A Comprehensive Approach for the Conceptual Modeling of Genomic Data

Abstract

The human genome is traditionally represented as a DNA sequence of three billion base pairs. However, its intricacies are captured by many more complex signals, representing DNA variations, the expression of gene activity, or DNA's structural rearrangements; a rich set of data formats is used to represent such signals. Different conceptual models explain such elaborate structure and behavior. Among them, the Conceptual Schema of the Human Genome (CSG) provides a concept-oriented, top-down representation of the genome behaviorindependent of data formats. The Genomic Conceptual Model (GCM) instead provides a data-oriented, bottom-up representation, targeting a well-organized, unified description of these formats. We hereby propose to join these two approaches to achieve a more complete vision, linking (1) a concepts layer, describing genome elements and their conceptual connections, with (2) a data layer, describing datasets derived from genome sequencing with specific technologies. The link is established when specific genomic data types are chosen in the data layer, thereby triggering the selection of a view in the concepts layer. The benefit is mutual, as data records can be semantically described by high-level concepts and exploit their links. In turn, the continuously evolving abstract model can be extended thanks to the input provided by real datasets. As a result, it will be possible to express queries that employ a holistic conceptual perspective on the genome, directly translated onto data-oriented terms and organization. The approach is here exemplified using the DNA variation data type but is applicable to all genomic information.

Conceptual modelling for life sciences based on systemist foundations

“…This approach would facilitate the description of a unified conceptual model that integrates higher-level genome concepts and a data layer where these concepts are represented as data that are obtained from practice. The initial results of this promising scientific task are already in progress [18]. The use of the systemist modelling approach would enable us to approach this task in a more natural, clear and, subsequently, valuable and effective manner.…”

A Reference Meta-model to Understand DNA Variant Interpretation Guidelines

“…More specifically, conceptual modeling techniques have proven to be an effective tool to achieve high levels of concreteness and standardization. A recent work [7], has considered general genomic data types represented in datasets for analysis and connected them to an abstract conceptual representation, with the purpose to resolve their heterogeneity. Other modeling efforts have targeted the inherent temporal dimension associated with genomics data by mapping their evolution over time [15]; such an approach is particularly sensitive in cases of changes in variant interpretation due to generelated data being updated [48].…”

“…A suitable approach to clarify this complex domain is Conceptual Modeling. Conceptual Modeling techniques have proven to be effective to achieve high levels of concreteness and standardization in genomics [42,38,45,7,15].…”

Study on the aesthetic laws of VR digital media art on the reception of film art

“…The literature [11][12] points out that film, as an art about "people," can only create works with eternal artistic vitality if it satisfies people's deep aesthetic needs both in terms of "audio-visual" senses and spirit. The literature [13][14][15][16], starting from film art itself, believes that film, as a comprehensive art, has become one of the most popular art forms because of its ability to fully and realistically present the world of human existence and the ideal of human existence. It is also born, exists, and develops because it can satisfy the aesthetic needs of human life.…”