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Model, Integrate, Search... Repeat [[electronic resource] ] : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi
Model, Integrate, Search... Repeat [[electronic resource] ] : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi
Autore Bernasconi Anna
Edizione [1st ed. 2023.]
Pubbl/distr/stampa Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023
Descrizione fisica 1 online resource (277 pages)
Disciplina 572.860285
Collana Lecture Notes in Business Information Processing
Soggetto topico Application software
Bioinformatics
Quantitative research
Artificial intelligence - Data processing
Computer and Information Systems Applications
Data Analysis and Big Data
Data Science
ISBN 3-031-44907-X
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto Intro -- Foreword -- Preface -- Acknowledgements -- Contents -- Acronyms -- Introduction -- Genomic Data Integration -- Thesis Contribution within the GeCo Project -- The Recent COVID-19 Pandemic -- Thesis Structure -- Part I Human Genomic Data Integration -- Genomic Data Players and Processes -- Technological Pipeline of Genomic Data -- Production -- Integration -- Services and Access -- Taxonomy of Players Involved in Data Production and Integration -- Main Genomic Data Players -- Contributors -- Repository Hosts -- Consortia -- Integrators -- Modeling Genomic Data -- The Genomic Data Model -- The Genomic Conceptual Model -- Analysis of Metadata Attributes -- Model Design -- Validation: Source-Specific Views of GCM -- Related Works -- Integrating Genomic Data -- Theoretical Rationale -- Approach Overview -- Data Download -- Data Transformation -- Data Cleaning -- Data Mapping -- Data Normalization and Enrichment -- Search Service and Ontology Selection -- Enrichment Process -- Data Constraint Checking -- Architecture Implementation -- Data Persistence -- Architecture Validation -- Lossless Integration -- Semantic Enrichment -- User Evaluation -- Related Works -- Snapshot of the Data Repository -- Included Data Sources -- OpenGDC: Integrating Cancer Genomic Data and Metadata -- Towards Automated Integration of Unstructured Metadata -- Experiments -- Related Works -- Searching Genomic Data -- Issues in Exploiting Semantic Knowledge in Genomics -- Inference Explanation -- GeKnowGraph: Exploration-Based Interface -- Exploration Interaction -- GenoSurf: a Web-Based Search Server for Genomic Datasets -- Data Search -- Key-Value Search -- Query Sessions -- Result Visualization -- Additional Functionalities -- Use Cases -- Validation of GenoSurf -- Related Works -- Future Directions of the Data Repository -- Including New Data Sources.
Improving Genomic Data Quality Dimensions -- Towards Better Interoperability -- Simplifying Data and Tools for End Users -- Monitoring Integration and Search Value -- Part II Viral Sequence Data Integration -- Viral Sequences Data Management Resources -- Landscape of Data Resources for Viral Sequences -- Fully Open-Source Resources -- GISAID and its Resources -- Integration of Sources of Viral Sequences -- Metadata Integration -- Value Harmonization and Ontological Efforts -- Replicated Sequences in Multiple Sources -- SARS-CoV-2 Search Systems -- Portals to NCBI and GISAID Resources -- Integrative Search Systems -- Comparison -- Discussion -- GISAID Restrictions -- Metadata Quality -- (Un)Willingness to Share Sequence Data -- Modeling Viral Sequence Data -- Conceptual Modeling for Viral Genomics -- Answering Complex Biological Queries -- Related Works -- Integrating Viral Sequence Data -- Database Content -- Relational Schema -- Data Import -- Annotation and Variant Calling -- Data Curation -- Searching Viral Sequence Data -- Requirements Analysis -- Lessons Learnt -- Web Interface -- Example Queries -- Discussion -- Related Works -- Future Directions of the Viral Sequence Repository -- Research Agenda -- ViruSurf Extensions -- Visualization Support: VirusViz -- Active Monitoring of SARS-CoV-2 Variations -- Integrating Host-Pathogen Information -- The Virus Genotype - Host Phenotype Connection -- The Host Genotype - Host Phenotype Connection -- Part III Epilogue -- Conclusions and Vision -- Summary of Thesis Contributions -- Achievements within GeCo Project -- Outlook -- META-BASE tool configuration -- User Manual -- Process Configuration -- Mapper Configuration -- Experimental setup GEO metadata extraction -- Mappings of viral sources attributes into ViruSurf -- References.
