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Conceptual Modeling for Genomics: Building an Integrated Repository of Open Data

  • Anna Bernasconi
  • Stefano Ceri
  • Alessandro Campi
  • Marco Masseroli
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10650)

Abstract

Many repositories of open data for genomics, collected by world-wide consortia, are important enablers of biological research; moreover, all experimental datasets leading to publications in genomics must be deposited to public repositories and made available to the research community. These datasets are typically used by biologists for validating or enriching their experiments; their content is documented by metadata. However, emphasis on data sharing is not matched by accuracy in data documentation; metadata are not standardized across the sources and often unstructured and incomplete.

In this paper, we propose a conceptual model of genomic metadata, whose purpose is to query the underlying data sources for locating relevant experimental datasets. First, we analyze the most typical metadata attributes of genomic sources and define their semantic properties. Then, we use a top-down method for building a global-as-view integrated schema, by abstracting the most important conceptual properties of genomic sources. Finally, we describe the validation of the conceptual model by mapping it to three well-known data sources: TCGA, ENCODE, and Gene Expression Omnibus.

Keywords

Conceptual model Data integration Genomics Next Generation Sequencing Open data 

Notes

Acknowledgement

This research is funded by the ERC Advanced Grant project GeCo (Data-Driven Genomic Computing), 2016–2021.

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Anna Bernasconi
    • 1
  • Stefano Ceri
    • 1
  • Alessandro Campi
    • 1
  • Marco Masseroli
    • 1
  1. 1.Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanItaly

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