Empowering Virus Sequence Research Through Conceptual Modeling

Bernasconi, Anna; Canakoglu, Arif; Pinoli, Pietro; Ceri, Stefano

doi:10.1007/978-3-030-62522-1_29

Cited by 20 publications

(19 citation statements)

References 47 publications

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“…The most specific kind of data relates to genomic aspects of both the virus and the host organism, i.e., the patient, and it is typically produced in sequencing laboratories; these data are described by conceptual models such as the Genomic Conceptual Model [30], the Conceptual Schema of the Human Genome [31], and the Viral Conceptual Model [32]. Genomic data are produced and hosted at many consortia and initiatives' sites (see in [33] for a complete review).…”

Section: Data Typesmentioning

confidence: 99%

A Conceptual Model for Geo-Online Exploratory Data Visualization: The Case of the COVID-19 Pandemic

Bernasconi

Grandi

2021

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Responding to the recent COVID-19 outbreak, several organizations and private citizens considered the opportunity to design and publish online explanatory data visualization tools for the communication of disease data supported by a spatial dimension. They responded to the need of receiving instant information arising from the broad research community, the public health authorities, and the general public. In addition, the growing maturity of information and mapping technologies, as well as of social networks, has greatly supported the diffusion of web-based dashboards and infographics, blending geographical, graphical, and statistical representation approaches. We propose a broad conceptualization of Web visualization tools for geo-spatial information, exceptionally employed to communicate the current pandemic; to this end, we study a significant number of publicly available platforms that track, visualize, and communicate indicators related to COVID-19. Our methodology is based on (i) a preliminary systematization of actors, data types, providers, and visualization tools, and on (ii) the creation of a rich collection of relevant sites clustered according to significant parameters. Ultimately, the contribution of this work includes a critical analysis of collected evidence and an extensive modeling effort of Geo-Online Exploratory Data Visualization (Geo-OEDV) tools, synthesized in terms of an Entity-Relationship schema. The COVID-19 pandemic outbreak has offered a significant case to study how and how much modern public communication needs spatially related data and effective implementation of tools whose inspection can impact decision-making at different levels. Our resulting model will allow several stakeholders (general users, policy-makers, and researchers/analysts) to gain awareness on the assets of structured online communication and resource owners to direct future development of these important tools.

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Section: Data Typesmentioning

confidence: 99%

A Conceptual Model for Geo-Online Exploratory Data Visualization: The Case of the COVID-19 Pandemic

Bernasconi

Grandi

2021

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“…1 represents the logical schema of ViruSurf databases. While the complete ViruSurf schema can be appreciated in [5] based on the Viral Conceptual Model [3], we here report the essential aspects: it is centered on the Sequence table, connected to SequencingProject, Virus, HostSample/HostSpecies, and ExperimentType. The "analytical" perspective of the schema contains information about Annotations (characterization of sub-parts of the sequence), Nu-cleotideVariants and AminoacidVariants.…”

Section: Integration With Sequence Datamentioning

confidence: 99%

CoV2K: A Knowledge Base of SARS-CoV-2 Variant Impacts

Khalaf

Alfonsi

Ceri

et al. 2021

Lecture Notes in Business Information Processing

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In spite of the current relevance of the topic, there is no universally recognized knowledge base about SARS-CoV-2 variants; viral sequences deposited at recognized repositories are still very few, and the process of tracking new variants is not coordinated. CoV2K is a manually curated knowledge base providing an organized collection of information about SARS-CoV-2 variants, extracted from the scientific literature; it features a taxonomy of variant impacts, organized according to three main categories (protein stability, epidemiology, and immunology) and including levels for these effects (higher, lower, null) resulting from a coherent interpretation of research articles. CoV2K is integrated with ViruSurf, hosted at Politecnico di Milano; ViruSurf is globally the largest database of curated viral sequences and variants, integrated from deposition repositories such as COG-UK, Gen-Bank, and GISAID. Thanks to such integration, variants documented in CoV2K can be analyzed and searched over large volumes of nucleotide and amino acid sequences, e.g., for co-occurrence and impact agreement; the paper sketches some of the data analysis tests that are currently under development.

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“…The Viral Conceptual Model (VCM) [4] is organized into four perspectives and centered around the notion of a virus genome Sequence. A viral sequence can be either DNA or RNA.…”

Section: The Viral Conceptual Model (Vcm)mentioning

confidence: 99%

“…Pastor et al proposed the Conceptual Schema of Human Genome [14,16]; Bernasconi et al introduced the Genomic Conceptual Model [5]. The Viral Conceptual Model (VCM) [4] was motivated by interest in representing the genomic aspects of COVID-19 so they can be shared among the scientific and medical communities that are attempting to understand SARS-CoV-2 and similar pathogens. The model is being used for designing: an integrated data warehouse and search system [8]; a linked Phenotype Data Dictionary [3]; a knowledge base of variant impacts [1]; and a visualization engine [6].…”

Section: Introductionmentioning

confidence: 99%

Ontological Unpacking as Explanation: The Case of the Viral Conceptual Model

Guizzardi

Bernasconi

Pastor

2021

Conceptual Modeling

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Inspired by the need to understand the genomic aspects of COVID-19, the Viral Conceptual Model captures and represents the sequencing of viruses. Although the model has already been successfully used, it should have a strong ontological foundation to ensure that it can be consistently applied and expanded. We apply an ontological analysis of the Viral Conceptual Model, using OntoUML, to unpack and identify its core components. The analysis illustrates the feasibility of bringing ontological clarity to complex models. The process of revealing the ontological semantics of a data structuring model provides a fundamental type of explanation for symbolic models, including conceptual models.

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Empowering Virus Sequence Research Through Conceptual Modeling

Cited by 20 publications

References 47 publications

A Conceptual Model for Geo-Online Exploratory Data Visualization: The Case of the COVID-19 Pandemic

A Conceptual Model for Geo-Online Exploratory Data Visualization: The Case of the COVID-19 Pandemic

CoV2K: A Knowledge Base of SARS-CoV-2 Variant Impacts

Ontological Unpacking as Explanation: The Case of the Viral Conceptual Model

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