The human genome complexity is captured by many signals, representing for instance DNA variations, the expression of gene activity, or DNA’s structural rearrangements; a rich set of data types and formats is used to record these signals. Conceptual models can support the description and explanation of the genome’s elaborate structure and behavior. Among others, the Conceptual Schema of the Human Genome (CSG) provides a concept-oriented, top-down representation of the genome behavior, which is independent of data formats. The Genomic Conceptual Model (GCM) provides instead a data-oriented, bottom-up representation, targeting a well-organized, unified description of these formats. In this research, we join the two approaches to achieve PoliViews, a comprehensive model that links (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. Their dynamic connection 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: data records can be semantically described by high-level concepts exploiting their links and, in turn, the continuously evolving abstract model can be extended thanks to the input provided by real datasets. PoliViews enables expressing queries that employ a holistic conceptual perspective on the genome, directly translated onto data-oriented terms and organization. Here, we demonstrate the approach by linking two major genomic data types, namely DNA variation and gene expression. For each type, we consider different eminent data sources; we describe their mapping with the corresponding view in the concepts layer, enabling an intra-data-type integration. Then, leveraging on the connections available in the concepts layer, we show how the distinct data types can be interoperated, enabling an inter-data-type integration. The PoliViews approach is shown through several examples of biological interest and can be further extended to any kind of genomic information.

Although the knowledge about human genomics is available to all scientists, information about this scientific breakthrough can often be difficult to fully comprehend and share. A Conceptual Schema of the Human Genome was previously developed to assist in describing human genome-related knowledge, by representing a holistic view of the relevant concepts regarding its biology and underlying mechanisms. This model should become helpful for any researcher who works with human genomics data. We, therefore, perform the process of ontological unpacking on a portion of the model, to facilitate domain understanding and data exchange among heterogeneous systems. The ontological unpacking is a transformation of an input conceptual model into an enriched model based on a foundational ontology. The preliminary analysis and enrichment process are supported by the ontological conceptual modeling language OntoUML, which has been applied previously to complex models to gain ontological clarity. The value of the used method is first assessed from a theoretical point of view: the transformation results in significant, diverse modeling implications regarding the characterization of biological entities, the representation of their changes over time, and, more specifically, the description of chemical compounds. Since the ontological unpacking process is costly, an empirical evaluation is conducted to study the practical implications of applying it in a real learning setting. A particularly complex domain such as metabolic pathways is either described by adopting a traditional conceptual model or explained through an ontologically unpacked model obtained from a traditional model. Our research is evidence that including a strong ontological foundation in traditional conceptual models is useful. It contributes to designing models that convey biological domains better than the original models.