A Method to Identify Relevant Genome Data: Conceptual Modeling for the Medicine of Precision

Briefings in Bioinformatics

Canakoglu

Masseroli

et al. 2020

With the outbreak of the COVID-19 disease, the research community is producing unprecedented efforts dedicated to better understand and mitigate the effects of the pandemic. In this context, we review the data integration efforts required for accessing and searching genome sequences and metadata of SARS-CoV2, the virus responsible for the COVID-19 disease, which have been deposited into the most important repositories of viral sequences. Organizations that were already present in the virus domain are now dedicating special interest to the emergence of COVID-19 pandemics, by emphasizing specific SARS-CoV2 data and services. At the same time, novel organizations and resources were born in this critical period to serve specifically the purposes of COVID-19 mitigation while setting the research ground for contrasting possible future pandemics. Accessibility and integration of viral sequence data, possibly in conjunction with the human host genotype and clinical data, are paramount to better understand the COVID-19 disease and mitigate its effects. Few examples of host-pathogen integrated datasets exist so far, but we expect them to grow together with the knowledge of COVID-19 disease; once such datasets will be available, useful integrative surveillance mechanisms can be put in place by observing how common variants distribute in time and space, relating them to the phenotypic impact evidenced in the literature.

Section: Integration Of Sources Of Viral Sequencesmentioning

confidence: 99%

A review on viral data sources and search systems for perspective mitigation of COVID-19

Briefings in Bioinformatics

Canakoglu

Masseroli

et al. 2020

“…Later, a stream of works developed conceptual modeling-based data warehouses, including: the GEDAW UML Conceptual schema [21] (for a gene-centric data warehouse), the Genomics Unified Schema [2], the Genome Information Management System [14] (a genome-centric data warehouse), and the GeneMapper Warehouse [16] (integrating expression data from genomic sources). More recently, there has been a solid stream of works dedicated to data quality-oriented conceptual modeling: [18] presents an ontological approach, [39] introduces the Human Genome Conceptual Model and [34] applies it to uncover relevant information hidden in genomics data lakes. Conceptual modeling has been mainly concerned with aspects of the human genome, even when more general approaches were adopted; in [8] we presented GCM, describing metadata associated with genomic experimental datasets available for model organisms.…”

Section: Related Workmentioning

confidence: 99%

Empowering Virus Sequence Research Through Conceptual Modeling

Canakoglu

Pinoli

et al. 2020

Conceptual Modeling

The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations, nucleotide and amino acid variants), organizational (sequencing project) and technical (experimental technology). VCM is inspired by GCM, our previously developed Genomic Conceptual Model, but it introduces many novel concepts, as viral sequences significantly differ from human genomes. When applied to SARS-CoV-2 virus, complex conceptual queries upon VCM are able to replicate the search results of recent articles, hence demonstrating huge potential in supporting virology research. Our effort is part of a broad vision: availability of conceptual models for both human genomics and viruses will provide important opportunities for research, especially if interconnected by the same human being, playing the role of virus host as well as provider of genomic and phenotype information.

“…More recently, there has been a solid stream of works dedicated to data quality-oriented conceptual modeling: [33] presents the Human Genome Con-ceptual Model and [29] applies it to uncover relevant information hidden in genomics data lakes. Conceptual modeling has been mainly concerned with aspects of the human genome, even when more general approaches were adopted; in [6] we presented the Genomic Conceptual Model (GCM), describing the metadata associated with genomic experimental datasets available for humans or other model organisms; GCM was essential for driving the data integration pipeline and building search interfaces [8].…”

Section: Related Workmentioning

confidence: 99%

Empowering Virus Sequences Research through Conceptual Modeling

Canakoglu²,

Pinoli³

et al. 2020

Preprint

The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and described from four perspectives: biological (virus type and hosts/sample), analytical (annotations and variants), organizational (sequencing project) and technical (experimental technology). VCM is inspired by GCM, our previously developed Genomic Conceptual Model, but it introduces many novel concepts, as viral sequences significantly differ from human genomes. When applied to SARS-CoV2 virus, complex conceptual queries upon VCM are able to replicate the search results of recent articles, hence demonstrating huge potential in supporting virology research. In addition to VCM, we also illustrate the data dictionary for patient's phenotype used by the COVID-19 Host Genetic Initiative. Our effort is part of a broad vision: availability of conceptual models for both human genomics and viruses will provide important opportunities for research, especially if interconnected by the same human being, playing the role of virus host as well as provider of genomic and phenotype information.