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Extension of the Genomic Conceptual Model to Integrate Genome-Wide Association Studies

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Advances in Conceptual Modeling (ER 2021)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 13012))

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Abstract

The first human genome has been sequenced at the turn of the year 2000. Since then, modern biology has made great progresses, also thanks to the introduction of Next-generation sequencing in the mid-2000s. The growing availability of genomic data led to the birth of tertiary analysis, concerning sense-making and extraction of useful biological information. To deal with data heterogeneity, in the last decade many tools have been introduced to achieve genomic data integration: among them, the Genomic Conceptual Model (GCM) and the META-BASE architecture. The latter one allows to map data from many projects into the GCM through an integration pipeline.

In this work, we proposed an extension of the GCM to integrate two additional sources into the META-BASE architecture, namely: GWAS Catalog (curated by the NHGRI and EBI institutes) and FinnGen (curated by the University of Helsinki). These two sources host Genome-Wide Association Studies (GWAS), useful for explaining the connection between genome variations of single nucleotides and particular traits. They are organized according to different data models but share the same data semantics. As a result of our integration efforts, we enable the interoperable use and querying of GWAS datasets with several other genomic datasets (including TCGA, ENCODE, Roadmap Epigenomics, 1000 Genomes Project, and GENCODE).

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Acknowledgements

This research is funded by the ERC Advanced Grant 693174 GeCo (data-driven Genomic Computing).

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Authors and Affiliations

  1. Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy

    Federico Comolli

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  1. Federico Comolli
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Correspondence to Federico Comolli .

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Editors and Affiliations

  1. University of Haifa, Haifa, Israel

    Iris Reinhartz-Berger

  2. The University of Queensland, Brisbane, QLD, Australia

    Shazia Sadiq

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Comolli, F. (2021). Extension of the Genomic Conceptual Model to Integrate Genome-Wide Association Studies. In: Reinhartz-Berger, I., Sadiq, S. (eds) Advances in Conceptual Modeling. ER 2021. Lecture Notes in Computer Science(), vol 13012. Springer, Cham. https://doi.org/10.1007/978-3-030-88358-4_10

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  • DOI: https://doi.org/10.1007/978-3-030-88358-4_10

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-88357-7

  • Online ISBN: 978-3-030-88358-4

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