Abstract
Nowadays, the diagnosis of disease based on genomic information is feasible by searching genetic variations on DNA sequences. However, geneticists struggle with bioinformatic tools that are supposed to simplify DNA sequence analysis. As a universal tool to support every requirement is far from be implemented, geneticists themselves must solve the data exchange among several tools. Due to the fact that there are no standards to support this integration task, it must be managed in every analysis. This paper addresses this integration by means of a model-driven framework. The Diagen framework is a software implementation based on conceptual modeling principles that formalizes data exchange and simplifies bioinformatic tool integration. First, we analyze how conceptual modeling can be used to deal with data exchange among tools. Then, the presented framework is used to search for variations on the BRCA2 gene using real DNA samples and a set of specific bioinformatic tools.
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Hamburg, M.A., Collins, F.S.: The Path to Personalized Medicine. New England Journal of Medicine 363(4), 301–304 (2010)
Rusk, N.: Focus on Next-Generation Sequencing Data Analysis. Nature Methods 6(11s), S1 (2009)
Pastor, O., Levin, A.M., Celma, M., Casamayor, J.C., Virrueta, A., Eraso, L.E.: Model-Based Engineering Applied to the Interpretation of the Human Genome. In: Kaschek, R., Delcambre, L. (eds.) The Evolution of Conceptual Modeling. LNCS, vol. 6520, pp. 306–330. Springer, Heidelberg (2011)
Nayanah, S.: 1000 Genomes Project. Nat. Biotech. 26(3), 256 (2008)
Reese, M.G., et al.: A Standard Variation File Format for Human Genome Sequences. Genome Biology 11(8), R88 (2010)
Eilbeck, K., et al.: The Sequence Ontology: A Tool for the Unification of Genome Annotations. Genome Biology 6(5), R44 (2005)
Li, H., et al.: The Sequence Alignment/Map Format and SAMtools. Bioinformatics 25(16), 2078–2079 (2009)
Holland, R.C.G., et al.: BioJava: An Open-Source Framework for Bioinformatics. Bioinformatics 24(18), 2096–2097 (2008)
Cock, P., et al.: Biopython: Freely Available Python Tools for Computational Molecular Biology and Bioinformatics. Bioinformatics 25(11), 1422–1423 (2009)
Stajich, J.E., et al.: The Bioperl Toolkit: Perl Modules for the Life Sciences. Genome Research 12(10), 1611–1618 (2002)
Hull, D., et al.: Taverna: a tool for building and running workflows of services. Nucleic Acids Research 34(Web Server issue), 729–732 (2006)
Garwood, K., et al.: Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it. BMC Bioinformatics 7, 532 (2006)
Fogh, R.H., et al.: MEMOPS: Data modelling and automatic code generation. Journal of Integrative Bioinformatics 7 (2010)
Villanueva, M.J., Valverde, F., Pastor, O.: Applying Conceptual Modeling to Alignment Tools: One Step towards the Automation of DNA Sequence Analysis. Bioinformatics 2011 (2011)
Dunnen, J.T., Antonarakis, S.E.: Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion. Human Mutation 15, 7–12 (2000)
Ort, E., Mehta, B.: Java Architecture for XML Binding (JAXB). Technical Report Sun Developer Network (2003)
Curtis, P., Bromberg, C., Cash, H., Goebel, J.C.: Sequencher, Gene Codes Corporation, Ann Arbor, Michigan (1995)
NCBI BLAST (Basic Local Alignment Search Tool), http://blast.ncbi.nlm.nih.gov
Hubbard, T., et al.: The ENSEMBL Genome Database Project. Nucleic Acids Research 30(1), 38–41 (2002)
Pastor, O., et al.: Enforcing Conceptual Modeling to Improve the Understanding of Human Genome. In: Research Challenges in Information Science (RCIS), pp. 85–92 (2010)
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Villanueva, M.J., Valverde, F., Levín, A.M., Pastor Lopez, O. (2012). Diagen: A Model-Driven Framework for Integrating Bioinformatic Tools. In: Nurcan, S. (eds) IS Olympics: Information Systems in a Diverse World. CAiSE 2011. Lecture Notes in Business Information Processing, vol 107. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29749-6_4
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DOI: https://doi.org/10.1007/978-3-642-29749-6_4
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