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Open-source tools for cancer genomics researchers, clinicians, geneticists, molecular biologists

GenoSurf (http://gmql.eu/genosurf): multi-ontology semantic search system providing access to a consolidated collection of human genome datasets for bioinformatic tertiary analysis.

OpenGDC (http://www.bioinformatics.deib.polimi.it/opengdc/): extraction and integration tool for cancer genomics data.

GeMI (http://gmql.eu/gemi): interactive interface to annotate genomic samples exploiting a deep-learning-based prediction model, accelerating genomic metadata extraction into structured formats.

VarSum API (http://gmql.eu/popstudy): API computing summary statistics on user-defined populations and their variants, using a large genomic data repository.

META-BASE (https://github.com/DEIB-GECO/Metadata-Manager): tool that integrates and enriches heterogeneous biological and clinical data sources, exploiting several configurations to build a repository.

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Open-source tools for experts in virology, phylogenetics, epidemiology, pathogenesis, immunology, focusing on SARS-CoV-2 and other viral species

ViruSurf (http://gmql.eu/virusurf): search system for public viral sequences described by their metadata and exhibiting nucleotide and amino acid mutational patterns.

EpiViruSurf (http://gmql.eu/epivirusurf/): search system for evaluating the impact of viral mutational patterns on epitopes, i.e., areas of the virus recognized by the human immune system.

VirusViz (http://gmql.eu/virusviz): visualization tool for the comparison of the mutational distributions of user-selected viral populations.

ViruClust (http://gmql.eu/viruclust): data analysis tool to perform temporal and spatial comparison of mutational patterns of SARS-CoV-2 sequences.

VariantHunter (http://gmql.eu/variant_hunter): tool for fast detection of emerging SARS-CoV-2 variants and sub-variants.

CoV2K API (http://gmql.eu/cov2k/api/): knowledge base of SARS-CoV-2 sequence mutations, variants, and their effects.

CoVEffect (http://gmql.eu/coveffect): interactive web interface for deep learning-assisted scientific text annotation with effects of SARS-CoV-2 mutations and variants.

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Open-source tools for the exploration of COVID-19-related research literature

GRAPH-SEARCH (http://gmql.eu/graph-search): explorer of COIVD-19-related literature using graph-based queries with shortest paths and sophisticated ranking.

CORToViz (http://gmql.eu/cortoviz): user-friendly visualizer for trends of topics extracted from COVID-19 scientific research abstracts, with easy-to-drive statistical testing. This is the first prototype developed in the context of the NGI Search Program (TETYS project), aiming to build the next-generation open-source Web topics explorer (applicable to many other text document corpora).

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Participation in standardization initiatives

Participation in the COVID-19 Host Genetics Initiative for designing the COVID-19 clinical data dictionary for describing COVID-19 patients’ phenotype; our work was used in the publication https://doi.org/10.1038/s41586-021-03767-x on Nature and adopted within ELIXIR-CONVERGE, as deemed appropriate as standardization guidelines (https://doi.org/10.5281/zenodo.4893222)

Participation in the FAIRification of Genomic Annotations RDA Working Group, for the standardization of Genomic Annotations and FAIRification data processing pipelines (https://www.rd-alliance.org/fairification-genomic-tracks-data-driven-life-science-through-granular-discovery-biological-sequence