Record Nr. UNINA-9910770265603321
Bernasconi Anna  
Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
Model, Integrate, Search... Repeat [[electronic resource] ] : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi
Model, Integrate, Search... Repeat [[electronic resource] ] : A Sound Approach to Building Integrated Repositories of Genomic Data / / by Anna Bernasconi
Autore Bernasconi Anna
Edizione [1st ed. 2023.]
Pubbl/distr/stampa Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023
Descrizione fisica 1 online resource (277 pages)
Disciplina 572.860285
Collana Lecture Notes in Business Information Processing
Soggetto topico Application software
Bioinformatics
Quantitative research
Artificial intelligence - Data processing
Computer and Information Systems Applications
Data Analysis and Big Data
Data Science
ISBN 3-031-44907-X
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto Intro -- Foreword -- Preface -- Acknowledgements -- Contents -- Acronyms -- Introduction -- Genomic Data Integration -- Thesis Contribution within the GeCo Project -- The Recent COVID-19 Pandemic -- Thesis Structure -- Part I Human Genomic Data Integration -- Genomic Data Players and Processes -- Technological Pipeline of Genomic Data -- Production -- Integration -- Services and Access -- Taxonomy of Players Involved in Data Production and Integration -- Main Genomic Data Players -- Contributors -- Repository Hosts -- Consortia -- Integrators -- Modeling Genomic Data -- The Genomic Data Model -- The Genomic Conceptual Model -- Analysis of Metadata Attributes -- Model Design -- Validation: Source-Specific Views of GCM -- Related Works -- Integrating Genomic Data -- Theoretical Rationale -- Approach Overview -- Data Download -- Data Transformation -- Data Cleaning -- Data Mapping -- Data Normalization and Enrichment -- Search Service and Ontology Selection -- Enrichment Process -- Data Constraint Checking -- Architecture Implementation -- Data Persistence -- Architecture Validation -- Lossless Integration -- Semantic Enrichment -- User Evaluation -- Related Works -- Snapshot of the Data Repository -- Included Data Sources -- OpenGDC: Integrating Cancer Genomic Data and Metadata -- Towards Automated Integration of Unstructured Metadata -- Experiments -- Related Works -- Searching Genomic Data -- Issues in Exploiting Semantic Knowledge in Genomics -- Inference Explanation -- GeKnowGraph: Exploration-Based Interface -- Exploration Interaction -- GenoSurf: a Web-Based Search Server for Genomic Datasets -- Data Search -- Key-Value Search -- Query Sessions -- Result Visualization -- Additional Functionalities -- Use Cases -- Validation of GenoSurf -- Related Works -- Future Directions of the Data Repository -- Including New Data Sources.
Improving Genomic Data Quality Dimensions -- Towards Better Interoperability -- Simplifying Data and Tools for End Users -- Monitoring Integration and Search Value -- Part II Viral Sequence Data Integration -- Viral Sequences Data Management Resources -- Landscape of Data Resources for Viral Sequences -- Fully Open-Source Resources -- GISAID and its Resources -- Integration of Sources of Viral Sequences -- Metadata Integration -- Value Harmonization and Ontological Efforts -- Replicated Sequences in Multiple Sources -- SARS-CoV-2 Search Systems -- Portals to NCBI and GISAID Resources -- Integrative Search Systems -- Comparison -- Discussion -- GISAID Restrictions -- Metadata Quality -- (Un)Willingness to Share Sequence Data -- Modeling Viral Sequence Data -- Conceptual Modeling for Viral Genomics -- Answering Complex Biological Queries -- Related Works -- Integrating Viral Sequence Data -- Database Content -- Relational Schema -- Data Import -- Annotation and Variant Calling -- Data Curation -- Searching Viral Sequence Data -- Requirements Analysis -- Lessons Learnt -- Web Interface -- Example Queries -- Discussion -- Related Works -- Future Directions of the Viral Sequence Repository -- Research Agenda -- ViruSurf Extensions -- Visualization Support: VirusViz -- Active Monitoring of SARS-CoV-2 Variations -- Integrating Host-Pathogen Information -- The Virus Genotype - Host Phenotype Connection -- The Host Genotype - Host Phenotype Connection -- Part III Epilogue -- Conclusions and Vision -- Summary of Thesis Contributions -- Achievements within GeCo Project -- Outlook -- META-BASE tool configuration -- User Manual -- Process Configuration -- Mapper Configuration -- Experimental setup GEO metadata extraction -- Mappings of viral sources attributes into ViruSurf -- References.
Record Nr. UNISA-996574259503316
Bernasconi Anna  
Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023
Materiale a stampa
Lo trovi qui: Univ. di Salerno
Opac: Controlla la disponibilità qui