Semalytics: a semantic analytics platform for the exploration of distributed and heterogeneous cancer data in translational research

• Published in: Database : the journal of biological databases and curation 2019, Vol.2019
• Main Authors: Mignone, Andrea, Grand, Alberto, Fiori, Alessandro, Medico, Enzo, Bertotti, Andrea
• Format: Article
• Language: English
• Subjects: Biomarkers, Tumor; Databases, Factual; Humans; Information Dissemination; Neoplasms; Original; Semantic Web; Translational Medical Research
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/baz080

Each cancer is a complex system with unique molecular features determining its dynamics, such as its prognosis and response to therapies. Understanding the role of these biological traits is fundamental in order to personalize cancer clinical care according to the characteristics of each patient's disease. To achieve this, translational researchers propagate patients' samples through in vivo and in vitro cultures to test different therapies on the same tumor and to compare their outcomes with the molecular profile of the disease. This in turn generates information that can be subsequently translated into the development of predictive biomarkers for clinical use. These large-scale experiments generate huge collections of hierarchical data (i.e. experimental trees) with relative annotations that are extremely difficult to analyze. To address such issues in data analyses, we came up with the Semalytics data framework, the core of an analytical platform that processes experimental information through Semantic Web technologies. Semalytics allows (i) the efficient exploration of experimental trees with irregular structures together with their annotations. Moreover, (ii) the platform links its data to a wider open knowledge base (i.e. Wikidata) to add an extended knowledge layer without the need to manage and curate those data locally. Altogether, Semalytics provides augmented perspectives on experimental data, allowing the generation of new hypotheses, which were not anticipated by the user a priori. In this work, we present the data core we created for Semalytics, focusing on its semantic nucleus and on how it exploits semantic reasoning and data integration to tackle issues of this kind of analyses. Finally, we describe a proof-of-concept study based on the examination of several dozen cases of metastatic colorectal cancer in order to illustrate how Semalytics can help researchers generate hypotheses about the role of genes alterations in causing resistance or sensitivity of cancer cells to specific drugs.