Abstract
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, leading to the generation of conceptual schemes whose intent is to provide a precise ontological characterization of the components involved in biological processes. However, the heterogeneity and idiosyncrasy of genomic use cases mean that, although the genome and its internal processes remain the same among eukaryote species, conceptual modeling techniques are used to generate conceptual schemes that focus on particular scenarios (i.e., they are species-specific conceptual schemes). We claim that instead of having different, species-specific conceptual schemes, it is feasible to provide a holistic conceptual schema valid to work with every eukaryote species by generating conceptual views that are inferred from that global conceptual schema. We report our preliminary work towards the possibility of generating such a conceptual schema by ontologically comparing two existing, species-specific conceptual schemes. Those changes that are necessary to provide an expanded conceptual schema that is suitable for both use cases are identified and discussed.
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Belmont, J.W., et al.: A haplotype map of the human genome. Nature 437(7063), 1299–1320 (2005). https://doi.org/10.1038/nature04226
Campbell, P.N.P.N., Smith, A.D.A.D., Peters, T.J.: Biochemistry Illustrated: Biochemistry and Molecular Biology in the Post-genomic Era, 5th edn. Elsevier Churchill Livingstone, Edinburgh (2005). https://searchworks.stanford.edu/view/5961093
Chen, C., Gmitter, F.G.: Mining of haplotype-based expressed sequence tag single nucleotide polymorphismsin citrus. BMC Genom. 14(1) (2013). https://doi.org/10.1186/1471-2164-14-746
Delcambre, L., Liddle, S., Pastor, O., Storey, V.: A reference framework for conceptual modeling: focusing on conceptual modeling research. Technical report, November 2018. https://doi.org/10.13140/RG.2.2.33041.07521
García S., A., Pastor, O.: CSCG: conceptual schema of the citrus genome. Technical report (2020). http://hdl.handle.net/10251/144234
García S., A., Reyes Román, J.F., Casamayor, J.C., Pastor, O.: Towards an effective and efficient management of genome data: an information systems engineering perspective. In: Cappiello, C., Ruiz, M. (eds.) CAiSE 2019. LNBIP, vol. 350, pp. 99–110. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-21297-1_9
Ghada, B., Amel, O., Aymen, M., Aymen, A., Amel, S.H.: Phylogenetic patterns and molecular evolution among ‘True citrus fruit trees’ group (Rutaceae family and Aurantioideae subfamily). Scientia Horticulturae 253, 87–98 (2019). https://doi.org/10.1016/j.scienta.2019.04.011
Heger, A., Holm, L.: Exhaustive enumeration of protein domain families. J. Mol. Biol. 328(3), 749–767 (2003). https://doi.org/10.1016/S0022-2836(03)00269-9
Heinzelmann, R., et al.: Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae. Heredity 124(6), 699–713 (2020). https://doi.org/10.1038/s41437-020-0306-z
Janzen, G.M., Wang, L., Hufford, M.B.: The extent of adaptive wild introgression in crops (2019). https://doi.org/10.1111/nph.15457
Miller, J.B., Pickett, B.D., Ridge, P.G.: JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. Bioinformatics 35(4), 546–552 (2019). https://doi.org/10.1093/bioinformatics/bty669
Mylopoulos, J.: Conceptual modelling and Telos, pp. 49–68 (1992)
Palacio, A.L., Fernández, I.P., López, O.P.: Genomic information systems applied to precision medicine: genomic data management for Alzheimer’s disease treatment. In: International Conference on Information Systems Development (ISD), October 2018. https://aisel.aisnet.org/isd2014/proceedings2018/eHealth/6
Palacio, A.L., López, Ó.P.: Towards an effective medicine of precision by using conceptual modelling of the genome. In: Proceedings - International Conference on Software Engineering, pp. 14–17. IEEE Computer Society, New York, May 2018. https://doi.org/10.1145/3194696.3194700
Pearson, H.: What is a gene?, May 2006. https://doi.org/10.1038/441398a
Reyes Román, J.F.: Diseño y Desarrollo de un Sistema de Información Genómica Basado en un Modelo Conceptual Holístico del Genoma Humano. Ph.D. thesis, Universitat Politècnica de València (2018). https://riunet.upv.es/handle/10251/99565
Reyes Román, J.F., Martínez, D.R., Simón, A.G., 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, ENASE 2018, vol. 2018-March, pp. 328–350. SCITEPRESS - Science and Technology Publications (2018). https://doi.org/10.5220/0006781103280334
Smirnov, A., Schneider, C., Hör, J., Vogel, J.: Discovery of new RNA classes and global RNA-binding proteins, October 2017. https://doi.org/10.1016/j.mib.2017.11.016
Train, C.M., Glover, N.M., Gonnet, G.H., Altenhoff, A.M., Dessimoz, C.: Orthologous matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. Bioinformatics 33(14), i75–i82 (2017). https://doi.org/10.1093/bioinformatics/btx229
Whiffin, N., et al.: Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals. Nat. Commun. 11(1), 1–12 (2020). https://doi.org/10.1038/s41467-019-10717-9
Acknowledgment
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).
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García S., A., Casamayor, J.C. (2020). Towards the Generation of a Species-Independent Conceptual Schema of the Genome. In: Grossmann, G., Ram, S. (eds) Advances in Conceptual Modeling. ER 2020. Lecture Notes in Computer Science(), vol 12584. Springer, Cham. https://doi.org/10.1007/978-3-030-65847-2_6
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