Using conceptual modeling to improve genome data management

Abstract

With advances in genomic sequencing technology, a large amount of data is publicly available for the research community to extract meaningful and reliable associations among risk genes and the mechanisms of disease. However, this exponential growth of data is spread in over thousand heterogeneous repositories, represented in multiple formats and with different levels of quality what hinders the differentiation of clinically valid relationships from those that are less well-sustained and that could lead to wrong diagnosis. This paper presents how conceptual models can play a key role to efficiently manage genomic data. These data must be accessible, informative and reliable enough to extract valuable knowledge in the context of the identification of evidence supporting the relationship between DNA variants and disease. The approach presented in this paper provides a solution that help researchers to organize, store and process information focusing only on the data that are relevant and minimizing the impact that the information overload has in clinical and research contexts. A case-study (epilepsy) is also presented, to demonstrate its application in a real context.

Conceptual modelling for life sciences based on systemist foundations

“…If these procedural steps are related to specific biological objects, a Class Diagram (CD) that includes these relevant structural participants should be introduced, facilitating an explicit identification and an accurate representation of the concrete relationships between PAD data components, Their UML CD counterpart must be explicitly stated. Figure 2 shows an excerpt of a Conceptual Schema of the Human Genome from (CSHG [118]). The purpose of the CSHG is to identify the relevant concepts that characterize genomic knowledge.…”

Conceptual modeling in the era of Big Data and Artificial Intelligence: Research topics and introduction to the special issue

“…The conceptual model of the human genome needs a precise ontological commitment that identifies its main conceptual notions together with their various set of relationships. An example can be found in the work of Pastor and colleagues [79], [24], [24], [61], and Ceri and colleagues [6], [4]. For the past decade, they have generated a continuous evolution of the modeling of the human genome, followed by a characterization of its ontological commitment.…”

An Ontological Characterization of a Conceptual Model of the Human Genome

“…Conceptual models are appropriate because they facilitate the exchange of information [13], while providing a sound basis to make a conceptualization process explicit and facilitate a shared understanding of a domain [11]. For the human genome domain, applying conceptual modeling can: improve communication among physicians, geneticists, biologists, and other researchers; assist in knowledge transfer; and, ultimately, enable efficient exploitation of information for progressing the understanding of the human genome [12].…”