tag single nucleotide polymorphismsin citrus. BMC Genomics. 2013. https://doi.org/10.1186/1471-2164-14-746.

Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004;32(suppl 1):277–80. https://doi.org/10.1093/nar/gkh063.

Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB), Enzyme Supplement 5 (1999). European Journal of Biochemistry. 1999;264(2):610–50.

Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Jang W, Karapetyan K, Katz K, Liu C, Maddipatla Z, Malheiro A, McDaniel K, Ovetsky M, Riley G, Zhou G, Holmes J, Kattman BL, Maglott DR. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018;46(D1):1062–7. https://doi.org/10.1093/nar/gkx1153.

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