The road towards data integration in human genomics: players, steps and interactions

A Bernasconi, A Canakoglu… - Briefings in …, 2021 - academic.oup.com
Thousands of new experimental datasets are becoming available every day; in many cases,
they are produced within the scope of large cooperative efforts, involving a variety of …

GeCoAgent: a conversational agent for empowering genomic data extraction and analysis

P Crovari, S Pidò, P Pinoli, A Bernasconi… - ACM Transactions on …, 2021 - dl.acm.org
With the availability of reliable and low-cost DNA sequencing, human genomics is relevant
to a growing number of end-users, including biologists and clinicians. Typical interactions …

GeMI: interactive interface for transformer-based Genomic Metadata Integration

G Serna Garcia, M Leone, A Bernasconi… - Database, 2022 - academic.oup.com
Abstract The Gene Expression Omnibus (GEO) is a public archive containing> 4 million
digital samples from functional genomics experiments collected over almost two decades …

[HTML][HTML] Data quality-aware genomic data integration

A Bernasconi - Computer Methods and Programs in Biomedicine …, 2021 - Elsevier
Genomic data are growing at unprecedented pace, along with new protocols, update
polices, formats and guidelines, terminologies and ontologies, which are made available …

The challenge of managing the evolution of genomics data over time: a conceptual model-based approach

A García S, M Costa, A Leon, O Pastor - BMC bioinformatics, 2022 - Springer
Background Precision medicine is a promising approach that has revolutionized disease
prevention and individualized treatment. The DELFOS oracle is a model-driven genomics …

A comprehensive approach for the conceptual modeling of genomic data

A Bernasconi, A García S, S Ceri, O Pastor - International Conference on …, 2022 - Springer
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 …

[HTML][HTML] PoliViews: A comprehensive and modular approach to the conceptual modeling of genomic data

A Bernasconi, A García, S Ceri, O Pastor - Data & Knowledge Engineering, 2023 - Elsevier
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 …

Improving NoSQL storage schema based on Z-curve for spatial vector data

D Zhang, Y Wang, Z Liu, S Dai - IEEE Access, 2019 - ieeexplore.ieee.org
NoSQL database can provide massive, high concurrency, and scalable services for storing
different types of data. HBase, a type of NoSQL database, in which columns are grouped …

Conceptual modelling for life sciences based on systemist foundations

R Lukyanenko, VC Storey, O Pastor - BMC bioinformatics, 2022 - Springer
Background All aspects of our society, including the life sciences, need a mechanism for
people working within them to represent the concepts they employ to carry out their …

Processing genome-wide association studies within a repository of heterogeneous genomic datasets

A Bernasconi, A Canakoglu, F Comolli - BMC genomic data, 2023 - Springer
Abstract Background Genome Wide Association Studies (GWAS) are based on the
observation of genome-wide sets of genetic variants–typically single-nucleotide …