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D3.1 A multi-omics data integration and pathway enrichment module that integrates information from literature and hidden relationships among molecular entities - Executive Summary

A multi-omics integration module has been designed that enables interrogating molecular entities of interest (genes, proteins, metabolites, etc.) against literature and hidden relationships data from the GLOMICAVE knowledgebase, i.e., integrates data from different structured and unstructured sources. First, we developed a multi-omics integration module to be embedded into the cloud platform (under development, WP5), and capable of integrating different omics data uploaded by users and projecting the results onto biological pathways. Next, we integrated data extracted from unstructured scientific publications obtained by WP2, phenotype and hidden relationship information obtained by WP4, and additional information into a single datatype. To this end, we have developed four modules that are responsible to integrate the different data sources, to store the data in a graph database, and to provide access to the data for other work packages. Altogether, this deliverable enables multi-omics integration of data uploaded by users and results projection onto biological pathways. Additionally, it enables linking dysregulated entities (genes, proteins, metabolites, etc.) with related scientific papers via different approaches (e.g., by ranking publications according to their relevance, or grouping scientific publications according to their similarity), and linking dysregulated entities with other entities using the hidden relationships database.