Conceptual Modeling for Genomics: Building an Integrated Repository of Open Data

Abstract

Many repositories of open data for genomics, collected by worldwide consortia, are important enablers of biological research; moreover, all experimental datasets leading to publications in genomics must be deposited to public repositories and made available to the research community. These datasets are typically used by biologists for validating or enriching their experiments; their content is documented by metadata. However, emphasis on data sharing is not matched by accuracy in data documentation; metadata are not standardized across the sources and often unstructured and incomplete. In this paper, we propose a conceptual model of genomic metadata, whose purpose is to query the underlying data sources for locating relevant experimental datasets. First, we analyze the most typical metadata attributes of genomic sources and define their semantic properties. Then, we use a top-down method for building a global-as-view integrated schema, by abstracting the most important conceptual properties of genomic sources. Finally, we describe the validation of the conceptual model by mapping it to three well-known data sources: TCGA, ENCODE, and Gene Expression Omnibus.

Empowering Virus Sequences Research through Conceptual Modeling

“…We previously proposed the Genomic Conceptual Model (GCM, [6]), an Entity-Relationship diagram that recognizes a common organization for a limited set of concepts supported by most genomic data sources, although with different 6 https://www.ncbi.nlm.nih.gov/labs/virus 7 https://www.ebi.ac.uk/ena/pathogens/ 8 https://4virology.net/virology-ca-tools/vgo/ 9 http://cov-glue.cvr.gla.ac.uk/ 10 http://clinicaltrials.gov/ names and formats. The model is centered on the Item entity, representing an elementary experimental file of genomic regions and their attributes.…”

“…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].…”

“…However, the model applies to any type of virus, and will be at the basis for the development of new instruments. In the past, we first presented the conceptual model for human genomics [6], then we developed the Web-based search system GenoSurf [8]; our ongoing effort is to develop a search system for viral conceptual schemas, inspired by GenoSurf.…”

“…Our recent work is focused on data-driven genomic computing, providing contributions in the area of modeling, integration, search and query answering. We have previously proposed a conceptual model focused on human genomics [6], which was based on a central entity Item, representing files of genomic regions. The simple schema evolved into a knowledge graph [5], including ontological representation of many relevant attributes (e.g., diseases, cell lines, tissue types...).…”

“…-We propose a new Viral Conceptual Model (VCM), a general conceptual model for describing viral sequences, organized along specific dimensions that highlight a conceptual schema similar to GCM [6]; -Focusing on SARS-CoV2, we show how VCM can be profitably linked to a phenotype database with information on COVID-19 infected patients; -We provide a list of interesting queries replicating newly released literature on infectious diseases; these can be easily performed on VCM.…”